recording logs

Got it runnign currently

.gitattributes

@@ -0,0 +1,8 @@
+*.sql.gzip filter=lfs diff=lfs merge=lfs -text
+*.xlsx filter=lfs diff=lfs merge=lfs -text
+containers/AACT_Reloader/2023-09-06_aactdb_with_matches.sql.gz filter=lfs diff=lfs merge=lfs -text
+other_data/USP[[:space:]]DC/usp_dc_pub_2023_release_2.0_updated_final.csv filter=lfs diff=lfs merge=lfs -text
+other_data/USP[[:space:]]MMG/MMG_v8.0_Alignment_File.csv filter=lfs diff=lfs merge=lfs -text
+other_data/VA[[:space:]]Formulary/PharmacyProductSystem_NationalDrugCodeExtract.csv filter=lfs diff=lfs merge=lfs -text
+containers/AACT_Reloader/backup/aact_db_backup_20250106_184236.sql.gz filter=lfs diff=lfs merge=lfs -text
+containers/AACT_Reloader/backup/aact_db_backup_20250107_133822.sql.gz filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -180,8 +180,18 @@ Manifest.toml
 
 
 ###### Custom #####
-*_clinical_trials/
-*_clinical_trials.zip
 NCT*.html
-/Orangebook/EOBZIP_*/
-/Orangebook/Orangebooks/
+*.json
+*.zip
+#Ignore stuff from RxNavInABox
+containers/RxNav-In-a-box/rxnav_data/*
+containers/RxNav-In-a-box/rxnav-in-a-box-*
+#Ignore stuff from AACT_downlaoder
+containers/AACT_downloader/postgresql/*
+containers/AACT_downloader/aact_downloads/*
+#ignore stuff in DrugCentral Downloader
+containers/drugcentral/docker-entrypoint-initdb.d/*.sql
+containers/drugcentral/docker-entrypoint-initdb.d/*.sql.gz
+containers/drugcentral/db_store/*
+
+.dbeaver/

.project

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ClinicalTrialsDataProcessing</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+		<nature>org.jkiss.dbeaver.DBeaverNature</nature>
+	</natures>
+</projectDescription>

AACT_downloader/ClinicalTrialHistory/Dockerfile

@@ -1,7 +0,0 @@
-FROM  youainti/aact_from_dump
-LABEL AUTHOR 'Will King (youainti@protonmail.com)'
-LABEL DESCRIPTION 'add extra processing to the aact database in preparation for downloading history.'
-
-#copy additional init scripts
-COPY ./docker-entrypoint-initdb.d/ /docker-entrypoint-initdb.d/
-#these will be run after the database is initialized

AACT_downloader/ClinicalTrialHistory/docker-entrypoint-initdb.d/030_HistoricalSchema.sql

@@ -1,26 +0,0 @@
--- Create a schema handling trial history.
-CREATE SCHEMA history;
-
---Create role for anyone who needs to both select and insert on historical data
-CREATE ROLE history_writer;
-GRANT CONNECT ON DATABASE aact_db to history_writer;
-
-GRANT USAGE ON SCHEMA history TO history_writer;
-
-GRANT INSERT,SELECT ON ALL TABLES IN SCHEMA http TO history_writer;
-
-
---Create role for anyone who only needs selection access to historical data, such as for analysis
-CREATE ROLE history_reader;
-GRANT CONNECT ON DATABASE aact_db to history_reader;
-
-GRANT USAGE ON SCHEMA history TO history_reader;
-
-GRANT SELECT ON ALL TABLES IN SCHEMA http TO history_reader;
-
-
-
-/* History Tables
-Below is where I would construct the parsed trial history tables that I need.
-*/
-

AACT_downloader/docker-compose.yaml

@@ -1,21 +0,0 @@
-version: '3'
-
-volumes:
-  aact_pg_database: #This is to hold the database.
-
-services:
-
-  aact:
-    build: ./ClinicalTrialHistory #build and use the clinical trial history db.
-    container_name: aact_db
-    #restart: always #restart after crashes
-    environment:
-      POSTGRES_USER: root
-      POSTGRES_PASSWORD: root
-      POSTGRES_DB: aact_db
-    ports:
-      - "5432:5432" #host:container
-    volumes: #host:container is the format.
-      - aact_pg_database:/var/lib/postgresql/ # this is persistant storage for the database 
-      - ./20220201_clinical_trials/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
-

Orangebook/CidParser.py

@@ -1,93 +0,0 @@
-# Adobe Pdf Character ID (cid:\d+) parser
-# The purpose is to allow someone to create their own table equivalent to the "\toUnicode" that
-# should be provided in every PDF using cid's (but is often mangled).
-
-def get_digits(string):
-    """
-    Extract leading the digits from a cid tag.
-    """
-    splat = string.split(")")
-    num = splat[0]
-    l = len(num)
-    return int(num),l
-
-def token_generator(string):
-    """
-    An iterable that returns tokens describing a string in a pdf.
-    Tokens take two forms:
-        - Integers: these represend CID codes
-        - Characters: these represent the arbitrary characters often returned amidst cid's.
-    
-    It is a python generator becasue that simplifies the ordering and allows us to avoid recursion.
-    """
-    start = 0
-    str_len = len(string)
-    
-    while start < str_len:
-        substring = string[start:]
-        
-        #check for cid
-        if (str_len - start > 6) and (substring[0:5] == "(cid:"):
-            
-            num,length = get_digits(substring[5:])
-            start += length + 6
-            yield num
-            
-        elif (str_len - start > 1):
-            start += 1
-            yield substring[0]
-        else:
-            start += 1
-            yield substring
-
-
-class UnknownSymbol():
-    """
-    Represents a token that is not in the parser's dictionary.
-    """
-    def __init__(self, symbol):
-        self.symbol = symbol
-        
-    def __repr__(self):
-        return "UnknownSymbol: {} of type {}".format(self.symbol, type(self.symbol))
-    
-    def __str__(self):
-        return "\uFFFD"
-
-class Parser:
-    """
-    Translates from tokens to character arrays or strings, handling errors as it goes.
-    
-    It requires a dictionary during instantiation. 
-    This dictionary is what is used to perform lookups.
-    
-    It exposes 3 methods
-        - convert attempts to convert a single token
-        - convert_stream will try to convert an iterable of tokens into an iterable of text.
-        - check_list_of_strings will try to convert a list of strings containing cids and other symbols into 
-            - strings, if there are no Unknown symbols.
-            - lists, containing characters and Unknown symbols.
-    """
-    def __init__(self, lookup_table):
-        self._lookup_table = lookup_table
-        
-    def convert(self,token):
-        try:
-            return self._lookup_table[token]
-        except:
-            return  UnknownSymbol(token)
-    
-    def convert_list(self,token_stream):
-        for token in token_stream:
-            yield self.convert(token)
-    
-    def convert_list_of_strings(self, list_of_strings):
-        for token_stream in list_of_stings:
-            arr = [x for x in ob2020.convert_stream(token_generator(token_stream))]
-            try:
-                print("".join(arr))
-            except:
-                print(arr)
-                
-if __name__ == "__main__":
-    print("Plan was to accept and proceess a symbol table and text. Apparently it has not been implemented."

Orangebook/Untitled.ipynb

@@ -1,371 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 18,
-   "id": "40358f02-c376-4431-be39-cdd477f17e7a",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import polars as pl"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 25,
-   "id": "8fb27ee2-72c1-4e80-9d00-de54f2834fe8",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "polars.datatypes.Datetime"
-      ]
-     },
-     "execution_count": 25,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "pl.datatypes.Datetime"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 55,
-   "id": "2c0edd77-c2d0-4184-a094-8c01783d2f0e",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "products = pl.scan_csv(file=\"./EOBZIP_2022_04/products.txt\", sep=\"~\")\n",
-    "patents = pl.scan_csv(file=\"./EOBZIP_2022_04/patent.txt\", sep=\"~\")\n",
-    "exclusivity = pl.scan_csv(file=\"./EOBZIP_2022_04/exclusivity.txt\", sep=\"~\", parse_dates=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 58,
-   "id": "023f211d-23aa-4a2c-843d-1b60cec91079",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def set_exclusivity_types(df):\n",
-    "    return df.with_columns([\n",
-    "        pl.col(\"Exclusivity_Date\").str.strptime(pl.Date, fmt=\"%b %-d, %Y\")\n",
-    "    ])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 61,
-   "id": "a1da42c9-e47a-4437-b089-e9b91f789a0c",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1 \"class=\"dataframe \">\n",
-       "<thead>\n",
-       "<tr>\n",
-       "<th>\n",
-       "Appl_Type\n",
-       "</th>\n",
-       "<th>\n",
-       "Appl_No\n",
-       "</th>\n",
-       "<th>\n",
-       "Product_No\n",
-       "</th>\n",
-       "<th>\n",
-       "Exclusivity_Code\n",
-       "</th>\n",
-       "<th>\n",
-       "Exclusivity_Date\n",
-       "</th>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "str\n",
-       "</td>\n",
-       "<td>\n",
-       "i64\n",
-       "</td>\n",
-       "<td>\n",
-       "i64\n",
-       "</td>\n",
-       "<td>\n",
-       "str\n",
-       "</td>\n",
-       "<td>\n",
-       "date\n",
-       "</td>\n",
-       "</tr>\n",
-       "</thead>\n",
-       "<tbody>\n",
-       "<tr>\n",
-       "<td>\n",
-       "\"N\"\n",
-       "</td>\n",
-       "<td>\n",
-       "11366\n",
-       "</td>\n",
-       "<td>\n",
-       "2\n",
-       "</td>\n",
-       "<td>\n",
-       "\"ODE-96\"\n",
-       "</td>\n",
-       "<td>\n",
-       "2022-08-07\n",
-       "</td>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "\"N\"\n",
-       "</td>\n",
-       "<td>\n",
-       "20287\n",
-       "</td>\n",
-       "<td>\n",
-       "11\n",
-       "</td>\n",
-       "<td>\n",
-       "\"NPP\"\n",
-       "</td>\n",
-       "<td>\n",
-       "2022-05-16\n",
-       "</td>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "\"N\"\n",
-       "</td>\n",
-       "<td>\n",
-       "20287\n",
-       "</td>\n",
-       "<td>\n",
-       "10\n",
-       "</td>\n",
-       "<td>\n",
-       "\"NPP\"\n",
-       "</td>\n",
-       "<td>\n",
-       "2022-05-16\n",
-       "</td>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "\"N\"\n",
-       "</td>\n",
-       "<td>\n",
-       "20287\n",
-       "</td>\n",
-       "<td>\n",
-       "9\n",
-       "</td>\n",
-       "<td>\n",
-       "\"NPP\"\n",
-       "</td>\n",
-       "<td>\n",
-       "2022-05-16\n",
-       "</td>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "\"N\"\n",
-       "</td>\n",
-       "<td>\n",
-       "20287\n",
-       "</td>\n",
-       "<td>\n",
-       "8\n",
-       "</td>\n",
-       "<td>\n",
-       "\"NPP\"\n",
-       "</td>\n",
-       "<td>\n",
-       "2022-05-16\n",
-       "</td>\n",
-       "</tr>\n",
-       "</tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "shape: (5, 5)\n",
-       "┌───────────┬─────────┬────────────┬──────────────────┬──────────────────┐\n",
-       "│ Appl_Type ┆ Appl_No ┆ Product_No ┆ Exclusivity_Code ┆ Exclusivity_Date │\n",
-       "│ ---       ┆ ---     ┆ ---        ┆ ---              ┆ ---              │\n",
-       "│ str       ┆ i64     ┆ i64        ┆ str              ┆ date             │\n",
-       "╞═══════════╪═════════╪════════════╪══════════════════╪══════════════════╡\n",
-       "│ N         ┆ 11366   ┆ 2          ┆ ODE-96           ┆ 2022-08-07       │\n",
-       "├╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤\n",
-       "│ N         ┆ 20287   ┆ 11         ┆ NPP              ┆ 2022-05-16       │\n",
-       "├╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤\n",
-       "│ N         ┆ 20287   ┆ 10         ┆ NPP              ┆ 2022-05-16       │\n",
-       "├╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤\n",
-       "│ N         ┆ 20287   ┆ 9          ┆ NPP              ┆ 2022-05-16       │\n",
-       "├╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┼╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌╌┤\n",
-       "│ N         ┆ 20287   ┆ 8          ┆ NPP              ┆ 2022-05-16       │\n",
-       "└───────────┴─────────┴────────────┴──────────────────┴──────────────────┘"
-      ]
-     },
-     "execution_count": 61,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "exclusivity.pipe(set_exclusivity_types).head(5).collect()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 85,
-   "id": "92fe99fa-1963-460c-99ea-7f614b4b2e25",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def set_patent_types(df):\n",
-    "    return df.with_columns([\n",
-    "        pl.col(\"Patent_Expire_Date_Text\").str.strptime(pl.Date, fmt=\"%b %-d, %Y\"),\n",
-    "        pl.col(\"Submission_Date\").str.strptime(pl.Date, fmt=\"%b %-d, %Y\"),\n",
-    "        pl.col(\"Drug_Substance_Flag\") == \"Y\",\n",
-    "        pl.col(\"Drug_Product_Flag\") == \"Y\",\n",
-    "        pl.col(\"Delist_Flag\") == \"Y\"\n",
-    "    ])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 90,
-   "id": "13707ca6-094f-4ed7-94cb-824087e97874",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/html": [
-       "<div>\n",
-       "<style scoped>\n",
-       "    .dataframe tbody tr th:only-of-type {\n",
-       "        vertical-align: middle;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe tbody tr th {\n",
-       "        vertical-align: top;\n",
-       "    }\n",
-       "\n",
-       "    .dataframe thead th {\n",
-       "        text-align: right;\n",
-       "    }\n",
-       "</style>\n",
-       "<table border=\"1 \"class=\"dataframe \">\n",
-       "<thead>\n",
-       "<tr>\n",
-       "<th>\n",
-       "Patent_Expire_Date_Text\n",
-       "</th>\n",
-       "</tr>\n",
-       "<tr>\n",
-       "<td>\n",
-       "date\n",
-       "</td>\n",
-       "</tr>\n",
-       "</thead>\n",
-       "<tbody>\n",
-       "<tr>\n",
-       "<td>\n",
-       "2022-01-02\n",
-       "</td>\n",
-       "</tr>\n",
-       "</tbody>\n",
-       "</table>\n",
-       "</div>"
-      ],
-      "text/plain": [
-       "shape: (1, 1)\n",
-       "┌─────────────────────────┐\n",
-       "│ Patent_Expire_Date_Text │\n",
-       "│ ---                     │\n",
-       "│ date                    │\n",
-       "╞═════════════════════════╡\n",
-       "│ 2022-01-02              │\n",
-       "└─────────────────────────┘"
-      ]
-     },
-     "execution_count": 90,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "patents.pipe(set_patent_types).select(\"Patent_Expire_Date_Text\").min().collect()"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 81,
-   "id": "18ad8df7-45d5-4454-8955-c5f28a7d7f1e",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "polars.datatypes.Null"
-      ]
-     },
-     "execution_count": 81,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "pl.datatypes.Null"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "79e4b3d9-29ae-4302-bee1-4be02e0ba654",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.13"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

Orangebook/Untitled2.ipynb

@@ -1,216 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 196,
-   "id": "2f61df31-f3c1-4b2e-ae96-96bf06089b17",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "def get_digits(string):\n",
-    "    splat = string.split(\")\")\n",
-    "    num = splat[0]\n",
-    "    l = len(num)\n",
-    "    return int(num),l\n",
-    "\n",
-    "def token_generator(string):\n",
-    "    \n",
-    "    start = 0\n",
-    "    str_len = len(string)\n",
-    "    \n",
-    "    \n",
-    "    while start < str_len:\n",
-    "        substring = string[start:]\n",
-    "        \n",
-    "        #check for cid\n",
-    "        if (str_len - start > 6) and (substring[0:5] == \"(cid:\"):\n",
-    "            \n",
-    "            num,length = get_digits(substring[5:])\n",
-    "            start += length + 6\n",
-    "            yield num\n",
-    "            \n",
-    "        elif (str_len - start > 1):\n",
-    "            start += 1\n",
-    "            yield substring[0]\n",
-    "        else:\n",
-    "            start += 1\n",
-    "            yield substring\n",
-    "\n",
-    "class UnknownSymbol():\n",
-    "    def __init__(self, symbol):\n",
-    "        self.symbol = symbol\n",
-    "        \n",
-    "    def __repr__(self):\n",
-    "        return \"UnknownSymbol: {} of type {}\".format(self.symbol, type(self.symbol))\n",
-    "    \n",
-    "    def __str__(self):\n",
-    "        return \"\\uFFFD\"\n",
-    "\n",
-    "class Parser:\n",
-    "    def __init__(self, lookup_table):\n",
-    "        self._lookup_table = lookup_table\n",
-    "        \n",
-    "    def convert(self,symbol):\n",
-    "        try:\n",
-    "            return self._lookup_table[symbol]\n",
-    "        except:\n",
-    "            return  UnknownSymbol(symbol)\n",
-    "    \n",
-    "    def convert_stream(self,token_stream):\n",
-    "        for token in token_stream:\n",
-    "            yield self.convert(token)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 213,
-   "id": "e2c1e39b-0ac5-4ad7-9176-ef8ea69feeec",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ob2020 = Parser({\n",
-    "    23:\"4\"\n",
-    "    ,19:\"0\"\n",
-    "    ,\"7\":\"T\"\n",
-    "    ,\"+\":\"H\"\n",
-    "    ,3:\" \"\n",
-    "    ,\"(\":\"E\"\n",
-    "    ,\"’\":\"D\"\n",
-    "    ,\",\":\"I\"\n",
-    "    ,\"2\":\"O\"\n",
-    "    ,\"1\":\"N\"\n",
-    "    ,16:\"-\"\n",
-    "    ,21:\"2\"\n",
-    "    ,\"$\":\"A\"\n",
-    "    ,\"3\":\"P\"\n",
-    "    ,\"5\":\"R\"\n",
-    "    ,\"9\":\"V\"\n",
-    "    ,\"8\":\"U\"\n",
-    "    ,\"*\":\"G\"\n",
-    "    ,\"&\":\"C\"\n",
-    "    ,\"/\":\"L\"\n",
-    "    ,\"6\":\"S\"\n",
-    "    ,22:\"3\"\n",
-    "    ,20:\"1\"\n",
-    "    ,11:\" \"\n",
-    "    ,\"R\":\"(\"\n",
-    "    ,\"I\":\"of\"\n",
-    "    ,24:\"5\"\n",
-    "    ,12:\")\"\n",
-    "})"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 214,
-   "id": "c02896ab-fc75-44cc-bb27-a5dcf1b6d7f0",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'40TH EDITION - 2020 - APPROVED DRUG PRODUCT LIST'"
-      ]
-     },
-     "execution_count": 214,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "\"\".join([x for x in ob2020.convert_stream(token_generator(b))])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 215,
-   "id": "1794e826-fa1f-4aba-8eab-6d603a06dfe0",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "c = \"35(6&5,37,21(cid:3)’58*(cid:3)352’8&7(cid:3)/,67(cid:3)\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 216,
-   "id": "c8b67d79-81ad-4b3a-be8b-bace9a8d943a",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "'PRESCRIPTION DRUG PRODUCT LIST '"
-      ]
-     },
-     "execution_count": 216,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "\"\".join([x for x in ob2020.convert_stream(token_generator(c))])"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 217,
-   "id": "f76d9760-fe69-4743-ab47-41cf74866d70",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "d = \"(cid:22)(cid:16)(cid:20)(cid:11)RI(cid:3)(cid:23)(cid:24)(cid:22)(cid:12)\""
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 218,
-   "id": "ee925997-0701-4d8e-b713-6f39c6a50a5b",
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "text/plain": [
-       "['3', '-', '1', ' ', '(', 'of', ' ', '4', '5', '3', ')']"
-      ]
-     },
-     "execution_count": 218,
-     "metadata": {},
-     "output_type": "execute_result"
-    }
-   ],
-   "source": [
-    "[x for x in ob2020.convert_stream(token_generator(d))]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "ae152c75-5fd6-4756-a473-fcea2de5ee30",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.13"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

Orangebook/download.url.txt

@@ -1 +0,0 @@
-https://www.fda.gov/media/76860/download

Orangebook/testing-pyocr.ipynb

@@ -1,145 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "id": "51bf48a1-920a-4e64-ac5f-323ff3a27ebf",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Will use tool 'Tesseract (sh)'\n",
-      "Available languages: eng, osd\n",
-      "Will use language 'eng'\n"
-     ]
-    }
-   ],
-   "source": [
-    "# Import the required libraries\n",
-    "from wand.image import Image\n",
-    "from PIL import Image as PI\n",
-    "import pyocr\n",
-    "import pyocr.builders\n",
-    "import io, sys\n",
-    "\n",
-    "\n",
-    "# Get the handle of the OCR library (in this case, tesseract)\n",
-    "tools = pyocr.get_available_tools()\n",
-    "if len(tools) == 0:\n",
-    "\tprint(\"No OCR tool found!\")\n",
-    "\tsys.exit(1)\n",
-    "tool = tools[0]\n",
-    "print(\"Will use tool '%s'\" % (tool.get_name()))\n",
-    "\n",
-    "# Get the language\n",
-    "langs = tool.get_available_languages()\n",
-    "print(\"Available languages: %s\" % \", \".join(langs)) \n",
-    "lang = langs[0] # For English\n",
-    "print(\"Will use language '%s'\" % (lang))\n",
-    "\n",
-    "# Setup two lists which will be used to hold our images and final_text\n",
-    "req_image = []\n",
-    "final_text = []\n",
-    "\n",
-    "# Open the PDF file using wand and convert it to jpeg\n",
-    "image_pdf = Image(filename=\"/home/will/research/ClinicalTrialsDataProcessing/Orangebook/Orangebooks/testprint.pdf\", resolution=300)\n",
-    "image_jpeg = image_pdf.convert('pdf')\n",
-    "\n",
-    "# wand has converted all the separate pages in the PDF into separate image\n",
-    "# blobs. We can loop over them and append them as a blob into the req_image\n",
-    "# list.\n",
-    "for img in image_jpeg.sequence:\n",
-    "\timg_page = Image(image=img)\n",
-    "\treq_image.append(img_page.make_blob('jpeg'))\n",
-    "\n",
-    "# Now we just need to run OCR over the image blobs and store all of the \n",
-    "# recognized text in final_text.\n",
-    "for img in req_image:\n",
-    "\ttxt = tool.image_to_string(\n",
-    "\t\tPI.open(io.BytesIO(img)),\n",
-    "\t\tlang=lang,\n",
-    "\t\tbuilder=pyocr.builders.TextBuilder()\n",
-    "\t)\n",
-    "\tfinal_text.append(txt)\n",
-    "\n"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 7,
-   "id": "f0d5f1d6-7e15-4ee6-b4ee-cbd41c5afb99",
-   "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "\n",
-      "The final text is: \n",
-      "\n",
-      "40TH EDITION - 2020 - APPROVED DRUG PRODUCT LIST\n",
-      "\n",
-      "PRESCRIPTION DRUG PRODUCT LIST\n",
-      "\n",
-      "ABACAVIR SULFATE\n",
-      "SOLUTION; ORAL\n",
-      "ABACAVIR SULFATE\n",
-      "\n",
-      "EQ 2 5 /ML\n",
-      "\n",
-      "EQ 2 Ee /ML\n",
-      "\n",
-      "EQ 300MG BASE\n",
-      "EQ 300MG BASE\n",
-      "EQ 300MG BASE\n",
-      "\n",
-      "\n"
-     ]
-    }
-   ],
-   "source": [
-    "print(\"\\nThe final text is: \\n\")\n",
-    "print(final_text[0][0:200])"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "id": "1cac17e7-079d-4e32-bdbf-ae49194b2078",
-   "metadata": {},
-   "source": [
-    "it appears taht this does not have the required precision. I'll need to do this some other way."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "2283e290-fab3-4cda-8ce9-55a0b3533c98",
-   "metadata": {},
-   "outputs": [],
-   "source": []
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "Python 3 (ipykernel)",
-   "language": "python",
-   "name": "python3"
-  },
-  "language_info": {
-   "codemirror_mode": {
-    "name": "ipython",
-    "version": 3
-   },
-   "file_extension": ".py",
-   "mimetype": "text/x-python",
-   "name": "python",
-   "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.8.13"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 5
-}

README.md

@@ -1,56 +1,91 @@
 # ClinicalTrialsDataProcessing
 
-This is used to build tools which process and standardize the data.
+This represents my 
 
-More data later.
+## Prerequisites
 
-# Outline
+> Python >= 3.10 (requires match statement)
+> Docker >= 20.10
+> Curl >= 7
+> Just >= 1.9
 
-## Directory Tree
-AACT_downloader
 
+# Usage
 
-## Key files index
 
-# Background on Docker
-Docker uses the following flow
+## Basic usage
 
-1. configuration using `docker-compose.yaml` or a `Dockerfile`
-2. `docker build .` to generate an image
-3. `docker run xxxxxx` to take the image and create a container.
-    - when the container is created, it starts, running commands as configured in the dockerfile.
-    - Consequently, the AACT database image when run must initialize the postgres db, then run the initalization details.
-    - Here is where bind mounts come into play.
+Check prerequisites
+```bash
+just check-status
+```
 
-## Multistage builds
-https://stackoverflow.com/questions/53659993/docker-multi-stage-how-to-split-up-into-multiple-dockerfiles
+Setup the underlying AACT database including downloading both 
+the AACT dump and historical data.
+```bash
+just create
+just select-trials
+just count=1000 get-histories
+```
+replacing the 1000 in `count=1000` with the number of trials you want to download.
 
-https://docs.docker.com/develop/develop-images/multistage-build/
+## Advanced Usage
 
-Basically
+If you need to reset the db without downloading the AACT dump
+```bash
+just rebuild
+just select-trials
+just count=1000 get-histories
+```
 
-## Dockerfile vs docker-compose.yaml
 
-A `Dockerfile` is used to create images.
+### Description of all the `just` recipes
 
-A `docker-compose.yaml` is used to automate the deployment of containers.
+# Background information
 
-## Types of storage
+This is designed to run on a linux machine with bash.
+If you are using a shell other than bash you should be aware of what
+is needed to run all of this using bash
 
-### COPY/ADD (Dockerfile)
+If any of the discussions below don't make sense, talk to your sysadmin,
+a local linux user, or reach out to the author.
 
-In a dockerfile, this adds a file permanently to the image.
+## Just installation
 
-This adds files one way to or from the container when initialized.
+I use the command runner `just` to automate/simplfy setting up the 
+docker containers and running many of the python scripts.
+It is similar to `make` in many ways but is designed to do less.
 
-### Volumes (docker-compose.yaml && Dockerfile)
+Just can be installed from https://github.com/casey/just/
 
-Useable in both docker-compose and Dockerfile's, this creates a permanent storage. 
-It can be maintained by docker or stored in a particular location.
+## Python installation
 
-Good for longer term storage such as databases.
+This requires python 3.10 or above due to the use of match-case statements
+in the html parser.
 
-### Bind mounts (docker-compose.yaml)
+Check which version of python you have by typing `python --version`.
+If you do not have the required version, I would recommend installing 
+the conda python manager and setting up a conda environment with python 3.10.
+Instructions for doing so are on the internet.
 
-Bind mounts are used to make a host filesystem resource
-available
+## Docker and Postgres
+Docker is a tool to manage and run OCI containers. 
+What this means in regards to this project is that docker makes it 
+easy to setup containers.
+
+Install docker based on instructions for your linux distribution.
+I use podman (an alternative from RedHat) because it allows for running without root permissions.
+
+### Docker networking
+
+It is helpful to construct an external docker network by running
+
+`docker network create network_name`
+
+and then including that network in the docker-compose.yaml
+
+# Environment Variables (`.env` file)
+I use an single .env file to setup the docker containers and pass configuration variables to 
+the python scripts. I would suggest changing the default values in `sample.env` to match your needs.
+If you do need to think about the security of your database I would recommend 
+you start by changing these.

Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql

@@ -0,0 +1,133 @@
+
+/* OVERVIEW
+ * 
+ * This links trials to the first date each drug (indexed by NDA/ANDA etc) is
+ * put on the market.
+ * 
+ * It takes 3 views to build up to it.
+ * */
+
+--Match trials to brands and ingredients
+create or replace view public.match_trials_to_bn_in as
+with trialncts as (
+        SELECT DISTINCT nct_id  FROM history.trial_snapshots TS
+    )
+SELECT 
+    bi.nct_id ,
+    bi.downcase_mesh_term, 
+    rr.tty2 ,
+    rr.rxcui2 as bn_or_in_cui, --brand or ingredient
+    count(*)
+FROM ctgov.browse_interventions bi
+    left outer JOIN rxnorm_migrated.rxnorm_props AS rp
+        on bi.downcase_mesh_term  = rp.propvalue1 --link names to drug cuis ()
+    left outer join rxnorm_migrated.rxnorm_relations rr 
+    	on rr.rxcui1 = rp.rxcui 
+WHERE
+    bi.nct_id in (
+        SELECT nct_id  FROM trialncts
+        )
+    and
+    bi.mesh_type='mesh-list'
+    and rp.propname = 'Active_ingredient_name'
+    and rr.tty2 in ('BN', 'IN', 'MIN')
+group by bi.nct_id, bi.downcase_mesh_term , rr.tty2 ,rr.rxcui2 
+order by bi.nct_id 
+;
+--running out of space.
+
+-- get list of interventions assoicated with trials of interest
+create temp table tmp_interventions as
+select * from ctgov.browse_interventions bi 
+where 
+	bi.mesh_type ='mesh-list'
+	and
+	bi.nct_id in (select distinct nct_id from history.trial_snapshots)
+;
+select * from tmp_interventions;
+
+--drop table tmp_join_interv_rxcui;
+create temp table tmp_join_interv_rxcui as
+select *
+from
+	tmp_interventions tint
+	inner join
+	rxnorm_migrated.rxnorm_props rp 
+		on tint.downcase_mesh_term = rp.propvalue1 
+where propname='RxNorm Name'
+;-- get the rxcui for ingredients
+
+select * from tmp_join_interv_rxcui;
+
+--filter rxcui -> is human prescribable
+create temp view tmp_view_prescribable as
+select count(*) from rxnorm_migrated.rxnorm_props rp 
+where 
+	rp.propname = 'PRESCRIBABLE' 
+	and 
+	rp.propvalue1 = 'Y'
+;
+
+--link prescribable to brand ingredients or brand names.
+	
+
+--get relationships of IN -> BN
+select *
+from 
+	rxnorm_migrated.rxnorm_relations rr 
+where 
+	rr.tty1 in ('IN','MIN')
+	and rr.rxcui1 in (select distinct rxcui from tmp_join_interv_rxcui tjir)
+	and rr.tty2 = 'BN'
+;
+
+
+
+--match trials to through brands NDC11
+create or replace view public.match_trial_to_ndc11 as
+select 
+	mttbi.nct_id,
+	ah.ndc,
+	count(*)
+from public.match_trials_to_bn_in as mttbi
+    left outer join rxnorm_migrated.rxnorm_relations as rr 
+    	on mttbi.bn_or_in_cui = rr.rxcui1
+    left outer join rxnorm_migrated."ALLNDC_HISTORY" as ah 
+        on rr.rxcui2 = ah.rxcui 
+where 
+    rr.tty1 = 'BN' 
+    and
+    rr.tty2 in ('SBD', 'BPCK')
+    and 
+    ah.sab='RXNORM' 
+group by mttbi.nct_id, ah.ndc
+order by mttbi.nct_id, ah.ndc
+;
+
+
+
+---associate trials to marketing start dates
+create or replace view public.match_trial_to_marketing_start_date as
+select 
+	mttn.nct_id,
+	n.application_number_or_citation,
+	min(n.marketing_start_date )
+from match_trial_to_ndc11 mttn 
+	inner join spl.nsde n 
+		on mttn.ndc = n.package_ndc11 
+where 	
+	n.product_type = 'HUMAN PRESCRIPTION DRUG'
+	and
+	n.marketing_category in ('NDA','ANDA','BLA', 'NDA authorized generic', 'NDA AUTHORIZED GENERIC')
+group by mttn.nct_id,n.application_number_or_citation 
+order by mttn.nct_id 
+;
+
+---Number of trials after a certain date
+select nct_id,count(distinct application_number_or_citation) 
+from public.match_trial_to_marketing_start_date mttmsd
+where "min" > '2012-06-01'
+group by nct_id
+;
+
+

Scripts/Backup_AACT_work.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+backup_dir="/mnt/will/large_data/Research_large_data/ClinicalTrialsDataProcessing/containers/AACT_Reloader/backup/"
+date_stamp=$(date +%Y%m%d_%H%M%S)
+filename="aact_db_backup_${date_stamp}.sql"
+container_name = ${1:-aact_db}
+
+podman exec "$container_name" pg_dump -U root aact_db > "${backup_dir}/${filename}"
+
+# Optional: compress the backup
+gzip "${backup_dir}/${filename}"

Scripts/ConfiguringFormularies.sql

@@ -0,0 +1,117 @@
+/*
+I started by creating a formularies schema,
+then importing the usp - dc formulary data through DBeaver's csv import.
+*/
+
+-- DROP SCHEMA "Formularies";
+
+CREATE SCHEMA "Formularies" AUTHORIZATION root;
+
+-- "Formularies".usp_dc_2023 definition
+
+-- Drop table
+
+-- DROP TABLE "Formularies".usp_dc_2023;
+
+CREATE TABLE "Formularies".usp_dc_2023 (
+	rxcui varchar(15) NULL, --yes even though this is a number, it is represented as a string elsewhere.
+	tty varchar(10) NULL,
+	"Name" varchar(256) NULL,
+	"Related BN" varchar(250) NULL,
+	"Related DF" varchar(25050) NULL,
+	"USP Category" varchar(250) NULL,
+	"USP Class" varchar(250) NULL,
+	"USP Pharmacotherapeutic Group" varchar(250) NULL,
+	"API Concept" varchar(250) NULL
+);
+
+/*
+I then linked the data back on itself with a materialized view, using claude.ai for simplicity.
+
+Claude.ai > I need a postres sql statement to create a materialized view that will take the following table and link from a given rxcui to the other rxcui's that share the same category and class
+
+```sql
+CREATE TABLE "Formularies".usp_dc_2023 (
+	rxcui int4 NULL,
+	tty varchar(10) NULL,
+	"Name" varchar(256) NULL,
+	"Related BN" varchar(250) NULL,
+	"Related DF" varchar(25050) NULL,
+	"USP Category" varchar(250) NULL,
+	"USP Class" varchar(250) NULL,
+	"USP Pharmacotherapeutic Group" varchar(250) NULL,
+	"API Concept" varchar(250) NULL
+);
+```
+
+It links rxcuis to other rxcuis where they have a matching USP Categories and Class
+This gives alternative RXCUIs based on category an class.
+*/
+CREATE MATERIALIZED VIEW "Formularies".rxcui_category_class_links AS
+WITH base AS (
+    SELECT DISTINCT
+        a.rxcui as source_rxcui,
+        b.rxcui as linked_rxcui,
+        a."USP Category" as category,
+        a."USP Class" as class
+    FROM "Formularies".usp_dc_2023 a
+    JOIN "Formularies".usp_dc_2023 b
+        ON a."USP Category" = b."USP Category"
+        AND a."USP Class" = b."USP Class"
+        AND a.rxcui != b.rxcui
+    WHERE a.rxcui IS NOT NULL
+    AND b.rxcui IS NOT NULL
+)
+SELECT * FROM base;
+
+-- Add indexes for better query performance
+CREATE INDEX ON "Formularies".rxcui_category_class_links (source_rxcui);
+CREATE INDEX ON "Formularies".rxcui_category_class_links (linked_rxcui);
+
+/*
+Next step is linking a given nct -> compounds -> formulary alternatives -> compounds -> brands/generics.
+I'll' break this into two steps.
+
+1. link formulary alternatives to compounds and brands,
+2. link nct_id to formulary alternatives
+*/
+drop if exists materialized view "Formularies".match_trial_compound_to_alternate_bn_rxcuis;
+drop if exists materialized view "Formularies".rxcui_to_brand_through_uspdc cascade;
+
+create materialized view "Formularies".rxcui_to_brand_through_uspdc AS
+select distinct
+	rccl.source_rxcui
+	,rccl.linked_rxcui
+	,rccl.category
+	,rccl."class"
+	,rr.tty1
+	--,rr.tty2
+	,rr.rxcui2
+from "Formularies".rxcui_category_class_links rccl
+join rxnorm_migrated.rxnorm_relations rr on rr.rxcui1 = rccl.linked_rxcui
+where rr.tty2 = 'BN'
+;
+
+/* So this one takes each RXCUI and it's associated RXCUIs from the same 
+category and class, and filters it down to associated RXCUI's that 
+represent brand names.
+ */
+
+create materialized view "Formularies".match_trial_compound_to_alternate_bn_rxcuis as
+select distinct mttbi.nct_id,  rtbtu.rxcui2 as brand_rxcuis
+from match_trials_to_bn_in mttbi
+join "Formularies".rxcui_to_brand_through_uspdc rtbtu
+	on mttbi.bn_or_in_cui = rtbtu.rxcui2
+;
+
+/*
+This takes the list of ingredients and brands associated with a trial, and 
+links it to the list of alternative brand names.
+*/
+
+--renamed the view
+CREATE OR REPLACE VIEW "Formularies".nct_to_brand_counts_through_uspdc
+AS SELECT mtctabr.nct_id,
+    count(*) AS brand_name_counts
+   FROM "Formularies".match_trial_compound_to_alternate_bn_rxcuis mtctabr
+  GROUP BY mtctabr.nct_id;

Scripts/Data_summaries.sql

@@ -0,0 +1,100 @@
+
+/* How many trials were included?
+ * How many trial were inspected?
+ * How many trials were reserved for downloaded?
+ * How many trials didn't get included for some technical reason?
+ * 
+********* Data from 2023-03-29 ***********
+Of Interest  1981
+Reserved    1709 #I believe this is lower than the downloaded number because I reserved them earlier
+Downloaded  1960
+Incomplete  3 #there were are few http 500 and 404 codes
+******************************************
+ * Note there were 21 missing trials of interest.
+ * */
+select status,count(distinct nct_id) from http.download_status ds 
+group by status;
+
+/* Get a list of trials
+ * -- There are currently 304 trials for which I was able to extract unique snapshots (2023-03-29)
+ * -- There are currently 1138 trials for which I was able to extract unique snapshots (2023-04-03)
+ * */
+select count(distinct nct_id) from history.trial_snapshots ts
+
+/* Get the number of listed conditions
+ * -- There are only 609 listed (MeSH classified) conditions from 284 trials(2023-03-29)
+ * I may need to expand how I address conditions
+ */
+select count(*)
+from ctgov.browse_conditions bc
+where
+mesh_type = 'mesh-list'
+and
+nct_id in (select distinct nct_id from history.trial_snapshots ts)
+;
+
+select count(distinct nct_id)
+from ctgov.browse_conditions bc
+where
+mesh_type = 'mesh-list'
+and
+nct_id in (select distinct nct_id from history.trial_snapshots ts)
+;
+
+/*
+ * If I were to expand that to non-coded conditions that would be
+ * 304 trials with 398 conditions
+ * */
+select count(distinct nct_id)
+from ctgov.conditions bc
+where
+nct_id in (select distinct nct_id from history.trial_snapshots ts)
+;
+select count(*) from ctgov.conditions c 
+where 
+nct_id in (select distinct nct_id from history.trial_snapshots ts)
+
+
+/* Get the number of matches from UMLS
+ * There are about 5,808 proposed matches.
+ * 
+ */
+select count(*) from "DiseaseBurden".trial_to_icd10 tti ;
+--1383 before run at 8pm 2023-03-29
+--5209 at 2023-04-03T11:21
+
+
+/*Get the number of trials that have links to icd10 trials*/
+select tti.approved,count(distinct nct_id) from "DiseaseBurden".trial_to_icd10 tti 
+group by tti.approved;
+
+-- finding and removing duplicates from the trial linking stuff. Useful when you redownload trials.
+/*
+with CTE as (
+    select row_number() over (partition by nct_id, "condition",ui) as rownum, *
+    from "DiseaseBurden".trial_to_icd10 tti 
+)
+delete from "DiseaseBurden".trial_to_icd10 tti2 
+where id in (
+    select id from cte where rownum > 1
+    );
+*/
+
+--get the number of completed vs terminated trials
+select overall_status,count(distinct nct_id) 
+from ctgov.studies s 
+where nct_id in (select distinct nct_id from "DiseaseBurden".trial_to_icd10 tti where tti.approved ='accepted' )
+group by overall_status 
+;
+
+select overall_status,count(distinct nct_id) 
+from ctgov.studies s 
+where nct_id in (select distinct nct_id from "DiseaseBurden".trial_to_icd10 tti)
+group by overall_status 
+;
+
+select overall_status,count(distinct nct_id) 
+from ctgov.studies s 
+where nct_id in (select distinct nct_id from history.trial_snapshots ts  )
+group by overall_status 
+;

Scripts/DevelopingLinks.sql

@@ -0,0 +1,38 @@
+--TODO: Document and migrate to setup
+
+drop table if exists "DiseaseBurden".trial_to_icd10;
+drop type if exists "DiseaseBurden".validation_type;
+
+create type "DiseaseBurden".validation_type as enum ('accepted', 'rejected', 'unmatched');
+comment on type "DiseaseBurden".validation_type is 'This is used to record interactions with each type. It can be accepted (yes this should be used), rejected (no this doesn`t match), or unmatched (where non of the proposed options match)';
+
+
+CREATE TABLE "DiseaseBurden".trial_to_icd10 (
+    id integer NOT NULL GENERATED ALWAYS AS IDENTITY,
+    nct_id varchar NOT NULL,
+    "condition" varchar NOT NULL,
+    ui varchar NULL,
+    uri varchar NULL,
+    rootsource varchar NULL,
+    "name" varchar NULL,
+    "source" varchar null,
+    approved "DiseaseBurden".validation_type,
+    approval_timestamp timestamp,
+        CONSTRAINT trial_to_icd10_pk PRIMARY KEY (id)
+);
+comment on type "DiseaseBurden".trial_to_icd10 is 'This represents potential links between trials and icd10 codes. Most of the links are both automatic and wrong.';
+
+
+
+DROP TABLE if exists "DiseaseBurden".icd10_to_cause;
+ 
+CREATE TABLE "DiseaseBurden".icd10_to_cause (
+    id SERIAL NOT NULL ,
+    code varchar NOT NULL,
+    cause_text varchar NOT NULL,
+    CONSTRAINT icd10_to_cause_pk PRIMARY KEY (id)
+);
+
+
+
+

Scripts/Extracting Tables Views and MatViews.sql

@@ -0,0 +1,38 @@
+SELECT 
+    'CREATE OR REPLACE VIEW ' || schemaname || '.' || viewname || ' AS ' || definition
+FROM pg_views 
+    WHERE schemaname != 'pg_catalog'  
+        and schemaname != 'information_schema' -- Replace with your schema name
+;
+
+SELECT 
+    'CREATE OR REPLACE MATERIALIZED VIEW ' || schemaname || '.' || viewname || ' AS ' || definition
+FROM pg_views 
+    WHERE schemaname != 'pg_catalog'  
+    and schemaname != 'information_schema'
+;
+
+SELECT 
+    'CREATE TABLE ' || schemaname || '.' || tablename || E'\n(\n' ||
+    string_agg(column_definition, E',\n') || E'\n);\n'
+FROM (
+    SELECT 
+        schemaname,
+        tablename,
+        column_name || ' ' || data_type ||
+        CASE 
+            WHEN character_maximum_length IS NOT NULL THEN '(' || character_maximum_length || ')'
+            ELSE ''
+        END ||
+        CASE 
+            WHEN is_nullable = 'NO' THEN ' NOT NULL'
+            ELSE ''
+        END as column_definition
+    FROM pg_catalog.pg_tables t
+    JOIN information_schema.columns c 
+        ON t.schemaname = c.table_schema 
+        AND t.tablename = c.table_name
+    WHERE schemaname != 'pg_catalog'  
+    	and schemaname != 'information_schema'-- Replace with your schema name
+) t
+GROUP BY schemaname, tablename;

Scripts/ExtractingData.sql

@@ -0,0 +1,658 @@
+create extension tablefunc;
+
+/*Getting Trial Data all together
+ * There are 3 main datasets to join per trial:
+ * 
+ * - Trial Data (still need to stick it together)
+ *   - Duration and enrollment data
+ * - Compound Marketing (can get for any trial)
+ *   - how many individual brands per compound at the start of the trial
+ * - Disease Data (can get for verified trials)
+ *   - Population upper limit (Global Burdens of Disease)
+ *   - Category (ICD10 2nd level groups)
+ */
+
+/*Disease Data*/
+-- ICD10 Category and GBD data
+with cte as (
+    select 
+        nct_id,
+        max("level") as max_level
+    from trial_to_cause
+    group by nct_id
+), cte2 as (
+    select 
+        ttc.nct_id,
+        ttc.ui,
+        ttc."condition",
+        ttc.cause_text,
+        ttc.cause_id,
+        cte.max_level
+    from trial_to_cause ttc
+        join cte 
+            on cte.nct_id=ttc.nct_id
+    where ttc."level"=cte.max_level
+    group by 
+        ttc.nct_id,
+        ttc.ui,
+        ttc."condition",
+        ttc.cause_text,
+        ttc.cause_id,
+        cte.max_level
+    order by nct_id,ui
+), cte3 as (
+select 
+    nct_id,
+    substring(cte2.ui for 3) as code,
+    cte2."condition",
+    cte2.cause_text,
+    cte2.cause_id,
+    ic.id as category_id,
+    ic.group_name 
+from cte2
+    join "DiseaseBurden".icd10_categories ic 
+        on 
+            substring(cte2.ui for 3) <= ic.end_code
+            and         
+            substring(cte2.ui for 3) >= ic.start_code
+)
+select nct_id, cause_id,category_id
+from cte3
+group by nct_id, cause_id, category_id
+;
+--still need to link to actual disease burdens.
+
+/*Compound Marketing Data*/
+---Number of trials after a certain date
+with marketing_cte as (
+    select nct_id,count(distinct application_number_or_citation) 
+    from public.match_trial_to_marketing_start_date mttmsd
+    where "min" > '2012-06-01'
+    group by nct_id
+)
+select * from marketing_cte
+;
+
+/*Get versions*/
+/* Ignore this version
+with cte1 as (
+    select nct_id,min("version") over (partition by nct_id) as min_version
+    from history.trial_snapshots ts 
+    where 
+        ts.start_date < ts.submission_date
+), cte2 as (
+    select * from cte1
+    group by nct_id, min_version
+    order by nct_id 
+), cte3 as (
+    select 
+        ts2.nct_id, 
+        ts2."version", 
+        ts2.overall_status,
+        ts2.submission_date,
+        ts2.start_date,
+        ts2.enrollment,
+        ts2.enrollment_category,
+        ts2.primary_completion_date,
+        ts2.primary_completion_date_category ,
+        --mv.nct_id,
+        mv.min_version
+    from history.trial_snapshots ts2 
+        join cte2 mv 
+            on mv.nct_id = ts2.nct_id
+    where 
+        ts2."version" = mv.min_version
+    order by ts2.nct_id 
+), cte4 as (
+    select cte3.nct_id, cte3.submission_date - cte3.start_date as submission_presecence
+    from cte3
+)
+select avg(submission_presecence)
+from cte4
+;
+--avg 61 day difference
+ */
+
+--use this version 
+with cte1 as ( --get trials
+    select nct_id,max("version") over (partition by nct_id) as min_version
+    from history.trial_snapshots ts 
+    where 
+        ts.start_date > ts.submission_date
+), cte2 as ( --
+    select * from cte1
+    group by nct_id, min_version
+    order by nct_id 
+), cte3 as (
+    select 
+        ts2.nct_id, 
+        ts2."version", 
+        ts2.overall_status,
+        ts2.submission_date,
+        ts2.start_date,
+        ts2.enrollment,
+        ts2.enrollment_category,
+        ts2.primary_completion_date,
+        ts2.primary_completion_date_category ,
+        --mv.nct_id,
+        mv.min_version
+    from history.trial_snapshots ts2 
+        join cte2 mv 
+            on mv.nct_id = ts2.nct_id
+    where 
+        ts2."version" = mv.min_version
+    order by ts2.nct_id 
+)
+select * 
+from cte3
+    where 
+        enrollment is null 
+        or enrollment_category is null 
+        or primary_completion_date is null 
+        or primary_completion_date_category is null 
+        or start_date is null
+/*, cte4 as (
+    select cte3.nct_id, cte3.submission_date - cte3.start_date as submission_presecence
+    from cte3
+)
+select avg(submission_presecence)
+from cte4
+; -- -33 day difference on average
+*/
+
+
+        
+        
+        
+        
+        
+        
+        
+with cte1_min as (
+    select nct_id,min("version") over (partition by nct_id) as min_version
+    from history.trial_snapshots ts 
+    where 
+        ts.start_date <= ts.submission_date
+),cte1_max as (
+    select nct_id,max("version") over (partition by nct_id) as max_version
+    from history.trial_snapshots ts 
+    where 
+        ts.start_date >= ts.submission_date
+), cte2_min as (
+    select * from cte1_min
+    group by nct_id, min_version
+), cte2_max as (
+    select * from cte1_max
+    group by nct_id, max_version
+)
+select *
+from cte2_min 
+    join cte2_max
+        on cte2_min.nct_id=cte2_max.nct_id
+where min_version >= max_version
+        
+        
+        
+        
+        
+        
+        
+        
+
+
+/* Neet to take a different tack in filling out the is version of the data.
+ * The idea is that we need the latest of each major category
+ * before the start date.
+ * */
+
+--get the set of trials which have 
+with cte as ( 
+    /* Get the absolute difference between the start date and the 
+     * submission_date for each version of the trial (measured in days)
+     * 
+     */
+    select 
+        s.nct_id,
+        s.start_date,
+        ts."version",
+        ts.submission_date,
+        abs(extract(epoch from ts.submission_date - s.start_date)::float/(24*60*60)) as start_deviance
+    from ctgov.studies s 
+        join history.trial_snapshots ts 
+            on s.nct_id = ts.nct_id 
+    where s.nct_id in (select distinct nct_id from "DiseaseBurden".trial_to_icd10 tti)
+),cte2 as (
+    /* Rank each version based on it's proximity to the start date
+     * */
+    select 
+        cte.nct_id,
+        cte."version", 
+        row_number() over (partition by cte.nct_id order by cte.start_deviance) as rownum,
+        cte.submission_date,
+        cte.start_deviance,
+        cte.start_date,
+        ts.primary_completion_date ,
+        ts.primary_completion_date_category ,
+        ts.overall_status ,
+        ts.enrollment ,
+        ts.enrollment_category 
+    from cte
+        join history.trial_snapshots ts 
+            on cte.nct_id=ts.nct_id and cte."version"=ts."version"
+), cte3_primary_completion as (
+    /* for each trial
+     * select the version with a filled out primary_completion_source
+     * that is closest to the start date.
+     * */
+    select cte2.nct_id, min(cte2.rownum) as primary_completion_source
+    from cte2
+    where cte2.primary_completion_date is not null
+    group by cte2.nct_id
+), cte3_enrollment as (
+    /* for each trial
+     * select the version with a filled out enrollment
+     * that is closest to the start date.
+     * */
+    select cte2.nct_id, min(cte2.rownum) as enrollment_source
+    from cte2
+    where cte2.enrollment is not null
+    group by cte2.nct_id
+), cte4 as (
+/* join the best options together to get the data of interest.
+ * 
+ * On further inspection there are just a view of those, with 
+ * many of them having a 7+ month difference between the two versions.
+ * I think I am going to drop them.
+ * */
+select 
+    c3e.nct_id,
+    --c2a.submission_date as submission_date_a,
+    --c2b.submission_date as submission_date_b,
+    --c3e.enrollment_source,
+    c2a."version" as version_a,
+    c2a.enrollment,
+    c2a.enrollment_category,
+    --c3p.primary_completion_source ,
+    c2b."version" as version_b,
+    c2b.primary_completion_date,
+    c2b.primary_completion_date_category
+from cte3_enrollment c3e
+    join cte2 c2a
+        on c3e.nct_id = c2a.nct_id and c3e.enrollment_source = c2a.rownum
+    join cte3_primary_completion c3p
+        on c3e.nct_id = c3p.nct_id
+    join cte2 c2b 
+        on c3p.nct_id=c2b.nct_id and c3p.primary_completion_source = c2b.rownum
+), cte5 as (
+    select nct_id
+    from cte4 where version_a != version_b
+)
+select 
+    c.nct_id,
+    s2.overall_status,
+    c.enrollment as planned_enrollment,
+    s2.enrollment, 
+    s2.start_date,
+    c.primary_completion_date as planned_primary_completion_date,
+    s2.primary_completion_date,
+    extract(epoch from c.primary_completion_date - s2.start_date)/(24*60*60) as planned_duration,
+    s2.primary_completion_date - s2.start_date as actual_duration
+from cte4 c
+    join ctgov.studies s2 
+        on c.nct_id = s2.nct_id 
+where c.nct_id not in (select nct_id from cte5)
+;
+
+
+/*
+ * Concern about causal inference
+ * 
+ * When putting the data together for CBO it looked like we got occasional updates about 
+ * the status of trials that included enrollment updates.
+ * That doesn't appear to be the case, but that messes with the ability to causally identify
+ * any results. I need to be careful about this data is used.
+ * 
+ * I created the statements below to get the data that I need.
+ */
+
+
+
+----get the set of trial snapshots
+create or replace view public.view_cte as 
+select 
+    nct_id, 
+    primary_completion_date, 
+    primary_completion_date_category, 
+    enrollment, 
+    start_date,
+    enrollment_category ,
+    overall_status,
+    --count("version"),
+    min(submission_date) as earliest_date_observed
+from history.trial_snapshots ts 
+where 
+    nct_id in (select distinct nct_id from "DiseaseBurden".trial_to_icd10 tti where tti.approved='accepted')
+    and submission_date >= start_date 
+    and overall_status not in ('Completed','Terminated')
+group by 
+    nct_id, 
+    primary_completion_date, 
+    primary_completion_date_category,
+    start_date,
+    enrollment, 
+    enrollment_category ,
+    overall_status
+;
+create or replace view public.view_disbur_cte0 as 
+select tti.nct_id, tti.ui , tti."condition",itc.cause_text, ch.cause_id, ch."level" 
+from "DiseaseBurden".trial_to_icd10 tti 
+    join "DiseaseBurden".icd10_to_cause itc
+        on replace(REPLACE(tti.ui,'-',''),'.','') = replace(REPLACE(itc.code ,'-',''),'.','')
+    join "DiseaseBurden".cause_hierarchy  ch
+        on itc.cause_text = ch.cause_name
+where 
+    tti.approved = 'accepted'
+;
+create or replace view  public.view_trial_to_cause as 
+select tti.nct_id, tti.ui , tti."condition",itc.cause_text, ch.cause_id, ch."level" 
+from "DiseaseBurden".trial_to_icd10 tti 
+    join "DiseaseBurden".icd10_to_cause itc
+        on replace(REPLACE(tti.ui,'-',''),'.','') = replace(REPLACE(itc.code ,'-',''),'.','')
+    join "DiseaseBurden".cause_hierarchy  ch
+        on itc.cause_text = ch.cause_name
+where 
+    tti.approved = 'accepted'
+order by nct_id 
+;--does this duplicate the view above?
+
+create or replace view  public.view_disbur_cte as 
+select 
+    nct_id,
+    max("level") as max_level
+from view_disbur_cte0
+group by nct_id
+
+;
+create or replace view  public.view_disbur_cte2 as 
+select 
+    ttc.nct_id,
+    ttc.ui,
+    ttc."condition",
+    ttc.cause_text,
+    ttc.cause_id,
+    disbur_cte.max_level
+from view_trial_to_cause ttc
+    join view_disbur_cte as disbur_cte
+        on disbur_cte.nct_id=ttc.nct_id
+where ttc."level"=disbur_cte.max_level
+group by 
+    ttc.nct_id,
+    ttc.ui,
+    ttc."condition",
+    ttc.cause_text,
+    ttc.cause_id,
+    disbur_cte.max_level
+order by nct_id,ui
+;
+create or replace view  public.view_disbur_cte3 as 
+select 
+    nct_id,
+    substring(disbur_cte2.ui for 3) as code,
+    disbur_cte2."condition",
+    disbur_cte2.cause_text,
+    disbur_cte2.cause_id,
+    ic.chapter_code  as category_id,
+    ic.group_name,
+    disbur_cte2.max_level
+from view_disbur_cte2 as disbur_cte2
+    join "DiseaseBurden".icd10_categories ic 
+        on 
+            substring(disbur_cte2.ui for 3) <= ic.end_code
+            and         
+            substring(disbur_cte2.ui for 3) >= ic.start_code
+where ic."level" = 1
+    
+;
+create or replace view  public.view_burdens_cte as 
+select * 
+from "DiseaseBurden".burdens b 
+where  b.sex_id = 3 --both sexes
+    and b.metric_id = 1 --number/count
+    and b.measure_id = 2 --DALYs
+    and b.age_id =22 --all ages
+;
+create or replace view  public.view_burdens_cte2 as 
+select 
+    --c1.location_id,
+    c1.cause_id,
+    c1."year",
+    --high sdi
+    c1.val as h_sdi_val,
+    c1.upper_95 as h_sdi_u95,
+    c1.lower_95 as h_sdi_l95,
+    --high-middle sdi
+    c2.val as hm_sdi_val,
+    c2.upper_95 as hm_sdi_u95,
+    c2.lower_95 as hm_sdi_l95,
+    --middle sdi
+    c3.val as m_sdi_val,
+    c3.upper_95 as m_sdi_u95,
+    c3.lower_95 as m_sdi_l95,
+    --low-middle sdi
+    c4.val as lm_sdi_val,
+    c4.upper_95 as lm_sdi_u95,
+    c4.lower_95 as lm_sdi_l95,
+    --low sdi
+    c5.val as l_sdi_val,
+    c5.upper_95 as l_sdi_u95,
+    c5.lower_95 as l_sdi_l95
+from view_burdens_cte c1
+    join view_burdens_cte c2
+        on c1.cause_id = c2.cause_id
+            and c1."year" = c2."year"
+    join view_burdens_cte c3
+        on c1.cause_id = c3.cause_id
+            and c1."year" = c3."year"
+    join view_burdens_cte c4
+        on c1.cause_id = c4.cause_id
+            and c1."year" = c4."year"
+    join view_burdens_cte c5
+        on c1.cause_id = c5.cause_id
+            and c1."year" = c5."year"
+where c1.location_id = 44635
+    and c2.location_id = 44634
+    and c3.location_id = 44639
+    and c4.location_id = 44636
+    and c5.location_id = 44637
+;
+--drop view if exists public.formatted_data cascade;
+create or replace view public.formatted_data as 
+select 
+    cte.nct_id,
+    cte.start_date,
+    cte.enrollment as current_enrollment,
+    cte.enrollment_category,
+    cte.overall_status  as current_status,
+    cte.earliest_date_observed,
+    extract( epoch from (cte.earliest_date_observed - cte.start_date))/extract( epoch from (cte.primary_completion_date - cte.start_date)) as elapsed_duration
+    ,count(distinct mttmsd."application_number_or_citation") as n_brands
+    ,dbc3.code
+    ,dbc3."condition"
+    ,dbc3.cause_text
+    ,dbc3.cause_id
+    ,dbc3.category_id
+    ,dbc3.group_name
+    ,dbc3.max_level
+    --c1.location_id,
+    --,b.cause_id
+    ,b."year",
+    --high sdi
+    b.h_sdi_val,
+    b.h_sdi_u95,
+    b.h_sdi_l95,
+    --high-middle sdi
+    b.hm_sdi_val,
+    b.hm_sdi_u95,
+    b.hm_sdi_l95,
+    --middle sdi
+    b.m_sdi_val,
+    b.m_sdi_u95,
+    b.m_sdi_l95,
+    --low-middle sdi
+    b.lm_sdi_val,
+    b.lm_sdi_u95,
+    b.lm_sdi_l95,
+    --low sdi
+    b.l_sdi_val,
+    b.l_sdi_u95,
+    b.l_sdi_l95
+from view_cte as cte
+    join public.match_trial_to_marketing_start_date mttmsd 
+        on cte.nct_id = mttmsd."nct_id"
+    join view_disbur_cte3 dbc3
+        on dbc3.nct_id = cte.nct_id
+    join view_burdens_cte2 b 
+        on b.cause_id = dbc3.cause_id and extract(year from b."year") = extract(year from cte.earliest_date_observed)
+where 
+    mttmsd."min" <= cte.earliest_date_observed
+group by 
+    cte.nct_id,
+    cte.start_date,
+    cte.enrollment,
+    cte.enrollment_category,
+    cte.overall_status,
+    cte.earliest_date_observed,
+    elapsed_duration
+    ,dbc3.code
+    ,dbc3."condition"
+    ,dbc3.cause_text
+    ,dbc3.cause_id
+    ,dbc3.category_id
+    ,dbc3.group_name
+    ,dbc3.max_level
+    --c1.location_id,
+    ,b.cause_id,
+    b."year",
+    --high sdi
+    b.h_sdi_val,
+    b.h_sdi_u95,
+    b.h_sdi_l95,
+    --high-middle sdi
+    b.hm_sdi_val,
+    b.hm_sdi_u95,
+    b.hm_sdi_l95,
+    --middle sdi
+    b.m_sdi_val,
+    b.m_sdi_u95,
+    b.m_sdi_l95,
+    --low-middle sdi
+    b.lm_sdi_val,
+    b.lm_sdi_u95,
+    b.lm_sdi_l95,
+    --low sdi
+    b.l_sdi_val,
+    b.l_sdi_u95,
+    b.l_sdi_l95
+order by cte.nct_id ,cte.earliest_date_observed
+;--used this one 2023-04-05
+--get the planned enrollment
+create or replace view public.time_between_submission_and_start_view as 
+    /* Get the absolute difference between the start date and the 
+     * submission_date for each version of the trial (measured in days)
+     * 
+     */
+select 
+    s.nct_id,
+    s.start_date,
+    ts."version",
+    ts.submission_date,
+    abs(extract(epoch from ts.submission_date - s.start_date)::float/(24*60*60)) as start_deviance
+from ctgov.studies s 
+    join history.trial_snapshots ts 
+        on s.nct_id = ts.nct_id 
+where s.nct_id in (select distinct nct_id from "DiseaseBurden".trial_to_icd10 tti)
+;
+create or replace view rank_proximity_to_start_time_view as 
+    /* Rank each version based on it's proximity to the start date
+     * */
+    select 
+        cte.nct_id,
+        cte."version", 
+        row_number() over (partition by cte.nct_id order by cte.start_deviance) as rownum,
+        cte.submission_date,
+        cte.start_deviance,
+        cte.start_date,
+        ts.primary_completion_date ,
+        ts.primary_completion_date_category ,
+        ts.overall_status ,
+        ts.enrollment ,
+        ts.enrollment_category 
+    from public.time_between_submission_and_start_view cte
+        join history.trial_snapshots ts 
+            on cte.nct_id=ts.nct_id and cte."version"=ts."version"
+;
+create or replace view enrollment_closest_to_start_view as 
+    /* for each trial
+     * select the version with a filled out enrollment
+     * that is closest to the start date.
+     * */
+    select cte2.nct_id, min(cte2.rownum) as enrollment_source
+    from rank_proximity_to_start_time_view cte2
+    where cte2.enrollment is not null
+    group by cte2.nct_id
+;
+--drop view public.formatted_data_with_planned_enrollment ;
+create or replace view formatted_data_with_planned_enrollment as
+select 
+    f.*, 
+    s.overall_status as final_status,
+    c2a."version",
+    c2a.enrollment as planned_enrollment
+from formatted_data f
+    join ctgov.studies s 
+        on f.nct_id = s.nct_id 
+    join enrollment_closest_to_start_view c3e
+        on c3e.nct_id = f.nct_id
+    join rank_proximity_to_start_time_view c2a
+        on c3e.nct_id = c2a.nct_id and c3e.enrollment_source = c2a.rownum
+;
+select * from formatted_data_with_planned_enrollment
+
+-------------------GET COUNTS------------------
+select count(distinct nct_id) from public.view_cte; --88
+select count(distinct nct_id) from public.view_disbur_cte0; --130
+select count(distinct nct_id) from public.view_trial_to_cause; --130
+select count(distinct nct_id) from public.view_disbur_cte;--130
+select count(distinct nct_id) from public.view_disbur_cte2;--130
+select count(distinct nct_id) from public.view_disbur_cte3;--130
+select count(distinct nct_id) from public.formatted_data; --48 probably because there are so many trials that don't fall into a GBD category/cause
+select count(distinct nct_id) from public.time_between_submission_and_start_view;--1067
+select count(distinct nct_id) from rank_proximity_to_start_time_view;--1067
+select count(distinct nct_id) from enrollment_closest_to_start_view;--1067
+select count(distinct nct_id) from formatted_data_with_planned_enrollment;--48
+
+
+
+select count(distinct nct_id) from public.view_trial_to_cause; --130
+select count(distinct nct_id) from formatted_data_with_planned_enrollment;--48
+
+
+--get durations and count snapshots per trial per trial
+with cte1 as (
+select 
+    nct_id, 
+    start_date , 
+    primary_completion_date, 
+    overall_status ,
+    primary_completion_date - start_date as duration
+from ctgov.studies s 
+where nct_id in (select distinct nct_id from http.download_status ds)
+), cte2 as (
+select nct_id,count(*) as snapshot_count from formatted_data_with_planned_enrollment fdwpe
+group by nct_id
+)
+select a.nct_id, a.overall_status, a.duration,b.snapshot_count
+from cte1 as a
+    join cte2 as b
+        on a.nct_id=b.nct_id
+;

Scripts/GroupingTrials.sql

@@ -0,0 +1,104 @@
+select * from "DiseaseBurden".icd10_to_cause itc ;
+select * from "DiseaseBurden".cause c ;
+
+
+
+
+select c.id, count(distinct code)
+from "DiseaseBurden".cause c 
+    join "DiseaseBurden".icd10_to_cause itc 
+        on c.cause = itc.cause_text 
+group by c.id
+order by c.id
+;
+
+select tti.approved,count(distinct nct_id) from "DiseaseBurden".trial_to_icd10 tti 
+group by tti.approved;
+
+select nct_id, "condition", ui
+from "DiseaseBurden".trial_to_icd10 tti 
+where tti.approved = 'accepted';
+
+drop  view trial_to_cause;
+
+---Link trials to their causes
+
+create temp view trial_to_cause as
+select tti.nct_id, tti.ui , tti."condition",itc.cause_text, ch.cause_id, ch."level" 
+from "DiseaseBurden".trial_to_icd10 tti 
+    join "DiseaseBurden".icd10_to_cause itc
+        on replace(REPLACE(tti.ui,'-',''),'.','') = replace(REPLACE(itc.code ,'-',''),'.','')
+    join "DiseaseBurden".cause_hierarchy  ch
+        on itc.cause_text = ch.cause_name
+where 
+    tti.approved = 'accepted'
+order by nct_id 
+;
+
+select distinct nct_id, count(*), min("level"), max("level")
+from trial_to_cause ttc
+group by nct_id
+;
+
+select nct_id,cause_text,cause_id from trial_to_cause
+where level = 3
+group by nct_id,cause_text,cause_id
+order by cause_id
+;
+
+select cause_id,"condition",cause_text,count(distinct nct_id) as c
+from trial_to_cause
+where level >= 3
+group by cause_id,"condition",cause_text
+--having count(distinct nct_id) > 2
+order by cause_id
+;
+
+with cte as (
+    select 
+        nct_id,
+        max("level") as max_level
+    from trial_to_cause
+    group by nct_id
+), cte2 as (
+    select 
+        ttc.nct_id,
+        ttc.ui,
+        ttc."condition",
+        ttc.cause_text,
+        ttc.cause_id,
+        cte.max_level
+    from trial_to_cause ttc
+        join cte 
+            on cte.nct_id=ttc.nct_id
+    where ttc."level"=cte.max_level
+    group by 
+        ttc.nct_id,
+        ttc.ui,
+        ttc."condition",
+        ttc.cause_text,
+        ttc.cause_id,
+        cte.max_level
+    order by nct_id,ui
+), cte3 as (
+select 
+    nct_id,
+    substring(cte2.ui for 3) as code,
+    cte2."condition",
+    cte2.cause_text,
+    cte2.cause_id,
+    ic.id as category_id,
+    ic.group_name 
+from cte2
+    join "DiseaseBurden".icd10_categories ic 
+        on 
+            substring(cte2.ui for 3) <= ic.end_code
+            and         
+            substring(cte2.ui for 3) >= ic.start_code
+)
+select nct_id, cause_id,category_id
+from cte3
+group by nct_id, cause_id, category_id
+;
+
+

Scripts/TablesAndViews_Public.sql

@@ -0,0 +1,83 @@
+
+drop view if exists public.match_trial_to_marketing_start_date;
+DROP VIEW if exists public.match_trial_to_ndc11;
+drop view if exists public.match_trials_to_bn_in;
+
+drop view if exists history.match_drugs_to_trials;
+DROP TABLE IF EXISTS history.trial_snapshots;
+
+CREATE TABLE IF NOT EXISTS history.trial_snapshots
+(
+    nct_id character varying(15) COLLATE pg_catalog."default" NOT NULL,
+    version integer NOT NULL,
+    submission_date timestamp without time zone,
+    primary_completion_date timestamp without time zone,
+    primary_completion_date_category history.updatable_catetories,
+    start_date timestamp without time zone,
+    start_date_category history.updatable_catetories,
+    completion_date timestamp without time zone,
+    completion_date_category history.updatable_catetories,
+    overall_status history.study_statuses,
+    enrollment integer,
+    enrollment_category history.updatable_catetories,
+    sponsor character varying COLLATE pg_catalog."default",
+    responsible_party character varying COLLATE pg_catalog."default",
+    CONSTRAINT trial_snapshots_pkey PRIMARY KEY (nct_id, version)
+);
+
+
+ALTER TABLE IF EXISTS history.trial_snapshots
+    OWNER to root;
+
+
+CREATE OR REPLACE VIEW history.match_drugs_to_trials
+AS SELECT bi.nct_id,
+    rp.rxcui,
+    rp.propvalue1
+   FROM ctgov.browse_interventions bi
+     JOIN rxnorm_migrated.rxnorm_props rp ON bi.downcase_mesh_term::text = rp.propvalue1::text
+  WHERE rp.propname::text = 'RxNorm Name'::text AND (bi.nct_id::text IN ( SELECT trial_snapshots.nct_id
+           FROM history.trial_snapshots));
+           
+       
+CREATE OR REPLACE VIEW public.match_trials_to_bn_in
+AS WITH trialncts AS (
+         SELECT DISTINCT ts.nct_id
+           FROM history.trial_snapshots ts
+        )
+ SELECT bi.nct_id,
+    bi.downcase_mesh_term,
+    rr.tty2,
+    rr.rxcui2 AS bn_or_in_cui,
+    count(*) AS count
+   FROM ctgov.browse_interventions bi
+     LEFT JOIN rxnorm_migrated.rxnorm_props rp ON bi.downcase_mesh_term::text = rp.propvalue1::text
+     LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON rr.rxcui1 = rp.rxcui
+  WHERE (bi.nct_id::text IN ( SELECT trialncts.nct_id
+           FROM trialncts)) AND bi.mesh_type::text = 'mesh-list'::text AND rp.propname::text = 'Active_ingredient_name'::text AND (rr.tty2 = ANY (ARRAY['BN'::bpchar, 'IN'::bpchar, 'MIN'::bpchar]))
+  GROUP BY bi.nct_id, bi.downcase_mesh_term, rr.tty2, rr.rxcui2
+  ORDER BY bi.nct_id;
+  
+  
+CREATE OR REPLACE VIEW public.match_trial_to_ndc11
+AS SELECT mttbi.nct_id,
+    ah.ndc,
+    count(*) AS count
+   FROM match_trials_to_bn_in mttbi
+     LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON mttbi.bn_or_in_cui = rr.rxcui1
+     LEFT JOIN rxnorm_migrated."ALLNDC_HISTORY" ah ON rr.rxcui2 = ah.rxcui
+  WHERE rr.tty1 = 'BN'::bpchar AND (rr.tty2 = ANY (ARRAY['SBD'::bpchar, 'BPCK'::bpchar])) AND ah.sab::text = 'RXNORM'::text
+  GROUP BY mttbi.nct_id, ah.ndc
+  ORDER BY mttbi.nct_id, ah.ndc;
+  
+  
+CREATE OR REPLACE VIEW public.match_trial_to_marketing_start_date
+AS SELECT mttn.nct_id,
+    n.application_number_or_citation,
+    min(n.marketing_start_date) AS min
+   FROM match_trial_to_ndc11 mttn
+     JOIN spl.nsde n ON mttn.ndc = n.package_ndc11::bpchar
+  WHERE n.product_type::text = 'HUMAN PRESCRIPTION DRUG'::text AND (n.marketing_category::text = ANY (ARRAY['NDA'::character varying, 'ANDA'::character varying, 'BLA'::character varying, 'NDA authorized generic'::character varying, 'NDA AUTHORIZED GENERIC'::character varying]::text[]))
+  GROUP BY mttn.nct_id, n.application_number_or_citation
+  ORDER BY mttn.nct_id;
+  

Scripts/VariousDevelopmentsForAnalysis.sql

@@ -0,0 +1,308 @@
+select * from formatted_data_with_planned_enrollment fdwpe 
+;
+
+
+select * from formatted_data_mat fdm
+;
+
+select count(distinct condition ) from formatted_data_mat fdm
+
+select nct_id, fdm.current_status , count(*) 
+from formatted_data_mat fdm 
+group by nct_id  , fdm.current_status 
+order by nct_id 
+;
+
+select * from formatted_data_mat fdm ;
+
+
+-- group with trial split
+with cte as (
+select nct_id
+from formatted_data_mat fdm 
+group by nct_id
+having count(distinct current_status) > 1
+order by nct_id
+)
+select 
+    fdm.nct_id
+    , current_status
+    , earliest_date_observed 
+    , elapsed_duration 
+    , n_brands
+    , category_id
+    , h_sdi_val 
+    , h_sdi_u95
+    , h_sdi_l95
+    , hm_sdi_val 
+    , hm_sdi_u95
+    , hm_sdi_l95
+    , m_sdi_val 
+    , m_sdi_u95
+    , m_sdi_l95
+    , lm_sdi_val 
+    , lm_sdi_u95
+    , lm_sdi_l95
+    , l_sdi_val 
+    , l_sdi_u95
+    , l_sdi_l95
+from formatted_data_mat fdm
+    join cte on cte.nct_id = fdm.nct_id 
+group by 
+    fdm.nct_id
+    , current_status
+    , earliest_date_observed 
+    , elapsed_duration 
+    , n_brands
+    , category_id
+    , h_sdi_val 
+    , h_sdi_u95
+    , h_sdi_l95
+    , hm_sdi_val 
+    , hm_sdi_u95
+    , hm_sdi_l95
+    , m_sdi_val 
+    , m_sdi_u95
+    , m_sdi_l95
+    , lm_sdi_val 
+    , lm_sdi_u95
+    , lm_sdi_l95
+    , l_sdi_val 
+    , l_sdi_u95
+    , l_sdi_l95
+order by nct_id , earliest_date_observed 
+;
+
+select count(distinct category_id ) from 
+
+
+select distinct category_id  from formatted_data_mat fdm 
+;
+
+
+
+
+
+-- group with trial split
+with cte as (
+select nct_id
+from formatted_data_mat fdm 
+group by nct_id
+having count(distinct current_status) > 1
+order by nct_id
+)
+select 
+    fdm.nct_id
+    , current_status
+    , earliest_date_observed 
+    , elapsed_duration 
+    , n_brands
+    , category_id
+    , h_sdi_val 
+    , h_sdi_u95
+    , h_sdi_l95
+    , hm_sdi_val 
+    , hm_sdi_u95
+    , hm_sdi_l95
+    , m_sdi_val 
+    , m_sdi_u95
+    , m_sdi_l95
+    , lm_sdi_val 
+    , lm_sdi_u95
+    , lm_sdi_l95
+    , l_sdi_val 
+    , l_sdi_u95
+    , l_sdi_l95
+from formatted_data_mat fdm
+    join cte on cte.nct_id = fdm.nct_id 
+group by 
+    fdm.nct_id
+    , current_status
+    , earliest_date_observed 
+    , elapsed_duration 
+    , n_brands
+    , category_id
+    , h_sdi_val 
+    , h_sdi_u95
+    , h_sdi_l95
+    , hm_sdi_val 
+    , hm_sdi_u95
+    , hm_sdi_l95
+    , m_sdi_val 
+    , m_sdi_u95
+    , m_sdi_l95
+    , lm_sdi_val 
+    , lm_sdi_u95
+    , lm_sdi_l95
+    , l_sdi_val 
+    , l_sdi_u95
+    , l_sdi_l95
+order by nct_id , earliest_date_observed 
+; --TODO: join to usp dc dataset
+
+
+
+
+WITH trialncts AS (
+         SELECT DISTINCT ts.nct_id
+           FROM history.trial_snapshots ts
+), nct_to_cui AS (
+         SELECT bi.nct_id,
+            bi.downcase_mesh_term,
+            rr.tty2,
+            rr.rxcui2 AS approved_drug_rxcui,
+            count(*) AS count
+           FROM ctgov.browse_interventions bi
+             LEFT JOIN rxnorm_migrated.rxnorm_props rp ON bi.downcase_mesh_term::text = rp.propvalue1::text
+             LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON rr.rxcui1 = rp.rxcui
+          WHERE (bi.nct_id::text IN ( SELECT trialncts.nct_id
+                   FROM trialncts)) AND bi.mesh_type::text = 'mesh-list'::text AND rp.propname::text = 'Active_ingredient_name'::text AND (rr.tty2::text = ANY (ARRAY['BPCK'::text, 'SCD'::text, 'SBD'::text, 'GPCK'::text]))
+          GROUP BY bi.nct_id, bi.downcase_mesh_term, rr.tty2, rr.rxcui2
+        )   
+ SELECT nct_to_cui.nct_id,
+    ud."USP Category",
+    ud."USP Class"
+   FROM nct_to_cui
+     JOIN "Formularies".usp_dc ud ON ud.rxcui::bpchar = nct_to_cui.approved_drug_rxcui
+  GROUP BY nct_to_cui.nct_id, ud."USP Category", ud."USP Class"
+  ORDER BY nct_to_cui.nct_id;
+
+  
+  
+  
+CREATE MATERIALIZED VIEW "Formularies".nct_to_brands_through_uspdc
+AS
+WITH trialncts AS (
+         SELECT DISTINCT ts.nct_id
+           FROM history.trial_snapshots ts
+)
+SELECT 
+    bi.nct_id,
+    count( distinct rr2.rxcui2 ) as brand_name_count
+    FROM ctgov.browse_interventions bi
+      LEFT JOIN rxnorm_migrated.rxnorm_props rp ON bi.downcase_mesh_term::text = rp.propvalue1::text --match mesh terms to rxcui
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON rr.rxcui1 = rp.rxcui -- match rxcui to relations between rxcuis
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr2 ON rr.rxcui2 = rr2.rxcui1  -- match rxcui to relations between rxcuis
+WHERE 
+    (bi.nct_id::text IN (SELECT trialncts.nct_id FROM trialncts)) --check the nct_id is in our list 
+    AND 
+    bi.mesh_type::text = 'mesh-list'::text --we are only looking at mesh "list" rxcuis
+    AND rp.propname::text = 'Active_ingredient_name'::text  --and we only care about active ingredients linked to \/\/\/\/\/
+    AND (rr.tty2::text = ANY (ARRAY['BPCK'::text, 'SCD'::text, 'SBD'::text, 'GPCK'::text])) --and we are linking from active ingredients ^^^^ to branded packs
+    AND (rr2.tty2::text = 'BN') --and from branded packs back to brand names
+GROUP BY bi.nct_id --remove duplicates
+;
+
+
+
+/* 
+ * 
+ */
+
+
+select 
+    fdqpe.nct_id
+    --,fdqpe.start_date
+    --,fdqpe.current_enrollment
+    --,fdqpe.enrollment_category
+    ,fdqpe.current_status 
+    ,fdqpe.earliest_date_observed 
+    ,fdqpe.elapsed_duration
+    ,fdqpe.n_brands as identical_brands
+    ,ntbtu.brand_name_count 
+    ,fdqpe.category_id
+    ,fdqpe.final_status
+    ,fdqpe.h_sdi_val
+    --,fdqpe.h_sdi_u95
+    --,fdqpe.h_sdi_l95
+    ,fdqpe.hm_sdi_val
+    --,fdqpe.hm_sdi_u95
+    --,fdqpe.hm_sdi_l95
+    ,fdqpe.m_sdi_val
+    --,fdqpe.m_sdi_u95
+    --,fdqpe.m_sdi_l95
+    ,fdqpe.lm_sdi_val
+    --,fdqpe.lm_sdi_u95
+    --,fdqpe.lm_sdi_l95
+    ,fdqpe.l_sdi_val
+    --,fdqpe.l_sdi_u95
+    --,fdqpe.l_sdi_l95
+from formatted_data_mat fdqpe
+    join "Formularies".nct_to_brands_through_uspdc ntbtu
+        on fdqpe.nct_id = ntbtu.nct_id 
+;
+
+--example of multiple reopenings
+select * 
+from formatted_data_mat fdm 
+where nct_id = 'NCT01239797'
+
+--attempt to automatically find transition periods
+with cte1 as (
+	select nct_id, min(earliest_date_observed) over (partition by nct_id) as earliest_closed_enrollment
+	from formatted_data_mat fdm 
+	where current_status = 'Active, not recruiting'
+), cte2 as (
+	select nct_id, max(earliest_date_observed) over (partition by nct_id) latest_open_enrollment
+	from formatted_data_mat fdm 
+	where current_status != 'Active, not recruiting'
+)
+select 
+	cte1.nct_id
+	,cte1.earliest_closed_enrollment
+	,cte2.latest_open_enrollment
+	,cte1.earliest_closed_enrollment - cte2.latest_open_enrollment 
+from cte1
+	join cte2 on cte1.nct_id = cte2.nct_id
+/*group by 
+	cte1.nct_id
+	,cte1.earliest_closed_enrollment
+	,cte2.latest_open_enrollment
+*/
+
+	
+
+/* So ocassionally a study reopens enrollment.
+ * If that didn't happen, then I could just find the first enrollment matching X and/or last enrollment matching Y
+ * to get the transitions
+ * Instead I need to create shifts of statuses between snapshots, and then remove all of those that did not change. 
+ * 
+ * Better yet, just get the last shift to ANR.
+ * */
+
+	
+/* Take each entry and get the status from a lagged snapshot
+ * Then select each snapshot moving from previous_state to ANR
+ * and filter out everything except the last one.
+ * */
+with cte as (
+select 
+	nct_id
+	,lag(current_status, 1) over (partition by nct_id order by earliest_date_observed)  as previous_status
+	,current_status
+	,earliest_date_observed as date_current
+from formatted_data_mat fdm
+), cte2 as (
+select 	
+	nct_id 
+	,previous_status
+	,current_status 
+	,max(date_current) as date_current_max
+from cte
+where 
+	previous_status != current_status 
+	and
+	current_status = 'Active, not recruiting'
+group by 
+	nct_id
+	,previous_status
+	,current_status
+	,date_current
+)
+select * 
+from formatted_data_mat fdm
+	join cte2 
+		on cte2.nct_id = fdm.nct_id 
+		and cte2.date_current_max = fdm.earliest_date_observed 
+; --join back into 
+	

Scripts/export_tables.sh

@@ -0,0 +1,35 @@
+#!/bin/bash 
+set -x
+
+# Uses 
+#
+# Defauls
+if [[ $# -lt 1 ]]; then
+    echo "Usage: pg_export container_name [database_name] [username]"
+    return 1
+fi
+
+CONTAINER=$1
+DBNAME=${2:-aact_db}
+USER=${3:-root}
+    
+#
+# for sqlfile in ../export/export_data_*.sql; do
+#     if [[ -f "$sqlfile" ]]; then
+#         outfile="../export/output_$(date -I)_$(basename ${sqlfile%.sql}).sql"
+#         # podman exec -t "$CONTAINER" psql -U "$USER" -d "$DBNAME" -t -A -f - < "$sqlfile" > "$outfile"
+#         # podman exec "$CONTAINER" psql -U "$USER" -d "$DBNAME" -t -A -f "$sqlfile" > "$outfile"
+#         podman cp "$sqlfile" "$CONTAINER":/tmp/query.sql
+#         podman exec "$CONTAINER" psql -U "$USER" -d "$DBNAME" -t -A -f /tmp/query.sql > "$outfile"
+#     fi
+# done
+#
+
+for sqlfile in ../export/export_data_*.sql; do
+    if [[ -f "$sqlfile" ]]; then
+        outfile="../export/output_$(date -I)_$(basename ${sqlfile%.sql}).sql"
+        podman cp "$sqlfile" "$CONTAINER":/tmp/query.sql
+        podman exec "$CONTAINER" psql -U "$USER" -d "$DBNAME" -f "/tmp/query.sql" > "$outfile"
+    fi
+done
+

Scripts/views to history.sql

@@ -0,0 +1,30 @@
+/***************CREATE VIEWS*******************/
+create or replace view 
+	history.match_drugs_to_trials as
+select nct_id,  rxcui, propvalue1
+from 
+	ctgov.browse_interventions as bi
+	join
+	rxnorm_migrated.rxnorm_props as rp
+	on bi.downcase_mesh_term = rp.propvalue1 
+where 
+	propname='RxNorm Name'
+	and 
+	nct_id in (select nct_id from history.trial_snapshots)
+;
+
+
+/********************IN DEVLEOPMENT*********************/
+
+/* Get the count of brand names attached to each trial
+ * I should develop this into a view that matches trials to brands
+ * then create a view that gets the counts.
+ */
+select rxcui1,count(rxcui2) from rxnorm_migrated.rxnorm_relations rr 
+where 
+	rxcui1 in (select rxcui from history.match_drugs_to_trials)
+	and
+	tty2 = 'BN'
+group by rxcui1 
+order by count(rxcui2) desc 
+;

TODO.md

@@ -0,0 +1,3 @@
+# TODO
+
+Code up a data extraction tool that uses llama3 or a similar quality source to extract the data that I need from the extended aact_database

assorted/examining the db.sql

@@ -1,44 +0,0 @@
-SELECT why_stopped FROM ctgov.studies
-WHERE why_stopped IS NOT NULL
-LIMIT 100;
-
-SELECT study_type, count(*) from ctgov.studies
-group by study_type;
-
-SELECT is_fda_regulated_drug, count(*) from ctgov.studies
-GROUP BY is_fda_regulated_drug;
-
-
-
-/*
-Note that there is a decent number of trials that have expanded access
-*/
-SELECT 
-	study_type
-	, phase
-	, has_expanded_access
-	, has_dmc
-	, count(*) 
-FROM ctgov.studies
-WHERE 
-	is_fda_regulated_drug is true
-	AND
-	study_type = 'Interventional'
-	AND 
-	start_date > date('2007-01-01')
-group by study_type, phase, has_expanded_access, has_dmc;
-
-
-
-
-/*
- Find different mesh terms as assigned by clinicaltrials.gov
- */
-select * from ctgov.browse_conditions
-order by nct_id desc,mesh_type
-limit 200;
-
-select * from ctgov.browse_interventions
-order by nct_id desc
-limit 200;
-

classifications/classify_terminations.py

@@ -1,48 +0,0 @@
-import psycopg2 as psyco
-import pandas as pd
-import nltk
-from nltk.corpus import stopwords
-from sklearn.feature_extraction.text import TfidfVectorizer
-from sklearn.cluster import KMeans
-import re
-
-
-def preporcess_text(text):
-    
-    text = text.lower()
-    text = re.sub("[^A-Za-z]+", " ", text)
-    #make tokens
-    tokens = nltk.word_tokenize(text)
-
-    #remove stopwords
-    tokens = [ w for w in tokens if not w in stopwords.words("english")]
-
-    #rejoin
-    return " ".join(tokens).strip()
-
-if __name__ == "__main__":
-    conn = psyco.connect(dbname="aact_db", user="analysis", host="localhost", password="test")
-
-    curse = conn.cursor()
-
-    curse.execute("SELECT why_stopped FROM ctgov.studies WHERE why_stopped IS NOT NULL LIMIT 2000;")
-    results = curse.fetchall()
-
-    curse.close()
-    conn.close()
-
-    data = pd.DataFrame(results, columns = ["corpus"])
-    data["cleaned"] = data.corpus.apply(preporcess_text)
-
-    vectorizer = TfidfVectorizer(sublinear_tf=True)
-
-    X = vectorizer.fit_transform(data.cleaned)
-
-    kmeans = KMeans(n_clusters=10, random_state=11021585)
-    kmeans.fit(X)
-
-    data["cluster"] = kmeans.labels_
-
-    print(data.groupby(["cluster"])["cleaned"].count())
-
-    

containers/AACT_Reloader/.gitattributes

@@ -0,0 +1 @@
+backup/2023-09-06_aactdb_with_matches.sql.gz filter=lfs diff=lfs merge=lfs -text

containers/AACT_Reloader/StartRestoreContainer.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+RESTORE_DUMP_GZ="${1:-aact_db_backup_20250107_133822.sql.gz}"
+POSTGRES_USER=root
+POSTGRES_PASSWORD=root
+POSTGRES_DB=aact_db
+
+CONTAINER_NAME="${POSTGRES_DB}-restored-$(date -I)"
+
+#start container
+podman run \
+    -e POSTGRES_PASSWORD="${POSTGRES_PASSWORD}" \
+    -e POSTGRES_USER="${POSTGRES_USER}" \
+    -e POSTGRES_DB="${POSTGRES_DB}" \
+    --name "${CONTAINER_NAME}" \
+    --detach \
+    --network research-network \
+    --shm-size=512mb \
+    --volume ./backup/:/backup/ \
+    -p 5432:5432\
+    postgres:14-alpine
+
+
+sleep 10
+
+# Function to check if PostgreSQL is ready
+function check_postgres {
+    podman exec -i "${CONTAINER_NAME}" psql -h localhost -U "${POSTGRES_USER}" -d "${POSTGRES_DB}" -c '\q' > /dev/null 2>&1    
+}
+
+# Wait for PostgreSQL to be ready
+until check_postgres; do
+  echo "Waiting for PostgreSQL to be ready..."
+  sleep 4
+done
+
+echo "PostgreSQL is ready. Restoring the database..."
+
+# Decompress the dump file and restore it to the database
+podman exec -i "${CONTAINER_NAME}" sh -c "gunzip -c /backup/${RESTORE_DUMP_GZ} | psql -h localhost -U ${POSTGRES_USER} -d ${POSTGRES_DB}"
+
+echo "Database restoration complete."

containers/AACT_downloader/docker-compose.yaml

@@ -0,0 +1,31 @@
+version: '3'
+
+networks:
+  pharmaceutical_research: #because it helps to have a way to link specifically to this. 
+
+services:
+  aact_db:
+    image: postgres:14-alpine
+    networks:
+      - pharmaceutical_research
+    shm_size: '4gb' #adjust the shared memeory /dev/shm when running
+      #https://stackoverflow.com/questions/30210362/how-to-increase-the-size-of-the-dev-shm-in-docker-container
+    container_name: aact_db
+    #restart: always #restart after crashes
+    environment:
+      POSTGRES_USER: root
+      POSTGRES_PASSWORD: root
+      POSTGRES_DB: aact_db
+    ports:
+      - "5432:5432" #host:container
+    volumes: #host:container is the format.
+      # this is persistant storage for the database  
+      - ./db_store/:/var/lib/postgresql/
+      # this is the database dump to restore from
+      - ./aact_downloads/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
+      # this is the folder containing entrypoint info.
+      - ./docker-entrypoint-initdb.d/:/docker-entrypoint-initdb.d/
+    env_file:
+      ../.env
+
+

containers/AACT_downloader/docker-entrypoint-initdb.d/005_CreateAactUsers.sql

@@ -0,0 +1,21 @@
+--Create ctti user and grant permissions
+CREATE ROLE ctti;
+GRANT ALL PRIVILEGES ON DATABASE aact_db TO ctti;
+
+/*
+Add the root user if it doesn't exist. 
+With the default configuration this shouldn't be an issue, 
+but I can see myself forgetting and changing the default POSTGRES_USER
+*/
+DO LANGUAGE plpgsql
+$do$
+BEGIN
+   IF NOT EXISTS (
+      SELECT FROM pg_catalog.pg_roles  -- SELECT list can be empty for this
+      WHERE  rolname = 'root') 
+    THEN
+      CREATE ROLE root LOGIN PASSWORD 'root'; --SECURITY ISSUE 
+      GRANT ALL PRIVILEGES ON DATABASE aact_db TO root;
+   END IF;
+END
+$do$

containers/AACT_downloader/docker-entrypoint-initdb.d/010_load_db_dump.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+set -e
+set -x
+
+
+# This file loads the database dump into the postgres database 
+
+dump_path="/mnt/host_data/postgres_data.dmp"
+
+#Double check the postgres user and database are set
+if [[ -z $POSTGRES_USER && -z $POSTGRES_DB ]]; #if either POSTGRES_USER or POSTGRES_DB are empty, throw an error.
+then
+    echo "Missing either the POSTGRESS_USER or the POSTGRES_DB environment variable"
+    exit 4
+else 
+    #restore the DB 
+    pg_restore -e -v -O -x --dbname="$POSTGRES_DB" --username="$POSTGRES_USER" --no-owner "$dump_path"
+fi

containers/AACT_downloader/docker-entrypoint-initdb.d/020_HttpSchema.sql

@@ -24,11 +24,11 @@ CREATE TABLE IF NOT EXISTS http.responses (
     id SERIAL PRIMARY KEY, 
     nct_id VARCHAR(15),
     version_a SMALLINT,
-	version_b SMALLINT,
+    version_b SMALLINT,
     url VARCHAR(255),
     response_code SMALLINT,
     response_date TIMESTAMP WITH TIME ZONE,
-	html TEXT
+    html TEXT
     );
 
 

containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql

@@ -0,0 +1,127 @@
+-- Create a schema handling trial history.
+CREATE SCHEMA history;
+
+--Create role for anyone who needs to both select and insert on historical data
+CREATE ROLE history_writer;
+GRANT CONNECT ON DATABASE aact_db to history_writer;
+
+GRANT USAGE ON SCHEMA history TO history_writer;
+
+GRANT INSERT,SELECT ON ALL TABLES IN SCHEMA http TO history_writer;
+
+
+--Create role for anyone who only needs selection access to historical data, such as for analysis
+CREATE ROLE history_reader;
+GRANT CONNECT ON DATABASE aact_db to history_reader;
+
+GRANT USAGE ON SCHEMA history TO history_reader;
+
+GRANT SELECT ON ALL TABLES IN SCHEMA http TO history_reader;
+
+
+/* History Tables
+Below is where I would construct the parsed trial history tables that I need.
+
+Possible fields
+    nct_id
+    version
+    --Study Status
+    overall_status^
+    primary_completion_date^
+    completion_date^
+    last_update_submitted_date
+    --SponsorCollaborators
+    sponsor (multi?)
+    collaborators (multi?)
+    --Oversight
+    fda_regulated_drug (ignore)
+    fda_regulated_device (ignore)
+    dmc (ignore)
+    --StuldyDescription
+    summary    
+    detailed_description
+    --Conditions
+    Conditions
+    Keywords
+    --StudyDesign
+    Study type
+    Primary Purpose
+    Study Phase
+    Interventional Study Model
+    Number of Arms
+    Masking
+    Allocation
+    Enrollment  ^
+    --ArmsAndInterventions
+    Arms (multiple) (Ignore)
+    --ProtocolOutcomeMeasures
+    --Eligibility
+    --ContactsLocation
+    --IPDSharing
+    --References
+    --ParticipantFlow
+    --BaselineCharacteristics
+    --ROutcomeMeasures
+    --AdverseEvents
+    --LimitationsAndCaveats
+    --More Information
+
+*/
+
+CREATE TYPE history.updatable_catetories AS ENUM
+    ('Actual', 'Anticipated', 'Expected');
+
+ALTER TYPE history.updatable_catetories
+    OWNER TO root;
+
+COMMENT ON TYPE history.updatable_catetories
+    IS 'This enum is used to capture the different types of categories that a date or enrollemnt figure may have.';
+
+
+
+CREATE TYPE history.study_statuses AS ENUM
+    ('Available', 'Withdrawn', 'Withheld', 'Temporarily not available', 'Active, not recruiting', 'Recruiting', 'Not yet recruiting', 'Enrolling by invitation', 'Suspended', 'No longer available', 'Approved for marketing', 'Unknown status', 'Completed', 'Terminated');
+
+ALTER TYPE history.study_statuses
+    OWNER TO root;
+
+COMMENT ON TYPE history.study_statuses
+    IS 'This enum is used to record study status. These are pulled from the ClinicalTrials.gov documentation.';
+
+
+-- Table: history.trial_snapshots
+
+DROP TABLE IF EXISTS history.trial_snapshots;
+
+CREATE TABLE IF NOT EXISTS history.trial_snapshots
+(
+    nct_id character varying(15) COLLATE pg_catalog."default" NOT NULL,
+    version integer NOT NULL,
+    submission_date timestamp NOT NULL,
+    primary_completion_date timestamp without time zone,
+    primary_completion_date_category history.updatable_catetories,
+    start_date timestamp without time zone,
+    start_date_category history.updatable_catetories,
+    completion_date timestamp without time zone,
+    completion_date_category history.updatable_catetories,
+    overall_status history.study_statuses,
+    enrollment integer,
+    enrollment_category history.updatable_catetories,
+    sponsor character varying COLLATE pg_catalog."default",
+    responsible_party character varying COLLATE pg_catalog."default",
+    CONSTRAINT trial_snapshots_pkey PRIMARY KEY (nct_id, version)
+);
+
+
+ALTER TABLE IF EXISTS history.trial_snapshots
+    OWNER to root;
+
+
+CREATE OR REPLACE VIEW history.match_drugs_to_trials
+AS SELECT bi.nct_id,
+    rp.rxcui,
+    rp.propvalue1
+   FROM ctgov.browse_interventions bi
+     JOIN rxnorm_migrated.rxnorm_props rp ON bi.downcase_mesh_term::text = rp.propvalue1::text
+  WHERE rp.propname::text = 'RxNorm Name'::text AND (bi.nct_id::text IN ( SELECT trial_snapshots.nct_id
+           FROM history.trial_snapshots));

containers/AACT_downloader/docker-entrypoint-initdb.d/040_StructuredProductLabels_Schema.sql

@@ -0,0 +1,40 @@
+CREATE SCHEMA spl AUTHORIZATION root;
+
+DROP TABLE IF EXISTS spl.nsde;
+
+CREATE SEQUENCE IF NOT EXISTS spl.nsde_id_seq
+    INCREMENT 1
+    START 1
+    MINVALUE 1
+    MAXVALUE 9223372036854775807
+    CACHE 1;
+
+ALTER SEQUENCE spl.nsde_id_seq
+    OWNER TO root;
+
+CREATE TABLE IF NOT EXISTS spl.nsde
+(
+    id integer NOT NULL DEFAULT nextval('spl.nsde_id_seq'::regclass),
+    package_ndc11 character varying(11) COLLATE pg_catalog."default",
+    application_number_or_citation character varying(25) COLLATE pg_catalog."default",
+    package_ndc character varying(50) COLLATE pg_catalog."default",
+    proprietary_name character varying(500) COLLATE pg_catalog."default",
+    product_type character varying(90) COLLATE pg_catalog."default",
+    marketing_category character varying(160) COLLATE pg_catalog."default",
+    dosage_form character varying(155) COLLATE pg_catalog."default",
+    billing_unit character varying(35) COLLATE pg_catalog."default",
+    marketing_start_date date,
+    marketing_end_date date,
+    inactivation_date date,
+    reactivation_date date,
+    CONSTRAINT nsde_pkey PRIMARY KEY (id)
+)
+
+TABLESPACE pg_default;
+
+ALTER TABLE IF EXISTS spl.nsde
+    OWNER to root;
+	
+-- if the table is dropped, the sequence is as well
+ALTER SEQUENCE spl.nsde_id_seq
+    OWNED BY spl.nsde.id;

containers/AACT_downloader/docker-entrypoint-initdb.d/050_RxNormMigrated_Schema.sql

@@ -0,0 +1,6 @@
+-- Create a schema handling trial history.
+CREATE SCHEMA rxnorm_migrated;
+
+--Create role for anyone who needs to both select and insert on historical data
+
+GRANT ALL ON ALL TABLES IN SCHEMA rxnorm_migrated TO root;

containers/RxNav-In-a-box/download_extract_rxnavinabox.md

@@ -0,0 +1,7 @@
+# Instructions:
+Go go [RxNavInABox](https://lhncbc.nlm.nih.gov/RxNav/applications/RxNav-in-a-Box.html) and download the most recent version. 
+
+I have included the version I use.
+
+Then unzip and run docker-compose.yaml
+

containers/docker-compose.yaml

@@ -0,0 +1,48 @@
+version: '3'
+
+networks:
+  pharmaceutical_research: #because it helps to have a way to link specifically to this. 
+    external: true
+
+services:
+  aact_db:
+    image: postgres:14-alpine
+    restart: "no"
+    networks:
+      - pharmaceutical_research
+    container_name: aact_db
+    #restart: always #restart after crashes
+    environment:
+      POSTGRES_USER: ${POSTGRES_USER}
+      POSTGRES_PASSWORD: ${POSTGRES_PASSWORD}
+      POSTGRES_DB: ${POSTGRES_DB}
+      VERSION: podman
+    ports:
+      - "5432:5432" #host:container
+    volumes: #host:container is the format.
+      # this is persistant storage for the database  
+      - ./AACT_downloader/postgresql/:/var/lib/postgresql/
+      # this is the database dump to restore from
+      - ./AACT_downloader/aact_downloads/postgres_data.dmp:/mnt/host_data/postgres_data.dmp
+      # this is the folder containing entrypoint info.
+      - ./AACT_downloader/docker-entrypoint-initdb.d/:/docker-entrypoint-initdb.d/
+    shm_size: 512mb
+
+
+  rxnav-db:
+    image: mariadb:10.4
+    restart: "no"
+    ports:
+      - "3306:3306"
+    volumes:
+      - ./RxNav-In-a-box/rxnav-in-a-box-20230103/mysql:/docker-entrypoint-initdb.d:ro
+      - ./RxNav-In-a-box/rxnav_data:/var/lib/mysql
+    environment:
+      MYSQL_RANDOM_ROOT_PASSWORD: "yes"
+      MYSQL_USER: ${MYSQL_USER}
+      MYSQL_PASSWORD: ${MYSQL_PASSWORD}
+      VERSION: podman
+    env_file:
+      .env
+    networks:
+      - pharmaceutical_research

containers/drugcentral/docker-compose.yaml

@@ -0,0 +1,23 @@
+version: '3'
+
+networks:
+  pharmaceutical_research: #because it helps to have a way to link specifically to this. 
+
+services:
+  aact_db:
+    image: postgres:14-alpine
+    networks:
+      - pharmaceutical_research
+    container_name: DrugCentral
+    #restart: always #restart after crashes
+    environment:
+      POSTGRES_PASSWORD: root
+    ports:
+      - "54320:5432" #host:container
+    volumes: #host:container is the format.
+      # this is persistant storage for the database  
+      - ./db_store/:/var/lib/postgresql/
+      # this is the folder containing entrypoint info.
+      - ./docker-entrypoint-initdb.d/:/docker-entrypoint-initdb.d/
+
+

containers/drugcentral/init.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+filename="drugcentral.dump.08222022.sql.gz"
+
+cd ./docker-entrypoint-initdb.d/
+
+curl "https://unmtid-shinyapps.net/download/$filename" --output "$filename"
+
+gzip -d $filename

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/__init__.py

@@ -0,0 +1,44 @@
+from flask import Flask
+import os
+from dotenv import dotenv_values
+
+
+
+env_path = "../../containers/.env"
+ENV = dotenv_values(env_path)
+
+def create_app(test_config=None):
+    # create and configure the app
+    app = Flask(__name__, instance_relative_config=True)
+    app.config.from_mapping(
+        SECRET_KEY='6e674d6e41b733270fd01c6257b3a1b4769eb80f3f773cd0fe8eff25f350fc1f',
+        POSTGRES_DB=ENV["POSTGRES_DB"],
+        POSTGRES_USER=ENV["POSTGRES_USER"],
+        POSTGRES_HOST=ENV["POSTGRES_HOST"],
+        POSTGRES_PORT=ENV["POSTGRES_PORT"],
+        POSTGRES_PASSWORD=ENV["POSTGRES_PASSWORD"],
+    )
+
+
+
+    # ensure the instance folder exists
+    try:
+        os.makedirs(app.instance_path)
+    except OSError:
+        pass
+
+    # a simple page that says hello
+    @app.route('/')
+    def hello():
+        return 'Hello, World!'
+
+
+    from . import db_interface
+    db_interface.init_database(app)
+
+    from . import validation
+    app.register_blueprint(validation.bp)
+
+    return app
+
+

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/db_interface.py

@@ -0,0 +1,175 @@
+import psycopg2 as psyco
+from psycopg2 import extras
+from datetime import datetime
+
+import click #used for cli commands. Not needed for what I am doing.
+from flask import current_app, g
+
+def get_db(**kwargs):
+
+    if "db" not in g:
+        g.db = psyco.connect(
+            dbname=current_app.config["POSTGRES_DB"]
+            ,user=current_app.config["POSTGRES_USER"]
+            ,host=current_app.config["POSTGRES_HOST"]
+            ,port=current_app.config["POSTGRES_PORT"]
+            ,password=current_app.config["POSTGRES_PASSWORD"]
+            ,**kwargs
+        )
+    return g.db
+
+def close_db(e=None):
+    db = g.pop('db', None)
+
+    if db is not None:
+        db.close()
+
+def check_initialization(app):
+    db = get_db()
+    with db.cursor() as curse:
+        curse.execute("select count(*) from \"DiseaseBurden\".trial_to_icd10")
+    curse.fetchall()
+    #just checking if everything is going to fail
+
+def init_database(app):
+    #check_initialization(app)
+    app.teardown_appcontext(close_db)
+
+
+
+
+def select_remaing_trials_to_analyze(db_conn):
+    '''
+    This will get the set of trials that need to be analyzed.
+    '''
+    sql = '''
+    select distinct nct_id 
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved is null
+    order by nct_id
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+
+def select_analyzed_trials(db_conn):
+    '''
+    This will get the set of trials that have been analyzed.
+    '''
+    sql = '''
+    select distinct nct_id, max(approval_timestamp)
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved in ('accepted','rejected')
+    group by nct_id
+    order by max(approval_timestamp) desc
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+def select_unmatched_trials(db_conn):
+    '''
+    This will get the set of trials that have been analyzed.
+    '''
+    sql = '''
+    select distinct nct_id
+    from "DiseaseBurden".trial_to_icd10 tti 
+    where tti.approved = 'unmatched'
+    order by nct_id
+    ;
+    '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql)
+        return cursor.fetchall()
+
+
+def get_trial_conditions_and_proposed_matches(db_conn, nct_id):
+    sql = '''
+        select *
+        from "DiseaseBurden".trial_to_icd10 tti 
+        where nct_id = %s
+        '''
+    with db_conn.cursor() as cursor:
+        cursor.execute(sql,[nct_id])
+        return cursor.fetchall()
+
+
+def store_validation(db_conn, list_of_insert_data):
+    sql = """
+    update "DiseaseBurden".trial_to_icd10
+    set approved=%s, approval_timestamp=%s
+    where id=%s
+    ; 
+    """
+    with db_conn.cursor() as cursor:
+        for l in list_of_insert_data:
+            cursor.execute(sql, l)
+    db_conn.commit()
+
+def get_trial_summary(db_conn,nct_id):
+    sql_summary ="""
+select 
+    s.nct_id,
+    brief_title ,
+    official_title ,
+    bs.description as brief_description,
+    dd.description as detailed_description
+from ctgov.studies s 
+    left join ctgov.brief_summaries bs
+        on bs.nct_id = s.nct_id 
+    left join ctgov.detailed_descriptions dd 
+        on dd.nct_id = s.nct_id 
+where s.nct_id = %s
+;
+"""
+    sql_conditions="""
+--conditions mentioned
+select * from ctgov.conditions c 
+where c.nct_id = %s
+;
+"""
+    sql_keywords="""
+select nct_id ,downcase_name 
+from ctgov.keywords k 
+where k.nct_id = %s
+;
+"""
+    with db_conn.cursor() as curse:
+        curse.execute(sql_summary,[nct_id])
+        summary = curse.fetchall()
+
+        curse.execute(sql_keywords,[nct_id])
+        keywords = curse.fetchall()
+
+        curse.execute(sql_conditions,[nct_id])
+        conditions = curse.fetchall()
+
+    return {"summary":summary, "keywords":keywords, "conditions":conditions}
+
+def get_list_icd10_codes(db_conn):
+    sql = """
+    select distinct code 
+    from "DiseaseBurden".icd10_to_cause itc 
+    order by code;
+    """
+    with db_conn.cursor() as curse:
+        curse.execute(sql)
+        codes = curse.fetchall()
+    
+    return [ x[0] for x in codes ]
+
+def record_suggested_matches(db_conn, nct_id,condition,icd10_code):
+    sql1 = """
+    INSERT INTO "DiseaseBurden".trial_to_icd10 
+    (nct_id,"condition",ui,"source",approved,approval_timestamp)
+    VALUES (%s,%s,%s,'hand matched','accepted',%s)
+    ;
+    """
+
+
+    with db_conn.cursor() as curse:
+        curse.execute(sql1,[nct_id,condition,icd10_code,datetime.now()])
+    db_conn.commit()

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/login.py

@@ -0,0 +1 @@
+#at some point I need to add a login or something.

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/templates/base.html

@@ -0,0 +1,25 @@
+<!doctype html>
+<title>{% block title %}{% endblock %} - ClinicalTrialsProject</title>
+<!--<link rel="stylesheet" href="{{ url_for('static', filename='style.css') }}">-->
+
+<nav>
+  <h1>Nav</h1>
+  <ul>
+    <li>
+      <a href="{{ url_for('validation.remaining') }}">Validation Home</a>
+    </li>
+    <li>
+      <a href="https://icd.who.int/browse10/2019/en">WHO ICD-10 Codes (2019)</a>
+    </li>
+    <li>
+      <a href="https://uts.nlm.nih.gov/uts/umls/home">UMLS Metathesaurs browser (requires login)</a>
+    </li>
+  </ul>
+</nav>
+
+<section class="content">
+  <header>
+    {% block header %}{% endblock %}
+  </header>
+  {% block content %}{% endblock %}
+</section>

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/templates/validation_index.html

@@ -0,0 +1,49 @@
+{% extends 'base.html' %}
+
+{% block header %}
+  <h1>{% block title %} ICD-10 to Trial Conditions Validation {% endblock %}</h1>
+{% endblock %}
+
+{% block content %}
+
+<h2>Trials to Validate</h2>
+
+<table>
+<th>Trials</th>
+{% for trial in list_to_validate %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that have been Validated</h2>
+
+<table>
+<th>Trials Links</th>
+{% for trial in validated_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a> 
+    (Most recently updated {{trial[1]}})
+</td></tr> 
+{% endfor %}
+</table>
+
+<h2>Trials that don't have a good match</h2>
+
+<table>
+<th>Trial Links</th>
+{% for trial in unmatched_list %}
+<tr><td>
+    <a href="{{ url_for('.validate_trial', nct_id=trial[0] ) }}">
+        {{ trial [0] }}
+    </a>
+</td></tr> 
+{% endfor %}
+</table>
+
+{% endblock %}

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/templates/validation_of_trial.html

@@ -0,0 +1,95 @@
+{% extends 'base.html' %}
+
+{% block header %}
+  <h1> ICD-10 to Trial Conditions Validation: {{ nct_id }} </h1>
+{% endblock %}
+
+{% block content %}
+
+<section class="summary">
+  <h3>Trial Summary</h3>
+
+  <div class="text_summary">
+    <ul>
+      <li>NCT: {{ summary_dats["summary"][0][0] }}</li>
+      <li>Brief Title: {{ summary_dats["summary"][0][1] }}</li>
+      <li>Long Title: {{ summary_dats["summary"][0][2] }}</li>
+      <li>Brief Description: {{ summary_dats["summary"][0][3] }}</li>
+      <li>Long Description: {{ summary_dats["summary"][0][4] }}</li>
+    </ul>
+  </div>
+  <div class="keywords">
+    <h4>Keywords</h4>
+    <ul>
+      {% for keyword in  summary_dats["keywords"] %}
+        <li>
+          {{ keyword[1] }}
+        </li>
+        {% endfor %}
+    </ul>
+  </div>
+  <div class="conditions">
+    <h4>Raw Conditions </h4>
+    <ul>
+      {% for condition in  summary_dats["conditions"] %}
+        <li>
+          {{ condition[3] }}
+        </li>
+        {% endfor %}
+    </ul>
+  </div>
+</section>
+
+<section class="proposed_conditions">
+  <h3>Proposed Conditions</h3>
+  <form method="post">
+    <table>
+      <tr>
+      <th>Approve</th>
+      <th>Condition (MeSH normalized)</th>
+      <th>Identifier</th>
+      <th>Source</th>
+      <th>Description</th>
+      <th>Source</th>
+      </tr>
+      {% for condition in condition_list %}
+
+      <tr>
+        <td> <input type="checkbox" id="{{ condition[0] }}" name="{{condition[0]}}" value="accepted" {% if condition[8] == "accepted" %}checked{% endif %}> </td>
+        <td> {{condition[2]}} </td>
+        <td> {{condition[3]}} </td>
+        <td> {{condition[5]}} </td>
+        <td> {{condition[6]}} </td>
+        <td> {{condition[7]}} </td>
+      </tr> 
+
+      {% endfor %}
+    </table>
+    <input type="submit" name="submission" value="Submit approvals">
+    <br/>
+    <input type="submit" name="marked_unmatched" value="Mark unmmatched">
+  </form>
+</section>
+
+<section class="submit_alternate">
+  <h3>Submit Alternate Conditions</h3>
+  <!--For each listed condition, provide a spot to enter a ICT10 code-->
+  <form method="post">
+    <label for="alternate_sub">Please enter the proposed code that appears to be the best match:</label>
+    <input name="alt_sub" id="alternate_sub">
+    <br/>
+    <label for="condition">
+      Please give a name to the condition you used to match this<br/>
+      Condition:
+    </label> 
+    <input name="condition", id="condition">
+    <br/>
+    <input type="submit" name="alternate_submission" value="Submit alternate ICD-10 code">
+  </form>
+</section>
+
+<section class="approved">
+  <!--TODO:This will list the already approved values-->
+</section>
+
+{% endblock %}

data_mgmt_scripts/Icd10ConditionsMatching/Icd10ConditionsMatching/validation.py

@@ -0,0 +1,98 @@
+import functools
+from flask import (Blueprint, flash, g, redirect, render_template, request, session, url_for)
+from Icd10ConditionsMatching.db_interface import (
+    get_db,select_remaing_trials_to_analyze, 
+    select_analyzed_trials,
+    select_unmatched_trials,
+    get_trial_conditions_and_proposed_matches,
+    store_validation,
+    get_trial_summary,
+    get_list_icd10_codes,
+    record_suggested_matches,
+    )
+from datetime import datetime
+
+#### First Blueprint: Checking Data
+bp = Blueprint("validation", __name__, url_prefix="/validation")
+
+
+
+@bp.route("/",methods=["GET"])
+def remaining():
+    db_conn = get_db()
+
+
+    to_validate = select_remaing_trials_to_analyze(db_conn)
+    validated = select_analyzed_trials(db_conn)
+    unmatched_list = select_unmatched_trials(db_conn)
+ 
+    
+    return render_template(
+        "validation_index.html", 
+        list_to_validate=to_validate,
+        validated_list = validated,
+        unmatched_list = unmatched_list
+        )
+
+
+@bp.route("/<nct_id>", methods=["GET","POST"])
+def validate_trial(nct_id):
+        
+    if request.method == "GET":
+        db_conn = get_db()
+
+        condition_list =  get_trial_conditions_and_proposed_matches(db_conn, nct_id)
+        summary_dats = get_trial_summary(db_conn, nct_id)
+
+        return render_template(
+            "validation_of_trial.html", 
+            nct_id=nct_id,
+            condition_list=condition_list,
+            summary_dats=summary_dats,
+            )
+    elif request.method == "POST":
+        db_conn = get_db()
+
+        list_of_insert_data = []
+        
+        db_conn = get_db()
+
+        condition_list =  get_trial_conditions_and_proposed_matches(db_conn, nct_id)
+
+        print(request.form)
+
+        if "submission" in request.form:
+            #if it is a submission: 
+                #grab all match ids from db
+                #if match id in submitted form, mark as approved, otherwise mark as rejected
+            for condition in condition_list:
+                id = condition[0]
+                list_of_insert_data.append((request.form.get(str(id),"rejected"), datetime.now(),id))
+               
+            store_validation(db_conn, list_of_insert_data)
+            return redirect(url_for("validation.remaining"))
+        elif "marked_unmatched" in request.form:
+            #if this was marked as "unmatched", store that for each entry.
+            for condition in condition_list:
+                id = condition[0]
+                list_of_insert_data.append(( "unmatched", datetime.now(), id))
+
+            store_validation(db_conn, list_of_insert_data)
+            return redirect(url_for("validation.remaining"))
+        elif "alternate_submission" in request.form:
+            code = request.form["alt_sub"]
+            code = code.strip().replace(".",'').ljust(7,"-")
+
+            condition = request.form["condition"].strip()
+
+            codelist = get_list_icd10_codes(db_conn)
+            if code in codelist:
+                record_suggested_matches(db_conn, nct_id, condition, code)
+                return redirect(request.path)
+            else:
+                record_suggested_matches(db_conn, nct_id, condition + "| Code not in GBD list", code)
+                return """
+                Entered `{}`, which is not in the list of available ICD-10 codes. <a href={}>Return to trial summary</a>
+                """.format(code.strip("-"),request.path), 422
+        
+

data_mgmt_scripts/Icd10ConditionsMatching/setup.py

@@ -0,0 +1,13 @@
+from setuptools import setup
+
+setup(
+    name='Icd10ConditionsMatching',
+    packages=['Icd10ConditionsMatching'],
+    include_package_data=True,
+    install_requires=[
+        'flask',
+        'psycopg2',
+        'datetime',
+        'python-dotenv',
+    ],
+)

data_mgmt_scripts/Icd10ConditionsMatching/start.sh

@@ -0,0 +1 @@
+waitress-serve --port=5000 --call 'Icd10ConditionsMatching:create_app'

data_mgmt_scripts/db_connection_test.py

@@ -0,0 +1,11 @@
+from drugtools.env_setup import postgres_conn, mariadb_conn, ENV
+
+print(ENV)
+
+with postgres_conn() as pconn, pconn.cursor() as curse:
+    curse.execute("select nct_id FROM ctgov.studies LIMIT 10;")
+    print(curse.fetchall())
+
+with mariadb_conn() as mconn, mconn.cursor() as mcurse:
+    mcurse.execute("select * FROM ALLNDC_HISTORY LIMIT 10;")
+    print(mcurse.fetchall())

data_mgmt_scripts/download_tests.py

@@ -1,9 +1,7 @@
-import downloader as download
+from drugtools.historical_nct_downloader import make_request, get_highest_version_number, step_generator 
+
+#this uses the history downloader script to test downloads
 
-def print_response_to_file(r):
-    pass
-def pretty_print_response(r):
-    pass
 
 def trial_downloads(nct_id):
     """
@@ -11,25 +9,25 @@ def trial_downloads(nct_id):
     Instead it writes to files
     """
     print("downloading {}".format(nct_id))
-    r = download.make_request(nct_id,1,2)
+    r = make_request(nct_id,1,2)
     responses = [ r ]
     print(r.url)
 
-    v = download.get_highest_version_number(r)
+    v = get_highest_version_number(r)
 
     if v == 2:
         pass
     elif v%2 == 0:
-        for version_a, version_b in download.step_generator(v):
+        for version_a, version_b in step_generator(v):
             print("\t versions {} & {}".format(version_a,version_b))
-            req = download.make_request(nct_id,version_a,version_b)
+            req = make_request(nct_id,version_a,version_b)
             responses.append(req)
     elif v %2 == 1:
-        for version_a, version_b in download.step_generator(v):
+        for version_a, version_b in step_generator(v):
             print("\t downloading versions {} & {}".format(version_a,version_b))
-            req = download.make_request(nct_id,version_a,version_b)
+            req = make_request(nct_id,version_a,version_b)
             responses.append(req)
-        responses.append(download.make_reqauest(nct_id,1,v))
+        responses.append(make_request(nct_id,1,v))
 
     print("\tDownloaded {} versions".format(v))
 

data_mgmt_scripts/drugtools/download_and_extract_nsde.py

@@ -0,0 +1,96 @@
+import json
+from psycopg2.extras import execute_values
+import datetime as dt
+from drugtools.env_setup import postgres_conn, ENV
+import requests
+import zipfile
+import io
+
+URL_STEM = 'https://download.open.fda.gov/other/nsde/'
+NUMBER_OF_NSDE_FILES = int(ENV["NUMBER_OF_NSDE_FILES"])
+
+def filename_generator(max_num):
+    for itt in range(1,max_num+1):
+        filename = "other-nsde-{:0>4}-of-{:0>4}.json.zip".format(itt,max_num)
+        yield filename
+
+def get_date(result,key):
+    r = result.get(key)
+    if r:
+        return dt.datetime.strptime(r, "%Y%m%d")
+    else:
+        return None
+
+def build_values(result):
+    #adjust types
+    proprietary_name = result.get("proprietary_name")
+    application_number_or_citation = result.get("application_number_or_citation")
+    product_type = result.get("product_type")
+    package_ndc = result.get("package_ndc")
+    marketing_category = result.get("marketing_category")
+    package_ndc11 = result.get("package_ndc11")
+    dosage_form = result.get("dosage_form")
+    billing_unit = result.get("billing_unit")
+    marketing_start_date = get_date(result,"marketing_start_date")
+    marketing_end_date = get_date(result, "marketing_end_date")
+    inactivation_date = get_date(result, "inactivation_date")
+    reactivation_date = get_date(result,"reactivation_date")
+
+    return (
+    proprietary_name
+    ,application_number_or_citation
+    ,product_type 
+    ,package_ndc 
+    ,marketing_category
+    ,package_ndc11 
+    ,dosage_form 
+    ,billing_unit 
+    ,marketing_start_date 
+    ,marketing_end_date 
+    ,inactivation_date 
+    ,reactivation_date
+            )
+
+def download_and_extract_zip(base_url,filename):
+    response = requests.get(base_url + filename)
+
+    with zipfile.ZipFile(io.BytesIO(response.content)) as the_zip:
+        contents_list = the_zip.infolist() 
+        for content_name in contents_list:
+            return the_zip.read(content_name)
+
+def run():
+    for filename in filename_generator(NUMBER_OF_NSDE_FILES):
+        #It would be nice to replace this^^ file_generator with something that retrieves and unzips the files directly.
+        with (postgres_conn() as con , con.cursor() as curse):
+            print(filename)
+
+            j = download_and_extract_zip(URL_STEM, filename)
+            results = json.loads(j)["results"]
+            query = """
+INSERT INTO spl.nsde (
+    proprietary_name
+    ,application_number_or_citation
+    ,product_type
+    ,package_ndc
+    ,marketing_category
+    ,package_ndc11
+    ,dosage_form
+    ,billing_unit
+    ,marketing_start_date
+    ,marketing_end_date
+    ,inactivation_date
+    ,reactivation_date
+) 
+VALUES %s;
+"""
+
+            values = [build_values(y) for y in results]
+            execute_values(curse,query,values)
+            
+            
+
+
+
+if __name__ == "__main__":
+    run()

data_mgmt_scripts/drugtools/env_setup.py

@@ -0,0 +1,43 @@
+import pymysql
+import psycopg2 as psyco
+from psycopg2.sql import SQL
+from dotenv import dotenv_values
+
+env_path = "../containers/.env"
+ENV = dotenv_values(env_path)
+
+def mariadb_conn(**kwargs):
+    return pymysql.connect(
+            database=ENV["MYSQL_DB"]
+            ,user=ENV["MYSQL_USER"]
+            ,host=ENV["MYSQL_HOST"]
+            ,port=int(ENV["MYSQL_PORT"])
+            ,password=ENV["MYSQL_PASSWORD"]
+            ,**kwargs
+        )
+
+def postgres_conn(**kwargs):
+    return psyco.connect(
+            dbname=ENV["POSTGRES_DB"]
+            ,user=ENV["POSTGRES_USER"]
+            ,host=ENV["POSTGRES_HOST"]
+            ,port=ENV["POSTGRES_PORT"]
+            ,password=ENV["POSTGRES_PASSWORD"]
+            ,**kwargs
+        )
+
+
+def get_tables_of_interest():
+    return ENV["TABLES_OF_INTEREST"].split(",")
+
+def postgres_table_delete_entries(schema,table):
+    with postgres_conn() as con:
+        with con.cursor() as curse:
+            delete_statement = SQL("delete from {schema}.{table}").format(
+                schema=Identifier(schema),
+                talbe=Identifier(table)
+                )
+            curse.execute(delete_statement)
+            con.commit()
+
+

data_mgmt_scripts/drugtools/historical_nct_downloader.py

@@ -1,13 +1,19 @@
-from tkinter import W
 import requests
-import psycopg2 as psyco
 from datetime import datetime
 from bs4 import BeautifulSoup
-from multiprocessing import Pool, Value
+from multiprocess import Pool, Value
 import math
 import time
-
-
+from drugtools.env_setup import postgres_conn, ENV
+from tqdm import tqdm
+
+############ GLOBALS
+RESET_TIME = Value('I',int(ENV["TRIAL_DOWNLOAD_RESET_TIME"]))
+DELAY_TIME = Value("I",int(ENV["TRIAL_DOWNLOAD_DELAY_TIME"]))
+TRIAL_RESERVATION_LIMIT=int(ENV["TRIAL_RESERVATION_LIMIT"])
+TRIAL_RESERVATION_BATCH_SIZE=int(ENV["TRIAL_RESERVATION_BATCH_SIZE"])
+    
+############ Functions
 def get_highest_version_number(response):
     """
     Navigate to the version table and and extract the highest posted version.
@@ -21,7 +27,10 @@ def get_highest_version_number(response):
 
     soup = BeautifulSoup(response.text, features="lxml")
     #get version table rows
-    table_rows = soup.findChildren("fieldset")[0].table.tbody.findChildren("tr")
+    try:
+        table_rows = soup.findChildren("fieldset")[0].table.tbody.findChildren("tr")
+    except IndexError as ie:
+        raise ie
 
     for row in reversed(table_rows):
         # if it is <td headers="VersionNumber">xx</td> then it contains what we need.
@@ -40,7 +49,11 @@ def make_request(nct_id,version1,version2):
     url = baseurl.format(nct_id,version1,version2)
 
     #make request
-    response = requests.get(url)
+    try:
+        time.sleep(0.02)
+        response = requests.get(url)
+    except requests.exceptions.ConnectionError as ce:
+        raise ce
 
     #return the response
     return response
@@ -81,16 +94,24 @@ def download_and_handle_errors(cursor, nct_id, version_a, version_b, delay_time,
     #check for 
     if r.status_code == 200:
         upload_response(cursor,nct_id,version_a, version_b, r)
+    elif r.status_code == 404:
+        upload_response(cursor, nct_id, version_a, version_b, r)
+        write_incomplete(cursor,nct_id)
+        return None
     elif r.status_code == 503:
         # write http code to http.responses
         upload_response(cursor, nct_id, version_a, version_b, r)
         # write incomplete to http.download_status
         write_incomplete(cursor,nct_id)
         # tell all other processes to slow down the request speed
-        delay_time.value += 1
         # Delay
-        print("Recieved 503 on {}, increasing delay count to {}".format(nct_id, delay_tiome))
-        time.sleep(reset_time)
+        with delay_time.get_lock():
+            delay_time.value += 1
+            time.sleep(reset_time.value)
+        print("Recieved 503 on {}, increasing delay count to {}".format(
+            nct_id, 
+            delay_time)
+        )
     else:
         #TODO: this should handle errors by
         # write http code to http.responses
@@ -100,8 +121,13 @@ def download_and_handle_errors(cursor, nct_id, version_a, version_b, delay_time,
         # raise exception
         #raise Exception("Download of {} (versions {},{}) returned http code {}".format(nct_id,version_a,version_b, r.status_code))
     
+        print("Recieved {} on {}, increasing delay count to {}".format(
+            r.status_code,
+            nct_id, 
+            delay_time))
         # Delay
-        time.sleep(reset_time)
+        with reset_time.get_lock():
+            time.sleep(reset_time.value)
     return r
 
 def write_incomplete(cursor, nct_id):
@@ -109,12 +135,12 @@ def write_incomplete(cursor, nct_id):
     Flags a trial as not having been fully downloaded.
     """
     query = """
-    INSERT INTO HTTP.DOWNLOAD_STATUS (NCT_ID,STATUS)
-        %s, 'Incomplete'::HTTP.HISTORY_DOWNLOAD_STATUS
+    INSERT INTO HTTP.DOWNLOAD_STATUS (NCT_ID,STATUS) VALUES
+        (%s, 'Incomplete'::HTTP.HISTORY_DOWNLOAD_STATUS);
     """
     cursor.execute(query, [nct_id] )
 
-def download_trial_records(nct_id, db_connection_specs, delay_time, reset_time):
+def download_trial_records(nct_id, delay_time, reset_time):
     """
     Manage the download of all records associated with a given trial.
     It uses a single connection and cursor for downloading the entire trial.
@@ -124,20 +150,23 @@ def download_trial_records(nct_id, db_connection_specs, delay_time, reset_time):
 
     This doesn't reserve a trial for download, but it does release the reservation.
     """
-    #for testing
-    print(nct_id)
-
 
     # A new connection is created every time the function is called so that this 
     # function can be run using a multiprocessing pool
-    with db_connection_specs.new() as db_conn:
+    with postgres_conn() as db_conn:
         with db_conn.cursor() as cursor:
 
             #upload the first two versions
             r = download_and_handle_errors(cursor, nct_id, 1, 2, delay_time, reset_time)
             #extract last version
-            v = get_highest_version_number(r)
+            if r is None:
+                return None
+
 
+            try:
+                v = get_highest_version_number(r)
+            except IndexError as ie:
+                raise RuntimeError(ie.__str__() + " | nct_id {}".format(nct_id))
 
             #download and upload the remaining versions
             if v == 2:
@@ -164,27 +193,6 @@ def download_trial_records(nct_id, db_connection_specs, delay_time, reset_time):
 
 
 
-class DBConnectionCreator():
-    """
-    Creates new database connections based on a specified set of parameters.
-    This simplifies connection creation by allowing the programmer to pass
-    around the preconfigured connection creator.
-    """
-    def __init__(self,dbname, user, host, port, password):
-        self.dbname = dbname
-        self.user = user
-        self.host = host
-        self.port = port
-        self.password=password
-
-    def new(self):
-        return psyco.connect(
-                dbname=self.dbname
-                ,user=self.user
-                ,host=self.host
-                ,port=self.port
-                ,password=self.password
-                )
 
 def step_generator(max_version):
     """
@@ -198,31 +206,6 @@ def step_generator(max_version):
         yield (old,i)
         old = i + 1
 
-def flag_trials_of_interest(db_connection):
-    """
-    Mark the queries of interest as "of interest"
-    INCOMPLETE
-    """
-
-    query = """
-    INSERT INTO http.download_status (nct_id, status)
-        SELECT nct_id, 'Of Interest'::http.history_download_status AS status
-        FROM ctgov.studies
-        WHERE 
-            is_fda_regulated_drug=TRUE
-            AND
-            study_type = 'Interventional'
-            AND
-            phase='Phase 3'
-            AND 
-            overall_status in ('Terminated', 'Completed')
-            AND 
-            start_date > '2008-01-01'
-            AND
-            completion_date < '2022-01-01'
-    ;
-    """
-    #TODO: actually send it to the database.
 
 def reserve_trials(db_connection, limit=10):
     """
@@ -247,37 +230,37 @@ def reserve_trials(db_connection, limit=10):
 
     return nctids_list
 
-if __name__ == "__main__":
-    """
-    Main!
-    """
-    #instantiate a database connnection creator
-    dbc = DBConnectionCreator(
-            dbname="aact_db"
-            ,user="python_downloader"
-            ,host="will-office"
-            ,port=5432
-            ,password="download")
-    
-
-    #db connection
-    with dbc.new() as con:
+def chunker(seq, size):
+    return [seq[pos:pos + size] for pos in range(0, len(seq), size)]
 
-        #get list of nct_ids
-        nctids = reserve_trials(con, 1500)
-        print(nctids)
+def reserve_and_download_versions(limit):
 
-    
-    reset_time = 10
-    delay_time = Value("I",1)
     #lambda that parameterizes the downloader, allowing it to be passed to the pool.
     def downloader(nct):
-        download_trial_records(nct, dbc, delay_time, reset_time)
+        download_trial_records(nct, DELAY_TIME, RESET_TIME)
 
-        #start analyzing them
-    with Pool(processes=12) as process_pool:
-        process_pool.map(downloader, nctids)
+    #db connection
+    with postgres_conn() as con:
+        itt = 0
+        while (nctids := reserve_trials(con,TRIAL_RESERVATION_BATCH_SIZE)) and \
+               itt < TRIAL_RESERVATION_LIMIT:
+            print(nctids)
+            with Pool(processes=12) as process_pool:
+                l = len(nctids)
+                itt += l
+                with tqdm(total=l) as prog_bar:
+                    for _ in process_pool.imap_unordered(downloader, nctids):
+                        prog_bar.update()
+                    con.commit()
 
 
 
+def run():
+    reserve_and_download_versions(TRIAL_RESERVATION_LIMIT)
 
+if __name__ == "__main__":
+    """
+    Main!
+    """
+    run()
+    #db connection

data_mgmt_scripts/drugtools/historical_nct_extractor.py

@@ -0,0 +1,465 @@
+from collections import namedtuple
+from copy import copy
+from datetime import datetime
+from bs4 import BeautifulSoup
+from drugtools.env_setup import ENV,postgres_conn
+from tqdm import tqdm
+#requires Python 3.10
+
+#### GLOBALS
+VERBOSE = True if ENV["VERBOSE"] == "True" else False
+
+###CLASSES AND CONSTRUCTORS
+
+TagDatePair = namedtuple("TagDatePair", ["tag","date"])
+TagTextPair = namedtuple("TagTextPair", ["tag","text"])
+
+#superclasses
+class VersionData():
+    """
+    This class holds two types of data:
+        - Data with a 1-to-1 relationship with the trial/version pair.
+        - Data with a child relationship with the trial/version pair.
+
+    This initializes with None attributes, and implements setter 
+    methods to load them (just to double check types)
+    That way I can just pass around the VersionData instance
+    and add data as I go.
+
+    It will also implement the ability to load the data to the database
+    """
+    def __init__(self,nct_id,version_id,submission_date):
+        #identifiers
+        self.nct_id = nct_id.strip()
+        self.version_id = version_id
+        self.submission_date = submission_date
+
+        #Study Status
+        self._primary_completion_date = None
+        self._primary_completion_date_category = None
+        self._start_date = None
+        self._start_date_category = None
+        self._completion_date = None
+        self._completion_date_category = None
+        self._overall_status = None
+        self._enrollment = None
+        self._enrollment_category = None
+        self._sponsor = None
+        #self._sponsor_category = None #I don't believe this is included in the raw data
+        self._responsible_party = None
+        #self._responsible_party_category = None #I don't believe this is included in the raw data
+        #self._collaborators = None #currently going to ignore as I've not fount it in AACT
+
+    def load_to_db(self,db_connection):
+        #load to initial table, then load any extra details into other tables
+        sql = """
+        INSERT INTO history.trial_snapshots
+            (
+                nct_id,
+                version,
+                submission_date,
+                primary_completion_date,
+                primary_completion_date_category,
+                start_date,
+                start_date_category,
+                completion_date,
+                completion_date_category,
+                overall_status,
+                enrollment,
+                enrollment_category,
+                sponsor,
+                responsible_party
+            )
+            VALUES
+            (
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s,
+                %s
+            )
+        """
+
+        with db_connection.cursor() as db_cursor:
+            try:
+                db_cursor.execute(
+                    sql,
+                    (
+                        self.nct_id,
+                        self.version_id,
+                        self.submission_date,
+                        self._primary_completion_date,
+                        self._primary_completion_date_category,
+                        self._start_date,
+                        self._start_date_category,
+                        self._completion_date,
+                        self._completion_date_category,
+                        self._overall_status,
+                        self._enrollment,
+                        self._enrollment_category,
+                        self._sponsor,
+                        self._responsible_party
+                    )
+                )
+            except Exception as err:
+                #catch any error, print the applicable information, and raise the error.
+                print(self)
+                raise err
+            
+            db_connection.commit()
+        
+############ Functions
+def extract_submission_dates(soup):
+    """
+    Extract dates for each version
+    """
+    table_rows = soup.findChildren("fieldset")[0].table.tbody.findChildren("tr")
+
+    version_date_dict = {}
+
+    for row in table_rows:
+        # if it is <td headers="VersionNumber">xx</td> then it contains what we need.
+        version_number = None
+        version_date = None
+        for td in row.findChildren("td"):
+            if ("headers" in td.attrs):
+                if (td.attrs["headers"][0]=="VersionNumber"):
+                    version_number = int(td.text)
+                elif (td.attrs["headers"][0]=="VersionDate"):
+                    version_date = datetime.strptime(td.text.strip() , "%B %d, %Y")
+
+        version_date_dict[version_number] = version_date
+    return version_date_dict
+
+def optional_strip(possible_string):
+    if type(possible_string) == str:
+        return possible_string.strip()
+    else:
+        return possible_string
+
+def extract_study_statuses(study_status_form, version_a,version_b):
+    """
+    This extracts data from a study_status form and returns one or two 
+    StudyStatusData objects, 
+
+    """
+
+    #get rows
+    rows = study_status_form.table.tbody.find_all("tr")
+    #iterate through rows, 
+    for trow in rows:
+        #matching on rowLabels
+
+        match tr_to_td(trow):
+            case ["Primary Completion:" as row_label, old,new]: 
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+
+                tagdate1 = extract_date_and_tag(old.text)
+                version_a._primary_completion_date = tagdate1.date
+                version_a._primary_completion_date_category = optional_strip(tagdate1.tag)
+                
+                tagdate2 = extract_date_and_tag(new.text)
+                version_b._primary_completion_date = tagdate2.date
+                version_b._primary_completion_date_category = optional_strip(tagdate2.tag)
+
+            case ["Study Start:" as row_label, old, new]: 
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                tagdate1 = extract_date_and_tag(old.text)
+                version_a._start_date = tagdate1.date
+                version_a._start_date_category = optional_strip(tagdate1.tag)
+                
+                tagdate2 = extract_date_and_tag(new.text)
+                version_b._start_date = tagdate2.date
+                version_b._start_date_category = optional_strip(tagdate2.tag)
+
+            case ["Study Completion:" as row_label, old,new]:
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                tagdate1 = extract_date_and_tag(old.text)
+                version_a._completion_date = tagdate1.date
+                version_a._completion_date_category = optional_strip(tagdate1.tag)              
+                tagdate2 = extract_date_and_tag(new.text)
+                version_b._completion_date = tagdate2.date
+                version_b._completion_date_category = optional_strip(tagdate2.tag)
+
+            case ["Overall Status:" as row_label, old,new]:
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                #split out any notes such as "Suspended [reason for suspenstion ]"
+                version_a._overall_status = optional_strip(old.text.split("[")[0])
+                #split out any notes such as "Suspended [reason for suspenstion ]"
+                version_b._overall_status = optional_strip(new.text.split("[")[0])
+                #FIX: There is an issue with NCT00789633 where the overall status includes information as to why it was suspended.
+
+            case _ as row_label:
+                print("row not matched: {}".format(row_label)) if VERBOSE else ""
+
+
+def extract_study_design(study_status_form, version_a,version_b):
+    """
+    This extracts data from a study_status form and returns one or two 
+    StudyStatusData objects, 
+
+    """
+    #get rows
+    rows = study_status_form.table.tbody.find_all("tr")
+    #iterate through rows, 
+    for trow in rows:
+        #matching on rowLabels
+        match tr_to_td(trow):
+            case ["Enrollment:" as row_label, old, new]: 
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+
+                #Extract tag and text, add them to preallocated object
+                tagtext1 = extract_text_and_tag(old.text)
+                version_a._enrollment = tagtext1.text
+                version_a._enrollment_category = optional_strip(tagtext1.tag)
+                
+                tagtext2 = extract_text_and_tag(new.text)
+                version_b._enrollment = tagtext2.text
+                version_b._enrollment_category = optional_strip(tagtext2.tag)
+
+            case _ as row_label:
+                print("row not matched: {}".format(row_label)) if VERBOSE else ""
+             
+def extract_sponsor_data(study_status_form, version_a,version_b):
+    """
+    This extracts data from a study_status form and returns one or two 
+    StudyStatusData objects, 
+
+    """
+    #get rows
+    rows = study_status_form.table.tbody.find_all("tr")
+    #iterate through rows, 
+    for trow in rows:
+        #matching on rowLabels
+        match tr_to_td(trow):
+            case ["Sponsor:" as row_label, old, new]:
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                version_a._sponsor = optional_strip(old.text)
+                version_b._sponsor = optional_strip(new.text)
+
+            case ["Responsible Party:" as row_label, old, new]: 
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                version_a._responsible_party = optional_strip(old.text)
+                version_b._responsible_party = optional_strip(new.text)
+
+            case ["Collaborators:" as row_label, old, new]: 
+                print("row matched: {}".format(row_label)) if VERBOSE else ""
+                #TODO: find a trial with multiple collaborators and figure out how to identify/count them:w
+                # So far can't figure out where this is in AACT, so I'm going to ignore it.
+                pass
+
+            case _ as row_label:
+                print("row not matched: {}".format(row_label)) if VERBOSE else ""
+
+
+def split_by_version(tag):
+    '''
+    OUTDATED: With the new format that separates old and new versions, I don't technically need this. It is a nice place to identify exact changes if those are every needed though and it removes the highlights cleanly.
+    '''
+    #clone elements and remove sub-tags that are not needed.
+    old = copy(tag)
+    for span in old.find_all(class_="add_hilite"):
+        span.extract()
+        
+    new = copy(tag)
+    for span in new.find_all(class_="drop_hilite"):
+        span.extract()
+    return old,new
+
+
+def extract_date_and_tag(text):
+    """
+    Extracts a datetype according to the date format
+    and the estimate tag based on 
+
+    """
+
+    text = text.strip()
+
+    #handle various empty cases
+    if not text or text == '':
+        return TagDatePair(None, None)
+        
+    date_split = text.split("[")
+    if len(date_split) > 1:
+        estimate_tag = date_split[1].split("]")[0].strip()
+    else:
+        estimate_tag = None
+    
+    try:
+        date_object = datetime.strptime(date_split[0].strip(), date_MMMM_YYYY)
+    except ValueError as ve:
+        date_object = datetime.strptime(date_split[0].strip(), date_MMMM_DD_YYYY)
+
+    return TagDatePair(estimate_tag, date_object)
+
+
+def extract_text_and_tag(text):
+    """
+    Extracts a datetype according to the date format
+    and the estimate tag based on 
+
+    """
+    text = text.strip()
+
+    #handle various empty cases
+    if not text or text == '':
+        return TagTextPair(None, None)
+        
+    date_split = text.split("[")
+    if len(date_split) > 1:
+        estimate_tag = date_split[1].split("]")[0].strip()
+    else:
+        estimate_tag = None
+    text_object = date_split[0].strip()
+    
+    return TagTextPair(estimate_tag, text_object)
+
+### FUNCTIONS
+
+def tr_to_td(tr) -> tuple[str, str, str]:
+    """
+    Takes an html data row of interest, extracts the record_name from the first <td>, and the data from the second <td>.
+
+    For the data, it just extracts the text. 
+    The text itself then needs processed separately, based on what it should contain.
+    """
+    #get list of cells 
+    td_list = tr.find_all("td")
+    if len(td_list) == 3:
+        return td_list[0].text, td_list[1], td_list[2]
+    else:
+        return None, None, None
+
+def get_forms(soup,version_a,version_b):
+
+    #extract all forms
+    for form in soup.body.find_all("form"):
+        #Match forms against ID types
+        if not "id" in form.attrs:
+            continue
+
+        #for each type of form (identified by the ID field) 
+        #  extract and add the data to the preallocated objects
+        match form.attrs["id"]:
+            case "form_StudyStatus":
+                extract_study_statuses(form,version_a,version_b)
+            case "form_SponsorCollaborators":
+                extract_sponsor_data(form, version_a, version_b)
+            case "form_Oversight":
+                pass
+            case "form_StudyDescription":
+                pass
+            case "form_Conditions":
+                pass
+            case "form_StudyDesign":
+                extract_study_design(form,version_a,version_b)
+            case "form_ArmsandInterventions":
+                pass
+            case "form_ProtocolOutcomeMeasures":
+                pass
+            case "form_Eligibility":
+                pass
+            case "form_ContactsLocations":
+                pass
+            case "form_IPDSharing":
+                pass
+            case "form_References":
+                pass
+            case "form_ParticipantFlow":
+                pass
+            case "form_BaselineCharacteristics":
+                pass
+            case "form_ROutcomeMeasures":
+                pass
+            case "form_AdverseEvents":
+                pass
+            case "form_LimitationsandCaveats":
+                pass
+            case "form_MoreInformation":
+                pass
+            case _ as form_name:
+                print("form not matched: {}".format(form_name)) if VERBOSE else ""
+
+
+### CONSTANTS
+date_MMMM_YYYY = "%B %Y"
+date_MMMM_DD_YYYY = "%B %d, %Y"
+
+def get_data_from_versions(nct_id,html, version_a_int, version_b_int):
+    soup = BeautifulSoup(html,"lxml")
+
+    version_date_dict = extract_submission_dates(soup)
+
+    #preallocate version data
+    version_a = VersionData(nct_id, version_a_int, version_date_dict.get(version_a_int))
+    version_b = VersionData(nct_id, version_b_int, version_date_dict.get(version_b_int))
+
+    #extract data from html and put it in the preallocated objects
+    get_forms(soup, version_a, version_b)
+
+    return version_a,version_b
+
+
+
+def run():
+    with postgres_conn() as db_connection:
+        #pull the requests from the db
+        with db_connection.cursor() as curse:
+            sql = """
+            SELECT nct_id, version_a,version_b, html
+            FROM http.responses
+            WHERE response_code = 200
+            """
+            curse.execute(sql)
+            for response in tqdm(curse.fetchall()):
+                nct_id, version_a, version_b, html = response
+
+                print(nct_id, version_a, version_b) if VERBOSE else ""
+
+                version1, version2 = get_data_from_versions(nct_id, html, version_a, version_b)
+            
+                if version_b == version_a + 1:
+                    version1.load_to_db(db_connection)
+                    version2.load_to_db(db_connection)
+                else:
+                    version2.load_to_db(db_connection)
+
+
+if __name__ == "__main__":
+    run()
+
+"""
+Documentation:
+
+TO add a new field to extraction-lib
+
+1. Locate the field in the HTML
+    - form id (e.g. <form id="form_StudyStatus> gives the form id "form_StudyStatus)
+    - Table row's data label. This corresponds to the text of first column in the row and will 
+    look something like 
+        <td class="rowLabel" style="min-width: 210px;">Record Verification:</td>.
+    "Record Verification:" is the data label in the example above.
+2. Identify what data you will be extracting 
+    - type (date, text, int, etc)
+    - if it contains a category ([Actual] vs [Anticipated] etc)
+3. Add data to:
+    - sql table: history.trial_snapshots
+    - the VersionData class
+    - the VersionData.load_to_db() function
+4. Ensure the field matcher in `get_forms(*)` is matching on the form ID and has a function processing the form
+5. Ensure the function processing the form has a match entry to proceess the row
+    - This should match on data label and then process the data by
+        - splitting into old and new versions
+        - Extracting the data for both old and new
+        - add the data to the passed VersionData objects
+"""

data_mgmt_scripts/drugtools/historical_trial_selector.py

@@ -0,0 +1,15 @@
+from .env_setup import postgres_conn
+from pathlib import Path
+
+
+def run():
+    #get relative path
+    p = Path(__file__).with_name("selected_trials.sql")
+    with open(p,'r') as fh:
+        sqlfile = fh.read()
+        with postgres_conn() as connection:
+            with connection.cursor() as curse:
+                curse.execute(sqlfile)
+
+if __name__ == "__main__":
+    run()

data_mgmt_scripts/drugtools/migrate_mysql2pgsql.py

@@ -0,0 +1,118 @@
+import psycopg2 as psyco
+from psycopg2 import sql
+from psycopg2 import extras
+import pymysql
+from dotenv import load_dotenv
+import os
+from .env_setup import postgres_conn, mariadb_conn, get_tables_of_interest
+
+
+##############NOTE
+'''
+
+
+mariadb --mariadb.connect--> incrementally fetched dict --psycopg2--> postgres
+
+I will have the ability to reduce memory usage and simplify what I am doing.
+
+
+'''
+
+############### GLOBALS
+#these are hardcoded so they shouldn't require any updates
+mschema="rxnorm_current" 
+pschema="rxnorm_migrated"
+
+########FUNCTIONS#################
+
+
+def convert_column(d):
+    """
+    Given the metadata about a column in mysql, make the portion of the `create table` 
+    statement that corresponds to that column in postgres
+    """
+    #extract
+    data_type = d["DATA_TYPE"]
+    position = d["ORDINAL_POSITION"]
+    table_name = d["TABLE_NAME"]
+    d["IS_NULLABLE"] = "NOT NULL" if d["IS_NULLABLE"] == "NO" else ""
+
+    #convert
+    if data_type=="varchar":
+        string = "{COLUMN_NAME} character varying({CHARACTER_MAXIMUM_LENGTH}) COLLATE pg_catalog.\"default\" {IS_NULLABLE}".format(**d)
+    elif data_type=="char":
+        string = "{COLUMN_NAME} character({CHARACTER_MAXIMUM_LENGTH}) COLLATE pg_catalog.\"default\" {IS_NULLABLE}".format(**d)
+    elif data_type=="tinyint":
+        string = "{COLUMN_NAME} smallint {IS_NULLABLE}".format(**d)
+    elif data_type=="decimal":
+        string = "{COLUMN_NAME} numeric({NUMERIC_PRECISION},{NUMERIC_SCALE}) {IS_NULLABLE}".format(**d)
+    elif data_type=="int":
+        string = "{COLUMN_NAME} integer {IS_NULLABLE}".format(**d)
+    elif data_type=="enum":
+        string = None
+    elif data_type=="text":
+        string = None
+
+    return string
+
+def run():
+    #get & convert datatypes for each table of interest
+    tables_of_interest = get_tables_of_interest()
+
+
+    with mariadb_conn(cursorclass=pymysql.cursors.DictCursor) as mcon, postgres_conn() as pcon:
+        with mcon.cursor() as mcurse, pcon.cursor(cursor_factory=extras.DictCursor) as pcurse:
+            for table in tables_of_interest: #create equivalent table in postgres
+
+                #get columns from mysql
+                q = "SELECT * FROM INFORMATION_SCHEMA.columns WHERE TABLE_SCHEMA=%s and TABLE_NAME=%s;"
+                mcurse.execute(q,[mschema,table])
+
+                #convert mysql column names and types to postgres column statements.
+                columns = [convert_column(a) for a in mcurse.fetchall() ] 
+                #TODO make sure this uses psycopg colums correctly.
+                column_sql = sql.SQL(",\n".join(columns))
+                
+                #build a header and footer
+                header=sql.SQL("CREATE TABLE IF NOT EXISTS {}\n(").format(sql.Identifier(pschema,table))
+                footer=sql.SQL(");")
+
+                #Joint the header, columns, and footer.
+                create_table_statement = sql.SQL("\n").join([header,column_sql,footer])
+                print(create_table_statement.as_string(pcon))
+
+                #Create the table in postgres
+                pcurse.execute(create_table_statement)
+                pcon.commit() 
+                
+                #Get the data from mysql
+                mcurse.execute("SELECT * FROM {schema}.{table}".format(schema=mschema,table=table))
+                #FIX setting up sql this^^^ way is improper.
+                results = mcurse.fetchall()
+
+                #build the insert statement template
+                #get list of field names
+                column_list = [sql.SQL(x) for x in results[0]]
+                column_inserts = [sql.SQL("%({})s".format(x)) for x in results[0]] #fix with sql.Placeholder
+                #generate insert statement
+                psql_insert = sql.SQL("INSERT INTO {table} ({columns}) VALUES  %s ").format(
+                    table=sql.Identifier(pschema,table)
+                    ,columns=sql.SQL(",").join(column_list)
+                )
+                #Note that this^^^^ does not contain parenthases around the placeholder
+
+                #Building the values template. 
+                #Note that it must include the parenthases so that the 
+                #VALUES portion is formatted correctly.
+                template = sql.SQL(",").join(column_inserts)
+                template = sql.Composed([
+                    sql.SQL("(")
+                    ,template
+                    ,sql.SQL(")")
+                    ])
+                
+                #insert the data with page_size
+                extras.execute_values(pcurse,psql_insert,argslist=results,template=template, page_size=1000)
+
+if __name__ == "__main__":
+    run()

data_mgmt_scripts/drugtools/selected_trials.sql

@@ -0,0 +1,21 @@
+DELETE FROM http.download_status;
+
+INSERT INTO http.download_status (nct_id, status)
+SELECT nct_id, 'Of Interest'::http.history_download_status AS status
+FROM ctgov.studies
+WHERE 
+    is_fda_regulated_drug=TRUE
+    AND
+    study_type = 'Interventional'
+    AND
+    phase='Phase 3'
+    AND 
+    overall_status in ('Terminated', 'Completed')
+    AND 
+    start_date > '2010-01-01'
+    AND
+    completion_date < '2022-01-01'
+;
+
+
+SELECT count(*) FROM http.download_status ;

data_mgmt_scripts/import-icd10_to_cause.py

@@ -0,0 +1,36 @@
+from drugtools.env_setup import ENV,postgres_conn
+from psycopg2 import extras
+from collections import namedtuple
+from tqdm import tqdm
+
+
+FILES=[
+    "../non-db_data_sources/GBD and ICD-10_(2019 version)/NONFATAL_cause2code.psv",
+    "../non-db_data_sources/GBD and ICD-10_(2019 version)/COD_cause2code.psv"
+]
+SEP="|"
+
+sql = """
+INSERT INTO "DiseaseBurden".icd10_to_cause
+    (code,cause_text)
+VALUES %s
+"""
+
+
+
+with postgres_conn() as pconn, pconn.cursor(cursor_factory=extras.DictCursor) as pcurse:
+    entries = []
+    for fpath in FILES:
+        print(fpath)
+
+        with open(fpath,"r") as fh:
+            for line in tqdm(fh.readlines(),desc=fpath):
+                code,cause = line.split(SEP)
+                code = code.strip()
+                cause = cause.strip()
+
+                entries.append((code,cause))
+    
+    extras.execute_values(pcurse, sql , entries)
+
+

data_mgmt_scripts/rm_data.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+rm -r ../containers/RxNav-In-a-box/rxnav_data/*
+
+rm -r ../containers/AACT_downloader/postgresql/data

data_mgmt_scripts/runall.py

@@ -0,0 +1,24 @@
+from drugtools import env_setup
+from drugtools import historical_trial_selector as hts
+from drugtools import historical_nct_downloader as hnd
+from drugtools import historical_nct_extractor as hne
+from drugtools import download_and_extract_nsde as daen
+from drugtools import migrate_mysql2pgsql as mm2p
+
+print("Current Environment")
+print(env_setup.ENV)
+
+cont = input("Are you willing to continue with the current environmnet? y/[n]")
+
+if cont == "Y" or cont == "y":
+    print("SelectingTrials")
+    #hts.run()
+    print("downloading trials")
+    #hnd.run()
+    print("extracting trials")
+    hne.run()
+    exit(0)
+    daen.run()
+    mm2p.run()
+else:
+    print("Please fix your .env file and try again")

data_mgmt_scripts/umls_requests.py

@@ -0,0 +1,87 @@
+import requests
+import json
+from drugtools.env_setup import ENV,postgres_conn
+from psycopg2 import extras
+from collections import namedtuple
+from tqdm import tqdm
+
+
+RecordStuff = namedtuple("RecordStuff", "nct_id condition ui uri rootSource name")
+
+class Requestor():
+    def __init__(self,api_key):
+        self.key = api_key
+
+    def search(self,search_term,inputType="sourceUi", returnIdType="code", addnl_terms={}):
+        query_terms = {
+            "apiKey":self.key,
+            "sabs":"ICD10",
+            "string":search_term,
+            "returnIdType":returnIdType,
+            "inputType":inputType
+        } | addnl_terms
+        query = "https://uts-ws.nlm.nih.gov/rest/search/current/"
+
+        r = requests.get(query,params=query_terms)
+        return r
+
+
+r = Requestor(ENV.get("UMLS_API_KEY"))
+
+
+with postgres_conn() as pconn, pconn.cursor(cursor_factory=extras.DictCursor) as pcurse:
+    sql = """
+    select nct_id, downcase_mesh_term
+    from ctgov.browse_conditions bc
+    where 
+    mesh_type = 'mesh-list'
+    and 
+    nct_id in (select distinct nct_id from history.trial_snapshots ts)
+    order by nct_id
+    ;
+    """
+    sql2 = """
+    with cte as (
+    /* Keywords added too much noise
+        select nct_id,downcase_name 
+        from ctgov.keywords k 
+        where nct_id in (select distinct nct_id from history.trial_snapshots ts)
+        union */
+        select nct_id, downcase_name  
+        from ctgov.conditions c 
+        union 
+        select nct_id ,downcase_mesh_term  as downcase_name
+        from ctgov.browse_conditions bc  
+        where mesh_type = 'mesh-list'
+    )
+    select nct_id, downcase_name  from cte
+    where nct_id in (select distinct nct_id from history.trial_snapshots ts)
+    order by nct_id 
+    """
+    pcurse.execute(sql2)
+    rows = pcurse.fetchall()
+
+    entries = []
+
+    for row in tqdm(rows,desc="Search MeSH terms"):
+        nctid = row[0]
+        condition = row[1]
+#        print(nctid,condition)
+
+        results = r.search(row[1]).json().get('result', Exception("No result entry in json")).get('results',Exception("No results entry in json"))
+
+        #if results are empty?
+        if not results:
+            entries.append(RecordStuff(nctid,condition,None,None,None,None))
+        else:
+            for entry in results:
+                entries.append(RecordStuff(nctid, condition, entry["ui"], entry["uri"], entry["rootSource"], entry["name"]))
+
+    sql_insert = """
+    INSERT INTO "DiseaseBurden".trial_to_icd10
+    (nct_id, "condition", ui,uri,rootsource,"name","source",approved,approval_timestamp)
+    VALUES
+    (%(nct_id)s, %(condition)s, %(ui)s, %(uri)s, %(rootSource)s, %(name)s, 'UMLS API search', null,null)
+    """
+    for entry in tqdm(entries,desc="Inserting entries to DB"):
+        pcurse.execute(sql_insert,entry._asdict())

export/export_data_postgres_materialized_views.sql

@@ -0,0 +1,6 @@
+ SELECT 
+    'CREATE OR REPLACE MATERIALIZED VIEW ' || schemaname || '.' || viewname || ' AS ' || definition
+FROM pg_views 
+    WHERE schemaname != 'pg_catalog'  
+    and schemaname != 'information_schema'
+;

export/export_data_postgres_tables.sql

@@ -0,0 +1,24 @@
+SELECT 
+    'CREATE TABLE ' || schemaname || '.' || tablename || E'\n(\n' ||
+    string_agg(column_definition, E',\n') || E'\n);\n'
+FROM (
+    SELECT 
+        schemaname,
+        tablename,
+        column_name || ' ' || data_type ||
+        CASE 
+            WHEN character_maximum_length IS NOT NULL THEN '(' || character_maximum_length || ')'
+            ELSE ''
+        END ||
+        CASE 
+            WHEN is_nullable = 'NO' THEN ' NOT NULL'
+            ELSE ''
+        END as column_definition
+    FROM pg_catalog.pg_tables t
+    JOIN information_schema.columns c 
+        ON t.schemaname = c.table_schema 
+        AND t.tablename = c.table_name
+    WHERE schemaname != 'pg_catalog'  
+    	and schemaname != 'information_schema'-- Replace with your schema name
+) t
+GROUP BY schemaname, tablename;

export/export_data_postgres_views.sql

@@ -0,0 +1,6 @@
+ SELECT 
+    'CREATE OR REPLACE VIEW ' || schemaname || '.' || viewname || ' AS ' || definition
+FROM pg_views 
+    WHERE schemaname != 'pg_catalog'  
+        and schemaname != 'information_schema' -- Replace with your schema name
+;

export/output_2025-01-06_export_data_postgres_materialized_views.sql

@@ -0,0 +1,415 @@
+                                                                                                                                                                                                                                                                                                      ?column?                                                                                                                                                                                                                                                                                                       
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_browse_conditions AS  SELECT browse_conditions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     array_to_string(array_agg(DISTINCT browse_conditions.mesh_term), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM ctgov.browse_conditions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY browse_conditions.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_browse_interventions AS  SELECT browse_interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     array_to_string(array_agg(browse_interventions.mesh_term), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+    FROM ctgov.browse_interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY browse_interventions.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_cities AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     array_to_string(array_agg(DISTINCT facilities.city), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_conditions AS  SELECT conditions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     array_to_string(array_agg(DISTINCT conditions.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ctgov.conditions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY conditions.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_countries AS  SELECT countries.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     array_to_string(array_agg(DISTINCT countries.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+    FROM ctgov.countries                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (countries.removed IS NOT TRUE)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   GROUP BY countries.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_design_outcomes AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_facilities AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     array_to_string(array_agg(facilities.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_group_types AS  SELECT design_groups.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     array_to_string(array_agg(DISTINCT design_groups.group_type), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ctgov.design_groups                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY design_groups.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_id_information AS  SELECT id_information.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     array_to_string(array_agg(DISTINCT id_information.id_value), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.id_information                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+   GROUP BY id_information.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_intervention_types AS  SELECT interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     array_to_string(array_agg(interventions.intervention_type), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY interventions.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_interventions AS  SELECT interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     array_to_string(array_agg(interventions.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM ctgov.interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY interventions.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_keywords AS  SELECT keywords.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     array_to_string(array_agg(DISTINCT keywords.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.keywords                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+   GROUP BY keywords.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_overall_official_affiliations AS  SELECT overall_officials.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     array_to_string(array_agg(overall_officials.affiliation), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+    FROM ctgov.overall_officials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY overall_officials.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_overall_officials AS  SELECT overall_officials.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     array_to_string(array_agg(overall_officials.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.overall_officials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY overall_officials.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_primary_outcome_measures AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   WHERE ((design_outcomes.outcome_type)::text = 'primary'::text)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_secondary_outcome_measures AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   WHERE ((design_outcomes.outcome_type)::text = 'secondary'::text)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_sponsors AS  SELECT sponsors.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     array_to_string(array_agg(DISTINCT sponsors.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.sponsors                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+   GROUP BY sponsors.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.all_states AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     array_to_string(array_agg(DISTINCT facilities.state), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.categories AS  SELECT search_results.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     search_results.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     search_results.name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     search_results.created_at,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results.updated_at,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results."grouping",                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results.study_search_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+    FROM ctgov.search_results;
+ CREATE OR REPLACE MATERIALIZED VIEW ctgov.covid_19_studies AS  SELECT s.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     s.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.study_type,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.official_title,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.acronym,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.phase,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     s.why_stopped,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     s.has_dmc,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.is_fda_regulated_device,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.is_fda_regulated_drug,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     s.is_unapproved_device,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     s.has_expanded_access,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     s.study_first_submitted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.last_update_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.results_first_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     s.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     s.study_first_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     cv.number_of_facilities,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     cv.has_single_facility,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     cv.nlm_download_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     s.number_of_arms,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.number_of_groups,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     sp.name AS lead_sponsor,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     aid.names AS other_ids,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     e.gender,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     e.gender_based,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     e.gender_description,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     e.population,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     e.minimum_age,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     e.maximum_age,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     e.criteria,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     e.healthy_volunteers,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ak.names AS keywords,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ai.names AS interventions,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     ac.names AS conditions,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     d.primary_purpose,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     d.allocation,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     d.observational_model,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     d.intervention_model,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     d.masking,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     d.subject_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     d.caregiver_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     d.investigator_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     d.outcomes_assessor_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ado.names AS design_outcomes,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     bs.description AS brief_summary,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dd.description AS detailed_description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM (((((((((((ctgov.studies s                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+      FULL JOIN ctgov.all_conditions ac ON (((s.nct_id)::text = (ac.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+      FULL JOIN ctgov.all_id_information aid ON (((s.nct_id)::text = (aid.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      FULL JOIN ctgov.all_design_outcomes ado ON (((s.nct_id)::text = (ado.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+      FULL JOIN ctgov.all_keywords ak ON (((s.nct_id)::text = (ak.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+      FULL JOIN ctgov.all_interventions ai ON (((s.nct_id)::text = (ai.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      FULL JOIN ctgov.sponsors sp ON (((s.nct_id)::text = (sp.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+      FULL JOIN ctgov.calculated_values cv ON (((s.nct_id)::text = (cv.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      FULL JOIN ctgov.designs d ON (((s.nct_id)::text = (d.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+      FULL JOIN ctgov.eligibilities e ON (((s.nct_id)::text = (e.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      FULL JOIN ctgov.brief_summaries bs ON (((s.nct_id)::text = (bs.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+      FULL JOIN ctgov.detailed_descriptions dd ON (((s.nct_id)::text = (dd.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+   WHERE (((sp.lead_or_collaborator)::text = 'lead'::text) AND ((s.nct_id)::text IN ( SELECT search_results.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+            FROM ctgov.search_results                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+           WHERE ((search_results.name)::text = 'covid-19'::text))));
+ CREATE OR REPLACE MATERIALIZED VIEW history.match_drugs_to_trials AS  SELECT bi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     rp.rxcui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     rp.propvalue1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+    FROM (ctgov.browse_interventions bi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      JOIN rxnorm_migrated.rxnorm_props rp ON (((bi.downcase_mesh_term)::text = (rp.propvalue1)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (((rp.propname)::text = 'RxNorm Name'::text) AND ((bi.nct_id)::text IN ( SELECT trial_snapshots.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+            FROM history.trial_snapshots)));
+ CREATE OR REPLACE MATERIALIZED VIEW http.most_recent_download_status AS  SELECT t.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     t.status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     t.update_timestamp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM ( SELECT download_status.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+             download_status.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+             download_status.status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+             download_status.update_timestamp,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+             row_number() OVER (PARTITION BY download_status.nct_id ORDER BY download_status.update_timestamp DESC) AS rn                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+            FROM http.download_status) t                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (t.rn = 1)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   ORDER BY t.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.time_between_submission_and_start_view AS  SELECT s.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     s.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     ts.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.submission_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     abs(((EXTRACT(epoch FROM (ts.submission_date - (s.start_date)::timestamp without time zone)))::double precision / (((24 * 60) * 60))::double precision)) AS start_deviance                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+    FROM (ctgov.studies s                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+      JOIN history.trial_snapshots ts ON (((s.nct_id)::text = (ts.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE ((s.nct_id)::text IN ( SELECT DISTINCT tti.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+            FROM "DiseaseBurden".trial_to_icd10 tti));
+ CREATE OR REPLACE MATERIALIZED VIEW public.rank_proximity_to_start_time_view AS  SELECT cte.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     cte.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     row_number() OVER (PARTITION BY cte.nct_id ORDER BY cte.start_deviance) AS rownum,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     cte.submission_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     cte.start_deviance,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     cte.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ts.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.primary_completion_date_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     ts.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     ts.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.enrollment_category                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM (time_between_submission_and_start_view cte                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+      JOIN history.trial_snapshots ts ON ((((cte.nct_id)::text = (ts.nct_id)::text) AND (cte.version = ts.version))));
+ CREATE OR REPLACE MATERIALIZED VIEW public.enrollment_closest_to_start_view AS  SELECT cte2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     min(cte2.rownum) AS enrollment_source                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+    FROM rank_proximity_to_start_time_view cte2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+   WHERE (cte2.enrollment IS NOT NULL)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+   GROUP BY cte2.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.match_trials_to_bn_in AS  WITH trialncts AS (                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+          SELECT DISTINCT ts.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+            FROM history.trial_snapshots ts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+         )                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+  SELECT bi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     bi.downcase_mesh_term,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     rr.tty2,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     rr.rxcui2 AS bn_or_in_cui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     count(*) AS count                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ((ctgov.browse_interventions bi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      LEFT JOIN rxnorm_migrated.rxnorm_props rp ON (((bi.downcase_mesh_term)::text = (rp.propvalue1)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON ((rr.rxcui1 = rp.rxcui)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   WHERE (((bi.nct_id)::text IN ( SELECT trialncts.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+            FROM trialncts)) AND ((bi.mesh_type)::text = 'mesh-list'::text) AND ((rp.propname)::text = 'Active_ingredient_name'::text) AND (rr.tty2 = ANY (ARRAY['BN'::bpchar, 'IN'::bpchar, 'MIN'::bpchar])))                                                                                                                                                                                                                                                                                                                                                                                                      +
+   GROUP BY bi.nct_id, bi.downcase_mesh_term, rr.tty2, rr.rxcui2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   ORDER BY bi.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.match_trial_to_ndc11 AS  SELECT mttbi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     ah.ndc,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     count(*) AS count                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ((match_trials_to_bn_in mttbi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON ((mttbi.bn_or_in_cui = rr.rxcui1)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      LEFT JOIN rxnorm_migrated."ALLNDC_HISTORY" ah ON ((rr.rxcui2 = ah.rxcui)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   WHERE ((rr.tty1 = 'BN'::bpchar) AND (rr.tty2 = ANY (ARRAY['SBD'::bpchar, 'BPCK'::bpchar])) AND ((ah.sab)::text = 'RXNORM'::text))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   GROUP BY mttbi.nct_id, ah.ndc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   ORDER BY mttbi.nct_id, ah.ndc;
+ CREATE OR REPLACE MATERIALIZED VIEW public.match_trial_to_marketing_start_date AS  SELECT mttn.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     n.application_number_or_citation,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     min(n.marketing_start_date) AS min                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM (match_trial_to_ndc11 mttn                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+      JOIN spl.nsde n ON ((mttn.ndc = (n.package_ndc11)::bpchar)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE (((n.product_type)::text = 'HUMAN PRESCRIPTION DRUG'::text) AND ((n.marketing_category)::text = ANY (ARRAY[('NDA'::character varying)::text, ('ANDA'::character varying)::text, ('BLA'::character varying)::text, ('NDA authorized generic'::character varying)::text, ('NDA AUTHORIZED GENERIC'::character varying)::text])))                                                                                                                                                                                                                                                                             +
+   GROUP BY mttn.nct_id, n.application_number_or_citation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   ORDER BY mttn.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_burdens_cte AS  SELECT b.measure_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     b.location_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     b.sex_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     b.age_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     b.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.metric_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     b.val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     b.upper_95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.lower_95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.key_column                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+    FROM "DiseaseBurden".burdens b                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE ((b.sex_id = 3) AND (b.metric_id = 1) AND (b.measure_id = 2) AND (b.age_id = 22));
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_burdens_cte2 AS  SELECT c1.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     c1.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     c1.val AS h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c1.upper_95 AS h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c1.lower_95 AS h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c2.val AS hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     c2.upper_95 AS hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c2.lower_95 AS hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c3.val AS m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c3.upper_95 AS m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c3.lower_95 AS m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c4.val AS lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     c4.upper_95 AS lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c4.lower_95 AS lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c5.val AS l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c5.upper_95 AS l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c5.lower_95 AS l_sdi_l95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ((((view_burdens_cte c1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+      JOIN view_burdens_cte c2 ON (((c1.cause_id = c2.cause_id) AND (c1.year = c2.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c3 ON (((c1.cause_id = c3.cause_id) AND (c1.year = c3.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c4 ON (((c1.cause_id = c4.cause_id) AND (c1.year = c4.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c5 ON (((c1.cause_id = c5.cause_id) AND (c1.year = c5.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+   WHERE ((c1.location_id = 44635) AND (c2.location_id = 44634) AND (c3.location_id = 44639) AND (c4.location_id = 44636) AND (c5.location_id = 44637));
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_cte AS  SELECT ts.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ts.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.primary_completion_date_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     ts.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     ts.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     min(ts.submission_date) AS earliest_date_observed                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM history.trial_snapshots ts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   WHERE (((ts.nct_id)::text IN ( SELECT DISTINCT tti.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+            FROM "DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+           WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type))) AND (ts.submission_date >= ts.start_date) AND (ts.overall_status <> ALL (ARRAY['Completed'::history.study_statuses, 'Terminated'::history.study_statuses])))                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY ts.nct_id, ts.primary_completion_date, ts.primary_completion_date_category, ts.start_date, ts.enrollment, ts.enrollment_category, ts.overall_status;
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_disbur_cte0 AS  SELECT tti.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     tti.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     tti.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     itc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ch.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     ch.level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM (("DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN "DiseaseBurden".icd10_to_cause itc ON ((replace(replace((tti.ui)::text, '-'::text, ''::text), '.'::text, ''::text) = replace(replace((itc.code)::text, '-'::text, ''::text), '.'::text, ''::text))))                                                                                                                                                                                                                                                                                                                                                                                                     +
+      JOIN "DiseaseBurden".cause_hierarchy ch ON (((itc.cause_text)::text = (ch.cause_name)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type);
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_disbur_cte AS  SELECT view_disbur_cte0.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     max(view_disbur_cte0.level) AS max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM view_disbur_cte0                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY view_disbur_cte0.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_trial_to_cause AS  SELECT tti.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     tti.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     tti.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     itc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ch.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     ch.level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM (("DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN "DiseaseBurden".icd10_to_cause itc ON ((replace(replace((tti.ui)::text, '-'::text, ''::text), '.'::text, ''::text) = replace(replace((itc.code)::text, '-'::text, ''::text), '.'::text, ''::text))))                                                                                                                                                                                                                                                                                                                                                                                                     +
+      JOIN "DiseaseBurden".cause_hierarchy ch ON (((itc.cause_text)::text = (ch.cause_name)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+   ORDER BY tti.nct_id;
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_disbur_cte2 AS  SELECT ttc.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ttc.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     ttc.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ttc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ttc.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     disbur_cte.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM (view_trial_to_cause ttc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      JOIN view_disbur_cte disbur_cte ON (((disbur_cte.nct_id)::text = (ttc.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   WHERE (ttc.level = disbur_cte.max_level)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+   GROUP BY ttc.nct_id, ttc.ui, ttc.condition, ttc.cause_text, ttc.cause_id, disbur_cte.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+   ORDER BY ttc.nct_id, ttc.ui;
+ CREATE OR REPLACE MATERIALIZED VIEW public.view_disbur_cte3 AS  SELECT disbur_cte2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) AS code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     disbur_cte2.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     disbur_cte2.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     disbur_cte2.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ic.chapter_code AS category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ic.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     disbur_cte2.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+    FROM (view_disbur_cte2 disbur_cte2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      JOIN "DiseaseBurden".icd10_categories ic ON (((SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) <= (ic.end_code)::text) AND (SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) >= (ic.start_code)::text))))                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   WHERE (ic.level = 1);
+ CREATE OR REPLACE MATERIALIZED VIEW public.formatted_data AS  SELECT cte.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     cte.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     cte.enrollment AS current_enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     cte.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     cte.overall_status AS current_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     cte.earliest_date_observed,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     (EXTRACT(epoch FROM (cte.earliest_date_observed - cte.start_date)) / EXTRACT(epoch FROM (cte.primary_completion_date - cte.start_date))) AS elapsed_duration,                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     count(DISTINCT mttmsd.application_number_or_citation) AS n_brands,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     dbc3.code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     dbc3.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     dbc3.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dbc3.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     dbc3.category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     dbc3.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dbc3.max_level,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     b.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     b.h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.l_sdi_l95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+    FROM (((view_cte cte                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      JOIN match_trial_to_marketing_start_date mttmsd ON (((cte.nct_id)::text = (mttmsd.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      JOIN view_disbur_cte3 dbc3 ON (((dbc3.nct_id)::text = (cte.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      JOIN view_burdens_cte2 b ON (((b.cause_id = dbc3.cause_id) AND (EXTRACT(year FROM b.year) = EXTRACT(year FROM cte.earliest_date_observed)))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   WHERE (mttmsd.min <= cte.earliest_date_observed)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY cte.nct_id, cte.start_date, cte.enrollment, cte.enrollment_category, cte.overall_status, cte.earliest_date_observed, (EXTRACT(epoch FROM (cte.earliest_date_observed - cte.start_date)) / EXTRACT(epoch FROM (cte.primary_completion_date - cte.start_date))), dbc3.code, dbc3.condition, dbc3.cause_text, dbc3.cause_id, dbc3.category_id, dbc3.group_name, dbc3.max_level, b.cause_id, b.year, b.h_sdi_val, b.h_sdi_u95, b.h_sdi_l95, b.hm_sdi_val, b.hm_sdi_u95, b.hm_sdi_l95, b.m_sdi_val, b.m_sdi_u95, b.m_sdi_l95, b.lm_sdi_val, b.lm_sdi_u95, b.lm_sdi_l95, b.l_sdi_val, b.l_sdi_u95, b.l_sdi_l95+
+   ORDER BY cte.nct_id, cte.earliest_date_observed;
+ CREATE OR REPLACE MATERIALIZED VIEW public.formatted_data_with_planned_enrollment AS  SELECT f.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     f.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.current_enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     f.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     f.current_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     f.earliest_date_observed,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     f.elapsed_duration,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     f.n_brands,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     f.code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     f.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     f.category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     f.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.max_level,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     f.h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.l_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     s.overall_status AS final_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     c2a.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     c2a.enrollment AS planned_enrollment                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM (((formatted_data f                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+      JOIN ctgov.studies s ON (((f.nct_id)::text = (s.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      JOIN enrollment_closest_to_start_view c3e ON (((c3e.nct_id)::text = (f.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN rank_proximity_to_start_time_view c2a ON ((((c3e.nct_id)::text = (c2a.nct_id)::text) AND (c3e.enrollment_source = c2a.rownum))));
+ CREATE OR REPLACE MATERIALIZED VIEW http.trials_to_download AS  SELECT most_recent_download_status.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+    FROM http.most_recent_download_status                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   WHERE (most_recent_download_status.status = 'Of Interest'::http.history_download_status);
+ CREATE OR REPLACE MATERIALIZED VIEW public.primary_design_outcomes AS  SELECT do2.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     do2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     do2.outcome_type,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     do2.measure,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     do2.time_frame,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     do2.population,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     do2.description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.design_outcomes do2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE (((do2.outcome_type)::text = 'primary'::text) AND ((do2.nct_id)::text IN ( SELECT DISTINCT fd.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+            FROM formatted_data fd)));
+(40 rows)
+

export/output_2025-01-06_export_data_postgres_tables.sql

@@ -0,0 +1,920 @@
+                       ?column?                        
+-------------------------------------------------------
+ CREATE TABLE DiseaseBurden.age_group                 +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ age_group character varying NOT NULL                 +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.burdens                   +
+ (                                                    +
+ measure_id integer NOT NULL,                         +
+ location_id integer NOT NULL,                        +
+ sex_id integer NOT NULL,                             +
+ age_id integer NOT NULL,                             +
+ cause_id integer NOT NULL,                           +
+ metric_id integer NOT NULL,                          +
+ year date NOT NULL,                                  +
+ val double precision NOT NULL,                       +
+ upper_95 double precision NOT NULL,                  +
+ lower_95 double precision NOT NULL,                  +
+ key_column integer NOT NULL                          +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.cause                     +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ cause character varying NOT NULL                     +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.cause_hierarchy           +
+ (                                                    +
+ cause_id integer NOT NULL,                           +
+ cause_name character varying,                        +
+ parent_id integer NOT NULL,                          +
+ parent_nae character varying,                        +
+ level integer NOT NULL                               +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.icd10_categories          +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ start_code character varying NOT NULL,               +
+ end_code character varying NOT NULL,                 +
+ group_name character varying NOT NULL,               +
+ level integer NOT NULL,                              +
+ chapter character varying NOT NULL,                  +
+ chapter_code integer NOT NULL                        +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.icd10_to_cause            +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ code character varying NOT NULL,                     +
+ cause_text character varying NOT NULL                +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.location                  +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ location character varying NOT NULL                  +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.measures                  +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ label character varying NOT NULL                     +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.metric                    +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ metric_label character varying NOT NULL              +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.rei                       +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ rei_label character varying NOT NULL                 +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.sex                       +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ sex character varying NOT NULL                       +
+ );                                                   +
+ 
+ CREATE TABLE DiseaseBurden.trial_to_icd10            +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ nct_id character varying NOT NULL,                   +
+ condition character varying NOT NULL,                +
+ ui character varying,                                +
+ uri character varying,                               +
+ rootsource character varying,                        +
+ name character varying,                              +
+ source character varying,                            +
+ approved USER-DEFINED,                               +
+ approval_timestamp timestamp without time zone       +
+ );                                                   +
+ 
+ CREATE TABLE Formularies.usp_dc_2023                 +
+ (                                                    +
+ USP Class character varying(250),                    +
+ USP Pharmacotherapeutic Group character varying(250),+
+ API Concept character varying(250),                  +
+ rxcui character varying(15),                         +
+ tty character varying(10),                           +
+ Name character varying(256),                         +
+ Related BN character varying(250),                   +
+ Related DF character varying(25050),                 +
+ USP Category character varying(250)                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.active_storage_attachments        +
+ (                                                    +
+ id bigint NOT NULL,                                  +
+ name character varying NOT NULL,                     +
+ record_type character varying NOT NULL,              +
+ record_id bigint NOT NULL,                           +
+ blob_id bigint NOT NULL,                             +
+ created_at timestamp without time zone NOT NULL      +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.active_storage_blobs              +
+ (                                                    +
+ metadata text,                                       +
+ checksum character varying NOT NULL,                 +
+ byte_size bigint NOT NULL,                           +
+ created_at timestamp without time zone NOT NULL,     +
+ id bigint NOT NULL,                                  +
+ key character varying NOT NULL,                      +
+ filename character varying NOT NULL,                 +
+ content_type character varying                       +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.baseline_counts                   +
+ (                                                    +
+ count integer,                                       +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ ctgov_group_code character varying,                  +
+ units character varying,                             +
+ scope character varying,                             +
+ result_group_id integer                              +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.baseline_measurements             +
+ (                                                    +
+ param_value character varying,                       +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ result_group_id integer,                             +
+ ctgov_group_code character varying,                  +
+ classification character varying,                    +
+ category character varying,                          +
+ title character varying,                             +
+ description text,                                    +
+ units character varying,                             +
+ param_type character varying,                        +
+ param_value_num numeric,                             +
+ dispersion_type character varying,                   +
+ dispersion_value character varying,                  +
+ dispersion_value_num numeric,                        +
+ dispersion_lower_limit numeric,                      +
+ dispersion_upper_limit numeric,                      +
+ explanation_of_na character varying,                 +
+ number_analyzed integer,                             +
+ number_analyzed_units character varying,             +
+ population_description character varying,            +
+ calculate_percentage character varying               +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.brief_summaries                   +
+ (                                                    +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ description text                                     +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.browse_conditions                 +
+ (                                                    +
+ mesh_term character varying,                         +
+ id integer NOT NULL,                                 +
+ mesh_type character varying,                         +
+ downcase_mesh_term character varying,                +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.browse_interventions              +
+ (                                                    +
+ downcase_mesh_term character varying,                +
+ mesh_term character varying,                         +
+ mesh_type character varying,                         +
+ id integer NOT NULL,                                 +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.calculated_values                 +
+ (                                                    +
+ number_of_secondary_outcomes_to_measure integer,     +
+ maximum_age_unit character varying,                  +
+ minimum_age_unit character varying,                  +
+ maximum_age_num integer,                             +
+ minimum_age_num integer,                             +
+ has_single_facility boolean,                         +
+ has_us_facility boolean,                             +
+ months_to_report_results integer,                    +
+ number_of_sae_subjects integer,                      +
+ were_results_reported boolean,                       +
+ registered_in_calendar_year integer,                 +
+ nlm_download_date date,                              +
+ actual_duration integer,                             +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ number_of_facilities integer,                        +
+ number_of_nsae_subjects integer,                     +
+ number_of_other_outcomes_to_measure integer,         +
+ number_of_primary_outcomes_to_measure integer        +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.central_contacts                  +
+ (                                                    +
+ phone_extension character varying,                   +
+ nct_id character varying,                            +
+ role character varying,                              +
+ id integer NOT NULL,                                 +
+ contact_type character varying,                      +
+ name character varying,                              +
+ phone character varying,                             +
+ email character varying                              +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.conditions                        +
+ (                                                    +
+ downcase_name character varying,                     +
+ name character varying,                              +
+ id integer NOT NULL,                                 +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.countries                         +
+ (                                                    +
+ name character varying,                              +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ removed boolean                                      +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.design_group_interventions        +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ design_group_id integer,                             +
+ intervention_id integer,                             +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.design_groups                     +
+ (                                                    +
+ group_type character varying,                        +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ title character varying,                             +
+ description text                                     +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.design_outcomes                   +
+ (                                                    +
+ description text,                                    +
+ measure text,                                        +
+ outcome_type character varying,                      +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ time_frame text,                                     +
+ population character varying                         +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.designs                           +
+ (                                                    +
+ masking_description text,                            +
+ subject_masked boolean,                              +
+ caregiver_masked boolean,                            +
+ investigator_masked boolean,                         +
+ outcomes_assessor_masked boolean,                    +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ allocation character varying,                        +
+ intervention_model character varying,                +
+ observational_model character varying,               +
+ primary_purpose character varying,                   +
+ time_perspective character varying,                  +
+ masking character varying,                           +
+ intervention_model_description text                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.detailed_descriptions             +
+ (                                                    +
+ description text,                                    +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.documents                         +
+ (                                                    +
+ comment text,                                        +
+ id integer NOT NULL,                                 +
+ url character varying,                               +
+ document_type character varying,                     +
+ nct_id character varying,                            +
+ document_id character varying                        +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.drop_withdrawals                  +
+ (                                                    +
+ period character varying,                            +
+ reason character varying,                            +
+ count integer,                                       +
+ ctgov_group_code character varying,                  +
+ result_group_id integer,                             +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.eligibilities                     +
+ (                                                    +
+ older_adult boolean,                                 +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ sampling_method character varying,                   +
+ gender character varying,                            +
+ minimum_age character varying,                       +
+ maximum_age character varying,                       +
+ healthy_volunteers character varying,                +
+ population text,                                     +
+ criteria text,                                       +
+ gender_description text,                             +
+ gender_based boolean,                                +
+ adult boolean,                                       +
+ child boolean                                        +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.facilities                        +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ status character varying,                            +
+ name character varying,                              +
+ city character varying,                              +
+ state character varying,                             +
+ zip character varying,                               +
+ country character varying                            +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.facility_contacts                 +
+ (                                                    +
+ contact_type character varying,                      +
+ name character varying,                              +
+ email character varying,                             +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ phone character varying,                             +
+ phone_extension character varying,                   +
+ facility_id integer                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.facility_investigators            +
+ (                                                    +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ facility_id integer,                                 +
+ role character varying,                              +
+ name character varying                               +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.file_records                      +
+ (                                                    +
+ url character varying,                               +
+ id bigint NOT NULL,                                  +
+ filename character varying,                          +
+ file_size bigint,                                    +
+ file_type character varying,                         +
+ created_at timestamp without time zone NOT NULL,     +
+ updated_at timestamp without time zone NOT NULL      +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.id_information                    +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ id_source character varying,                         +
+ nct_id character varying,                            +
+ id_link character varying,                           +
+ id_value character varying,                          +
+ id_type_description character varying,               +
+ id_type character varying                            +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.intervention_other_names          +
+ (                                                    +
+ name character varying,                              +
+ nct_id character varying,                            +
+ intervention_id integer,                             +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.interventions                     +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ name character varying,                              +
+ intervention_type character varying,                 +
+ description text,                                    +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.ipd_information_types             +
+ (                                                    +
+ name character varying,                              +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.keywords                          +
+ (                                                    +
+ name character varying,                              +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ downcase_name character varying                      +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.links                             +
+ (                                                    +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ description text,                                    +
+ url character varying                                +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.mesh_headings                     +
+ (                                                    +
+ qualifier character varying,                         +
+ id integer NOT NULL,                                 +
+ subcategory character varying,                       +
+ heading character varying                            +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.mesh_terms                        +
+ (                                                    +
+ description character varying,                       +
+ tree_number character varying,                       +
+ qualifier character varying,                         +
+ id integer NOT NULL,                                 +
+ downcase_mesh_term character varying,                +
+ mesh_term character varying                          +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.milestones                        +
+ (                                                    +
+ count_units character varying,                       +
+ count integer,                                       +
+ description text,                                    +
+ period character varying,                            +
+ title character varying,                             +
+ ctgov_group_code character varying,                  +
+ result_group_id integer,                             +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ milestone_description character varying              +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.outcome_analyses                  +
+ (                                                    +
+ other_analysis_description text,                     +
+ param_type character varying,                        +
+ non_inferiority_type character varying,              +
+ outcome_id integer,                                  +
+ nct_id character varying,                            +
+ id integer NOT NULL,                                 +
+ param_value numeric,                                 +
+ dispersion_type character varying,                   +
+ dispersion_value numeric,                            +
+ p_value_modifier character varying,                  +
+ p_value double precision,                            +
+ ci_n_sides character varying,                        +
+ ci_percent numeric,                                  +
+ ci_lower_limit numeric,                              +
+ ci_upper_limit numeric,                              +
+ ci_upper_limit_na_comment character varying,         +
+ p_value_description character varying,               +
+ method character varying,                            +
+ method_description text,                             +
+ estimate_description text,                           +
+ groups_description text,                             +
+ non_inferiority_description text                     +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.outcome_analysis_groups           +
+ (                                                    +
+ result_group_id integer,                             +
+ ctgov_group_code character varying,                  +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ outcome_analysis_id integer                          +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.outcome_counts                    +
+ (                                                    +
+ result_group_id integer,                             +
+ ctgov_group_code character varying,                  +
+ scope character varying,                             +
+ units character varying,                             +
+ count integer,                                       +
+ outcome_id integer,                                  +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.outcome_measurements              +
+ (                                                    +
+ result_group_id integer,                             +
+ ctgov_group_code character varying,                  +
+ classification character varying,                    +
+ category character varying,                          +
+ title character varying,                             +
+ description text,                                    +
+ units character varying,                             +
+ param_type character varying,                        +
+ param_value character varying,                       +
+ param_value_num numeric,                             +
+ dispersion_type character varying,                   +
+ dispersion_value character varying,                  +
+ dispersion_value_num numeric,                        +
+ dispersion_lower_limit numeric,                      +
+ dispersion_upper_limit numeric,                      +
+ explanation_of_na text,                              +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ outcome_id integer                                   +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.outcomes                          +
+ (                                                    +
+ population text,                                     +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ outcome_type character varying,                      +
+ title text,                                          +
+ description text,                                    +
+ time_frame text,                                     +
+ anticipated_posting_date date,                       +
+ anticipated_posting_month_year character varying,    +
+ units character varying,                             +
+ units_analyzed character varying,                    +
+ dispersion_type character varying,                   +
+ param_type character varying                         +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.overall_officials                 +
+ (                                                    +
+ name character varying,                              +
+ affiliation character varying,                       +
+ role character varying,                              +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.participant_flows                 +
+ (                                                    +
+ count_units integer,                                 +
+ nct_id character varying,                            +
+ pre_assignment_details text,                         +
+ units_analyzed character varying,                    +
+ drop_withdraw_comment character varying,             +
+ reason_comment character varying,                    +
+ recruitment_details text,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.pending_results                   +
+ (                                                    +
+ event_date_description character varying,            +
+ event_date date,                                     +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ event character varying                              +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.provided_documents                +
+ (                                                    +
+ has_sap boolean,                                     +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ document_type character varying,                     +
+ has_protocol boolean,                                +
+ has_icf boolean,                                     +
+ document_date date,                                  +
+ url character varying                                +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.reported_event_totals             +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ updated_at timestamp without time zone NOT NULL,     +
+ created_at timestamp without time zone NOT NULL,     +
+ subjects_at_risk integer,                            +
+ subjects_affected integer,                           +
+ classification character varying NOT NULL,           +
+ event_type character varying,                        +
+ ctgov_group_code character varying NOT NULL,         +
+ nct_id character varying NOT NULL                    +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.reported_events                   +
+ (                                                    +
+ vocab character varying,                             +
+ nct_id character varying,                            +
+ result_group_id integer,                             +
+ ctgov_group_code character varying,                  +
+ time_frame text,                                     +
+ event_type character varying,                        +
+ default_vocab character varying,                     +
+ default_assessment character varying,                +
+ subjects_affected integer,                           +
+ subjects_at_risk integer,                            +
+ description text,                                    +
+ event_count integer,                                 +
+ organ_system character varying,                      +
+ adverse_event_term character varying,                +
+ frequency_threshold integer,                         +
+ assessment character varying,                        +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.responsible_parties               +
+ (                                                    +
+ affiliation text,                                    +
+ nct_id character varying,                            +
+ responsible_party_type character varying,            +
+ name character varying,                              +
+ title character varying,                             +
+ organization character varying,                      +
+ id integer NOT NULL,                                 +
+ old_name_title character varying                     +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.result_agreements                 +
+ (                                                    +
+ other_details text,                                  +
+ restrictive_agreement character varying,             +
+ restriction_type character varying,                  +
+ agreement text,                                      +
+ pi_employee character varying,                       +
+ nct_id character varying,                            +
+ id integer NOT NULL                                  +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.result_contacts                   +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ organization character varying,                      +
+ name character varying,                              +
+ phone character varying,                             +
+ email character varying,                             +
+ extension character varying,                         +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.result_groups                     +
+ (                                                    +
+ result_type character varying,                       +
+ title character varying,                             +
+ description text,                                    +
+ id integer NOT NULL,                                 +
+ nct_id character varying,                            +
+ ctgov_group_code character varying                   +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.retractions                       +
+ (                                                    +
+ pmid character varying,                              +
+ id bigint NOT NULL,                                  +
+ nct_id character varying,                            +
+ source character varying,                            +
+ reference_id integer                                 +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.search_results                    +
+ (                                                    +
+ created_at timestamp without time zone NOT NULL,     +
+ nct_id character varying NOT NULL,                   +
+ id integer NOT NULL,                                 +
+ updated_at timestamp without time zone NOT NULL,     +
+ grouping character varying NOT NULL,                 +
+ study_search_id integer,                             +
+ name character varying NOT NULL                      +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.sponsors                          +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ name character varying,                              +
+ lead_or_collaborator character varying,              +
+ agency_class character varying,                      +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.studies                           +
+ (                                                    +
+ phase character varying,                             +
+ delayed_posting character varying,                   +
+ source_class character varying,                      +
+ updated_at timestamp without time zone NOT NULL,     +
+ created_at timestamp without time zone NOT NULL,     +
+ plan_to_share_ipd_description character varying,     +
+ plan_to_share_ipd character varying,                 +
+ ipd_url character varying,                           +
+ ipd_access_criteria character varying,               +
+ ipd_time_frame character varying,                    +
+ biospec_description text,                            +
+ biospec_retention character varying,                 +
+ is_us_export boolean,                                +
+ is_ppsd boolean,                                     +
+ is_unapproved_device boolean,                        +
+ is_fda_regulated_device boolean,                     +
+ is_fda_regulated_drug boolean,                       +
+ has_dmc boolean,                                     +
+ expanded_access_type_treatment boolean,              +
+ expanded_access_type_intermediate boolean,           +
+ expanded_access_type_individual boolean,             +
+ has_expanded_access boolean,                         +
+ why_stopped character varying,                       +
+ number_of_groups integer,                            +
+ number_of_arms integer,                              +
+ limitations_and_caveats character varying,           +
+ source character varying,                            +
+ enrollment_type character varying,                   +
+ enrollment integer,                                  +
+ expanded_access_nctid character varying,             +
+ last_known_status character varying,                 +
+ overall_status character varying,                    +
+ official_title text,                                 +
+ brief_title text,                                    +
+ baseline_population text,                            +
+ acronym character varying,                           +
+ study_type character varying,                        +
+ target_duration character varying,                   +
+ results_first_submitted_date date,                   +
+ study_first_submitted_date date,                     +
+ nlm_download_date_description character varying,     +
+ primary_completion_date date,                        +
+ nct_id character varying,                            +
+ primary_completion_date_type character varying,      +
+ primary_completion_month_year character varying,     +
+ completion_date date,                                +
+ completion_date_type character varying,              +
+ completion_month_year character varying,             +
+ verification_date date,                              +
+ verification_month_year character varying,           +
+ start_date date,                                     +
+ start_date_type character varying,                   +
+ start_month_year character varying,                  +
+ last_update_posted_date_type character varying,      +
+ last_update_posted_date date,                        +
+ last_update_submitted_qc_date date,                  +
+ disposition_first_posted_date_type character varying,+
+ disposition_first_posted_date date,                  +
+ disposition_first_submitted_qc_date date,            +
+ results_first_posted_date_type character varying,    +
+ results_first_posted_date date,                      +
+ results_first_submitted_qc_date date,                +
+ study_first_posted_date_type character varying,      +
+ study_first_posted_date date,                        +
+ study_first_submitted_qc_date date,                  +
+ last_update_submitted_date date,                     +
+ disposition_first_submitted_date date,               +
+ baseline_type_units_analyzed character varying,      +
+ fdaaa801_violation boolean,                          +
+ expanded_access_status_for_nctid character varying   +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.study_records                     +
+ (                                                    +
+ nct_id character varying,                            +
+ sha character varying,                               +
+ created_at timestamp without time zone NOT NULL,     +
+ updated_at timestamp without time zone NOT NULL,     +
+ type character varying,                              +
+ content json,                                        +
+ id bigint NOT NULL                                   +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.study_references                  +
+ (                                                    +
+ id integer NOT NULL,                                 +
+ citation text,                                       +
+ reference_type character varying,                    +
+ pmid character varying,                              +
+ nct_id character varying                             +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.study_searches                    +
+ (                                                    +
+ query character varying NOT NULL,                    +
+ id integer NOT NULL,                                 +
+ updated_at timestamp without time zone NOT NULL,     +
+ created_at timestamp without time zone NOT NULL,     +
+ beta_api boolean NOT NULL,                           +
+ name character varying NOT NULL,                     +
+ grouping character varying NOT NULL,                 +
+ save_tsv boolean NOT NULL                            +
+ );                                                   +
+ 
+ CREATE TABLE ctgov.verifiers                         +
+ (                                                    +
+ id bigint NOT NULL,                                  +
+ created_at timestamp without time zone NOT NULL,     +
+ source json,                                         +
+ updated_at timestamp without time zone NOT NULL,     +
+ load_event_id integer,                               +
+ last_run timestamp without time zone,                +
+ differences json NOT NULL                            +
+ );                                                   +
+ 
+ CREATE TABLE history.trial_snapshots                 +
+ (                                                    +
+ completion_date timestamp without time zone,         +
+ nct_id character varying(15) NOT NULL,               +
+ version integer NOT NULL,                            +
+ submission_date timestamp without time zone,         +
+ primary_completion_date timestamp without time zone, +
+ primary_completion_date_category USER-DEFINED,       +
+ start_date timestamp without time zone,              +
+ start_date_category USER-DEFINED,                    +
+ completion_date_category USER-DEFINED,               +
+ overall_status USER-DEFINED,                         +
+ enrollment integer,                                  +
+ enrollment_category USER-DEFINED,                    +
+ sponsor character varying,                           +
+ responsible_party character varying                  +
+ );                                                   +
+ 
+ CREATE TABLE http.download_status                    +
+ (                                                    +
+ status USER-DEFINED NOT NULL,                        +
+ nct_id character varying(15) NOT NULL,               +
+ id integer NOT NULL,                                 +
+ update_timestamp timestamp with time zone            +
+ );                                                   +
+ 
+ CREATE TABLE http.responses                          +
+ (                                                    +
+ nct_id character varying(15),                        +
+ version_a smallint,                                  +
+ version_b smallint,                                  +
+ url character varying(255),                          +
+ response_code smallint,                              +
+ response_date timestamp with time zone,              +
+ id integer NOT NULL,                                 +
+ html text                                            +
+ );                                                   +
+ 
+ CREATE TABLE rxnorm_migrated.ALLNDC_HISTORY          +
+ (                                                    +
+ sab character varying(10),                           +
+ ndc11_left9 character(9) NOT NULL,                   +
+ rowid integer NOT NULL,                              +
+ ndc character(13) NOT NULL,                          +
+ suppress character(1),                               +
+ edate character(6),                                  +
+ sdate character(6),                                  +
+ rxcui character(16)                                  +
+ );                                                   +
+ 
+ CREATE TABLE rxnorm_migrated.ALLRXCUI_HISTORY        +
+ (                                                    +
+ tty character varying(5),                            +
+ sts character(1),                                    +
+ rxindb character(1),                                 +
+ indb character(1),                                   +
+ rowid integer NOT NULL,                              +
+ rxcui character(16) NOT NULL,                        +
+ sab character varying(20),                           +
+ str character varying(3000),                         +
+ sdate character(6),                                  +
+ edate character(6)                                   +
+ );                                                   +
+ 
+ CREATE TABLE rxnorm_migrated.rxnorm_props            +
+ (                                                    +
+ rxcui character(8) NOT NULL,                         +
+ pres smallint NOT NULL,                              +
+ propvalue1 character varying(4000) NOT NULL,         +
+ propname character varying(30) NOT NULL              +
+ );                                                   +
+ 
+ CREATE TABLE rxnorm_migrated.rxnorm_relations        +
+ (                                                    +
+ tty2 character(4) NOT NULL,                          +
+ rxcui1 character(8) NOT NULL,                        +
+ tty1 character(4) NOT NULL,                          +
+ cvf character(4) NOT NULL,                           +
+ rxcui2 character(8) NOT NULL                         +
+ );                                                   +
+ 
+ CREATE TABLE spl.nsde                                +
+ (                                                    +
+ proprietary_name character varying(500),             +
+ package_ndc character varying(50),                   +
+ application_number_or_citation character varying(25),+
+ package_ndc11 character varying(11),                 +
+ id integer NOT NULL,                                 +
+ reactivation_date date,                              +
+ inactivation_date date,                              +
+ marketing_start_date date,                           +
+ marketing_end_date date,                             +
+ billing_unit character varying(35),                  +
+ dosage_form character varying(155),                  +
+ marketing_category character varying(160),           +
+ product_type character varying(90)                   +
+ );                                                   +
+ 
+(76 rows)
+

export/output_2025-01-06_export_data_postgres_views.sql

@@ -0,0 +1,415 @@
+                                                                                                                                                                                                                                                                                                      ?column?                                                                                                                                                                                                                                                                                                       
+---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+ CREATE OR REPLACE VIEW ctgov.all_browse_conditions AS  SELECT browse_conditions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     array_to_string(array_agg(DISTINCT browse_conditions.mesh_term), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM ctgov.browse_conditions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY browse_conditions.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_browse_interventions AS  SELECT browse_interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     array_to_string(array_agg(browse_interventions.mesh_term), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+    FROM ctgov.browse_interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY browse_interventions.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_cities AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     array_to_string(array_agg(DISTINCT facilities.city), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_conditions AS  SELECT conditions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     array_to_string(array_agg(DISTINCT conditions.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ctgov.conditions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY conditions.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_countries AS  SELECT countries.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     array_to_string(array_agg(DISTINCT countries.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+    FROM ctgov.countries                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (countries.removed IS NOT TRUE)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   GROUP BY countries.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_design_outcomes AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_facilities AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     array_to_string(array_agg(facilities.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_group_types AS  SELECT design_groups.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     array_to_string(array_agg(DISTINCT design_groups.group_type), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ctgov.design_groups                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY design_groups.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_id_information AS  SELECT id_information.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     array_to_string(array_agg(DISTINCT id_information.id_value), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.id_information                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+   GROUP BY id_information.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_intervention_types AS  SELECT interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     array_to_string(array_agg(interventions.intervention_type), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY interventions.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_interventions AS  SELECT interventions.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     array_to_string(array_agg(interventions.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM ctgov.interventions                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY interventions.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_keywords AS  SELECT keywords.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     array_to_string(array_agg(DISTINCT keywords.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.keywords                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+   GROUP BY keywords.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_overall_official_affiliations AS  SELECT overall_officials.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     array_to_string(array_agg(overall_officials.affiliation), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+    FROM ctgov.overall_officials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY overall_officials.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_overall_officials AS  SELECT overall_officials.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     array_to_string(array_agg(overall_officials.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.overall_officials                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   GROUP BY overall_officials.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_primary_outcome_measures AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   WHERE ((design_outcomes.outcome_type)::text = 'primary'::text)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_secondary_outcome_measures AS  SELECT design_outcomes.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     array_to_string(array_agg(DISTINCT design_outcomes.measure), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+    FROM ctgov.design_outcomes                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+   WHERE ((design_outcomes.outcome_type)::text = 'secondary'::text)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY design_outcomes.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_sponsors AS  SELECT sponsors.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     array_to_string(array_agg(DISTINCT sponsors.name), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM ctgov.sponsors                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+   GROUP BY sponsors.nct_id;
+ CREATE OR REPLACE VIEW ctgov.all_states AS  SELECT facilities.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     array_to_string(array_agg(DISTINCT facilities.state), '|'::text) AS names                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+    FROM ctgov.facilities                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY facilities.nct_id;
+ CREATE OR REPLACE VIEW ctgov.categories AS  SELECT search_results.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     search_results.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     search_results.name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     search_results.created_at,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results.updated_at,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results."grouping",                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     search_results.study_search_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+    FROM ctgov.search_results;
+ CREATE OR REPLACE VIEW ctgov.covid_19_studies AS  SELECT s.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     s.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.study_type,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.official_title,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.acronym,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.phase,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     s.why_stopped,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     s.has_dmc,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.is_fda_regulated_device,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.is_fda_regulated_drug,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     s.is_unapproved_device,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     s.has_expanded_access,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     s.study_first_submitted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.last_update_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.results_first_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     s.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     s.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     s.completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     s.study_first_posted_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     cv.number_of_facilities,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     cv.has_single_facility,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     cv.nlm_download_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     s.number_of_arms,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     s.number_of_groups,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     sp.name AS lead_sponsor,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     aid.names AS other_ids,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     e.gender,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     e.gender_based,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     e.gender_description,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     e.population,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     e.minimum_age,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     e.maximum_age,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     e.criteria,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     e.healthy_volunteers,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ak.names AS keywords,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ai.names AS interventions,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     ac.names AS conditions,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     d.primary_purpose,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     d.allocation,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     d.observational_model,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     d.intervention_model,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     d.masking,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     d.subject_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     d.caregiver_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     d.investigator_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     d.outcomes_assessor_masked,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ado.names AS design_outcomes,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     bs.description AS brief_summary,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dd.description AS detailed_description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM (((((((((((ctgov.studies s                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+      FULL JOIN ctgov.all_conditions ac ON (((s.nct_id)::text = (ac.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+      FULL JOIN ctgov.all_id_information aid ON (((s.nct_id)::text = (aid.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      FULL JOIN ctgov.all_design_outcomes ado ON (((s.nct_id)::text = (ado.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+      FULL JOIN ctgov.all_keywords ak ON (((s.nct_id)::text = (ak.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+      FULL JOIN ctgov.all_interventions ai ON (((s.nct_id)::text = (ai.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      FULL JOIN ctgov.sponsors sp ON (((s.nct_id)::text = (sp.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+      FULL JOIN ctgov.calculated_values cv ON (((s.nct_id)::text = (cv.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      FULL JOIN ctgov.designs d ON (((s.nct_id)::text = (d.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+      FULL JOIN ctgov.eligibilities e ON (((s.nct_id)::text = (e.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      FULL JOIN ctgov.brief_summaries bs ON (((s.nct_id)::text = (bs.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+      FULL JOIN ctgov.detailed_descriptions dd ON (((s.nct_id)::text = (dd.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+   WHERE (((sp.lead_or_collaborator)::text = 'lead'::text) AND ((s.nct_id)::text IN ( SELECT search_results.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+            FROM ctgov.search_results                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+           WHERE ((search_results.name)::text = 'covid-19'::text))));
+ CREATE OR REPLACE VIEW history.match_drugs_to_trials AS  SELECT bi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     rp.rxcui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     rp.propvalue1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+    FROM (ctgov.browse_interventions bi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+      JOIN rxnorm_migrated.rxnorm_props rp ON (((bi.downcase_mesh_term)::text = (rp.propvalue1)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (((rp.propname)::text = 'RxNorm Name'::text) AND ((bi.nct_id)::text IN ( SELECT trial_snapshots.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+            FROM history.trial_snapshots)));
+ CREATE OR REPLACE VIEW http.most_recent_download_status AS  SELECT t.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     t.status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     t.update_timestamp                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM ( SELECT download_status.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+             download_status.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+             download_status.status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+             download_status.update_timestamp,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+             row_number() OVER (PARTITION BY download_status.nct_id ORDER BY download_status.update_timestamp DESC) AS rn                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+            FROM http.download_status) t                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+   WHERE (t.rn = 1)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   ORDER BY t.nct_id;
+ CREATE OR REPLACE VIEW public.time_between_submission_and_start_view AS  SELECT s.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     s.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     ts.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.submission_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     abs(((EXTRACT(epoch FROM (ts.submission_date - (s.start_date)::timestamp without time zone)))::double precision / (((24 * 60) * 60))::double precision)) AS start_deviance                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+    FROM (ctgov.studies s                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+      JOIN history.trial_snapshots ts ON (((s.nct_id)::text = (ts.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE ((s.nct_id)::text IN ( SELECT DISTINCT tti.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+            FROM "DiseaseBurden".trial_to_icd10 tti));
+ CREATE OR REPLACE VIEW public.rank_proximity_to_start_time_view AS  SELECT cte.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     cte.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     row_number() OVER (PARTITION BY cte.nct_id ORDER BY cte.start_deviance) AS rownum,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     cte.submission_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     cte.start_deviance,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     cte.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ts.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.primary_completion_date_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     ts.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     ts.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.enrollment_category                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+    FROM (time_between_submission_and_start_view cte                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+      JOIN history.trial_snapshots ts ON ((((cte.nct_id)::text = (ts.nct_id)::text) AND (cte.version = ts.version))));
+ CREATE OR REPLACE VIEW public.enrollment_closest_to_start_view AS  SELECT cte2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     min(cte2.rownum) AS enrollment_source                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+    FROM rank_proximity_to_start_time_view cte2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+   WHERE (cte2.enrollment IS NOT NULL)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+   GROUP BY cte2.nct_id;
+ CREATE OR REPLACE VIEW public.match_trials_to_bn_in AS  WITH trialncts AS (                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+          SELECT DISTINCT ts.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+            FROM history.trial_snapshots ts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+         )                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+  SELECT bi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     bi.downcase_mesh_term,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     rr.tty2,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     rr.rxcui2 AS bn_or_in_cui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     count(*) AS count                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ((ctgov.browse_interventions bi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      LEFT JOIN rxnorm_migrated.rxnorm_props rp ON (((bi.downcase_mesh_term)::text = (rp.propvalue1)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON ((rr.rxcui1 = rp.rxcui)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   WHERE (((bi.nct_id)::text IN ( SELECT trialncts.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+            FROM trialncts)) AND ((bi.mesh_type)::text = 'mesh-list'::text) AND ((rp.propname)::text = 'Active_ingredient_name'::text) AND (rr.tty2 = ANY (ARRAY['BN'::bpchar, 'IN'::bpchar, 'MIN'::bpchar])))                                                                                                                                                                                                                                                                                                                                                                                                      +
+   GROUP BY bi.nct_id, bi.downcase_mesh_term, rr.tty2, rr.rxcui2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   ORDER BY bi.nct_id;
+ CREATE OR REPLACE VIEW public.match_trial_to_ndc11 AS  SELECT mttbi.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     ah.ndc,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     count(*) AS count                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM ((match_trials_to_bn_in mttbi                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      LEFT JOIN rxnorm_migrated.rxnorm_relations rr ON ((mttbi.bn_or_in_cui = rr.rxcui1)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      LEFT JOIN rxnorm_migrated."ALLNDC_HISTORY" ah ON ((rr.rxcui2 = ah.rxcui)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   WHERE ((rr.tty1 = 'BN'::bpchar) AND (rr.tty2 = ANY (ARRAY['SBD'::bpchar, 'BPCK'::bpchar])) AND ((ah.sab)::text = 'RXNORM'::text))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   GROUP BY mttbi.nct_id, ah.ndc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+   ORDER BY mttbi.nct_id, ah.ndc;
+ CREATE OR REPLACE VIEW public.match_trial_to_marketing_start_date AS  SELECT mttn.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     n.application_number_or_citation,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     min(n.marketing_start_date) AS min                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+    FROM (match_trial_to_ndc11 mttn                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+      JOIN spl.nsde n ON ((mttn.ndc = (n.package_ndc11)::bpchar)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE (((n.product_type)::text = 'HUMAN PRESCRIPTION DRUG'::text) AND ((n.marketing_category)::text = ANY (ARRAY[('NDA'::character varying)::text, ('ANDA'::character varying)::text, ('BLA'::character varying)::text, ('NDA authorized generic'::character varying)::text, ('NDA AUTHORIZED GENERIC'::character varying)::text])))                                                                                                                                                                                                                                                                             +
+   GROUP BY mttn.nct_id, n.application_number_or_citation                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   ORDER BY mttn.nct_id;
+ CREATE OR REPLACE VIEW public.view_burdens_cte AS  SELECT b.measure_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     b.location_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     b.sex_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     b.age_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     b.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.metric_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     b.val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     b.upper_95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.lower_95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     b.key_column                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+    FROM "DiseaseBurden".burdens b                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE ((b.sex_id = 3) AND (b.metric_id = 1) AND (b.measure_id = 2) AND (b.age_id = 22));
+ CREATE OR REPLACE VIEW public.view_burdens_cte2 AS  SELECT c1.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     c1.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     c1.val AS h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c1.upper_95 AS h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c1.lower_95 AS h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c2.val AS hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     c2.upper_95 AS hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c2.lower_95 AS hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c3.val AS m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c3.upper_95 AS m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c3.lower_95 AS m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c4.val AS lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     c4.upper_95 AS lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c4.lower_95 AS lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     c5.val AS l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     c5.upper_95 AS l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     c5.lower_95 AS l_sdi_l95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM ((((view_burdens_cte c1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+      JOIN view_burdens_cte c2 ON (((c1.cause_id = c2.cause_id) AND (c1.year = c2.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c3 ON (((c1.cause_id = c3.cause_id) AND (c1.year = c3.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c4 ON (((c1.cause_id = c4.cause_id) AND (c1.year = c4.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+      JOIN view_burdens_cte c5 ON (((c1.cause_id = c5.cause_id) AND (c1.year = c5.year))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+   WHERE ((c1.location_id = 44635) AND (c2.location_id = 44634) AND (c3.location_id = 44639) AND (c4.location_id = 44636) AND (c5.location_id = 44637));
+ CREATE OR REPLACE VIEW public.view_cte AS  SELECT ts.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     ts.primary_completion_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     ts.primary_completion_date_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     ts.enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ts.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     ts.overall_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     min(ts.submission_date) AS earliest_date_observed                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+    FROM history.trial_snapshots ts                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   WHERE (((ts.nct_id)::text IN ( SELECT DISTINCT tti.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+            FROM "DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+           WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type))) AND (ts.submission_date >= ts.start_date) AND (ts.overall_status <> ALL (ARRAY['Completed'::history.study_statuses, 'Terminated'::history.study_statuses])))                                                                                                                                                                                                                                                                                                                                                                        +
+   GROUP BY ts.nct_id, ts.primary_completion_date, ts.primary_completion_date_category, ts.start_date, ts.enrollment, ts.enrollment_category, ts.overall_status;
+ CREATE OR REPLACE VIEW public.view_disbur_cte0 AS  SELECT tti.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     tti.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     tti.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     itc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ch.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     ch.level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM (("DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN "DiseaseBurden".icd10_to_cause itc ON ((replace(replace((tti.ui)::text, '-'::text, ''::text), '.'::text, ''::text) = replace(replace((itc.code)::text, '-'::text, ''::text), '.'::text, ''::text))))                                                                                                                                                                                                                                                                                                                                                                                                     +
+      JOIN "DiseaseBurden".cause_hierarchy ch ON (((itc.cause_text)::text = (ch.cause_name)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type);
+ CREATE OR REPLACE VIEW public.view_disbur_cte AS  SELECT view_disbur_cte0.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     max(view_disbur_cte0.level) AS max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM view_disbur_cte0                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   GROUP BY view_disbur_cte0.nct_id;
+ CREATE OR REPLACE VIEW public.view_trial_to_cause AS  SELECT tti.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     tti.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     tti.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     itc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ch.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     ch.level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM (("DiseaseBurden".trial_to_icd10 tti                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN "DiseaseBurden".icd10_to_cause itc ON ((replace(replace((tti.ui)::text, '-'::text, ''::text), '.'::text, ''::text) = replace(replace((itc.code)::text, '-'::text, ''::text), '.'::text, ''::text))))                                                                                                                                                                                                                                                                                                                                                                                                     +
+      JOIN "DiseaseBurden".cause_hierarchy ch ON (((itc.cause_text)::text = (ch.cause_name)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+   WHERE (tti.approved = 'accepted'::"DiseaseBurden".validation_type)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+   ORDER BY tti.nct_id;
+ CREATE OR REPLACE VIEW public.view_disbur_cte2 AS  SELECT ttc.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     ttc.ui,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     ttc.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     ttc.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ttc.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     disbur_cte.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM (view_trial_to_cause ttc                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      JOIN view_disbur_cte disbur_cte ON (((disbur_cte.nct_id)::text = (ttc.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   WHERE (ttc.level = disbur_cte.max_level)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+   GROUP BY ttc.nct_id, ttc.ui, ttc.condition, ttc.cause_text, ttc.cause_id, disbur_cte.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+   ORDER BY ttc.nct_id, ttc.ui;
+ CREATE OR REPLACE VIEW public.view_disbur_cte3 AS  SELECT disbur_cte2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) AS code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     disbur_cte2.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     disbur_cte2.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     disbur_cte2.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     ic.chapter_code AS category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     ic.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     disbur_cte2.max_level                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+    FROM (view_disbur_cte2 disbur_cte2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      JOIN "DiseaseBurden".icd10_categories ic ON (((SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) <= (ic.end_code)::text) AND (SUBSTRING(disbur_cte2.ui FROM 1 FOR 3) >= (ic.start_code)::text))))                                                                                                                                                                                                                                                                                                                                                                                                                        +
+   WHERE (ic.level = 1);
+ CREATE OR REPLACE VIEW public.formatted_data AS  SELECT cte.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     cte.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     cte.enrollment AS current_enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     cte.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+     cte.overall_status AS current_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     cte.earliest_date_observed,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     (EXTRACT(epoch FROM (cte.earliest_date_observed - cte.start_date)) / EXTRACT(epoch FROM (cte.primary_completion_date - cte.start_date))) AS elapsed_duration,                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     count(DISTINCT mttmsd.application_number_or_citation) AS n_brands,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             +
+     dbc3.code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     +
+     dbc3.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     dbc3.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dbc3.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     dbc3.category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     dbc3.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               +
+     dbc3.max_level,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     b.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     b.h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     b.l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     b.l_sdi_l95                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+    FROM (((view_cte cte                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      JOIN match_trial_to_marketing_start_date mttmsd ON (((cte.nct_id)::text = (mttmsd.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+      JOIN view_disbur_cte3 dbc3 ON (((dbc3.nct_id)::text = (cte.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+      JOIN view_burdens_cte2 b ON (((b.cause_id = dbc3.cause_id) AND (EXTRACT(year FROM b.year) = EXTRACT(year FROM cte.earliest_date_observed)))))                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   WHERE (mttmsd.min <= cte.earliest_date_observed)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+   GROUP BY cte.nct_id, cte.start_date, cte.enrollment, cte.enrollment_category, cte.overall_status, cte.earliest_date_observed, (EXTRACT(epoch FROM (cte.earliest_date_observed - cte.start_date)) / EXTRACT(epoch FROM (cte.primary_completion_date - cte.start_date))), dbc3.code, dbc3.condition, dbc3.cause_text, dbc3.cause_id, dbc3.category_id, dbc3.group_name, dbc3.max_level, b.cause_id, b.year, b.h_sdi_val, b.h_sdi_u95, b.h_sdi_l95, b.hm_sdi_val, b.hm_sdi_u95, b.hm_sdi_l95, b.m_sdi_val, b.m_sdi_u95, b.m_sdi_l95, b.lm_sdi_val, b.lm_sdi_u95, b.lm_sdi_l95, b.l_sdi_val, b.l_sdi_u95, b.l_sdi_l95+
+   ORDER BY cte.nct_id, cte.earliest_date_observed;
+ CREATE OR REPLACE VIEW public.formatted_data_with_planned_enrollment AS  SELECT f.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     f.start_date,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.current_enrollment,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          +
+     f.enrollment_category,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         +
+     f.current_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     f.earliest_date_observed,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      +
+     f.elapsed_duration,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            +
+     f.n_brands,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     f.code,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     f.condition,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.cause_text,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.cause_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     f.category_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 +
+     f.group_name,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.max_level,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.year,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+     f.h_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.h_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.h_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.hm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.hm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.hm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.m_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.m_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.m_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.lm_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.lm_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.lm_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+     f.l_sdi_val,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.l_sdi_u95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     f.l_sdi_l95,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     s.overall_status AS final_status,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     c2a.version,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     c2a.enrollment AS planned_enrollment                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+    FROM (((formatted_data f                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        +
+      JOIN ctgov.studies s ON (((f.nct_id)::text = (s.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+      JOIN enrollment_closest_to_start_view c3e ON (((c3e.nct_id)::text = (f.nct_id)::text)))                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+      JOIN rank_proximity_to_start_time_view c2a ON ((((c3e.nct_id)::text = (c2a.nct_id)::text) AND (c3e.enrollment_source = c2a.rownum))));
+ CREATE OR REPLACE VIEW http.trials_to_download AS  SELECT most_recent_download_status.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+    FROM http.most_recent_download_status                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+   WHERE (most_recent_download_status.status = 'Of Interest'::http.history_download_status);
+ CREATE OR REPLACE VIEW public.primary_design_outcomes AS  SELECT do2.id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           +
+     do2.nct_id,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    +
+     do2.outcome_type,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              +
+     do2.measure,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   +
+     do2.time_frame,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     do2.population,                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+     do2.description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                +
+    FROM ctgov.design_outcomes do2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  +
+   WHERE (((do2.outcome_type)::text = 'primary'::text) AND ((do2.nct_id)::text IN ( SELECT DISTINCT fd.nct_id                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       +
+            FROM formatted_data fd)));
+(40 rows)
+

history_downloader/db_connection.py

@@ -1,11 +0,0 @@
-import psycopg2 as psyco
-
-conn = psyco.connect(dbname="aact_db", user="root", host="will-office", password="root")
-
-curse = conn.cursor()
-
-curse.execute("select * FROM http.responses LIMIT 100;")
-print(curse.fetchall())
-
-curse.close()
-conn.close()

history_downloader/downloader_prep.sql

@@ -1,21 +0,0 @@
-DELETE FROM http.download_status;
-
-INSERT INTO http.download_status (nct_id, status)
-SELECT nct_id, 'Of Interest'::http.history_download_status AS status
-FROM ctgov.studies
-WHERE 
-is_fda_regulated_drug=TRUE
-AND
-study_type = 'Interventional'
-AND
-phase='Phase 3'
-AND 
-overall_status in ('Terminated', 'Completed')
-AND 
-start_date > '2008-01-01'
-AND
-completion_date < '2022-01-01'
-;
-
-
-SELECT count(*) FROM http.download_status ;

justfile

@@ -0,0 +1,112 @@
+#justfile, used for automating build/setup
+# TODO
+# - setup a .env file so things can be shared between just and docker
+#   - move network name to .env
+#   - move postgress login credentials (allow them to be printed from just while setting up)
+
+
+data_link := "https://ctti-aact.nyc3.digitaloceanspaces.com/27grtsnhtccplxapj2o8ak9aotvv"
+data_file := "2022-12-23_postgres_data.zip"
+data_path := "./containers/AACT_downloader/aact_downloads"
+data_filepath := data_path / data_file
+
+#must match the 'container name: aact_db' in the docker-compose.yaml
+docker_container := `docker container ls -a | grep aact_db | cut -f 1 -d " " | tr "\n" " "`
+
+#Various paths for docker stuff
+docker-compose_path := "./AACT_downloader/docker-compose.yaml"
+
+#rxnorm_mappings
+rxnorm_mappings_url := "https://dailymed-data.nlm.nih.gov/public-release-files/rxnorm_mappings.zip"
+
+#Number of historical trials to download.
+count := "100"
+
+
+#check for necessary dependencies
+check-status:
+    docker --version
+    #check if python version > 3.10. 
+    python --version
+    python -c 'import sys; exit(sys.hexversion >= 50859504)'
+    curl --version
+    echo "current docker containers:{{docker_container}}"
+
+#Setup the AACT container
+setup-containers: 
+    @echo "Check for downloaded data"
+    [ -s {{data_path}}/postgres_data.dmp ]
+
+    #run docker compose
+    @echo "Setting up AACT container"
+    docker-compose -f {{docker-compose_path}} up -d
+
+#Stop the appropriate docker container
+stop-containers:
+    #stop all docker containers if they are currently running.
+    #The if [empty string] statement because sometimes there are no running containers
+    if [ -n "{{docker_container}}" ]; then  docker stop {{docker_container}}; fi
+    @echo "confirmed that docker containers {{docker_container}} are stopped"
+
+#Remove the appropriate docker container as well as associated volumes
+clean-docker: stop-containers
+    # remove docker containers
+    if [ -n "{{docker_container}}" ]; then  docker rm {{docker_container}}; fi
+    # cleanup docker network
+    docker network prune
+    # cleanup docker volumes
+    docker volume prune
+
+
+#Download the AACT data
+download-aact-data:
+    curl {{data_link}} > ./AACT_downloader/aact_downloads/{{data_file}}
+    unzip {{data_filepath}} -d {{data_path}}
+    rm {{data_filepath}}
+
+
+#build based on previously downloaded data
+build: check-status setup-containers
+    #system built from downloaded data
+
+#remove containers and rebuild based on previously downloaded data
+rebuild: clean-docker build 
+    #system will be built from scratch, using previously downloaded data
+
+#download data and create the containers
+create: check-status download-aact-data build
+    # downloaded data and built from scratch
+
+#remove containers, redownload data, then rebuild containers
+recreate: clean-docker create
+    # removed containers, redownloaded data, then rebuilt containers
+
+#Register trials of interest in the database based on ./history_downloader/selected_trials.sql
+select-trials:
+    cd history_downloader && python ./select_trials.py
+
+#Download trial histories based on registered trials of interest.
+download-trial-histories:
+    cd history_downloader && python ./downloader.py --count {{count}}
+
+#Check if you can connect to the db
+test-db-connection:
+    cd history_downloader && python db_connection.py
+
+#Parse previously downloaded histories into tables.
+parse-trial-histories:
+    cd Parser && python extraction_lib.py
+
+#Download and install 
+get-histories: download-trial-histories parse-trial-histories
+
+#download market data
+get-nsde:
+    cd market_data && bash download_nsde.sh
+    cd market_data && python extract_nsde.py
+
+get-rxnorm-mappings:
+    #this may not be needed, all it does is match spls to rxcuis and I think I already have that.
+    curl {{rxnorm_mappings_url}} > ./market_data/rxnorm_mappings.zip
+    cd ./market_data && unzip ./rxnorm_mappings.zip
+    rm ./market_data/rxnorm_mappings.zip

llm-extractor/llm_extractor.py

@@ -0,0 +1,55 @@
+import ollama
+
+import psycopg
+from psycopg.rows import dict_row
+from typing import List, Dict
+
+def fetch_all_rows(conn_params: dict) -> List[Dict]:
+    # Establish a connection to the PostgreSQL database
+    conn = psycopg.connect(**conn_params, row_factory=dict_row)
+    cursor = conn.cursor()
+    
+    # Define your SQL query to select all rows from the table
+    sql_query = "SELECT * FROM public.primary_design_outcomes;"
+    
+    # Execute the query
+    cursor.execute(sql_query)
+    
+    # Fetch all rows from the result set
+    rows = cursor.fetchall()
+    
+    # Close the cursor and connection
+    cursor.close()
+    conn.close()
+    
+    return rows
+
+# Example usage
+conn_params = {
+    "dbname": "aact_db",
+    "user": "root",
+    "password": "root",
+    "host": "localhost",
+    "port": "5432"
+}
+
+outcome_description = '''
+Measure: {measure}
+Time Frame: {time_frame}
+Description: {description}
+'''
+
+
+if __name__ == "__main__":
+    #check for model
+
+    #get information
+    rows_dicts = fetch_all_rows(conn_params)
+
+    for row in rows_dicts[:3]:
+        text_data = outcome_description.format(**row)
+        r = ollama.generate(model='youainti/llama3.1-extractor:2024-08-28.2', prompt=text_data)
+
+        print(text_data)
+        print(r["response"])
+

llm-extractor/modfile_llm_extractor

@@ -0,0 +1,31 @@
+FROM llama3.1
+PARAMETER num_ctx 8192
+PARAMETER seed 11021585
+SYSTEM """
+You are a Natural Language Processor, tasked with extracting data about outcome measures from textual tables. 
+You are to extract the longest observation time from the primary objectives for this clinical trial.
+I need you to distinguish between trials that have a specified period during which they track participants
+and those trials that don't.
+
+Return results as JSON, with the format 
+```json
+{
+    "longest_observation_scalar": <number>,
+    "longest_observation_unit: <string: minutes, hours, days, weeks, months, years>
+}
+```
+Do not return any other commentary.
+If the study does not have a specified end of observation, set the values to `null`.
+If the text does not appear to be related to clinical trials, return `{ null }`
+
+For example:
+- 'baseline to week 3' should give: `{ "longest_observation_scalar": 3, "longest_observation_unit": "weeks" }`
+- 'tracked 4 months' should give: `{ "longest_observation_scalar": 4,   "longest_observation_unit": "months"}`
+- 'randomization to 14 months' should give `{ "longest_observation_scalar": 14,   "longest_observation_unit": "months"}`
+- 'After day 1 to week 48' should give `{ "longest_observation_scalar": 48,   "longest_observation_unit": "weeks"}`
+- 'randomization to 14 months' should give `{ "longest_observation_scalar": 14,   "longest_observation_unit": "months"}`
+- 'baseline until death' should give: `{ "longest_observation_scalar": null, "longest_observation_unit": null }`
+- 'progression free survival up to 4 years' should give: `{ "longest_observation_scalar": null, "longest_observation_unit": null }`
+- 'the quick brown fox jumped over the lazy dog for one hour' should give: `{null}`
+
+"""

llm-extractor/primary_design_outcomes_202408281954.csv

@@ -0,0 +1,448 @@
+id,nct_id,outcome_type,measure,time_frame,population,description,Scalar,Unit,,,,
+65857719,NCT00967798,primary,Number of Participants With Conversion to Cystic Fibrosis Related Diabetes,Month 15,,The number of participants with conversion to cystic fibrosis related diabetes was determined.,15,months,,,,
+65857602,NCT00968968,primary,Progression-free Survival,"Time from randomization until disease progression or death, approximately 4 years",,"Progression-free survival (PFS) with lapatinib plus trastuzumab versus trastuzumab alone.
+
+Progression-free survival (PFS) is defined as the time from randomization to the earliest date of disease progression (with radiological evidence) or death from any cause, or to last contact date up to 21Feb2014.
+
+Disease Progression was defined using Response Evaluation Criteria In Solid Tumors (RECIST v1.1), a 20% increase in the sum of the diameters of target lesions, taking as a reference, the smallest sum diameters recorded since the treatment started (the sum must have an absolute increase from nadir of 5mm), or an unequivocal progression of existing non-target lesions, or the appearance of new lesions.",??,??,,,,
+66348662,NCT01067521,primary,Total Number of Confirmed Relapses During the Placebo Controlled (PC) Treatment Period Estimated by Negative Binomial Regression,Day 1 to 12 months,,"Relapses were monitored throughout the study. During the PC Period, two neurologists/physicians assessed subjects' general medical and neurological evaluations separately. A relapse was defined as the appearance of 1+ new neurological abnormalities or the reappearance of 1+ previously observed neurological abnormalities lasting >= 48 hours and immediately preceded by an improving neurological state of at >=30 days from onset of previous relapse. An event was counted as a relapse only when the subject's symptoms were accompanied by observed objective neurological changes, consistent with >= one of the following: - An increase of >= 0.5 in the Expanded Disability Status Scale (EDSS) score as compared to previous evaluation. - An increase of one grade in the actual score of >=2 of the 7 functional systems (FS), as compared to previous evaluation. - An increase of 2 grades in the actual score of one FS as compared to the previous evaluation. Adjusted mean values are displayed.",12,months,,,,
+66348663,NCT01067521,primary,Annualized Rate of Confirmed Relapses Comparing Early Starters to Delayed Starters Estimated by Negative Binomial Regression,Day 1 up to 6.5 years,,"The annualized relapse rate (ARR) was calculated for the study by dividing the cumulative number of confirmed relapses by the number of person-years of exposure to treatment. The analysis of the annualized relapse rate is based on estimating a contrast (early start vs delayed start) derived from a baseline-adjusted, Negative Binomial Regression model to the number of confirmed relapses observed during study (post randomization) with an ""offset"" based on the log of exposure to treatment.",??,??,,,,
+65846774,NCT01069705,primary,Number of Participants With Adverse Events (AEs),From time of first administration of study drug until study completion (up to 169 days),,"An AE was defined as any unfavorable and unintended sign, symptom, or disease temporally associated with the use of study drug, whether or not related to study drug.",??,??,,,,
+65846775,NCT01069705,primary,Number of Participants With Serious Adverse Events (SAEs),From time of consent to 4 weeks after study completion (up to 199 days),,"A SAE was defined as an event which was fatal or life threatening, required or prolonged hospitalization, was significantly or permanently disabling or incapacitating, constituted a congenital anomaly or a birth defect, or encompassed any other clinically significant event that could jeopardize the participant or require medical or surgical intervention to prevent one of the aforementioned outcomes.",??,??,,,,
+65846776,NCT01069705,primary,Percentage of Participants With a Decrease of ≥20% in Forced Expiratory Value in One Second (FEV1) Percent (%) Predicted From Pre-dose to 30-minute Post-dose,"Pre-dose and post-dose of Day 1 and Day 29 of every Cycle (5, 6, 7)",,Airway Reactivity >= 20% relative decrease in FEV1% predicted from pre-dose to 30 minutes post-dose. Relative Change = 100 * (30 minutes Post-dose - Pre-dose)/Pre-dose assessed by the number and percentage of participants with a decrease of ≥ 20% in FEV1 % predicted from pre-dose to 30 minutes post-dose.,29,days,,,,
+65846777,NCT01069705,primary,Percentage of Participants With Frequency Decrease From Baseline in the Post-baseline Audiology Tests,"Cycles 5, 6, 7 (Days 1, 29) and Follow-up (Week 57/Day 57)",,"Auditory acuity of participants was measured using a standard dual-channel audiometer at frequencies from 250 to 8000 Hertz, and an audiogram (pure-tone air conduction) and tympanogram were performed by an audiologist. The categories reported includes >= 10dB decrease in 3 consecutive frequencies in either ear, >= 15dB decrease in 2 consecutive frequencies in either ear, and >= 20dB decrease in at least one frequency in either ear",,,,,,
+65846254,NCT01074047,primary,Kaplan-Meier Estimates for Overall Survival,Day 1 (randomization) to 40 months,,Overall Survival was defined as the time from randomization to death from any cause. Overall survival was calculated by the formula: date of death - date of randomization + 1. Participants surviving at the end of the follow-up period or who withdrew consent to follow-up were censored at the date of last contact. Participants who were lost to follow-up were censored at the date last known alive.,,,,,,
+65845812,NCT01077518,primary,Progression-free Survival (PFS) as Assessed by the Independent Review Committee (IRC),From randomization to the date of first documented disease progression or death due to any cause (67.5 months),,PFS is defined as the time interval between randomization until disease progression or death (due to any cause).,,,,,,
+65845533,NCT01079806,primary,Percentage of Participants Who Achieved a Combination of Hepatitis B Virus (HBV) DNA Suppression and Hepatitis B e Antigen (HBeAg) Seroconversion at Week 48,At Week 48,,"Suppression=HBV DNA<50 IU/mL (approximately 300 copies/mL) using the Roche COBAS TaqMan HBV Test for use with the High Pure System assay; seroconversion=undetectable HBeAg and detectable anti-hepatitis B e antibodies. While the analysis of the primary endpoint was based on a randomized sample size of 123 participants (the Primary Cohort), the size of the overall study population was augmented to 180 randomized participants to meet global regulatory requirements.",,,,,,
+65843612,NCT01099579,primary,"Number of Participants With Death as Outcome, Serious Adverse Events (SAEs), Adverse Events (AEs) Leading to Discontinuation",From Day 1 to Week 48,,"AE=any new unfavorable symptom, sign, or disease or worsening of a preexisting condition that may not have a causal relationship with treatment. SAE=a medical event that at any dose results in death, persistent or significant disability/incapacity, or drug dependency/abuse; is life-threatening, an important medical event, or a congenital anomaly/birth defect; or requires or prolongs hospitalization.",,,,,,
+65843613,NCT01099579,primary,Number of Participants With Laboratory Test Results With Worst Toxicity of Grade 3-4,After Day 1 to Week 48,,"ALT=alanine aminotransferase; SGPT=serum glutamic-pyruvic transaminase; AST=aspartate aminotransferase; SGOT=serum glutamic-oxaloacetic transaminase; ULN=upper limit of normal. Grading by the National Institute of Health Division of AIDs and World Health Organization criteria. Hemoglobin (g/dL): Grade (Gr)1=9.5-11.0; Gr 2=8.0-9.4; Gr 3=6.5-7.9; Gr 4=<6.5. Neutrophils, absolute (/mm^3): Gr 1=>=1000-<1500; Gr 2= >=750-<1000; Gr 3=>=500-<750; Gr 4=<500. ALT/SGPT (*ULN): Gr 1=1.25-2.5; Gr 2=2.6-5; Gr 3=5.1-10; Gr 4=>10. AST/SGOT (*ULN): Gr 1=1.25-2.5; Gr 2=2.6-5; Gr 3=5.1-10; Gr 4=>10. Alkaline phosphatase(*ULN): Gr 1=1.25-2.5; Gr 2=2.6-5: Gr 3=5.1-10; Gr 4=>10. Total bilirubin (*ULN): Gr 1=1.1-1; Gr 2=1.6-2.5; Gr 3=2.6-5; Gr 4=>5. Amylase (*ULN): Gr 1=1.10-39; Gr 2=1.40-2; Gr 3=2.10-5.0; Gr 4=>5.0. Lipase (*ULN): Gr 1=1.10-1.39: Gr 2=1.40-2; Gr 3=2.10-5.0; Gr 4=>5.0. Uric acid (mg/dL): Gr 1=7.5-10.0; Gr 2=10.1-12.0; Gr 3=12.1-15.0; Gr 4=>15.",,,,,,
+65843614,NCT01099579,primary,"Electrocardiogram Changes From Baseline in PR Interval, QTC Bazett, and QTC Fridericia at Week 48",From Baseline to Week 48,,"Electrocardiogram parameters were measured at baseline for QTC Bazett, QTC Fridericia, and PR interval. The mean change from baseline at week 48 is reported by arm in milliseconds.",,,,,,
+65843615,NCT01099579,primary,Number of Participants With Centers for Disease Control (CDC) Class C AIDS Events,From Day 1 to Week 48,,"CDC Class C events are AIDS-defining events that include recurrent bacterial pneumonia (>=2 episodes in 12 months); candidiasis of the bronchi, trachea, lungs, or esophagus; invasive cervical carcinoma; disseminated or extrapulmonary coccidioidomycosis; extrapulmonary cryptococcosis; chronic intestinal cryptosporidiosis (>1 month); cytomegalovirus disease; HIV-related encephalopathy; herpes simplex: chronic ulcers, or bronchitis, pneumonitis, or esophagitis; disseminated or extrapulmonary histoplasmosis; chronic intestinal isosporiasis; Kaposi sarcoma; immunoblastic or primary brain Burkitt lymphoma; mycobacterium avium complex, kansasii, or tuberculosis; mycobacterium, other species; Pneumocystis carinii pneumonia; progressive multifocal leukoencephalopathy; Salmonella septicemia; recurrent toxoplasmosis of brain; HIV wasting syndrome (involuntary weight loss >10% of baseline body weight) with chronic diarrhea or chronic weakness and documented fever for ≥1 month.",,,,,,
+65843546,NCT01100502,primary,Progression-free Survival by Independent Review,Up to approximately 4 years,,"Time from date of randomization to the first documentation of disease progression by independent review or to death due to any cause, whichever comes first",,,,,,
+65842497,NCT01111539,primary,Phase C: Mean Change From End of Phase B (Week 8) in the Montgomery-Asberg Depression Rating Scale (MADRS) Total Score to End of Phase C (Week 14),Week 8 to Week 14,,"The MADRS assessed severity of depressive symptoms. It ranges from a minimum of 0 to a maximum of 60 (higher scores indicating a greater severity of depressive symptoms). Participants are rated on 10 items (feelings of sadness, lassitude, pessimism, inner tension, suicidality, reduced sleep or appetite, difficulty concentrating, and a lack of interest) each on a 7-point scale from 0 (no symptoms) to 6 (symptoms of maximum severity). A negative change from Week 8 indicates improvement.",,,,,,
+65842494,NCT01111552,primary,Phase C: Mean Change From End of Phase B (Week 8) in the Montgomery-Asberg Depression Rating Scale (MADRS) Total Score to End of Phase C (Week 14),Week 8 to Week 14,,"The MADRS assessed severity of depressive symptoms. It ranges from a minimum of 0 to a maximum of 60 (higher scores indicating a greater severity of depressive symptoms). Participants are rated on 10 items (feelings of sadness, lassitude, pessimism, inner tension, suicidality, reduced sleep or appetite, difficulty concentrating, and a lack of interest) each on a 7-point scale from 0 (no symptoms) to 6 (symptoms of maximum severity). A negative change from Week 8 indicates improvement. Last observation carried forward (LOCF) method was used for analyses.",,,,,,
+66377721,NCT01111565,primary,Phase C: Mean Change From End of Phase B (Week 8) in the Montgomery-Asberg Depression Rating Scale (MADRS) Total Score to End of Phase C (Week 14),Week 8 to Week 14,,"The MADRS assessed severity of depressive symptoms. It ranges from a minimum of 0 to a maximum of 60 (higher scores indicating a greater severity of depressive symptoms). Participants are rated on 10 items (feelings of sadness, lassitude, pessimism, inner tension, suicidality, reduced sleep or appetite, difficulty concentrating, and a lack of interest) each on a 7-point scale from 0 (no symptoms) to 6 (symptoms of maximum severity). A negative change (or decrease) from baseline indicates a reduction (or improvement) in symptoms. Last observation carried forward (LOCF) method was used for analyses.",,,,,,
+65841648,NCT01120184,primary,Percentage of Participants With Death or Disease Progression According to Independent Review Facility (IRF) Assessment,"Up to 48 months from randomization until clinical cutoff of 16-Sept-2014 (at Screening, every 9 weeks for 81 weeks, then every 12 weeks thereafter and/or up to 42 days after last dose)",,"Tumor assessments were performed according to Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1, using radiographic images submitted to the IRF up to and including the confirmatory tumor assessment 4 to 6 weeks after study drug discontinuation. Disease progression was defined as a greater than or equal to (≥) 20 percent (%) and 5-millimeter (mm) increase in sum of diameters of target lesions, taking as reference the smallest sum obtained during the study, or appearance of new lesion(s). The percentage of participants with death or disease progression was calculated as [number of participants with event divided by the number analyzed] multiplied by 100.",,,,,,
+65841649,NCT01120184,primary,Progression-Free Survival (PFS) According to IRF Assessment,"Up to 48 months from randomization until clinical cutoff of 16-Sept-2014 (at Screening, every 9 weeks for 81 weeks, then every 12 weeks thereafter and/or up to 42 days after last dose)",,"Tumor assessments were performed according to RECIST version 1.1, using radiographic images submitted to the IRF up to and including the confirmatory tumor assessment 4 to 6 weeks after study drug discontinuation. PFS was defined as the time from randomization to first documented disease progression or death from any cause. Disease progression was defined as a ≥20% and 5-mm increase in sum of diameters of target lesions, taking as reference the smallest sum obtained during the study, or appearance of new lesion(s). Median duration of PFS was estimated using Kaplan-Meier analysis, and corresponding confidence intervals (CIs) were computed using the Brookmeyer-Crowley method.",,,,,,
+65841587,NCT01120600,primary,Percentage Change From Baseline in Lumbar Spine Bone Mineral Density (BMD) at Month 24,Baseline and Month 24,,Lumbar spine BMD was assessed by dual energy X-ray absorptiometry (DXA) at Baseline and at Month 24.,,,,,,
+65841588,NCT01120600,primary,Number of Participants Who Experienced an Adverse Event (AE),Up to 24 months (plus 14 days) after first dose of study drug,,"An AE is defined as any unfavorable and unintended sign (including an abnormal laboratory finding), symptom, or disease temporally associated with the use of a study drug, whether or not it is considered related to the study drug.",,,,,,
+65841589,NCT01120600,primary,Number of Participants Who Discontinued Treatment Due to an AE,Up to 24 months after first dose of study drug,,"An AE is defined as any unfavorable and unintended sign (including an abnormal laboratory finding), symptom, or disease temporally associated with the use of a study drug, whether or not it is considered related to the study drug.",,,,,,
+66384256,NCT01123707,primary,"Percentage of Participants With Treatment-Emergent Adverse Events (TEAEs), Serious TEAEs (STEAEs), Severe (Grade 3 or Higher) TEAEs, and Discontinuations From the Trial Due to TEAEs",From first dose up to 30 days post last dose (Up to approximately 40 weeks),,"An AE was defined as any untoward medical occurrence in a clinical investigation participant administered a drug; it did not necessarily have to have a causal relationship with this treatment. An AE was considered serious if it was fatal; life-threatening; persistently or significantly disabling or incapacitating; required in-patient hospitalization or prolonged hospitalization; a congenital anomaly/birth defect; or other medically significant event that, based upon appropriate medical judgment, may have jeopardized the participant and may have required medical or surgical intervention. TEAE is defined as an adverse event that started after start of study drug treatment. The Common Terminology Criteria for Adverse Events v3.0 (CTCAE) was used to determine the severity wherein Grade 1=mild AE, Grade 2=moderate AE, Grade 3=severe AE, Grade 4=life-threatening or disabling AE, Grade 5=death related to AE.",,,,,,
+65840407,NCT01129882,primary,Number Of Participants Reporting Severe Treatment-Emergent Adverse Events (TEAE),Baseline to Month 97 (+/- 3 days),,"A TEAE was defined as an AE that started after start of investigational medicinal product (IMP) treatment or if the event was continuous from baseline and was serious, IMP-related, or resulted in death, discontinuation, interruption, or reduction of IMP. A severe AE was one that caused inability to work or perform normal daily activity.
+
+A summary of serious and all other non-serious adverse events, regardless of causality, is located in the Reported Adverse Events module.",,,,,,
+65838665,NCT01148225,primary,Number of Participants With Adverse Events,Baseline to Final Visit (up to 366 weeks),,"An adverse event (AE) is defined as any untoward medical occurrence in a patient or clinical investigation subject administered a pharmaceutical product and which does not necessarily have a causal relationship with this treatment. The investigator assessed the relationship of each event to the use of study drug as either probably related, possibly related, probably not related or not related. A serious adverse event (SAE) is an event that results in death, is life-threatening, requires or prolongs hospitalization, results in a congenital anomaly, persistent or significant disability/incapacity or is an important medical event that, based on medical judgment, may jeopardize the subject and may require medical or surgical intervention to prevent any of the outcomes listed above. Treatment-emergent events (TEAEs/TESAEs) are defined as any event with an onset date on or after the first dose of study drug and up to 70 days after the last dose. See the Adverse Event section for details.",,,,,,
+65838666,NCT01148225,primary,Hematology: Number of Participants With Potentially Clinically Significant (PCS) Values,Baseline to Final Visit (Up to 366 weeks),,PCS laboratory values were defined as Common Toxicity Criteria (CTC) according to the National Cancer Institute Common Terminology for Adverse Events (NCI CTCAE) v3.0 ≥ Grade 3. Abbreviations used include g=grams, L=liters.,,,,,
+65838667,NCT01148225,primary,Chemistry: Number of Participants With PCS Values,Baseline to Final Visit (Up to 366 weeks),,PCS laboratory values were defined as Common Toxicity Criteria (CTC) according to the National Cancer Institute Common Terminology for Adverse Events (NCI CTCAE) v3.0 ≥ Grade 3. Abbreviations include ALT/SGPT=alanine aminotransferase/serum glutamate pyruvate transaminase, AST/SGOT=aspartate aminotransferase/serum glutamate oxaloacetate transaminase, g/L=grams/liter, mmol/L=millimoles/liter, ULN=upper limit of normal.,,
+65838668,NCT01148225,primary,Pulse (Sitting): Mean Change (Beats Per Minute) From Baseline To Final Visit,Baseline to Final Visit (Up to 366 weeks),,Heart rate (beats per minute) was measured while the participant was sitting.,,,,,,
+65838669,NCT01148225,primary,Respiratory Rate (Sitting): Mean Change (Respirations Per Minute) From Baseline To Final Visit,Baseline to Final Visit (Up to 366 weeks),,Respiratory rate (respirations per minute) was measured while the participant was sitting.,,,,,,
+65838670,NCT01148225,primary,Temperature (Sitting): Mean Change (Centigrade) From Baseline To Final Visit,Baseline to Final Visit (Up to 366 weeks),,Temperature was measured while the participant was sitting.,,,,,,
+65838671,NCT01148225,primary,Diastolic and Systolic Blood Pressure (Sitting): Mean Change (mmHg) From Baseline To Final Visit,Baseline to Final Visit (Up to 366 weeks),,Blood pressure was measured while the participant was sitting. Abbreviations used include mmHg=millimeters of mercury.,,,,,,
+65832687,NCT01201356,primary,"Parts I and II: Number of Participants With Adverse Events, Serious Adverse Event, and Death","Baseline (Part I) to Month 6 Follow-up (Part II), up to 8 years",,"Analysis of absolute and relative frequencies for Adverse Event (AE), Serious Adverse Event (SAE) and Deaths by primary System Organ Class (SOC) to demonstrate that Fingolimod 0.5 mg/day is safe in patients with relapsing forms of Multiple Sclerosis (MS) through the monitoring of relevant clinical and laboratory safety parameters. Only descriptive analysis performed.",,,,,,
+65968081,NCT01213017,primary,the change from baseline in synovitis and bone edema RAMRIS score.,6 weeks,,,,,,,,
+65831375,NCT01214421,primary,Percent Change From the Baseline in Total Kidney Volume (TKV) for Study 156-04-251 Participants Enrolled in This Study (156-08-271),Study Baseline (Prior to Day 1 in Study 156-04-251) to Month 24 in this study (Study 156-08-271),,"Total kidney volume is a measure of disease progression in the ADPKD participants. Kidney volume was assessed in T1-weighted magnetic resonance images collected at each study site and sent to a central reviewing facility. At the central reviewing facility, radiologists used proprietary software to measure the volume of both kidneys in participants continuing from previous study (156-04-251) at Month 24 of this study (156-08-271) comparing change in TKV for the early-treated (those previously treated with tolvaptan) to delayed-treated (those previously treated with placebo). The percent change in the volume of both kidneys combined was analysed using mixed-effect model repeated measures (MMRM) analysis and reported. This outcome measure was analyzed only in the participants enrolled from the previous study - 156-04-251, as pre-specified in the protocol.",,,,,,
+65829319,NCT01234337,primary,Progression-free Survival (PFS) Assessed by the Independent Review Panel According to Response Evaluation Criteria for Solid Tumors (RECIST) 1.1,From randomization of the first participant until approximately 3 years or until disease radiological progression,,"PFS was defined as the time from date of randomization to disease progression, radiological or death due to any cause, whichever occurs first. Per RECIST version 1.1, progressive disease was determined when there was at least 20% increase in the sum of diameters of the target lesions, taking as a reference the smallest sum on study (this included the baseline sum if that was the smallest sum on trial). In addition to a relative increase of 20%, the sum had demonstrated an absolute increase of at least 5 mm. Appearance of new lesions and unequivocal progression of existing non-target lesions was also interpreted as progressive disease. Participants without progression or death at the time of analysis were censored at their last date of evaluable tumor evaluation. Median and other 95% confidence intervals (CIs) computed using Kaplan-Meier estimates.",,,,,,
+66377362,NCT01239797,primary,Median Progression Free Survival (PFS),From randomization up to 326 events (up to approximately 38 months),,Primary definition of Progression-free survival (PFS) defined as the time from randomization to the date of first documented tumor progression or death due to any cause. Participants were censored at the last adequate assessment prior to the start of any subsequent systemic-therapy or at the last adequate assessment prior to 2 missing assessments (> 10 weeks). Participants who died more than 10 weeks after the randomization date and had no on-treatment assessment were censored at the randomization date. Clinical deterioration was not considered progression. The primary analysis of PFS was based on the primary definition using the Independent Review Committee (IRC) tumor assessment using the European Group for Blood and Bone Marrow Transplant (EBMT) criteria. Tumor assessments were made every 4 weeks (±1 week) relative to the first dose of study medication.,,,,,,
+66377363,NCT01239797,primary,Objective Response Rate (ORR),From randomization up to approximately 38 months,,"Objective response rate (ORR) defined as the percentage of participants with a best response on-study of partial response (PR) or better (stringent CR [sCR], complete response [CR], very good partial response [VGPR], and partial response [PR]) based on the Independent Review Committee (IRC) assessment of best response using the European Group for Blood and Bone Marrow Transplant (EBMT) assessment criteria. Participants were censored at the last adequate assessment prior to the start of any subsequent systemic-therapy or at the last adequate assessment prior to 2 missing assessments (> 10 weeks). Participants who died more than 10 weeks after the randomization date and had no on-treatment assessment were censored at the randomization date. Clinical deterioration was not considered progression. Assessments were made every 4 weeks.",,,,,,
+64468586,NCT01285557,primary,Overall Survival (OS),"From the date of randomization until disease progression or death, cut-off date: 15 August 2014 (approximately 40 months)",,OS was defined as the time from randomization to the date of death for the ITT population. Participants who did not die were censored at the date last known to be alive. Analysis was performed by using Kaplan-Meier method.,,,,,,
+65818940,NCT01335698,primary,"Number of Participants Who Died and With Adverse Events (AEs) Leading to Discontinuation, Hyperbilirubinemia, Jaundice, First-degree Arterioventricular Block, Tachycardia, and Rash on ATV Powder",Day one to week 300 (approximately 22-Jan-2018),,"AE=any new unfavorable symptom, sign, or disease or worsening of a preexisting condition that may not have a causal relationship with treatment.",,,,,,
+65818941,NCT01335698,primary,Number of Participants Who Experienced a SAE on ATV Powder,Day one to week 300 (approximately 22-Jan-2018),,"SAE= any of the the following: is life-threatening (defined as an event in which the subject was at risk of death at the time of the event; it does not refer to an event which hypothetically might have caused death if it were more severe), requires inpatient hospitalization or causes prolongation of existing hospitalization, results in persistent or significant disability/incapacity, is a congenital anomaly/birth defect, is an important medical event (defined as a medical event(s) that may not be immediately life threatening or result in death or hospitalization but, based upon appropriate medical and scientific judgment, may jeopardize the subject or may require intervention [eg, medical, surgical] to prevent one of the other serious outcomes listed in the definition above.) Examples of such events include, but are not limited to, intensive treatment in an emergency room or at home for allergic bronchospasm; blood dyscrasias or convulsions that do not result in hospitalization",,,,,,
+65818942,NCT01335698,primary,Number of Participants With A Center of Disease Control and Prevention (CDC) Class C AIDS Event on ATV Powder,Day one to week 300 (approximately 22-Jan-2018),,"The CDC disease staging system assesses the severity of HIV disease by CD4 cell counts and by the presence of specific HIV-related conditions. CD4 counts are classified as 1: ≥500 cells/µL, 2: 200-499 cells/µL, and 3: <200 cells/µL. Children with HIV infection are also classified in each of several categories. Category N: Not symptomatic. Category A: Mildly symptomatic. Category B: Moderately symptomatic. Category C: Severely symptomatic.",,,,,,
+65818943,NCT01335698,primary,Number of Participants With Laboratory Test Results Meeting the Criteria for Grade 3-4 Abnormality on ATV Powder,Day one to week 300 (approximately 22-Jan-2018),,"Criteria of the Division of AIDS for grading the severity of adult and pediatric adverse events as follows: Grade (Gr) 1=mild; Gr 2=moderate; Gr 3=severe; Gr 4=potentially life-threatening. Neutrophils (absolute) (adult and infants >7 days): Gr 1=1.000-1300/mm^3; Gr 2=750-999 mm^3; Gr 3=500-749 mm^3; Gr 4= <500 mm^3. Alanine aminotransferase, aspartate aminotransferase, alkaline phosphatase: Gr 1=1.25-2.5*upper limit of normal (ULN); Gr 2=2.6-5.0*ULN; Gr 3=5.1-10.0*ULN; Gr 4= >10.0*ULN. Bilirubin, total (adults and infants >14 days): Gr 1=1.1-1.5*ULN; Gr 2=1.6-2.5*ULN; Gr 3=2.6-5.0*ULN; Gr 4= >5.0*ULN. Lipase: Gr 1=1.1-1.5*ULN; Gr 2=1.6-3.0*ULN; Gr 3=3.1-5.0*ULN; Gr 4= >5.0*ULN. Bicarbonate, serum low: Gr 1=16.0 mEq/L-<lower limit of normal; Gr 2=11.0-15.9 mEq/L; Gr 3=8.0-10.9 mEq/L; Gr 4= <8 mEq/L. By criteria of the World Health Organization: Amylase: Gr 1=1.0-1.39*ULN; Gr 2=1.40-2.09*ULN; Gr 3.=2.10-5.0*ULN; Gr 4= >5.0*ULN.",,,,,,
+65815965,NCT01368497,primary,"Proportion of Participants With Hepatitis B e Antigen (HBeAg) Loss & Hepatitis B Virus (HBV) Deoxyribonucleic Acid (DNA) Levels ≤1,000 International Units (IU) Per Milliliter (mL)",End of follow-up (up to 96 weeks),,,,,,,,
+65815966,NCT01368497,primary,Incidence of Adverse Events (AEs) Per Person-Year,From first treatment to the end of treatment (up to 48 weeks) and the end of follow-up (up to 96 weeks),,"The number of AEs includes both AEs and Serious Adverse Events (SAEs). The incidence is calculated as the number of AEs divided by the number of person-years of observation, which is the sum, across all participants, of the number of years between the start of treatment and the end of treatment, or the end of follow-up, respectively.",,,,,,
+65815967,NCT01368497,primary,Incidence of Serious Adverse Events (SAEs) Per Person-Year,From first treatment to the end of treatment (up to 48 weeks) and the end of follow-up (up to 96 weeks),,"The incidence is calculated as the number of SAEs divided by the number of person-years of observation, which is the sum, across all participants, of the number of years between the start of treatment and the end of treatment, or the end of follow-up, respectively.",,,,,,
+65815899,NCT01369199,primary,"Proportion of Participants With HBeAg Loss (Lack of Detectable HBeAg) AND HBV DNA ≤1,000 IU/mL",End of follow-up (up to 96 weeks),,Lack of data was considered to be treatment failure.,,,,,,
+65815900,NCT01369199,primary,Incidence of Adverse Events (AEs) Per Person-Year of Observation,From first treatment to the end of treatment (up to 48 weeks) and the end of follow-up (up to 96 weeks),,"The number of AEs includes both AEs and Serious Adverse Events (SAEs). The incidence is calculated as the number of AEs divided by the number of person-years of observation, which is the sum, across all participants, of the number of years between the start of treatment and the end of treatment, or the end of follow-up, respectively.",,,,,,
+65815901,NCT01369199,primary,Incidence of Serious Adverse Events (SAEs) Per Person-Year,From first treatment to the end of treatment (up to 48 weeks) and the end of follow-up (up to 96 weeks),,"The incidence is calculated as the number of SAEs divided by the number of person-years of observation, which is the sum, across all participants, of the number of years between the start of treatment and the end of treatment, or the end of follow-up, respectively.",,,,,,
+64189362,NCT01400776,primary,Change From Baseline in Participant's Self-Assessment of Severity of Vaginal Dryness to Week 12/Final Visit,Baseline (Day 0) to Week 12/Final Visit,,"The severity of vaginal dryness was assessed and recorded on a questionnaire by the participants using the following 4 point scale where, 0=None (The symptom is not present), 1=Mild (The symptom is present but may be intermittent; does not interfere with participants activities or lifestyle), 2=Moderate (The symptom is present. Participant is usually aware of the symptom, but activities and lifestyle are only occasionally affected), and 3=Severe (The symptom is present. Participant is usually aware and bothered by the symptom and have modified participant's activities and/or lifestyle due to the symptom. The negative change from Baseline indicates improvement. Week 12/Final Visit is defined as the last available postbaseline assessment up to Week 12.",,,,,,
+64189363,NCT01400776,primary,Change From Baseline in Vaginal pH to Week 12/Final Visit,Baseline (Day 0) to Week 12/Final Visit,,"Vaginal pH was obtained at final visit of the study. The pH was a numeric value from a scale of 0 to 14 expressing the acidity or alkalinity of the vaginal fluids where 7 was neutral, lower values were more acidic (values of 0-6) and higher values more alkaline (values of 8-14). A negative change from Baseline indicates improvement. Week 12/Final Visit is defined as the last available postbaseline assessment up to Week 12.",,,,,,
+64189364,NCT01400776,primary,Change From Baseline in Percentage of Vaginal Superficial Cells to Week 12/Final Visit,Baseline (Day 0) to Week 12/Final Visit,,Vaginal wall smears were collected from each participant. The smears were sent to the central laboratory for analysis to determine the percentage of superficial cells. Week 12/Final Visit is defined as the last available postbaseline assessment up to Week 12.,,,,,,
+64189365,NCT01400776,primary,Change From Baseline in Percentage of Vaginal Parabasal Cells to Week 12/Final Visit,Baseline (Day 0) to Week 12/Final Visit,,Vaginal wall smears were collected from each participant. The smears were sent to the central laboratory for analysis to determine the percentage of parabasal cells. Week 12/Final Visit is defined as the last available postbaseline assessment up to Week 12.,,,,,,
+65812203,NCT01413178,primary,Progression-Free Survival (PFS),3 years after transplant,,Participants that are still alive and without Multiple Myeloma 3 years after Stem cell Transplantation.,,,,,,
+65811960,NCT01416441,primary,"Number of Participants With Treatment Emergent Adverse Events (TEAEs), Serious TEAEs, Severe TEAEs and TEAEs Leading Treatment Discontinuation",From signing of the informed consent up to 30 days after the last dose (Up to Week 52),,An Adverse Event (AE) is defined as any untoward medical occurrence in a participant enrolled in a clinical trial and which did not necessarily have a causal relationship with the study medication. Treatment emergent adverse events (TEAE) are adverse events occurring after the onset of study drug administration.,,,,,,
+65811961,NCT01416441,primary,Number of Participants With Clinically Significant Changes in Laboratory Parameter Values,Baseline to Week 52,,"The laboratory values were one of the parameters to measure the safety and tolerability of individual participants. Participants with potentially clinically significant lab values in serum chemistry, hematology, urinalyses and prolactin tests that were identified based on pre-defined criteria were reported. Any value outside the normal range was flagged for the attention of the investigator who assessed whether or not a flagged value is of clinical significance.",,,,,,
+65811962,NCT01416441,primary,Number of Participants With Clinically Significant Changes in Electrocardiogram (ECG) Values,Baseline to Week 52,,"Incidence of clinically relevant abnormal ECG values were reported as change from Baseline in heart rate (Tachycardia - ≥15 beats per minute (bpm), Bradycardia ≤15 bpm; Rhythm (Sinus tachycardia ≥15 bpm increase, Sinus bradycardia decrease of ≥15 bpm from Baseline); Presence of - supraventricular premature beat; ventricular premature beat; supraventricular tachycardia; ventricular tachycardia; atrial fibrillation and flutter. Conduction - Presence of primary, secondary or tertiary atrioventricular block, left bundle-branch block, right bundle-branch block, pre-excitation syndrome, other intraventricular conduction blocked QRS ≥0.12 second increase of ≥0.02 second. Acute, subacute or old Infarction, Presence of myocardial ischemia, symmetrical T-wave inversion. Increase in QTc - QTc ≥450 msec ≥10% increase. Any clinically significant change from Baseline assessed by the Investigator are reported.",,,,,,
+65811963,NCT01416441,primary,"Number of Participants With Emergence of Suicidal Ideation, TEAEs Related to Suicide and Suicidality and Suicide Ideation From the Potential Suicide Events Recorded on the Columbia-Suicide Severity Rating Scale (C-SSRS)",Baseline to Week 52,,"Suicidality was defined as reporting at least one occurrence of any suicidal behavior or suicidal ideation. Suicidal behavior was defined as reporting any type of suicidal behaviors (actual attempt, interrupted attempt, aborted attempt, and preparatory acts or behavior). Suicidal ideation was defined as reporting any type of suicidal ideation. The suicidal ideation intensity total score is the sum of intensity scores of 5 items (frequency, duration, controllability, deterrents, and reasons for ideation). The score of each intensity item ranges from 0 (none) to 5 (worst) which leads to the range of the total score from 0 to 25. A missing score of any item resulted in a missing total score. If no suicidal ideation was reported, a score of 0 was given to the intensity scale.",,,,,,
+65811964,NCT01416441,primary,Change From Baseline in Abnormal Involuntary Movement Scale (AIMS) Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32, 40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The AIMS Scale is an extrapyramidal symptoms (EPS) rating scale. The AIMS is a 12 item scale. The first 10 items e.g. facial and oral movements (items 1-4), extremity movements (items 5 and 6), trunk movements (item 7), investigators global assessment of dyskinesia (items 8 to 10) are rated from 0 to 4 (0=best, 4=worst). Items 11 and 12, related to dental status, have dichotomous responses, 0=no and 1=yes. The AIMS Total Score is the sum of the ratings for the first seven items. The possible total scores are from 0 to 28. A negative change from Baseline indicates improvement.",,,,,,
+65811965,NCT01416441,primary,Mean Change From Baseline in Body Mass Index (BMI),"Baseline and Weeks 12, 24, 52 and Last Visit (Week 52 or early termination Visit before Week 52)",,"The BMI kilogram/meter square (i.e. kg/m^2) was calculated from the Baseline height and the weight at the current visit using one of the following formulae, as appropriate: Weight (kg) divided by [Height (meters)]^2.",,,,,,
+65811966,NCT01416441,primary,Number of Participants With Clinically Significant Changes in Vital Signs,Baseline to Week 52,,"Vital signs assessments included orthostatic (supine and standing) blood pressure (BP) measured as millimeter of mercury [mmHg]), heart rate, (measured in beats per minute [bpm]), body weight (measured in kilograms [kg]) and body temperature. Incidence of clinically relevant abnormal values in heart rate, systolic and diastolic blood pressure and weight were identified based on pre-defined criteria. Orthostatic assessments of blood pressure and heart rate were made after the participant has been supine for at least 5 minutes and again after the participant has been standing for approximately 2 minutes, but not more than 3 minutes.",,,,,,
+65811967,NCT01416441,primary,Mean Change From Baseline in Simpson Angus Scale (SAS) Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32, 40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The SAS is a rating scale used to measure Extrapyramidal symptoms (EPS). The SAS scale consists of a list of 10 symptoms of parkinsonism (gait, arm dropping, shoulder shaking, elbow rigidity, wrist rigidity, head rotation, glabella tap, tremor, salivation, and akathisia), with each item rated from 0 to 4, with 0 being normal and 4 being the worst. The SAS Total score is sum of ratings for all 10 items, with possible Total scores from 0 to 40. A negative change from Baseline indicates improvement.",,,,,,
+65811968,NCT01416441,primary,Mean Change From Baseline in Barnes Akathisia Rating Scale (BARS) Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32,40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The BARS was an EPS rating scale. The BARS was used to assess the presence and severity of akathisia. This scale consists of 4 items. Only the 4th item, the Global Clinical Assessment of Akathisia, was evaluated in this trial. This item is rated on a 6 point scale, with 0 being best (absent) and 5 being worst (severe akathisia). A negative change from Baseline indicates improvement.",,,,,,
+65811969,NCT01416441,primary,"Mean Change From Baseline in Average Score of Attention-Deficit Disorder/Attention-Deficit Hyperactivity Disorder (ADD/ADHD) Sub-scale of the Swanson, Nolan and Pelham-IV (SNAP-IV)","Baseline and Weeks 4, 8, 12, 16, 20, 24, 32,40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The SNAP-IV, ADHD Inattention subscale contains 19 items, items 1 to 9 measure inattention, items 11 to 19 measure hyperactivity/impulsivity, and item 10 for inattention domain that scores the intensity of each item during the last seven days on a 0 to 3 scale (0=not at all, 1=just a little, 2=pretty much, 3=very much). The lowest possible score is 0; highest is 57. The negative change from Baseline indicates improvement.",,,,,,
+65811970,NCT01416441,primary,Mean Change From Baseline in Children's Yale-Brown Obsessive Compulsive Scale (CY-BOCS) Total Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32,40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The CY-BOCS is used to assess characteristics of obsession and compulsion for the week prior to the interview. Nineteen items are rated in the CY-BOCS, but the total score is the sum of only items 1 to 10 (excluding items 1b and 6b). The obsession and compulsion subtotals are the sums of items 1 to 5 (excluding 1b) and 6 to 10 (excluding 6b), respectively. A missing value for any CY-BOCS item scale could result in a missing total score or obsession and compulsion subtotals of which the item scale is a component. At baseline, the full CY-BOCS interview is conducted. At all post-baseline time points, the ""Questions on Obsessions"" (items 1 to 5) and ""Questions on Compulsions"" (items 6 to 10) are reviewed and the target symptoms identified at baseline are the primary focus for rating severity. CY-BOCS total score could range from 0 to 40. Higher scores indicate worse outcome. A negative change from Baseline indicates improvement.",,,,,,
+65811971,NCT01416441,primary,Mean Change From Baseline in Children's Depression Rating Scale Revised (CDRS-R) Total Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32,40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The CDRS-R is composed of 17 interviewer-rated symptom areas: impaired schoolwork, difficulty having fun, social withdrawal, appetite disturbance, sleep disturbance, excessive fatigue, physical complaints, irritability, excessive guilt, low self-esteem, depressed feelings, morbid ideas, suicidal ideas, excessive weeping, depressed facial affect, listless speech, and hypoactivity. The CDRS-R total score is the sum of scores for the 17 symptom areas. A missing value for any CDRS-R item scale or a not rated item scale (indicated by the value of 0) could result in a missing total score. The CDRS-R total score is the sum of scores for the 17 symptom areas and could range from 17 to 113 with higher values indicating worse outcome. A negative change from Baseline indicates improvement.",,,,,,
+65811972,NCT01416441,primary,Mean Change From Baseline in Pediatric Anxiety Rating Scale (PARS) Total Severity Score,"Baseline and Weeks 4, 8, 12, 16, 20, 24, 32,40, 52; Last Visit (Week 52 or early termination Visit before Week 52)",,"The PARS has 2 sections: the symptom checklist and the severity items. The symptom checklist is used to determine the child's repertoire of symptoms during the past week. Information is elicited from the child and parent(s) and the rater then combines information from all informants using his/her best judgment. The 7-item severity list is used to determine severity of symptoms and the PARS total score. The time frame for the PARS rating is the past week. Only those symptoms endorsed for the past week are included in the symptom checklist and rated on the severity items. The PARS total severity score is the sum of items 2, 3, 5, 6, and 7. The total severity score ranges from 0 to 25, with 25 being the worst. Codes ""8"" (Not applicable) and ""9"" (Does not know) are not included in the summation (ie, equivalent to a score of 0 in the summation). A negative change from Baseline indicates improvement.",,,,,,
+65811973,NCT01416441,primary,Mean Change From Baseline in Body Weight,"Baseline to Weeks 12, 24, 52 and Last Visit (Week 52 or early termination Visit before Week 52)",,,,,,,,
+65811974,NCT01416441,primary,Mean Change From Baseline in Waist Circumference,"Baseline to Weeks 12, 24, 52 and Last Visit (Week 52 or early termination Visit before Week 52)",,"Waist circumference was recorded before a participant's meal and at approximately the same time at each visit. Measurement was accomplished by locating the upper hip bone and the top of the right iliac crest and placing the measuring tape in a horizontal plane around the abdomen at the level of the crest. Before reading the tape measure, the assessor assured that the tape was snug, but did not compress the skin, and is parallel to the floor. The measurement was made at the end of a normal exhalation.",,,,,,
+65811875,NCT01418339,primary,Change From Baseline in Yale Global Tic Severity Scale (YGTSS) - Total Tic Score (TTS),Baseline to Week 8,,"The YGTSS is a semi-structured clinical interview designed to measure the tic severity. This scale consisted of a tic inventory, with 5 separate rating scales to rate the severity of symptoms, and an impairment ranking. Ratings were made along 5 different dimensions on a scale of 0 to 5 for motor and vocal tics, each including number, frequency, intensity, complexity, and interference. The YGTSS TTS was the summation of the severity scores of motor and vocal tics. The TTS ranged from 0 (none) to 50 (severe) with a higher score represent more severe symptoms (greater reduction from baseline for greater improvement). Mixed Effect Repeated Measure Model (MMRM) analysis was performed.",,,,,,
+65808618,NCT01449929,primary,Percentage of Participants With Plasma Human Immunodeficiency Virus-1 (HIV-1) Ribonucleic Acid (RNA) <50 Copies/Milliliter (c/mL) at Week 48,Week 48,,"Assessment was done using Missing, Switch or Discontinuation = Failure (MSDF), as codified by the Food and Drug Administration (FDA) ""snapshot"" algorithm.This algorithm treated all participants without HIV-1 RNA data at Week 48 as nonresponders, as well as participants who switched their concomitant ART prior to Week 48 as follows: background ART substitutions non-permitted per protocol (one background ART substitution was permitted for safety or tolerability); background ART substitutions permitted per protocol unless the decision to switch was documented as being before or at the first on-treatment visit where HIV-1 RNA was assessed. Otherwise, virologic success or failure was determined by the last available HIV-1 RNA assessment while the participant was on-treatment in the snapshot window (Week 48 +/- 6 weeks). Modified Intent-To-Treat Exposed (mITT-E) Population:all randomized participants who received at least one dose of investigational product",,,,,,
+64189352,NCT01455597,primary,Number of Participants With Endometrial Biopsy Results at Final Visit,Final Visit (Day closest to Day 281),,"The endometrial biopsy results was categorized as: normal results categorized as atrophic/inactive or proliferative, unsatisfactory with endometrial thickness ≤4 mm and missing biopsy with endometrial thickness ≤4 mm; abnormal results categorized as polyp, hyperplasia, and carcinoma; unknown result categorized as unsatisfactory with endometrial thickness >4 mm, missing biopsy with endometrial thickness >4 mm, unsatisfactory without transvaginal ultrasonography (TVU) result and missing biopsy without TVU result. The duration of estradiol exposure was combination of studies PR-04409.3 and PR-04509.",,,,,,
+64308049,NCT01459679,primary,Mean change in maximum corneal curvature (Kmax) from baseline,Month 6 or 12,,,,,,,,
+65807389,NCT01461928,primary,Maintenance II: Progression-free Survival (PFS) Using 1999 International Working Group (Cheson) Response Criteria for Lymphoma or by the Recommendations for Waldenström's Macroglobulinemia,"From randomization (Maintenance II) up to disease progression or death, whichever occurs first (up to approximately 24 months)",,"Progression free survival from randomization (PFSrand) is defined as the time from date of randomization to the date of first documented disease progression or death, whichever occurs first. One participant died in Induction before randomization and one participant died in Maintenance II Observation arm due to an SAE and were not considered in the analysis as no death page was completed. The Observation arm did not include one participant with AE outcome of death reported retrospectively 2 months after discontinuation from study (censored as having no event on Day 456 post-randomization).",,,,,,
+65807162,NCT01463306,primary,"Number of Participants With Treatment Emergent Adverse Events (AEs), Treatment Emergent Serious Adverse Events (SAEs), Treatment Related AEs and Treatment Related SAEs",Baseline (Day 1) up to 13 Months,,An AE was any untoward medical occurrence in a participant who received study drug without regard to possibility of causal relationship. An SAE was an AE resulting in any of the following outcomes or deemed significant for any other reason: death, initial or prolonged inpatient hospitalization, life-threatening experience (immediate risk of dying), persistent or significant disability/incapacity, congenital anomaly. Treatment emergent are events between first dose of study drug and up to 28 days after last dose of study drug (up to 13 months) that were absent before treatment or that worsened relative to pretreatment state. AEs included both serious and non-serious AEs. Treatment-related AE was any untoward medical occurrence attributed to study drug in a participant who received study drug. Relatedness to study drug was assessed by the investigator.,,
+65807163,NCT01463306,primary,Number of Participants With Clinically Significant Change From Baseline in Physical and Neurological Examination Findings up to 12 Months,Baseline up to 12 Months,,"Physical examination assessed: general appearance, dermatological, head and eyes, ears, nose, mouth, and throat, pulmonary, cardiovascular, abdominal, genitourinary (optional), lymphatic, musculoskeletal/extremities. Neurological examination assessed: level of consciousness, mental status, cranial nerve assessment, muscle strength and tone, reflexes, pin prick and vibratory sensation, coordination and gait. Investigator judged clinically significant change from baseline in physical and neurological examination findings.",,,,,,
+65807164,NCT01463306,primary,Number of Participants Meeting Pre-defined Criteria for Vital Signs Abnormalities,Baseline up to 12 months,,Pre-defined criteria of vital signs abnormalities: maximum (max.) increase or decrease from baseline in sitting/supine systolic blood pressure (SBP) >=30 millimeter of mercury (mmHg), maximum increase or decrease from baseline in sitting/supine diastolic blood pressure (DBP) >=20 mmHg.,,,,,
+65807165,NCT01463306,primary,Number of Participants With Tanner Staging Evaluation at Baseline,Baseline (Day 1),,"Tanner stage defines physical measurements of development based on external primary and secondary sex characteristics. Participants were evaluated for pubic hair distribution, breast development (only females) and genital development (only males), with values ranging from stage 1 (pre-pubertal characteristics) to stage 5 (adult or mature characteristics).",,,,,,
+65807166,NCT01463306,primary,Number of Participants With Tanner Staging Evaluation at Month 12,Month 12,,"Tanner stage defines physical measurements of development based on external primary and secondary sex characteristics. Participants were evaluated for pubic hair distribution, breast development (only females) and genital development (only males), with values ranging from stage 1 (pre-pubertal characteristics) to stage 5 (adult or mature characteristics).",,,,,,
+65807167,NCT01463306,primary,Number of Participants With >=7 Percent (%) Change From Baseline in Body Weight up to 12 Months,Baseline up to 12 Months,,"In this outcome measure number of participants with increase and decrease of >=7% in body weight, from baseline up to 12 months are reported.",,,,,,
+65807168,NCT01463306,primary,Absolute Values for Body Height at Baseline,Baseline,,,,,,,,
+65807169,NCT01463306,primary,Absolute Values for Body Height at Month 12,Month 12,,,,,,,,
+65807170,NCT01463306,primary,Number of Participants With Incidence of Laboratory Abnormalities,Baseline up to 12 Months,,"Criteria for laboratory abnormalities: Hemoglobin (Hgb), hematocrit, red blood cell(RBC) count: <0.8*lower limit of normal(LLN), platelet: <0.5*LLN/greater than (>)1.75*upper limit of normal (ULN), white blood cell (WBC): <0.6*LLN/>1.5*ULN, lymphocyte, neutrophil- absolute/%:<0.8*LLN/>1.2*ULN, basophil, eosinophil, monocyte- absolute/%:>1.2*ULN; total/direct/indirect bilirubin >1.5*ULN, aspartate aminotransferase (AT), alanine AT, gammaglutamyl transferase, alkaline phosphatase:> 3.0*ULN, total protein, albumin: <0.8*LLN/>1.2*ULN; thyroxine, thyroid stimulating hormone <0.8*LLN/>1.2*ULN; cholesterol, triglycerides:> >1.3*ULN; blood urea nitrogen, creatinine:>1.3*ULN; sodium <0.95*LLN/>1.05*ULN, potassium, chloride, calcium: <0.9*LLN or >1.1*ULN; glucose <0.6*LLN/>1.5*ULN, creatine kinase>2.0*ULN; urine (specific gravity <1.003/>1.030, pH <4.5/>8, glucose, ketones, protein: >=1, WBC, RBC:>=20, bacteria >20, hyaline casts/casts >1); prothrombin (PT), PT international ratio>1.1*ULN.",,,,,,
+65807171,NCT01463306,primary,Number of Participants With Maximum Change From Baseline up to 12 Months in 12-Lead Electrocardiogram (ECG) Parameters,Baseline up to 12 Months,,"Categories for which data is reported are: 1) maximum (max) PR interval increase from baseline (IFB) (millisecond [msec]) percent change (PctChg) >=25/50%; 2) maximum QRS complex increase from baseline (msec) PctChg>=50%; 3) maximum QTcB interval (Bazett's correction) increase from baseline (msec): change >=30 to <60; change >=60; 4) maximum QTcF interval (Fridericia's correction) increase from baseline (msec): change >=30 to <60; change >=60. 'PctChg>=25/50%': >= 25% increase from baseline when baseline ECG parameter is > 200 msec, and is >= 50% increase from baseline when baseline ECG parameter is non-missing and <=200 msec.",,,,,,
+65807172,NCT01463306,primary,28-Days Seizure Rate at Week 1,Week 1,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807173,NCT01463306,primary,28-Days Seizure Rate at Month 1,Month 1,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807174,NCT01463306,primary,28-Days Seizure Rate at Month 2,Month 2,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807175,NCT01463306,primary,28-Days Seizure Rate at Month 4,Month 4,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807176,NCT01463306,primary,28-Days Seizure Rate at Month 6,Month 6,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807177,NCT01463306,primary,28-Days Seizure Rate at Month 9,Month 9,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+65807178,NCT01463306,primary,28-Days Seizure Rate at Month 12/Early Termination,Month 12/Early Termination,,"28-days seizure rate was defined as number of seizures per 28-day period. 28-days seizure rate have been reported separately for partial onset seizure and primary generalized tonic clonic seizure. Partial onset seizure: a seizure that starts in one area of the brain. This kind of seizure is brief, lasting seconds to less than 2 minutes. Primary generalized tonic clonic seizure: a seizure that starts in one area of the brain, then spreads to both sides of the brain as a tonic-clonic seizure and usually last 1 to 3 minutes.",,,,,,
+64308011,NCT01470131,primary,Progression Free Survival,Analysis to be conducted after a minimum of 201 events,,,,,,,,
+66358803,NCT01471444,primary,Progression-Free Survival (PFS),"From day of transplant to disease of progression or death of any cause, whichever came first, assessed up to 5 years",,Number of events with progression free survival. (Progression is defined as more than 5% blast in the peripheral blood or bone marrow biopsy.) or expired from treatment related mortality post transplant.,,,,,,
+66358799,NCT01510184,primary,Overall Survival (OS) for Living Participants,"From randomization till death or end of study, whichever occurs first (Up to approximately 2.5 years)",,"OS was the time from randomization to death. In living participants, survival time was censored on the last date that participants were known to be alive. OS for living participant was calculated as (end of study date/last visit date - randomization date)+ 1/30.4375. Overall Survival was summarized separately for living participants as only few participants died in this study.",,,,,,
+66358800,NCT01510184,primary,Overall Survival for Death,"From randomization till death or end of study, whichever occurs first (Up to approximately 2.5 years)",,OS was the time from randomization to death. OS for death calculated as (date of death - randomization date)+ 1/30.4375. Overall Survival was summarized separately for participants who were died as only few participants died in this study.,,,,,,
+65801015,NCT01536392,primary,Percentage of Participants With Response Rate to Anti-Emetic Therapy Days 4-7 Each Chemotherapy Cycle,"Baseline, up to 7 days post-chemotherapy, through 5 cycles of chemotherapy measured each cycle, an average of 6 weeks",,"Response defined as no emetic or retching episodes and no rescue medication use during late onset phase (4-7 days post-chemotherapy) measured each cycle. Responses tabulated to 4 items of Morisky Medication Adherence measure for each treatment group by cycle of therapy. Elements summarized of Morrow Assessment of Nausea and Emesis and for pill counts/compliance for each treatment group by cycle of therapy. Descriptive statistics summarize total scores for Osoba Module, used to measure effect of nausea and vomiting on quality of life, for each treatment group by cycle of therapy. Osoba Nausea and Emesis Module; higher scores indicate worse quality of life. Morisky Medication Adherence Scale. Higher scores indicate higher compliance. Morisky Medication Adherence Scale is Yes=0 and No=1 , zero is the lowest level of medication adherence, and 4 is the highest level of medication adherence.",,,,,,
+65800672,NCT01541215,primary,Change in HbA1c (Glycosylated Haemoglobin),"Week 0, week 26",,"Change in HbA1c from baseline to week 26. All available data were used for the primary analysis, including data collected after treatment discontinuation and initiation of rescue medication.",,,,,,
+65798269,NCT01571284,primary,Number of Participants With Treatment-Emergent Adverse Events (TEAEs),Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Any untoward medical occurrence in a participant who received investigational medicinal product (IMP) was considered an adverse event (AE) without regard to possibility of causal relationship with this treatment. A serious AE (SAE): Any untoward medical occurrence that resulted in any of the following outcomes: death, life-threatening, required initial or prolonged in-patient hospitalization, persistent or significant disability/incapacity, congenital anomaly/birth defect, or considered as medically important event. Any TEAE included participants with both serious and non-serious AEs. National Cancer Institute Common Terminology Criteria (NCI-CTCAE) Version 4.03 was used to assess severity (Grade 1=mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling) of AEs.",,,,,,
+65798270,NCT01571284,primary,Number of Participants With Abnormal Hematological Parameters,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Abnormal hematological parameters included: anaemia, thrombocytopenia, leukopenia and neutropenia. Number of participants with each of these parameters were analyzed by grades (All Grades and Grades 3-4 as per NCI CTCAE (Version 4.03), where Grade 1=mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling. All Grades included Grades 1-4.",,,,,,
+65798271,NCT01571284,primary,Number of Participants With International Normalized Ratio (INR),Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,The INR is a derived measure of the prothrombin time. The INR is the ratio of a participant's prothrombin time to a normal control sample. Normal range (without anti coagulation therapy): 0.8-1.2, Targeted range (with anti coagulation therapy) 2.0-3.0.,,,,,
+65798272,NCT01571284,primary,Number of Participants With Abnormal Electrolytes Parameters,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Abnormal electrolytes parameters included: hyponatremia, hypernatremia, hypocalcemia, hypercalcemia, hypokalemia, and hyperkalemia. Number of participants with each of these parameters were analyzed by grades ( All Grades and Grades 3-4 as per NCI CTCAE Version 4.03, where Grade 1=mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling. All Grades included Grades 1-4.",,,,,,
+65798273,NCT01571284,primary,Number of Participants With Abnormal Renal and Liver Function Parameters,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Renal and liver function parameters included: creatinine, hyperbilirubinemia, aspartate aminotransferase (AST), alanine aminotransferase (ALT) and alkaline phosphatase. Number of participants with each of these parameters were analyzed by grades (All Grades and Grades 3-4) as per NCI CTCAE version 4.03, where Grade 1=mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling. All Grades included Grades 1-4.",,,,,,
+65798274,NCT01571284,primary,Creatinine Clearance of Aflibercept Plus FOLFIRI,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Creatinine clearance is a measure of kidney function. Creatinine clearance rate is the volume of blood plasma that is cleared of creatinine by the kidneys per unit time. Creatinine clearance can be measured directly or estimated using established formulas. For this study, the creatinine clearance was calculated using the Cockroft-Gault or Modification of Diet in Renal Disease (MDRD).",,,,,,
+65798275,NCT01571284,primary,Number of Participants With Other Abnormal Biochemistry Parameters,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Other abnormal biochemistry parameters included: hypoglycemia, hyperglycemia and hypoalbuminemia. Number of participants with each of these parameters were analyzed by grades (All Grades and Grades 3-4) as per NCI CTCAE Version 4.03, where Grade 1= mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling. All Grades included Grades 1-4.",,,,,,
+65798276,NCT01571284,primary,Number of Participants With Abnormal Non-Gradable Biochemistry Parameters,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Non-gradeable biochemistry parameters included; chloride, urea, total protein, blood urea nitrogen (BUN) and lactate dehydrogenase (LDH). Number of participants with <lower limit of normal ranges (LLN) and >upper limit of normal ranges (ULN) for each of these parameters were reported.",,,,,,
+65798277,NCT01571284,primary,Number of Participants With Proteinuria Events,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Proteinuria is defined as the ratio of protein to creatinine. Number of participants with proteinuria were analyzed by grades (Grades 1, 2, 3 ,4) as per NCI CTCAE Version 4.03 where Grade 1= mild, Grade 2= moderate, Grade 3= severe, Grade 4= life-threatening/disabling.",,,,,,
+65798278,NCT01571284,primary,Number of Participants With Proteinuria Grade >=2,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Proteinuria is defined as the ratio of protein to creatinine. Number of participants with proteinuria grade >=2 (graded as per NCI CTCAE Version 4.03), where Grade>=2 represents moderate to life-threatening/disabling event.",,,,,,
+65798279,NCT01571284,primary,Number of Participants With Urinary Protein-Creatinine Ratio (UPCR),Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,Urinary protein creatinine ratio (UPCR) corresponds to the ratio of the urinary protein and urinary creatinine concentration (expressed in mg/dL). This ratio provides an accurate quantification of 24-hours urinary protein excretion. There is a high correlation between morning UPCR and 24-hour proteinuria in participants with normal or reduced renal functions. Normal ratio is < or = 1.,,,,,,
+65798280,NCT01571284,primary,Number of Participants With Proteinuria (Grade>=2) Concomitant With Hematuria and /or Hypertension,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,"Proteinuria is defined as the presence of excess proteins in the urine (assessed either by spot sample, dipstick/ urine protein or 24 hour urine collection). Hematuria is defined as the presence of blood in urine (positive dipstick for RBC or reported AE). Number of participants with proteinuria grade >=2 (graded as per NCI CTCAE Version 4.03), where Grade>=2 represents moderate to life-threatening/disabling event. Hypertension (high blood pressure) is defined as having a blood pressure reading of more than 140/90 mmHg over a number of weeks.",,,,,,
+65798281,NCT01571284,primary,Number of Participants With Cycle Delay and/or Dose Modification,Baseline up to 30 days after the last treatment administration (either Aflibercept or FOLFIRI whichever comes last) (maximum exposure: 214 weeks),,A theoretical cycle is a 2 week period i.e. 14 days. A cycle is delayed if duration of previous cycle is greater than 14+2 days , dose modification includes dose reduction and dose omission.,,,,,
+65798168,NCT01571362,primary,Change in Weekly Average Electronic Diary (eDiary) Numeric Rating Scale -Pain (NRS-Pain) Score From Randomization Baseline to Final 2 Weeks (Average of Weeks 11 and 12),Weeks 11 and 12,,Weekly average diary NRS-Pain scores were derived from the daily NRS-pain scale and calculated as the mean of the last 7 days. NRS-Pain scores based on an 11-point numerical rating scale from 0 (no pain) to 10 (worst possible pain). Higher scores indicate greater pain.,,,,,,
+65798111,NCT01572038,primary,"Subgroup Analysis by Region of Enrollment: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798100,NCT01572038,primary,"Overview of the Number of Participants With at Least One Treatment-Emergent Adverse Event, Severity Determined According to National Cancer Institute Common Terminology Criteria for Adverse Events, Version 4.0 (NCI-CTCAE v4.0)","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. TEAEs to monitor included anaphylaxis and hypersensitivity, cardiac dysfunction, diarrhoea Grade ≥3, pregnancy-related AEs, interstitial lung disease, infusion-/administration-related reactions, mucositis, (febrile) neutropenia, rash/skin reactions, and suspected transmission of infectious agent. TEAEs of special interest included LVEF decreased, liver enzymes increased, and suspected transmission of infectious agent by the study drug.",,,,,,
+65798101,NCT01572038,primary,Number of Participants Who Died Over the Course of the Study by Reported Cause of Death (Adverse Events Leading to Death by System Organ Class and Preferred Term),The median (full range) duration of follow-up was 68.73 (0.03-87.29) months.,,"All adverse events leading to death, regardless of whether they were classified as treatment emergent, are listed by system organ class (SOC) and preferred term (PT) according to the Medical Dictionary for Regulatory Activities, version 22.1 (MedDRA version 22.1); PTs that are part of a given SOC are listed in the rows directly below each SOC within the results table. Admin. = administration; Mediast. = mediastinal",,,,,,
+65798102,NCT01572038,primary,Number of Participants Who Died Within 6 Months of Starting Study Treatment by Reported Cause of Death (Adverse Events Leading to Death by System Organ Class and Preferred Term),The median (full range) duration of follow-up was 68.73 (0.03-87.29) months.,,"All adverse events leading to death, regardless of whether they were classified as treatment emergent, are listed by system organ class (SOC) and preferred term (PT) according to the Medical Dictionary for Regulatory Activities, version 22.1 (MedDRA version 22.1); PTs that are part of a given SOC are listed in the rows directly below each SOC within the results table. Admin. = administration; Mediast. = mediastinal",,,,,,
+65798103,NCT01572038,primary,"Number of Participants With Grade ≥3 Treatment-Emergent Adverse Events, Occurring in ≥1% of Participants by System Organ Class and Preferred Term","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. MedDRA version 22.1 was used to code AEs by system organ class (SOC) and preferred term (PT); PTs that are part of a given SOC are listed in the rows directly below each SOC within the results table. If a participant experienced the same AE at more than one severity grade, only the most severe grade was presented.",,,,,,
+65798104,NCT01572038,primary,"Number of Participants With Treatment-Emergent Adverse Events of Any Grade That Were Related to Study Treatment (Pertuzumab, Trastuzumab, or Taxane), Occurring in ≥10% of Participants by System Organ Class","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. MedDRA version 22.1 was used to code AEs and the system organ classes are presented in descending order according to the total frequency of occurrence. If a participant experienced more than one event in a category, they were counted only once in that category.",,,,,,
+65798105,NCT01572038,primary,"Number of Participants With Grade ≥3 Treatment-Emergent Adverse Events That Were Related to Study Treatment (Pertuzumab, Trastuzumab, or Taxane), Occurring in ≥0.5% of Participants by Preferred Term","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. MedDRA version 22.1 was used to code AEs and the preferred terms are presented in descending order according to the total frequency of occurrence. If a participant experienced more than one event in a category, they were counted only once in that category.",,,,,,
+65798106,NCT01572038,primary,"Number of Participants With Treatment-Emergent Adverse Events Leading to Discontinuation of Study Treatment (Pertuzumab, Trastuzumab, or Taxane), Occurring in ≥0.2% of Participants by Preferred Term","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. MedDRA version 22.1 was used to code AEs and the preferred terms are presented in descending order according to the total frequency of occurrence. If a participant experienced more than one event in a category, they were counted only once in that category. Discont. = discontinuation; Ptz = pertuzumab; Tax = taxane; Trz = trastuzumab",,,,,,
+65798107,NCT01572038,primary,"Number of Participants With Treatment-Emergent Adverse Events Leading to Dose Interruption of Study Treatment (Pertuzumab, Trastuzumab, or Taxane), Occurring in ≥0.5% of Participants by Preferred Term","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. MedDRA version 22.1 was used to code AEs and the preferred terms are presented in descending order according to the total frequency of occurrence. If a participant experienced more than one event in a category, they were counted only once in that category. Interrupt. = interruption; Ptz = pertuzumab; Tax = taxane; Trz = trastuzumab",,,,,,
+65798108,NCT01572038,primary,"Number of Participants With Treatment-Emergent Adverse Events to Monitor of Any Grade, Occurring in ≥5% of Participants by Category","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first dose of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, it was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. If a participant had more than one event in a category, they were counted only once in that category. TEAEs to monitor included anaphylaxis and hypersensitivity, cardiac dysfunction, diarrhoea Grade ≥3, pregnancy-related AEs, interstitial lung disease, infusion-/administration-related reactions, mucositis, (febrile) neutropenia, rash/skin reactions, and suspected transmission of infectious agent. MedDRA version 22.1 was used to code AEs; AEs may fall within multiple categories.",,,,,,
+65798109,NCT01572038,primary,"Number of Participants With Grade ≥3 Treatment-Emergent Adverse Events to Monitor, Occurring in ≥0.5% of Participants by Category and Preferred Term","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first dose of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, it was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. If a participant had more than one event in a category, they were counted only once in that category. TEAEs to monitor included anaphylaxis and hypersensitivity, cardiac dysfunction, diarrhoea Grade ≥3, pregnancy-related AEs, interstitial lung disease, infusion-/administration-related reactions, mucositis, (febrile) neutropenia, rash/skin reactions, and suspected transmission of infectious agent. MedDRA version 22.1 was used to code AEs; preferred terms (PT) that are part of a given category are listed in the rows directly below each category within the results table.",,,,,,
+65798110,NCT01572038,primary,Number of Participants With Treatment-Emergent Adverse Events of Special Interest by Category and Preferred Term,"From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. TEAEs of special interest included LVEF decreased, liver enzymes (ALT or AST) increased, and suspected transmission of infectious agent by the study drug. MedDRA version 22.1 was used to code AEs; preferred terms (PT) that are part of a given category are listed in the rows directly below each category within the results table. If a participant experienced more than one event in a category, they were counted only once in that category.",,,,,,
+65798112,NCT01572038,primary,"Subgroup Analysis by Age (≤65 vs. >65 Years): Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), TEAEs Leading to Death, Grade ≥3 TEAEs, Any-Grade and Grade ≥3 TEAEs Related to Pertuzumab, and TEAEs to Monitor","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. TEAEs to monitor included anaphylaxis and hypersensitivity, cardiac dysfunction, diarrhoea Grade ≥3, pregnancy-related AEs, interstitial lung disease, infusion-/administration-related reactions, mucositis, (febrile) neutropenia, rash/skin reactions, and suspected transmission of infectious agent.",,,,,,
+65798113,NCT01572038,primary,"Subgroup Analysis by Taxane Chemotherapy: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), TEAEs Leading to Death, Grade ≥3 TEAEs, Any-Grade and Grade ≥3 TEAEs Related to Pertuzumab, and TEAEs to Monitor","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE. TEAEs to monitor included anaphylaxis and hypersensitivity, cardiac dysfunction, diarrhoea Grade ≥3, pregnancy-related AEs, interstitial lung disease, infusion-/administration-related reactions, mucositis, (febrile) neutropenia, rash/skin reactions, and suspected transmission of infectious agent.",,,,,,
+65798114,NCT01572038,primary,"Subgroup Analysis by ECOG Performance Status at Baseline: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798115,NCT01572038,primary,"Subgroup Analysis by Visceral Disease at Baseline: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798116,NCT01572038,primary,"Subgroup Analysis by Prior (Neo)Adjuvant Chemotherapy: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798117,NCT01572038,primary,"Subgroup Analysis by Hormone Receptor Status at Baseline: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798118,NCT01572038,primary,"Subgroup Analysis by Previous Trastuzumab Therapy: Overview of the Number of Participants With Serious Treatment-Emergent Adverse Events (TEAEs), Grade ≥3 TEAEs, and Grade ≥3 TEAEs Related to Pertuzumab","From Baseline until 28 days after, or 7 months after (only for serious AEs related to study drug), the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"Treatment-emergent adverse events (TEAEs) were adverse events (AEs) that started or worsened in severity on or after the first administration of study drug, up to and including 28 days after the last dose. The investigator graded all AEs for severity per NCI-CTCAE v4.0; if not listed, the AE was assessed as follows: Grade 1 = mild; Grade 2 = moderate; Grade 3 = severe; Grade 4 = life-threatening/disabling; Grade 5 = death. The investigator determined whether an AE was related to study drug and independently assessed severity and seriousness of each AE.",,,,,,
+65798119,NCT01572038,primary,Number of Participants With a Congestive Heart Failure Event,From Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,"Congestive heart failure was defined as the Standardised MedDRA Query (SMQ) 'Cardiac failure (wide)' from the Medical Dictionary for Regulatory Activities, version 22.1 (MedDRA version 22.1).",,,,,,
+65798120,NCT01572038,primary,Time to Onset of the First Episode of Congestive Heart Failure,From Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,Congestive heart failure was defined as SMQ 'Cardiac failure (wide)' from the MedDRA version 22.1. Time to onset of the first episode of congestive heart failure was analyzed using a Kaplan-Meier approach. Participants who did not experience any congestive heart failure at the time of data-cut were censored at the date of the last attended visit whilst on-treatment (including visits up to and including 28 days after last dose of study treatment). Only treatment emergent congestive heart failure events are included.,,,,,,
+65798121,NCT01572038,primary,Change From Baseline in Left Ventricular Ejection Fraction (LVEF) Values Over the Course of the Study,"Baseline, predose on Day 1 of every 3 cycles (1 cycle is 3 weeks) during treatment period, and 28 days post-treatment safety follow-up. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,"All participants must have had a baseline LVEF ≥50% to enroll in the study; patients with significant cardiac disease or baseline LVEF below 50% were not eligible for this study. The change from baseline LVEF values were reported at every 3 cycles over the course of the study and at the final treatment, worst treatment, and maximum decrease values. The final treatment value was defined as the last LVEF value observed before all study treatment discontinuation. The worst treatment value was defined as the lowest LVEF value observed before all study treatment discontinuation. The maximum decrease value was defined as the largest decrease of LVEF value from baseline, or minimum increase if a participant's post-baseline LVEF measures were all larger than the baseline value.",,,,,,
+65798122,NCT01572038,primary,Number of Participants by Change From Baseline in Left Ventricular Ejection Fraction (LVEF) Categories Over the Course of the Study,"Baseline, predose on Day 1 of every 3 cycles (1 cycle is 3 weeks) during treatment period, and 28 days post-treatment safety follow-up. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.",,All participants must have had a baseline LVEF greater than or equal to (≥)50% to enroll in the study, patients with significant cardiac disease or baseline LVEF below 50% were not eligible for this study. The number of participants are reported according to four change from baseline in LVEF value categories over the course of the study: 1) an increase or decrease from baseline LVEF less than (<)10% points or no change in LVEF, 2) an absolute LVEF value <45% points and a decrease from baseline LVEF ≥10% points to <15% points, 3) an absolute LVEF value <45% points and a decrease from baseline LVEF ≥15% points, or 4) an absolute LVEF value ≥45% points and a decrease from baseline LVEF ≥10% points. BL = baseline, Decr. = decrease, Incr. = increase
+65798123,NCT01572038,primary,Number of Participants With Laboratory Abnormalities in Hematology and Coagulation Parameters: Shift From Baseline to the Worst Post-Baseline Grade According to NCI-CTC v4.0,Predose at each treatment cycle (1 cycle is 3 weeks) from Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,"Clinical laboratory tests for hematology and coagulation parameters were performed at local laboratories. Laboratory toxicities were defined based on NCI-CTC v4.0 from Grades 1 (least severe) to 4 (most severe). Some laboratory parameters are bi-dimensional (i.e. can be graded in both the low and high direction). These parameters were split and presented in both directions. Baseline was defined as the last non-missing measurement taken prior to the first dose of study treatment (including unscheduled assessments). Values from all visits, including unscheduled visits, were included in the derivation of the worst post-baseline grade. Not every abnormal laboratory value qualified as an adverse event, only if it met any of the following criteria: was clinically significant (per investigator); was accompanied by clinical symptoms; resulted in a change in study treatment; or resulted in a medical intervention or a change in concomitant therapy.",,,,,,
+65798124,NCT01572038,primary,Number of Participants With Laboratory Abnormalities in Hematology and Coagulation Parameters: Shift From Baseline to the Worst Post-Baseline Grade According to Normal Range Criteria,Predose at each treatment cycle (1 cycle is 3 weeks) from Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,"Clinical laboratory tests for hematology and coagulation parameters were performed at local laboratories. Laboratory toxicities were defined based on local laboratory normal ranges (for parameters with NCI-CTC grade not defined). Some laboratory parameters are bi-dimensional (i.e. can be graded in both the low and high direction). These parameters were split and presented in both directions. Baseline was defined as the last non-missing measurement taken prior to the first dose of study treatment (including unscheduled assessments). Values from all visits, including unscheduled visits, were included in the derivation of the worst post-baseline grade. Not every abnormal laboratory value qualified as an adverse event, only if it met any of the following criteria: was clinically significant (per investigator); was accompanied by clinical symptoms; resulted in a change in study treatment; or resulted in a medical intervention or a change in concomitant therapy.",,,,,,
+65798125,NCT01572038,primary,Number of Participants With Laboratory Abnormalities in Biochemistry Parameters: Shift From Baseline to the Worst Post-Baseline Grade According to NCI-CTC v4.0,Predose at each treatment cycle (1 cycle is 3 weeks) from Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,"Clinical laboratory tests for biochemistry parameters were performed at local laboratories. Laboratory toxicities were defined based on NCI-CTC v4.0 from Grades 1 (least severe) to 4 (most severe). Some laboratory parameters are bi-dimensional (i.e. can be graded in both the low and high direction). These parameters were split and presented in both directions. Baseline was defined as the last non-missing measurement taken prior to the first dose of study treatment (including unscheduled assessments). Values from all visits, including unscheduled visits, were included in the derivation of the worst post-baseline grade. Not every abnormal laboratory value qualified as an adverse event, only if it met any of the following criteria: was clinically significant (per investigator); was accompanied by clinical symptoms; resulted in a change in study treatment; or resulted in a medical intervention or a change in concomitant therapy.",,,,,,
+65798126,NCT01572038,primary,Number of Participants With Laboratory Abnormalities in Biochemistry Parameters: Shift From Baseline to the Worst Post-Baseline Grade According to Normal Range Criteria,Predose at each treatment cycle (1 cycle is 3 weeks) from Baseline until 28 days after the last dose of study treatment. The median (full range) duration of exposure to any study treatment was 16.2 (0.0-86.4) months.,,"Clinical laboratory tests for biochemistry parameters were performed at local laboratories. Laboratory toxicities were defined based on local laboratory normal ranges (for parameters with NCI-CTC grade not defined). Some laboratory parameters are bi-dimensional (i.e. can be graded in both the low and high direction). These parameters were split and presented in both directions. Baseline was defined as the last non-missing measurement taken prior to the first dose of study treatment (including unscheduled assessments). Values from all visits, including unscheduled visits, were included in the derivation of the worst post-baseline grade. Not every abnormal laboratory value qualified as an adverse event, only if it met any of the following criteria: was clinically significant (per investigator); was accompanied by clinical symptoms; resulted in a change in study treatment; or resulted in a medical intervention or a change in concomitant therapy.",,,,,,
+65797515,NCT01578499,primary,Percentage of Participants Achieving an Objective Response That Lasts at Least 4 Months (ORR4),"Each Cycle until disease progression, death End of treatment (Median overall follow-up 38.8 months)",,"ORR4 was determined by an Independent Review Facility (IRF) based on Global Response Score (GRS) which consisted of a skin assessment by the investigator using the modified severity-weighted assessment tool (mSWAT), nodal and visceral radiographic assessment by an IRF and for the participants with mycosis fungoides (MF) only, detection of circulation Sezary cells. Participants whose first response occurred after the start of subsequent anticancer therapy were excluded. Response Criteria was based on International Society for Cutaneous Lymphomas (ISCL), United States Cutaneous Lymphoma Consortium (USCLC) and Cutaneous Lymphoma Task Force (CLTF) of the European Organisation for Research and Treatment of Cancer (EORTC) Consensus guidelines (Olsen, 2011).",,,,,,
+65795896,NCT01597908,primary,Overall Survival (OS),From the date of randomization until date of death due to any cause (up to approximately 6 years),,"Overall Survival (OS) was defined as the interval of time between the date of randomization and the date of death due to any cause. For patients who did not die, OS was censored at the date of last contact.",,,,,,
+65794590,NCT01610284,primary,"Progression Free Survival (PFS) Based on Local Investigator Assessment - Full Analysis Set (FAS) in Full Population, Main Study Cohort and PI3K Unknown Cohort","Date of randomization to the date of first documented tumor progression or death from any cause, whichever occurs first, reported between day of first patient randomized up to approximately 4 years",,"Progression Free Survival (PFS) is defined as the time from date of randomization to the date of first radiologically documented progression or death due to any cause. If a patient did not progress or die at the time of the analysis data cut-off or start of new antineoplastic therapy, PFS was censored at the date of the last adequate tumor assessment before the earliest of the cut-off date or the start date of additional anti-neoplastic therapy. Progression is defined using Response Evaluation Criteria In Solid Tumors Criteria RECIST v1.1, as 20% increase in the sum of diameter of all measured target lesions, taking as reference the smallest sum of diameter of all target lesions recorded at or after baseline and/or unequivocal progression of the non-target lesions and/or appearance of a new lesion. In addition to the relative increase of 20%, the sum must demonstrate an absolute increase of at least 5 mm.",,,,,,
+65792502,NCT01633060,primary,Progression Free Survival (PFS) Based on Local Investigator Assessment - Full Analysis Set (FAS),Every 6 weeks after randomization up to a maximum of 4 years,,"Progression Free Survival (PFS) is defined as the time from date of randomization to the date of first radiologically documented progression or death due to any cause. If a patient did not progress or die at the time of the analysis data cut-off or start of new antineoplastic therapy, PFS was censored at the date of the last adequate tumor assessment before the earliest of the cut-off date or the start date of additional anti-neoplastic therapy. Progression is defined using Response Evaluation Criteria In Solid Tumors Criteria RECIST v1.1, as 20% increase in the sum of diameter of all measured target lesions, taking as reference the smallest sum of diameter of all target lesions recorded at or after baseline and/or unequivocal progression of the non-target lesions and/or appearance of a new lesion. In addition to the relative increase of 20%, the sum must demonstrate an absolute increase of at least 5 mm. Patients were followed up for approximately every 6 weeks after randomization.",,,,,,
+65791562,NCT01642004,primary,Overall Survival (OS) Time in Months for All Randomized Participants at Primary Endpoint,"Randomization until 199 deaths, up to November 2014, approximately 25 months",,"OS was defined as the time between the date of randomization and the date of death from any cause. Participants were censored at the date they were last known to be alive. Median OS time was calculated using Kaplan-Meier (KM) method. Hazard ratio (HR) and the corresponding Confidence Interval (CI) were estimated in a stratified Cox proportional hazards model for distribution of OS in each randomized arm. Interim analysis (Primary Endpoint) was planned to occur after at least 196 deaths, with the actual analysis occurring at 199 deaths.",,,,,,
+65791563,NCT01642004,primary,Overall Survival (OS) Rate in All Randomized Participants,"Randomization to 18 months post-randomization, up to June 2015",,"The overall survival rate is the probability that a participant will be alive at 6, 12, and 18 months following randomization. Overall survival was defined as the time between the date of randomization and the date of death as a result of any cause. Survival rates were determined via Kaplan-Meier estimates.",,,,,,
+65791564,NCT01642004,primary,Number of Deaths From Any Cause in All Randomized Participants at Primary Endpoint,"Randomization until 199 deaths, up to November 2014, approximately 25 months",,"The number of participants who died from any cause was reported for each arm. Interim analysis (Primary Endpoint) was planned to occur after at least 196 deaths, with the actual analysis occurring at 199 deaths.",,,,,,
+65791148,NCT01646021,primary,Progression Free Survival (PFS),"Time from the date of randomization until the date of first documented evidence of progressive disease (or relapse for subjects who experience CR during the study) or death, whichever occurred first (approximately 48 months)",,"PFS is defined as the duration in months from the date of randomization to the date of progression disease (PD) or relapse from complete response (CR) or death whichever was reported first and was assessed based on the investigator assessment. Revised Response Criteria for Malignant Lymphoma categorizes the response of the treatment of a patient's tumour to CR (the disappearance of all evidence of disease), Relapsed Disease or PD (Any new lesion or increase by greater than or equal to [>=] 50 percent [%] of previously involved sites from nadir).",,,,,,
+65789596,NCT01663623,primary,Time to First Relapse,Approximately up to 4 years,,Time to relapse is defined as the number of days from Day 0 until the participant experienced a relapse (relapse date - treatment start date +1). Only post-baseline relapses were considered in these analyses. Only relapses occurring up to and including the last visit date in the double-blind treatment period were considered in these analyses. Intent-to-treat population comprised of all randomized participants who received at least one dose of study agent (belimumab or placebo). NA indicates that the data was not available as the Number of events is too low to estimate the value. Median and Inter-quartile range were presented and were based on Kaplan Meier estimates.,,,,,,
+64158296,NCT01673867,primary,Overall Survival (OS) Time in Months for All Randomized Participants at Primary Endpoint,"Randomization until 413 deaths, up to March 2015 (approximately 29 months)",,"OS was defined as the time between the date of randomization and the date of death from any cause. Participants were censored at the date they were last known to be alive. Median OS time was calculated using Kaplan-Meier (KM) method. Hazard ratio (HR) and the corresponding Confidence Interval (CI) were estimated in a stratified Cox proportional hazards model for distribution of OS in each randomized arm. Interim analysis (Primary Endpoint) was planned to occur after at least 380 deaths, with the actual analysis occurring at 413 deaths.",,,,,,
+64158297,NCT01673867,primary,One-year Overall Survival (OS) Rate in All Randomized Participants,12 months,,"The one-year overall survival rate is a percentage, representing the fraction of all randomized participants who were alive following one year of treatment. Overall survival was defined as the time between the date of randomization and the date of death as a result of any cause. Survival rates were determined via Kaplan-Meier estimates.",,,,,,
+64158298,NCT01673867,primary,Number of Deaths From Any Cause in All Randomized Participants at Primary Endpoint,"Randomization until 413 deaths, up to March 2015 (approximately 29 months)",,"The number of participants who died from any cause was reported for each arm. Interim analysis (Primary Endpoint) was planned to occur after at least 380 deaths, with the actual analysis occurring at 413 deaths.",,,,,,
+65784565,NCT01713946,primary,Core Phase: European Medicine Agency (EMA): Seizure Frequency Response Rate,"Baseline (8-week period before randomization), Week 7 to 18 (12-week maintenance period of the core phase)",,"Comparison of response rates in the everolimus low-trough treatment arm (3-7 ng/mL), high-trough treatment arm (9-15 ng/mL) and placebo arm. Response means at least a 50% reduction from baseline in partial-onset seizure frequency during the maintenance period of the core phase.",,,,,,
+65784566,NCT01713946,primary,Core Phase: Food & Drug Administration (FDA): Percentage Change From Baseline in Partial Onset-seizure Frequency,"Baseline (8-week period before randomization), Week 7 to 18 (12-week maintenance period of the core phase)",,"Comparison of median percent change from baseline in weekly seizure frequency in the everolimus low-trough treatment arm (3-7 ng/mL), high-trough treatment arm (9-15 ng/mL) and placebo arm during maintenance period of the core phase. Percentage change from baseline in average weekly seizure frequency during the maintenance period of the Core phase (SFcfb) = 100 × (SFB - SFM) ÷ SFB where:
+
+SFB is the average weekly seizure frequency in the Baseline phase SFM is the average weekly seizure frequency in the maintenance period of the Core phase A positive percentage change from baseline (SFcfb) means a reduction in seizure frequency whereas a negative percentage change from baseline (SFcfb) means an increase in seizure frequency.",,,,,,
+65783857,NCT01721772,primary,Overall Survival (OS),"From date of randomization to date of death. For those without documentation of death, to the last date the participant was known to be alive, assessed up to 17 months.",,OS is defined as the time between the date of randomization and the date of death or the last date the participant was known to be alive.,,,,,,
+65783858,NCT01721772,primary,Overall Survival (OS) Rate,From randomization to 6 months and or to 12 months,,OS rate is calculated as the percentage of participants alive at the indicated timepoints,,,,,,
+65782873,NCT01732913,primary,Progression Free Survival,,,Progression-free survival (PFS) is defined as the interval from randomization to the earlier of the first documentation of definitive indolent non-Hodgkin lymphoma (iNHL) disease progression or death from any cause. PFS was to be assessed by an independent review committee (IRC).,,,,,,
+65782868,NCT01732926,primary,Progression-free Survival (PFS),,,PFS is defined as the interval from randomization to the earlier of the first documentation of definitive indolent non-Hodgkin lymphomas (iNHL) disease progression or death from any cause. Definitive iNHL disease progression is progression based on standard criteria. PFS was to be assessed by an independent review committee (IRC).,,,,,,
+65781700,NCT01747915,primary,Log-transformed (Log) 28-day Seizure Rate for All Primary Generalized Tonic-Clonic (PGTC) Seizures During 12-Week Double-Blind Treatment Phase,Day 1 up to Week 12,,"All PGTC seizures experienced during treatment phase were recorded by the participants or their parents/legal guardian in a daily seizure diary. 28-day seizure rate for all PGTC seizures= ([number of seizures in the double blind treatment phase] divided by [number of days in double blind treatment phase minus {-} number of missing diary days in treatment phase])*28. For log-transformation, the quantity 1 was added to the 28-day seizure rate for all participants to account for any possible ""0"" seizure incidence. This resulted in final calculation as: log transformed (28-day seizure rate +1).",,,,,,
+65780474,NCT01764841,primary,Time to First Exacerbation Event Within 48 Weeks,Up to Week 48,,Time to first exacerbation was defined as the time from randomization until the visit at which the first qualifying exacerbation is recorded by the investigator. Exacerbation events are defined as exacerbations with systemic antibiotic use and presence of fever or malaise / fatigue and worsening of at least three signs/symptoms.,,,,,,
+65776795,NCT01808118,primary,Number of Participants Who Did Not Experience a Flare During Period 2 by Week 68,From Week 28 through 68,,"The Ankylosing Spondylitis Disease Activity Score (ASDAS) tool is a self-administered questionnaire/objective laboratory evaluation. The questionnaire assesses disease activity, back pain, and peripheral pain/swelling on a numeric rating scale (from 0 (normal) to 10 (very severe)) and duration of morning stiffness on a numeric rating scale (from 0 to 10, with 0 being none and 10 representing a duration of ≥2 hours). The laboratory parameter is a measurement of high-sensitivity C-reactive protein (mg/L) (hs-CRP). Data from five variables (disease activity, back pain, duration of morning stiffness, peripheral pain/swelling, and hs-CRP) are combined to yield a score (0 to no defined upper limit). During Period 2 participants visited study sites at Weeks 28, 32, 36, 40, 44, 48, 52, 56, 60, 64 and 68 or if they discontinued early from the study. A flare was defined as having any 2 consecutive study visits with ASDAS ≥ 2.100.",,,,,,
+65776714,NCT01808573,primary,Centrally Assessed Progression Free Survival,"From randomization date to recurrence, progression or death, assessed up to 38 months. The result is based on primary analysis data cut.",,"Progression Free Survival (PFS), Measured in Months, for Randomized Subjects of the Central Assessment. The time interval from the date of randomization until the first date on which recurrence, progression (per Response Evaluation Criteria in Solid Tumors Criteria (RECIST) v1.1), or death due to any cause, is documented. For subjects without recurrence, progression or death, it is censored at the last valid tumor assessment. Progression is defined using Response Evaluation Criteria in Solid Tumors Criteria (RECIST v1.1), as a 20% increase in the sum of the longest diameter of target lesions, or a measurable increase in a non-target lesion, or the appearance of new lesions. Here, the time to event was reported as the restricted mean survival time. The restricted mean survival time was defined as the area under the curve of the survival function up to 24 months.",,,,,,
+65776715,NCT01808573,primary,Overall Survival,"From randomization date to death, assessed up to 59 months.The result is based on primary analysis data cut.",,"Overall survival (OS) is defined as the time from randomization to death due to any cause, censored at the last date known alive on or prior to the data cutoff employed for the analysis, whichever was earlier. Here, the time to event was reported as the restricted mean survival time. The restricted mean survival time was defined as the area under the curve of the survival function up to 48 months.",,,,,,
+65775940,NCT01819129,primary,Change From Baseline in HbA1c,"Week 0, Week 26",,"The primary endpoint was change from baseline in HbA1c after 26 weeks of randomized treatment. For this endpoint baseline (week 0) and week 26 have been presented, where week 26 data is end of trial containing last available measurement.",,,,,,
+65772551,NCT01866319,primary,Progression-free Survival (PFS) According to Response Evaluation Criteria In Solid Tumors Version 1.1 (RECIST 1.1) as Assessed by Independent Radiology Plus Oncology Review (IRO),Up to approximately 12 months (through first pre-specified statistical analysis cut-off date of 03-Sep-2014),,"PFS was defined as the time from randomization to the first documented disease progression, based on blinded Independent Radiology plus Oncology review (IRO) using RECIST 1.1, or death due to any cause, whichever occurred first. Disease progression was defined as a 20% or greater increase in the sum of diameters of target lesions with an absolute increase of at least 5 mm or the appearance of new lesions. The primary analysis of PFS was performed at the time of the first protocol pre-specified statistical analysis, with data cut-off of 03-Sep-2014.",,,,,,
+65772552,NCT01866319,primary,Percentage of Participants With Overall Survival (OS) at 12 Months,Month 12,,"OS was defined as the time from randomization to death due to any cause. The percentage of participants with OS (OS rate) at 12 months was reported for each arm. The reported percentage was estimated using a product-limit (Kaplan-Meier) method for censored data; data were censored at the date of cut-off. The primary analysis of OS was performed at the time of the second protocol pre-specified statistical analysis, with data cut-off of 03-Mar-2015.",,,,,,
+65770619,NCT01891890,primary,Conners' Continuous Performance Test II (CPT-II) Confidence Index,"Baseline, Month 6",,"The Conners' Continuous Performance Test II (CPT-II) is a measure of sustained attention. Letters are individually presented on a computer screen, and participants are instructed to press the space bar when they are presented with any letter except the letter ""X"". For children younger than 6 years of age at enrollment, the Kiddie CPT will be used in which the child is instructed to press the space bar every time the ball appears on the screen. The outcome measure is a confidence index representing the probability that the respondent has a clinically relevant problem in sustained attention. Possible scores range from 0 to 100. Scores between 40 and 60 are considered inconclusive while scores above 60 indicate that the child exhibits inattentiveness.",,,,,,
+65769554,NCT01905592,primary,Progression Free Survival (PFS) - Central Review Assessment,"From the date of randomization to the date of disease progression or death due to any cause, whichever occurs earlier, up to 4 years",,"The primary objective of this study is to compare progression-free survival (PFS), as assessed by blinded central review, of participants with advanced/metastatic human epidermal growth factor receptor 2 (HER2)-negative gBRCA mutation breast cancer when treated with niraparib as compared to those treated with physician's choice single agent chemotherapy standards (eribulin, vinorelbine, gemcitabine or capecitabine). PFS is defined as the date of randomization to the date of disease progression or death due to any cause, whichever occurs earlier as per Response evaluation criteria in solid tumors (RECIST) version (v)1.1 as determined by central review assessment. Progressive Disease is defined as at least a 20 percent (%) increase in the sum of diameters of measured lesions taking as references the smallest sum of diameters recorded on study (including Baseline) and an absolute increase of >= 5 millimeter (mm).",,,,,,
+65769319,NCT01908829,primary,Change From Baseline to End of Treatment (EoT) in Mean Number of Incontinence Episodes Per 24 Hours,Baseline and end of treatment (up to 12 weeks),,"The mean number of incontinence episodes (complaint of any involuntary leakage of urine) per day was derived from number of incontinence episodes recorded on valid diary days during the 3-day micturition diary period divided by the number of valid diary days during the 3-day micturition diary period. The analysis population consisted of the Full Analysis Set (FAS) which comprised of all the Randomized Analysis Set's (RAS) participants who met the following criteria: took at least 1 dose of double-blind study drug after randomization, reported at least 1 micturition in the baseline diary & at least 1 micturition postbaseline & reported at least 1 incontinence episode in the baseline diary. For participants who withdrew before EoT (week 12) and have no measurement available for that diary period, the Last Observation Carried Forward (LOCF) value during the double-blind study period was used as EoT value to derive the primary variable.",,,,,,
+65768317,NCT01920477,primary,Number of Subjects Who Experienced Sustained Remission on Minimal Steroid Therapy,Baseline up to approximately 60 weeks,,Sustained remission = time from randomization to the time of the subject's initial reduction of prednisone/prednisolone dose to <=10 mg/day and maintenance of a dose <=10 mg/day with no new or nonhealing lesions for >=8 weeks and maintenance of the status until Week 60.,,,,,,
+65768318,NCT01920477,primary,Duration of Remission on Minimal Steroid Therapy,Baseline up to approximately 60 weeks,,Sum of all periods of absence of new or nonhealing lesions while on an oral prednisone/prednisolone dose of <=10 mg/day up to Week 60 was assessed.,,,,,,
+65768118,NCT01922011,primary,"Percentage of Participants With Clinical Improvement in the 3 General Categories of Pain, Inflammation, and Limb Function Based on the Investigator's Overall Assessment of Severity of Each of the Symptom Categories.",Up to study Day 5,,"Clinical improvement was based on the Investigator's overall assessment of severity of each of the 3 general symptom categories of Pain, Inflammation, and Limb Function. Based on this evaluation, a participant was considered to have met criteria for clinical improvement according to the following definition: If 3 general categories are present at baseline: at least a 1-point improvement (i.e. severe to moderate, moderate to mild, mild to absent) in at least 2 of the general categories and no worsening in the other. If 2 general categories are present at baseline: at least a 2-point improvement (i.e. severe to mild, moderate to absent) in at least 1 of the general categories and no worsening or new findings in the others OR at least a 1-point improvement in both and no new findings in the other. If 1 general category is present at baseline: at least a 2-point improvement (i.e., severe to mild, moderate to absent) in that category and no new findings in the others.",,,,,,
+65765979,NCT01940497,primary,Percentage of Participants With Treatment-Emergent Adverse Events (TEAEs),Day 1 up to 28 days after last dose of trastuzumab (up to approximately 1 year),,An AE was any untoward medical occurrence in a participant who received study drug without regard to possibility of causal relationship. TEAEs were the AEs occurring from starting on the day of or after first administration of trastuzumab and within 28 days after last dose of trastuzumab. Data for this outcome measure were analyzed and reported by adjuvant versus neoadjuvant chemotherapy groups within each treatment arm.,,,,,,
+65764383,NCT01958671,primary,Change From Baseline In A1C at Week 26,Baseline and Week 26,,A1C is measured as percent. The change from baseline is the Week 26 A1C percent minus the Week 0 A1C percent. Laboratory measurements were performed after an overnight fast ≥10 hours in duration. Data presented exclude data following the initiation of rescue therapy.,,,,,,
+65764384,NCT01958671,primary,Percentage of Participants Experiencing An Adverse Event (AE),Up to 54 weeks (including 2 weeks following last dose),,An AE is defined as any untoward medical occurrence in a patient or clinical investigation participant administered a pharmaceutical product and which does not necessarily have to have a causal relationship with this treatment. Data presented include data following the initiation of rescue therapy.,,,,,,
+65764385,NCT01958671,primary,Percentage of Participants Discontinuing Study Treatment Due to an AE,Up to 52 weeks,,An AE is defined as any untoward medical occurrence in a patient or clinical investigation participant administered a pharmaceutical product and which does not necessarily have to have a causal relationship with this treatment. Data presented include data following the initiation of rescue therapy.,,,,,,
+65764000,NCT01962441,primary,Percentage of Participants With Sustained Virologic Response (SVR) 12 Weeks After Discontinuation of Therapy (SVR12),Posttreatment Week 12,,"SVR12 was defined as HCV RNA < the lower limit of quantitation (LLOQ; ie, 15 IU/mL) at 12 weeks after stopping study treatment.",,,,,,
+65764001,NCT01962441,primary,Percentage of Participants Who Permanently Discontinued Any Study Drug Due to an Adverse Event,Up to 24 weeks,,,,,,,,
+65763600,NCT01967940,primary,Part 1: Percentage of Participants With Plasma HIV-1 RNA Decreases From Baseline Exceeding 0.5 log10 at Day 10,Day 10,,,,,,,,
+65762716,NCT01976364,primary,Percentage of Participants With Treatment-Emergent Adverse Events (AEs) and Serious Adverse Events (SAEs),Date of first dose of study medication up to 48 months (36 months of main study and 12 months of sub-study),,An AE was any untoward medical occurrence in a participant who received study drug without regard to possibility of causal relationship. SAE was an AE resulting in any of the following outcomes or deemed significant for any other reason: death, initial or prolonged inpatient hospitalization, life-threatening experience (immediate risk of dying), persistent or significant disability/incapacity, congenital anomaly. Treatment-emergent were events between first dose of study drug and up to 48 months that were absent before treatment or that worsened relative to pretreatment state. AEs included both serious and non-serious AEs.,,
+65762717,NCT01976364,primary,Number of Adverse Events (AEs) by Severity,Date of first dose of study medication up to 48 months (36 months of main study and 12 months of sub-study),,"An AE was any untoward medical occurrence attributed to study drug in a participant who received study drug. AEs were classified into 3 categories according to their severity as mild AEs (did not interfere with participant's usual function), moderate AEs (interfered to some extent with participant's usual function) and severe AEs (interfered significantly with participant's usual function).",,,,,,
+65762718,NCT01976364,primary,Number of Participants With Abnormal Clinical Laboratory Values,Date of first dose of study medication up to 48 months (36 months of main study and 12 months of sub-study),,"Laboratory tests: hematology (Hb, hematocrit, RBC count, platelets, reticulocytes, WBC count, count and absolute lymphocytes,neutrophils, basophils, eosinophils, monocytes. Liver function (bilirubin [total, direct, indirect], AST, ALT, alkaline phosphatase, gamma-glutamyl transferase, albumin, total protein), renal function (blood urea nitrogen, creatinine), Lipids (cholesterol, HDL, LDL, triglyceride, apolipoprotein [A-1, B]), electrolytes (sodium, potassium, chloride, calcium, biocarbonate), chemistry (glucose, HbA1c, creatinine kinapse), urinalysis dipstick(urine pH, glucose, ketones, protein, blood, leukocyte, esterase), urinalysis microscopy (urine- RBC, WBC, bacteria, epithelial cells),C-reactive protein. Laboratory abnormality: determined by investigator per pre-defined criteria.",,,,,,
+65762719,NCT01976364,primary,Number of Participants With Clinically Significant Change From Baseline in Clinical Laboratory Values,Date of first dose of study medication (Baseline) up to 48 months (36 months of main study and 12 months of sub-study),,"Laboratory tests: hematology (Hb, hematocrit, RBC count, platelets, reticulocytes, WBC count, count and absolute lymphocytes, neutrophils, basophils, eosinophils, monocytes. Liver function (bilirubin[total,direct,indirect], AST, ALT, alkaline phosphatase, gamma-glutamyl transferase, albumin, total protein), renal function (blood urea nitrogen, creatinine), Lipids(cholesterol, HDL, LDL, triglyceride, apolipoprotein [A-1, B]), electrolytes (sodium, potassium, chloride, calcium, biocarbonate), chemistry (glucose, HbA1c, creatinine kinapse), urinalysis dipstick(urine-pH, glucose, ketones, protein, blood, leukocyte, esterase), urinalysis microscopy(urine- RBC, WBC, bacteria, epithelial cells),C-reactive protein. Clinically significant change: determined by investigator per pre-defined criteria.",,,,,,
+65762720,NCT01976364,primary,Sub-study: Change From Baseline in Health Assessment Questionnaire - Disability Index (HAQ-DI) Score at Month 6,"Sub-study: Baseline (Day 1), Month 6",,"HAQ-DI assessed the degree of difficulty a participant had experienced during the past week in 8 domains of daily living activities: dressing/grooming, arising, eating, walking, reach, grip, hygiene, and other activities. There were total of 2-3 items distributed in each of these 8 domains. Each item was scored for level of difficulty on a 4-point scale from 0 to 3: 0= no difficulty; 1= some difficulty; 2= much difficulty; 3= unable to do. Overall score was computed as the sum of domain scores and divided by the number of domains answered. Total possible HAQ-DI score ranged from 0 (least difficulty) to 3 (extreme difficulty), where higher score indicated more difficulty while performing daily living activities.",,,,,,
+65762721,NCT01976364,primary,Sub-study: Change From Baseline in Psoriatic Arthritis Disease Activity Score (PASDAS) at Month 6,"Sub-study: Baseline (Day 1), Month 6",,"PASDAS was composite PsA disease activity score that included following components: Physician and patient global assessment of disease activity (assessed on a 0-100 VAS) in millimeter (mm), swollen (66 joints) and tender joint counts (68 joints), Leeds enthesitis index (enthesitis assessed at 6 sites; total score of 0-6), tender dactylitic digit score (scored on a scale of 0-3, where 0= no tenderness and 3= extreme tenderness), short form-36 questionnaire (SF-36) physical component summary (norm-based domain scores were used in analyses; with a population mean of 50 with a SD of 10 points, and ranges from minus infinity to plus infinity) and C-reactive protein (CRP) in milligram per liter (mg/L). PASDAS was composite score and was a weighted index with score range of 0 to 10, where higher score indicated more severe disease.",,,,,,
+65761723,NCT01987479,primary,Percentage of Participants With Adverse Events,Baseline up to Week 32,,An adverse event was any untoward medical occurrence in a participant who received study drug without regard to possibility of causal relationship. Adverse events included serious as well as non-serious adverse events.,,,,,,
+65761714,NCT01987505,primary,Percentage of Participants With Administration-Associated Reactions (AARs),From start of treatment to end of treatment (up to 32 months),,"AARs were defined as all adverse events (AEs) occurring within 24 hours of rituximab SC administration and which were considered related to study drug. AARs included infusion/injection-related reactions (IIRRs), injection-site reactions, administration site conditions and all symptoms thereof. Grading was completed according to the National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events (CTCAE), version 4.0.",,,,,,
+65760039,NCT02008227,primary,Percentage of Participants Who Died: PP-ITT,Baseline until death due to any cause (up to approximately 2.25 years),,,,,,,,
+65760040,NCT02008227,primary,Percentage of Participants Who Died: Tumor Cells (TC)1/2/3 or Tumor-Infiltrating Immune Cells (IC)1/2/3 Subgroup of PP,Baseline until death due to any cause (up to approximately 2.25 years),,"Percentage of participants who died among TC1/2/3 or IC1/2/3 subgroup of PP-ITT were reported. TC1 = presence of discernible programmed death-ligand 1 (PD-L1) staining of any intensity in >/=1% and <5% TCs; TC2: presence of discernible PD-L1 staining of any intensity in >/=5% and <50% TCs; TC3 = presence of discernible PD-L1 staining of any intensity in >/=50% TCs; IC1 = presence of discernible PD-L1 staining of any intensity in ICs covering between >/=1% and <5% of tumor area occupied by tumor cells, associated intratumoral, and contiguous peri-tumoral desmoplastic stroma; IC2 = presence of discernible PD-L1 staining of any intensity in ICs covering between >/=5% and <10% of tumor area occupied by tumor cells, associated intratumoral, and contiguous peri-tumoral desmoplastic stroma; IC3 = presence of discernible PD-L1 staining of any intensity in ICs covering >/=10% of tumor area occupied by tumor cells, associated intratumoral, and contiguous peri-tumoral desmoplastic stroma.",,,,,,
+65760041,NCT02008227,primary,Overall Survival (OS): PP-ITT,Baseline until death due to any cause (up to approximately 2.25 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65760042,NCT02008227,primary,OS: TC1/2/3 or IC1/2/3 Subgroup of PP,Baseline until death due to any cause (up to approximately 2.25 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65760043,NCT02008227,primary,OS: SP-ITT,Baseline until death due to any cause (up to approximately 2.87 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65760044,NCT02008227,primary,OS: TC1/2/3 Or IC1/2/3 Subgroup of SP,Baseline until death from any cause (approximately 2.87 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65760045,NCT02008227,primary,OS: TC2/3 or IC2/3 Subgroup of SP,Baseline until death due to any cause (up to approximately 2.87 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65760046,NCT02008227,primary,OS: TC3 or IC3 Subgroup of SP,Baseline until death due to any cause (up to approximately 2.87 years),,OS duration is defined as the difference in time from the date of randomization to the date of death due to any cause. Data for participants who were not reported as having died at the time of analysis were censored at the date they were last known to be alive. Participants who had no post-baseline information were censored at the date of randomization plus 1 day. OS was estimated using KM methodology.,,,,,,
+65759081,NCT02019420,primary,Number of Participants With All-Cause Mortality in the Intent-to-Treat (ITT) Population,Up to 28 days,,The numbers of participants with all-cause mortality within 28 days after randomization was determined in the ITT population. Any participants who were lost to follow-up and not known to be alive or deceased by Day 28 were imputed as deceased.,,,,,,
+64619564,NCT02032277,primary,Pathological Complete Response (pCR).,At the time of definitive surgery (approximately 24-36 weeks from first dose of study drug).,,Pathological complete response (pCR) in the breast tissue and the lymph node tissue will be assessed upon completion of pre-operative systemic therapy and definitive surgery.,,,,,,
+65757541,NCT02038920,primary,Induction Phase: Percentage of Participants With Crohn's Disease Activity Index (CDAI)-100 Response,Week 10,,"A response to therapy is considered a decrease from baseline of at least 100 points in the CDAI score at Week 10. CDAI is scoring system for the assessment of Crohn's disease activity. The total CDAI score ranges from 0 to approximately 600, where higher scores indicate more severe disease. Index values of 150 and below are associated with quiescent disease; values above that indicate active disease.",,,,,,
+65757542,NCT02038920,primary,Maintenance Phase: Percentage of Participants With Clinical Remission,Week 60,,Clinical remission is defined as the CDAI score ≤150. CDAI is scoring system for the assessment of Crohn's disease activity. Index values of 150 and below are associated with quiescent disease, values above that indicate active disease.,,,,,
+65757543,NCT02038920,primary,Number of Participants Who Experienced at Least One or More Treatment-Emergent Adverse Events (TEAEs),From Baseline up to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"An Adverse event (AE) is defined as any untoward medical occurrence in a study participant who received a drug (including a study drug); it does not necessarily have to have a causal relationship with this treatment. An AE can therefore be any unfavorable and unintended sign (e.g., a clinically significant abnormal laboratory finding), symptom, or disease temporally associated with the use of a drug whether or not it is considered related to the drug. A TEAE is defined as an adverse event with an onset that occurs after receiving study drug.",,,,,,
+65757544,NCT02038920,primary,Number of Participants With TEAE Related to Body Weight (Weight Decreased),From Baseline up to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"Reported events on this outcome measure were ""Weight Decreased"".",,,,,,
+65757545,NCT02038920,primary,Number of Participants With TEAE Related to Vital Signs,From Baseline up to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"Vital signs included body temperature (axilla), sitting blood pressure (after the participant has rested for at least 5 minutes), and pulse (bpm). Reported events on this outcome measure were ""Pyrexia"", ""Body temperature increased"", ""Hypertension"", and ""Orthostatic hypotension"".",,,,,,
+65757546,NCT02038920,primary,Number of Participants With TEAE Related to Electrocardiogram (ECG) [Bundle Branch Block Right],From Baseline up to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"Reported events on this outcome measure were ""Bundle Branch Block Right"".",,,,,,
+65757547,NCT02038920,primary,Number of Participants With Markedly Abnormal Values of Laboratory Parameters Values,From Baseline up to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"The laboratory values outside the range (Hemoglobin <=7 g/dL, Lymphocytes <500 /microL, White Blood Cell (WBC) <2000 /microL, Platelets <7.5 10^4/microL, Neutrophils <1000 /microL, Alanine Aminotransferase (ALT) (Glutamic Pyruvic Transaminase; GPT) >3.0 U/L x upper limit of normal (ULN), Aspartate Aminotransferase (AST) (Glutamic Oxaloacetic Transaminase; GOT) >3.0 U/L x ULN, Total Bilirubin >2.0 mg/dL x ULN, Amylase >2.0 (U/L) x ULN are considered markedly abnormal.",,,,,,
+65757473,NCT02039505,primary,Percentage of Participants With a Clinical Response at Week 10 in Induction Phase,Week 10,,"Clinical response is defined as a reduction in complete Mayo score of ≥3 points and ≥30% from Baseline with an accompanying decrease in rectal bleeding subscore of ≥1 point or absolute rectal bleeding subscore of ≤1 point. Mayo Score is a standard assessment tool to measure ulcerative colitis disease activity in clinical trials. The index consists of 4 subscores (rectal bleeding, stool frequency, findings on endoscopy, and physician's global assessment), a global assessment by the physician, and an endoscopic subscore. Each subscore is scored on a scale from 0 to 3 and the complete Mayo score ranges from 0 to 12 (higher scores indicate greater disease activity).",,,,,,
+65757474,NCT02039505,primary,Percentage of Participants With Clinical Remission at Week 60 in Maintenance Phase,Week 60,,"Clinical Remission is defined as a complete Mayo score of ≤2 points and no individual subscore >1 point. Mayo Score is a standard assessment tool to measure ulcerative colitis disease activity in clinical trials. The index consists of 4 subscores: rectal bleeding, stool frequency, findings on endoscopy, and physician's global assessment. Each subscore is scored on a scale from 0 to 3 and the complete Mayo score ranges from 0 to 12 (higher scores indicate greater disease activity).",,,,,,
+65757475,NCT02039505,primary,Number of Participants Who Experienced at Least One or More Treatment-Emergent Adverse Events (TEAEs),From Baseline to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"An Adverse Event (AE) is defined as any untoward medical occurrence in a clinical investigation participant administered a drug; it does not necessarily have to have a causal relationship with this treatment. An AE can therefore be any unfavorable and unintended sign (e.g., a clinically significant abnormal laboratory finding), symptom, or disease temporally associated with the use of a drug, whether or not it is considered related to the drug. A treatment-emergent adverse event (TEAE) is defined as an adverse event with an onset that occurs after receiving study drug.",,,,,,
+65757476,NCT02039505,primary,Number of Participants With TEAE Related to Body Weight,From Baseline to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,,,,,,,
+65757477,NCT02039505,primary,Number of Participants With TEAE Related to Vital Signs,From Baseline to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"Vital signs included body temperature (axilla), sitting blood pressure (after the participant has rested for at least 5 minutes), and pulse (bpm).",,,,,,
+65757478,NCT02039505,primary,Number of Participants With TEAE Related to Electrocardiogram (ECG),From Baseline to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,,,,,,,
+65757479,NCT02039505,primary,Number of Participants With Markedly Abnormal Laboratory Parameters Values,From Baseline to 16 weeks after the last dose of study drug (Up to approximately 170 weeks),,"The laboratory values outside the range (Hemoglobin <=7 g/dL, Lymphocytes <500 /µL, WBC <2000 /µL, Platelets <7.5 10^4/µL, Neutrophils <1000 /µL, alanine aminotransferase (ALT) >3.0 U/L x upper limit of normal (ULN), aspartate aminotransferase (AST) >3.0 U/L x ULN, Total Bilirubin >2.0 mg/dL x ULN, Amylase >2.0 (U/L) x ULN were considered markedly abnormal. Only laboratory parameters with events were represented.",,,,,,
+65757314,NCT02042183,primary,Number of Participants Classified as Overall Responders at Week 12,at Week 12,,"An overall responder is defined as a participant who qualified as a weekly responder for 9 of the 12 treatment weeks, with durability demonstrated by at least 3 of the responder weeks occurring during the last 4 weeks of the treatment period. A weekly responder is defined as a participant who has at least 3 spontaneous bowel movements during the week, and at least one more than at baseline.",,,,,,
+65756716,NCT02052310,primary,"US (FDA) Submission: Mean Hb Change From Baseline to The Average Level During The Evaluation Period (Week 28 to Week 52), Regardless of Rescue Therapy (ITT Population)","Baseline (Day 1, Week 0), Week 28 to 52",,"Hb values under the influence of rescue therapy were not censored for the primary analysis. Rescue therapy for roxadustat treated participants was defined as recombinant erythropoietin or analogue (erythropoiesis-stimulating agent [ESA]) or red blood cell (RBC) transfusion, and rescue therapy for epoetin alfa treated participants was defined as RBC transfusion. Baseline Hb was defined the mean of up to 4 last central lab values prior to the first dose of study treatment. The intermittent missing Hb data was imputed for each treatment relying on non-missing data from all participants within each treatment group using the Monte Carlo Markov Chain (MCMC) imputation model, Monotone missing data were imputed by regression from its own treatment group.",,,,,,
+65756717,NCT02052310,primary,"Ex-U.S. Submission: Hb Responder Rate- Percentage of Participants Who Achieved a Hb Response at 2 Consecutive Visits at Least 5 Days Apart During First 24 Weeks of Treatment, Without Rescue Therapy Within 6 Weeks Prior to the Hb Response (PPS Population)","Baseline (Day 1, Week 0) up to Week 24",,"Hb response was defined, using central laboratory values, as: Hb ≥11.0 g/dL and a Hb increase from baseline by ≥1.0 g/dL in participants whose baseline Hb >8.0 g/dL, or increase in Hb ≥2.0 g/dL in participants whose baseline Hb ≤8.0 g/dL. Rescue therapy for roxadustat treated participant was defined as recombinant erythropoietin or analogue (ESA) or RBC transfusion, and rescue therapy for epoetin alfa treated participants was defined as RBC transfusion.",,,,,,
+65755648,NCT02065557,primary,Co-Primary Endpoint 1: Percentage of Participants Who Achieved Clinical Remission as Measured by Partial Mayo Score (PMS) at Week 8 - Induction Period,Week 8,,"The Mayo score is a tool designed to measure disease activity for ulcerative colitis. The PMS (Mayo score without endoscopy) ranges from 0 (normal or inactive disease) to 9 (severe disease) and is calculated as the sum of 3 sub scores (stool frequency, rectal bleeding and physician's global assessment), each of which ranges from 0 (normal) to 3 (severe disease). A negative change in PMS indicates improvement. Clinical remission was defined as a PMS ≤ 2 and no individual subscore > 1.",,,,,,
+65755649,NCT02065557,primary,Co-Primary Endpoint 2: Percentage of Participants With Clinical Remission Per Full Mayo Score (FMS) at Week 52 in Week 8 Responders Per PMS - Maintenance Period,Week 52,,"The FMS ranges from 0 (normal or inactive disease) to 12 (severe disease) and is calculated as the sum of 4 subscores (stool frequency, rectal bleeding, endoscopy, and physician's global assessment), each of which ranges from 0 (normal) to 3 (severe disease). The PMS (Mayo score without endoscopy) ranges from 0 (normal or inactive disease) to 9 (severe disease) and is calculated as the sum of 3 subscores (stool frequency, rectal bleeding and physician's global assessment). Negative changes indicate improvement. PMS responders are defined as those with a decrease in PMS ≥ 2 points and ≥ 30% from Baseline. Clinical remission per FMS is defined as Mayo Score ≤ 2 and no individual subscore > 1.",,,,,,
+65755630,NCT02065570,primary,Percentage of Participants Who Achieved Clinical Remission at Week 4,Week 4,,"Crohn's Disease Activity Index (CDAI) is used to assess the symptoms of participants with Crohn's Disease. Scores generally range from 0 to 600, where clinical remission of Crohn's disease is defined as CDAI < 150, and very severe disease is defined as CDAI > 450.",,,,,,
+65755631,NCT02065570,primary,Percentage of Participants With Endoscopic Response at Week 12,Week 12,,"Endoscopic response was scored using the Simplified Endoscopic Score for Crohn's Disease (SES-CD). The SES-CD evaluates 4 endoscopic variables (ulcer size ranging from 0 [none] to 3 [very large]; ulcerated surface ranging from 0 [none] to 3 [>30%]; affected surface ranging from 0 [none] to 3 [>75%], and narrowing ranging from 0 [none] to 3 [cannot be passed]) in 5 segments assessed during ileocolonoscopy (ileum, right colon, transverse colon, sigmoid and left colon, and rectum). The total score is the sum of the 4 endoscopic variable scores and range from 0 to 56, where higher scores indicate more severe disease. Endoscopic response was defined as SES-CD total score > 50% from Baseline (or for a Baseline SES-CD of 4, at least a 2 point reduction from Baseline) at Week 12.",,,,,,
+65755632,NCT02065570,primary,Number of Participants With Treatment-Emergent Adverse Events (TEAEs),From first dose of study drug until 70 days following last dose of study drug in the induction study (up to 12 weeks) or maintenance study (up to 56 weeks).,,"Adverse event (AE): any untoward medical occurrence that does not necessarily have a causal relationship with this treatment. The investigator assessed the relationship of each event to the use of study drug as either probably related, possibly related, probably not related or not related. Serious AE (SAE) is an event that results in death, is life-threatening, requires or prolongs hospitalization, results in a congenital anomaly, persistent or significant disability/incapacity or is an important medical event that, based on medical judgment, may jeopardize the subject and may require medical or surgical intervention to prevent any of the outcomes listed above. TEAEs: any event that began or worsened in severity after the first dose of study drug in the induction or maintenance study. Events with unknown severity were counted as severe. Events with unknown relationship to study drug were counted as drug-related.",,,,,,
+65755607,NCT02065622,primary,Induction Period Primary Endpoint: Percentage of Participants With Clinical Remission Per Full Mayo Score (FMS) at Week 8,Week 8,,"The Mayo score is a tool designed to measure disease activity for ulcerative colitis. The FMS ranges from 0 (normal or inactive disease) to 12 (severe disease) and is calculated as the sum of 4 subscores (stool frequency, rectal bleeding, endoscopy [confirmed by a central reader], and physician's global assessment), each of which ranges from 0 (normal) to 3 (severe disease). Negative changes indicate improvement. Clinical remission per FMS is defined as Mayo Score ≤ 2 and no individual subscore > 1.",,,,,,
+65755608,NCT02065622,primary,Maintenance Period Primary Endpoint: Percentage of Week 8 Responders (Per FMS) With Clinical Remission (Per FMS) at Week 52,Week 52,,"The Mayo score is a tool designed to measure disease activity for ulcerative colitis. The FMS ranges from 0 (normal or inactive disease) to 12 (severe disease) and is calculated as the sum of 4 subscores (stool frequency, rectal bleeding, endoscopy [confirmed by a central reader], and physician's global assessment), each of which ranges from 0 (normal) to 3 (severe disease). Negative changes indicate improvement. Week 8 responders (per FMS) are defined as participants with a decrease in Full Mayo score of ≥ 3 points and ≥ 30% from Baseline plus a decrease from baseline in the rectal bleeding subscore (RBS) ≥ 1 or an absolute RBS ≤ 1. Clinical remission per FMS is defined as Mayo Score ≤ 2 and no individual subscore > 1.",,,,,,
+66112997,NCT02066636,primary,The Number of Participants With Treatment Related Select Adverse Events (Grade 3-4 and Grade 5),From first dose and 100 days after last dose (last dose up to randomization for cohort B) (up to approximately 88 months),,"A treatment related adverse event (AE) is defined as any new untoward medical occurrence or worsening of a preexisting medical condition in a clinical investigation participant administered an investigational (medicinal) product and that has a causal relationship with this treatment. The select AEs categories are those that are expected to be most commonly used to describe pneumonitis, interstitial nephritis, diarrhea/colitis, hepatitis, rash, and endocrinopathies and hypersensitivity/infusion reactions. AEs are graded according to NCI CTCAE (Version 4.0) guidelines where Grade 3= Severe, Grade 4 = Life-threatening, Grade 5 = Death.",,,,,,
+65755285,NCT02070757,primary,Percentage of Participants With All Cause Mortality in the Intent-to-Treat (ITT) Population - Day 28,Day 28,,"To demonstrate the non-inferiority of ceftolozane/tazobactam versus meropenem in stratified adult participants with ventilated nosocomial pneumonia (VNP) (participants with either ventilator-associated bacterial pneumonia [VABP] or ventilated hospital-acquired bacterial pneumonia [HABP]) based on the difference in all-cause mortality rates in the intent to treat (ITT) population using a non-inferiority margin of 10%. The estimated adjusted percentage was a weighted average across all strata, constructed using Mehrotra-Railkar continuity-corrected minimum risk (MRc) stratum weights.",,,,,,
+65755116,NCT02072824,primary,Log Transformed 24-Hour Seizure Rate for All Partial Onset Seizures During the Double-Blind Treatment Phase,Day 1 up to Day 14,,"All partial onset seizures experienced during treatment phase were recorded by central reader during the 48 to 72 hour video-electroencephalogram (EEG). Double Blind 24 hour EEG seizure rate for all partial onset seizures = ([Number of seizures in double blind 48 to 72 hour EEG assessment] divided by [number of hours of video-EEG monitoring])*24. The EEG assessment was done at the end of the fixed dose treatment. For log-transformation, the quantity 1 was added to the double blind 24 hour EEG seizure rate for all participants to account for any possible ""0"" seizure incidence. This resulted in final calculation as: log transformed (double-blind 24-hour EEG seizure rate + 1).",,,,,,
+65755005,NCT02074982,primary,Percentage of Participants With Moderate to Severe Plaque Psoriasis Who Achieved Psoriasis Area and Severity Index (PASI) 90 at Week 16,Week 16,,"Psoriasis Area and Severity Index (PASI) is a combined assessment of lesion severity and affected area into a single score: 0 (no disease) to 72(maximal disease). Body is divided into 4 areas for scoring (head, arms, trunk, legs; each area is scored by itself and scores are combined for final PASI. For each area, percent of skin involved is estimated: 0 (0%) to 6 (90-100%), and severity is estimated by clinical signs, erythema, induration and desquamation; scale 0 (none) to 4 (maximum). Final PASI = sum of severity parameters for each area* area score weight of section (head: 0.1, arms: 0.2 body: 0.3 legs: 0.4).
+
+PASI 90 responders were defined as participants achieving ≥ 90% improvement at Week 16",,,,,,
+65753127,NCT02099110,primary,Change From Baseline in A1C at Week 26: Excluding Rescue Approach,Baseline and Week 26,,"A1C is blood marker used to report average blood glucose levels over prolonged periods of time and is reported as a percentage (%). This change from baseline reflects the Week 26 A1C minus the Week 0 A1C. Excluding recue approach data analysis excluded all data following the initiation of rescue therapy at any time point, in order to avoid the confounding influence of the rescue therapy.",,,,,,
+65753128,NCT02099110,primary,Percentage of Participants Who Experienced an Adverse Event (AE): Including Rescue Approach,Up to 54 weeks,,"An AE is defined as any unfavorable and unintended sign including an abnormal laboratory finding, symptom or disease associated with the use of a medical treatment or procedure, regardless of whether it is considered related to the medical treatment or procedure, that occurs during the course of the study. Including rescue approach data analysis included data following the initiation of rescue therapy.",,,,,,
+65753129,NCT02099110,primary,Percentage of Participants Who Discontinued Study Treatment Due to an AE: Including Rescue Approach,Up to 52 weeks,,"An AE is defined as any unfavorable and unintended sign including an abnormal laboratory finding, symptom or disease associated with the use of a medical treatment or procedure, regardless of whether it is considered related to the medical treatment or procedure, that occurs during the course of the study. Including rescue approach data analysis included data following the initiation of rescue therapy.",,,,,,
+65752712,NCT02105636,primary,Overall Survival (OS),From date of randomization to date of death (Up to approximately 18 months),,OS was defined as the time from randomization to the date of death from any cause. Participants were censored at the date they were last known to be alive and at the date of randomization if they were randomized but had no follow-up. Median OS time was calculated using Kaplan-Meier (KM) method.,,,,,,
+64619059,NCT02106546,primary,Overall Survival (OS) in current smokers,Up to 3 years from first dose of study drug,,Time to death for a given subject will be defined as the number of days from the date that the subject was randomized to the date of the subject's death.,,,,,,
+65752557,NCT02106832,primary,Time to First Exacerbation Event Within 48 Weeks - Cipro 28 vs. Pooled Placebo,Up to Week 48,,Time to first exacerbation was defined as the time from randomization until the visit at which the first qualifying exacerbation is recorded by the investigator. Exacerbation events are defined as exacerbations with systemic antibiotic use and presence of fever or malaise / fatigue and worsening of at least three signs/symptoms.,,,,,,
+65752558,NCT02106832,primary,Time to First Exacerbation Event Within 48 Weeks - Cipro 14 vs. Pooled Placebo,Up to Week 48,,Time to first exacerbation was defined as the time from randomization until the visit at which the first qualifying exacerbation is recorded by the investigator. Exacerbation events are defined as exacerbations with systemic antibiotic use and presence of fever or malaise / fatigue and worsening of at least three signs/symptoms.,,,,,,
+65750571,NCT02130557,primary,Percentage of Participants With Major Molecular Response (MMR) at Month 12,Month 12,,MMR was defined as a ratio of breakpoint cluster region to abelson (BCR-ABL/ABL) less than or equal to (<=) 0.1 percent (%) on the international scale (IS) (greater than or equal to [>=] 3 log reduction from standardized baseline in ratio of BCR-ABL to ABL transcripts [>=3000 ABL required]) by quantitative reverse transcriptase polymerase chain reaction (RT-qPCR). The percentage of participants with MMR at Month 12 are reported.,,,,,,
+65750511,NCT02131233,primary,Percentage of Participants Achieving <40 Copies/mL Human Immunodeficiency Virus-1 (HIV-1) Ribonucleic Acid (RNA) at Week 48,Week 48,,"From blood samples collected at week 48, HIV-1 RNA levels were determined by the Abbott RealTime HIV-1 Assay, which has a limit of reliable quantification (LoQ) of 40 copies/mL. The NC=F approach as defined by FDA ""snapshot"" approach was used as the primary approach to analysis where all missing data were treated as failures regardless of the reason.",,,,,,
+66342088,NCT02136069,primary,"Percentage of Participants With Both Clinical Response at Week 10 and Clinical Remission at Week 54, as Determined by the Mayo Clinic Score (MCS)","Week 10, Week 54",,"Mayo Clinic Score (MCS) is a composite of 4 assessments, each rated from 0-3: stool frequency, rectal bleeding, endoscopy, and physician's global assessment. Higher scores indicate more severe disease.
+
+Clinical Response is MCS with ≥3-point decrease and 30% reduction from baseline as well as ≥1-point decrease in rectal bleeding subscore or an absolute rectal bleeding score of 0 or 1.
+
+Clinical Remission is MCS ≤2 with individual subscores ≤1.",,,,,,
+65750053,NCT02138136,primary,Median Number of Observed Weekly Spontaneous Bowel Movements (SBM) Per Month,within 9 months,,Spontaneous bowel movements are defined as bowel movements without the aid of drugs.,,,,,,
+64198800,NCT02142738,primary,Progression Free Survival (PFS) Rate at Month 6,Month 6,,"PFS was defined as the time from randomization to documented disease progression per Response Evaluation Criteria in Solid Tumors version 1.1 (RECIST 1.1) or death due to any cause, whichever occurred first and was based on blinded independent central radiologists' (BICR) review. Progressive Disease (PD) was defined as ≥20% increase in the sum of diameters of target lesions and an absolute increase of ≥5 mm. (Note: the appearance of one or more new lesions was also considered progression). Participants were evaluated every 9 weeks with radiographic imaging to assess their response to treatment. The data cutoff was 09-May-2016. The PFS rate at Month 6 was calculated.",,,,,,
+65749378,NCT02147158,primary,Percentage of Participants With Absence of Bleeding During the Last 35 Consecutive Days on Treatment in Treatment Course 1,Last 35 consecutive days on treatment in the 12-Week Treatment Course 1,,"Participants recorded bleeding in a daily diary. Absence of bleeding was defined as no bleeding days (i.e., no entries for bleeding or heavy bleeding; however, spotting was allowed), during the last 35 consecutive days on treatment in Treatment Course 1.",,,,,,
+65749379,NCT02147158,primary,Time to Absence of Bleeding on Treatment During Treatment Course 1,From first dose up to the end of the 12-Week Treatment Course 1,,Time to absence of bleeding was defined as the duration in days from first dose to the first day in the time interval in which absence of bleeding occurs and persists through the last dose in the first treatment course. The persistence of absence of bleeding occurred for a minimum of 35 consecutive days counting backward from the last dose in Treatment Course 1.,,,,,,
+66358764,NCT02149121,primary,Analysis of Serum AUC0-last of Rituximab During the 1st Course of the Main Study Period (Over the First 24 Weeks) (ANCOVA),over the first 24 weeks,,"For evaluation of pharmacokinetics (PK), the primary endpoint was defined as the analysis of serum AUC0-last, AUC0-inf and Cmax of rituximab during the 1st course of the Main Study Period (over the first 24 weeks). During the 1st course of the Main Study Period, blood samples for PK analysis were collected every week from Week 0 to Week 4, every 4 weeks from Week 4 to Week 16, followed by Week 24.
+
+AUC0-last: Area under the concentration-time curve from time to the last measurable concentration over both doses of the 1st course",,,,,,
+66358765,NCT02149121,primary,Analysis of Serum AUC0-inf of Rituximab During the 1st Course of the Main Study Period (Over the First 24 Weeks) (ANCOVA),at Week 24 of the Main Study Period,,"For evaluation of PK, the primary endpoint was defined as the analysis of serum AUC0-last, AUC0-inf and Cmax of rituximab during the 1st course of the Main Study Period (over the first 24 weeks). During the 1st course of the Main Study Period, blood samples for PK analysis were collected every week from Week 0 to Week 4, every 4 weeks from Week 4 to Week 16, followed by Week 24.
+
+AUC0-inf: Area under the concentration-time curve from time 0 extrapolated to infinity over both doses of the 1st course",,,,,,
+66358766,NCT02149121,primary,Analysis of Serum Cmax of Rituximab During the 1st Course of the Main Study Period (Over the First 24 Weeks) (ANCOVA),at Week 24 of the Main Study Period,,"For evaluation of pharmacokinetics (PK), the primary endpoint was defined as the analysis of serum AUC0-last, AUC0-inf and Cmax of rituximab during the 1st course of the Main Study Period (over the first 24 weeks). During the 1st course of the Main Study Period, blood samples for PK analysis were collected every week from Week 0 to Week 4, every 4 weeks from Week 4 to Week 16, followed by Week 24.
+
+Cmax: Observed maximum concentration after the seocnd infusion of the 1st course",,,,,,
+66358767,NCT02149121,primary,Analysis of Change From Baseline of DAS28 (CRP) at Week 24 (ANCOVA),at Week 24 of the Main Study Period,,"For evaluation of efficacy, the primary endpoint was defined as the analysis of change from baseline in disease activity measured by disease activity score 28 (DAS 28) C-reactive protein (CRP) at Week 24 between 2 treatment groups, CT-P10 and reference products (combined Rituxan and MabThera) groups. During the 1st course of the Main Study Period, DAS28 was assessed every 4 weeks from Week 0 to Week 24. DAS28 (CRP) was calculated using the following formula: DAS28 (CRP) = 0.56 X SQRT(TJC28) + 0.28 X SQRT(SJC28) + 0.36 X ln(CRP+1) + 0.014 X GH on VAS + 0.96. DAS28 (CRP) provides a number on a scale from 0 to 10 with higher values indicating greater RA disease activity.",,,,,,
+65748508,NCT02158936,primary,Number of Participants Who Were Platelet Transfusion Independent During Cycles 1-4 of Azacitidine Therapy,4 cycles (Cycle = 28 days),,A subject is defined as being platelet transfusion independent if they received no platelet transfusions within the first 4 cycles of treatment with azacitidine. Subjects who died or withdrew from investigational product within the first four cycles were treated as failures (i.e. not transfusion independent) in the analysis,,,,,,
+65748242,NCT02162771,primary,Area Under the Serum Concentration-time Curve at Steady State (AUCtau),Core Cycle 4 (Week 12),,"AUCtau: Area under the plasma drug concentration-time curve within a dosing interval at steady state.
+
+PK sampling was done at pre-dose and 1 hour after the end of infusion (EOI) at Core Cycles 1-3 and 5-8. At Core Cycle 4 (i.e. steady state), intensive PK samplings were done as follows: predose, EOI, 1 hour after EOI, 24 hour after EOI, 168 hour after EOI, 336 hour after EOI, 504 hour after EOI. Lastly, one sample at any time of the end of treatment (EOT) 1 visit was obtained.",,,,,,
+65748243,NCT02162771,primary,"Maximum Serum Concentration at Steady State (Cmax,ss)",Core Cycle 4 (Week 12),,"Cmax,ss: Maximum concentration of drug in plasma at steady state on administering a fixed dose at equal dosing intervals.
+
+PK sampling was done at pre-dose and 1 hour after the end of infusion (EOI) at Core Cycles 1-3 and 5-8. At Core Cycle 4 (i.e. steady state), intensive PK samplings were done as follows: predose, EOI, 1 hour after EOI, 24 hour after EOI, 168 hour after EOI, 336 hour after EOI, 504 hour after EOI. Lastly, one sample at any time of the end of treatment (EOT) 1 visit was obtained.",,,,,,
+65748244,NCT02162771,primary,Overall Response Rate (ORR) According to the 1999 International Working Group (IWG) Criteria,During the Core Study Period (up to 8 cycles, Week 24),,"ORR was defined as the proportion of patients with the best response of complete response (CR), unconfirmed complete response (CRu), or partial response (PR) by central review.
+
+Per 1999 IWG criteria, the disease status was assessed by using contrasted CT, and CR, CRu, and PR were defined as followings; CR=Disappearance of all clinical/radiographic evidence of disease: regression of lymph nodes to normal size, absence of B-symptoms, bone marrow involvement, and organomegaly, and normal LDH level; CRu=Regression of measurable disease: >=75% decrease in SPD of target lesions and in each target lesions. no increase in the size of non-target lesions, neither new lesion nor organomegaly measured; PR=Regression of measurable disease: >=50% decrease in SPD of target lesions and no evidence of disease progression.",,,,,
+65748156,NCT02163759,primary,"Percentage of Participants in Remission at Week 10 With Etrolizumab as Compared With Placebo, as Determined by the Mayo Clinic Score (MCS), GA28948 Population",Week 10,,"The Mayo Clinic Score (MCS) ranges from 0 to 12 and is a composite of the four following assessments of disease activity: stool frequency subscore, rectal bleeding subscore, endoscopy subscore, and physician's global assessment (PGA) subscore. Each of the four assessments was rated with a score from 0 to 3, with higher scores indicating more severe disease. Remission was defined as MCS less than or equal to (≤)2 with individual subscores ≤1 and a rectal bleeding subscore of 0. Participants were also classified as non-remitters if Week 10 assessments were missing or if they had received permitted/prohibited rescue therapy prior to assessment. Participants were stratified by concomitant treatment with corticosteroids or immunosuppressants at randomization and disease activity measured during screening (MCS ≤9/MCS ≥10); the Cochran-Mantel-Haenszel test adjusted the difference in remission rates and associated 95% confidence interval for the stratification factors.",,,,,,
+65748049,NCT02165397,primary,Progression Free Survival (PFS) Based on Independent Review Committee (IRC) Assessment - Kaplan Meier Landmark Estimates at Month 54,Month 54 (median time on study: 49.7 months [Ibr+R and Pbo+R] and 57.9 months [Open-Label Ibr]),,"PFS was defined as the time from date randomization to date of first IRC-confirmed disease progression (PD) assessed according to the modified VIth International Workshop on Waldenström's Macroglobulinemia (IWWM) criteria (National Comprehensive Cancer Network [NCCN] 2014) or death due to any cause, whichever occurs first, regardless of the use of subsequent antineoplastic therapy prior to documented PD or death.
+
+As the median PFS was not reached in the Ibrutinib + Rituximab arm at the time of the analysis, Kaplan Meier landmark estimate of the PFS rate at 54 months (that is, the estimated percentage of participants with PFS at Month 54) is presented.",,,,,,
+64455249,NCT02167945,primary,All-Cause Death: Time to Event,"At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to all-cause death was defined as the number of days from the first day of study drug dosing for the participant to the date of death. All deaths were to be included, regardless of whether the death occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant did not die, their data was to be censored at the date of their last available assessment of clinical outcomes. For participants with no post-baseline assessment, the participant's data was to be censored on the first day of study drug dosing. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. The pre-specified analysis of all-cause death included pooled data from TOPAZ-II (this study) and the companion study TOPAZ-I (M14-423; NCT02219490).",,,,,,
+64455250,NCT02167945,primary,Liver-Related Death: Time to Event,"At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to liver-related death was defined as number of days from the 1st day of study drug dosing for the participant to date of liver-related death. All liver-related deaths were to be included, regardless of whether the death occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant didn't experience the event of interest nor had died (all-cause death), their data was to be censored at the date of their last available assessment of clinical outcomes. For participants with no post-baseline assessment, their data was to be censored on the 1st day of study drug dosing. All-cause death was a censoring event for liver-related death. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. The pre-specified analysis of liver-related death included pooled data from TOPAZ-II (this study) and the companion study TOPAZ-I (M14-423; NCT02219490).",,,,,,
+64455251,NCT02167945,primary,Liver Decompensation: Time to Event,"At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to liver decompensation was defined as number of days from the 1st day of study drug dosing for the participant to the date of liver decompensation. All liver decompensation was to be included, regardless of whether it occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant didn't experience the event of interest nor had died (all-cause death), their data was to be censored at the date of their last available assessment of clinical outcomes. For participants with no post-baseline assessment, their data was to be censored on the 1st day of study drug dosing. All-cause death was a censoring event for liver decompensation. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. The pre-specified analysis of liver decompensation included pooled data from TOPAZ-II (this study) and the companion study TOPAZ-I (M14-423; NCT02219490).",,,,,,
+64455252,NCT02167945,primary,Liver Transplantation: Time to Event,"At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to liver transplantation was defined as number of days from the 1st day of study drug dosing for the participant to date of liver transplantation. All liver transplantation was to be included, regardless of whether it occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant didn't experience the event of interest nor had died (all-cause death), their data was to be censored at the date of their last available assessment of clinical outcomes. For participants with no post-baseline assessment, their data was to be censored on the 1st day of study drug dosing. All-cause death was a censoring event for liver transplantation. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. The pre-specified analysis of liver transplantation included pooled data from TOPAZ-II (this study) and the companion study TOPAZ-I (M14-423; NCT02219490).",,,,,,
+64455253,NCT02167945,primary,Hepatocellular Carcinoma: Time to Event,"At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to hepatocellular carcinoma was defined as number of days from the 1st day of study drug dosing for the participant to date of hepatocellular carcinoma. All hepatocellular carcinoma was to be included, whether it occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant didn't experience the event of interest nor had died (all-cause death), their data was to be censored at the date of their last available assessment of clinical outcomes. For those with no post-baseline assessment, their data was to be censored on the 1st day of study drug dosing. All-cause death was a censoring event for hepatocellular carcinoma. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. The pre-specified analysis of hepatocellular carcinoma included pooled data from TOPAZ-II (this study) and the companion study TOPAZ-I (M14-423; NCT02219490).",,,,,,
+64455254,NCT02167945,primary,"All-Cause Death, Liver-Related Death, Liver Decompensation, Liver Transplantation, Hepatocellular Carcinoma: Time to Event","At Post-Treatment Weeks 52, 104, 156, 208, and 260",,"Time to the composite of clinical outcomes is the time to the first occurrence of all-cause death, liver-related death, liver decompensation, liver transplantation, or hepatocellular carcinoma. All first occurrences were to be included, regardless of whether it occurred while the participant was still taking study drug or had previously discontinued study drug. If the participant did not experience any of these events, their data was to be censored at the date of their last available assessment of clinical outcomes. For participants with no post-baseline assessment, the participant's data was to be censored on the first day of study drug dosing. The event-free survival rates were estimated using Kaplan-Meier methodology and incidence estimates are presented with 95% confidence intervals. Pre-specified analysis included pooled data from this study and from TOPAZ-I; NCT02219490.",,,,,,
+65747703,NCT02171429,primary,"Percentage of Participants in Remission at Week 10 With Etrolizumab Compared With Placebo, as Determined by the Mayo Clinic Score (MCS), GA28949 Population",Week 10,,"The Mayo Clinic Score (MCS) ranges from 0 to 12 and is a composite of the four following assessments of disease activity: stool frequency subscore, rectal bleeding subscore, endoscopy subscore, and physician's global assessment (PGA) subscore. Each of the four assessments was rated with a score from 0 to 3, with higher scores indicating more severe disease. Remission was defined as MCS less than or equal to (≤)2 with individual subscores ≤1 and a rectal bleeding subscore of 0. Participants were also classified as non-remitters if Week 10 assessments were missing or if they had received permitted/prohibited rescue therapy prior to assessment. Participants were stratified by concomitant treatment with corticosteroids or immunosuppressants at randomization and disease activity measured during screening (MCS ≤9/MCS ≥10); the Cochran-Mantel-Haenszel test adjusted the difference in remission rates and associated 95% confidence interval for the stratification factors.",,,,,,
+65747271,NCT02175771,primary,Participants With Treatment-Emergent Adverse Experiences (TEAE) During the Treatment Period,Day 1 to Week 26 of the Treatment Period,,"An adverse event was defined as any untoward medical occurrence that develops or worsens in severity during the conduct of a clinical study and does not necessarily have a causal relationship to the study drug. Severity was rated by the investigator on a scale of mild, moderate and severe, with severe= an AE which prevents normal daily activities. Relationship of AE to treatment was determined by the investigator. Serious AEs include death, a life-threatening adverse event, inpatient hospitalization or prolongation of existing hospitalization, persistent or significant disability or incapacity, a congenital anomaly or birth defect, OR an important medical event that jeopardized the patient and required medical intervention to prevent the previously listed serious outcomes.",,,,,,
+65747136,NCT02177266,primary,Number of Patients With Post Cardiac Surgery Atrial Fibrillation or Post-pericardiotomy Syndrome.,Baseline to 3 months,,,,,,,,
+65746687,NCT02185014,primary,Percentage of Participants With Endoscopic Improvement at Week 40 in Participants With Endoscopic Improvement at Week 0,Week 40,,"Endoscopic improvement defined as a simple endoscopic score for Crohn's Disease (SES-CD) score of ≤4 and at least a 2-point reduction compared with Study M14-115 (NCT02185014) Baseline and no subscore greater than 1 in any individual endoscopic variable. The SES-CD evaluates 4 endoscopic variables (ulcer size ranging from 0 [none] to 3 [very large]; ulcerated surface ranging from 0 [none] to 3 [>30%]; affected surface ranging from 0 [none] to 3 [>75%], and narrowing ranging from 0 [none] to 3 [cannot be passed]) in 5 segments assessed during ileocolonoscopy (ileum, right colon, transverse colon, sigmoid and left colon, and rectum). The Total Score is the sum of the 4 endoscopic variable scores and range from 0 to 56, where higher scores indicate more severe disease. Nonresponder imputation (NRI) was used for missing data.",,,,,,
+65746600,NCT02186873,primary,Percentage of Participants Who Achieved at Least 20 Percent Improvement From Baseline in the Assessment of SpondyloArthritis International Society (ASAS 20) at Week 16,Week 16,,"ASAS 20 defined as 20 percent (%) improvement compared to baseline in the ASAS Working Group criteria: that is, greater than or equal to (>=)20% improvement from baseline in at least 3 of the 4 domains: patient's global assessment of disease activity (0=very well,10 =very poor), total back pain (0=no pain,10=most severe pain), function (self-assessment using BASFI [0=no functional impairment to 10= maximal impairment]), inflammation (0=none,10=very severe) with an absolute improvement of at least 1 (0-10 centimeter (cm) visual analogue scale [VAS]), and an absence of deterioration (defined as >=20% worsening and absolute worsening of at least 1 on a 0-10 cm scale) in the potential remaining domain.",,,,,,
+65746515,NCT02187159,primary,"Change From Baseline to Week 13 in Average Daily Pain Score (ADPS) in Participants Receiving DS-5565, Pregabalin, or Placebo",Baseline up to Week 13 postdose,,The patient reported pain intensity daily (over the past 24 hours) on a scale of 0 = no pain to 10 = worst possible pain. The daily pain scores were averaged over 7 days to calculate the weekly ADPS.,,,,,,
+65745390,NCT02203032,primary,Number of Visits at Which Participants Achieved an Investigator's Global Assessment (IGA) Response of Cleared (0) or Minimal (1) and at Least a 2 Grade Improvement (From Week 16) From Week 28 Through Week 40,Week 28 through Week 40,,"The IGA documents the investigator's assessment of the participants psoriasis at a given time point. Overall lesions are graded for induration, erythema, and scaling. The participants' psoriasis was assessed as cleared (0), minimal (1), mild (2), moderate (3), or severe (4).",,,,,,
+65745174,NCT02207231,primary,Percentage of Participants Who Achieved an Investigator's Global Assessment (IGA) Score of Cleared (0) or Minimal (1) in the Guselkumab Group Compared to the Placebo Group at Week 16,Week 16,,"The IGA documents the investigator's assessment of the participants' psoriasis at a given time point. Overall lesions are graded for induration, erythema, and scaling. The participants' psoriasis was assessed as cleared (0), minimal (1), mild (2), moderate (3), or severe (4).",,,,,,
+65745175,NCT02207231,primary,Percentage of Participants Who Achieved Psoriasis Area and Severity Index (PASI) 90 Response in the Guselkumab Group Compared to the Placebo Group at Week 16,Week 16,,"The PASI is a system used for assessing and grading the severity of psoriatic lesions. In the PASI system, the body is divided into 4 regions: the head, trunk, upper extremities, and lower extremities. Each of these areas were assessed separately for the percentage of the area involved, which translates to a numeric score that ranges from 0 to 6, and for erythema, induration, and scaling, which are each rated on a scale of 0 to 4. The PASI produces a numeric score that can range from 0 to 72. A higher score indicates more severe disease. A PASI 90 response represents participants who achieved at least a 90 percent improvement from baseline in the PASI score.",,,,,,
+65745154,NCT02207244,primary,Percentage of Participants Who Achieved an Investigator's Global Assessment (IGA) Score of Cleared (0) or Minimal (1) in the Guselkumab Group Compared to the Placebo Group at Week 16,Week 16,,"The IGA documents the investigator's assessment of the participants' psoriasis at a given time point. Overall lesions are graded for induration, erythema, and scaling. The participants' psoriasis was assessed as cleared (0), minimal (1), mild (2), moderate (3), or severe (4).",,,,,,
+65745155,NCT02207244,primary,Percentage of Participants Who Achieved Psoriasis Area and Severity Index (PASI) 90 Response in the Guselkumab Group Compared to the Placebo Group at Week 16,Week 16,,"The PASI is a system used for assessing and grading the severity of psoriatic lesions. In the PASI system, the body is divided into 4 regions: the head, trunk, upper extremities, and lower extremities. Each of these area was assessed separately for the percentage of the area involved, which translates to a numeric score that ranges from 0 to 6, and for erythema, induration, and scaling, which are each rated on a scale of 0 to 4. The PASI produces a numeric score that can range from 0 to 72. A higher score indicates more severe disease. A PASI 90 response represents participants who achieved at least a 90 percent improvement from baseline in the PASI score.",,,,,,
+65744359,NCT02218372,primary,Percentage of Participants With Confirmed Clinical Response (CCR) at End of Treatment (EOT) +2 Days,Up to day 12,,"Initial clinical response (ICR) for ages from birth to < 2 years was defined as absence of watery diarrhea for 2 consecutive treatment days, remaining well until study drug discontinuation. ICR for ages ≥ 2 years to < 18 years was defined as improvement in number and character of bowel movements as determined by < 3 unformed bowel movements (UBMs) per day for 2 consecutive treatment days, remaining well until study drug discontinuation. CCR was defined for both age groups as not requiring further CDAD therapy within 2 days after study drug completion, and was reported with a positive (Yes) or negative (No) outcome. Resolution of diarrhea was assessed during interviews of participant/parent/legal guardian, supplemented by review of personal records (if hospitalized) and checked for presence of watery diarrhea (ages from birth to < 2 years) or number of UBMs (for ages ≥ 2 years to < 18 years).",,,,,,
+65742195,NCT02247804,primary,Change From Baseline in IOP in the Study Eye at Week 12 (Hours 0 and 2),Baseline (Hours 0 and 2) to Week 12 (Hours 0 and 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. A mixed-effects model with repeated measures (MMRM) was used for analyses. A negative change from baseline indicates an improvement and a positive change from baseline indicates a worsening.",,,,,,
+65742196,NCT02247804,primary,IOP in the Study Eye at Week 2 (Hour 0),Week 2 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742197,NCT02247804,primary,IOP in the Study Eye at Week 2 (Hour 2),Week 2 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742198,NCT02247804,primary,IOP in the Study Eye at Week 6 (Hour 0),Week 6 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742199,NCT02247804,primary,IOP in the Study Eye at Week 6 (Hour 2),Week 6 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742200,NCT02247804,primary,IOP in the Study Eye at Week 12 (Hour 0),Week 12 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742201,NCT02247804,primary,IOP in the Study Eye at Week 12 (Hour 2),Week 12 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742039,NCT02250651,primary,Change From Baseline in Intraocular Pressure (IOP) in the Study Eye to Week 12 (Hours 0 and 2),Baseline (Up to 3 days prior to Day 1 at Hours 0 and 2) to Week 12 (Hours 0 and 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. A mixed-effects model with repeated measures (MMRM) was used for analyses. A negative change from baseline indicates an improvement and a positive change from baseline indicates a worsening.",,,,,,
+65742040,NCT02250651,primary,IOP in the Study Eye at Week 2 (Hour 0),Week 2 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742041,NCT02250651,primary,IOP in the Study Eye at Week 2 (Hour 2),Week 2 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742042,NCT02250651,primary,IOP in the Study Eye at Week 6 (Hour 0),Week 6 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742043,NCT02250651,primary,IOP in the Study Eye at Week 6 (Hour 2),Week 6 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742044,NCT02250651,primary,IOP in the Study Eye at Week 12 (Hour 0),Week 12 (Hour 0),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742045,NCT02250651,primary,IOP in the Study Eye at Week 12 (Hour 2),Week 12 (Hour 2),,"IOP is a measurement of the fluid pressure inside the study eye. Measurements were taken at Hours 0 and 2. The study eye is defined as the eye that meets the entry criteria. If both eyes meet the entry criteria, the eye with the higher IOP at Baseline Hour 0 will be selected as the study eye. If both eyes had the same IOP at Hour 0, then the right eye was designated as the study eye. MMRM was used for analyses.",,,,,,
+65742038,NCT02251275,primary,Number Of Participants Reporting Treatment-Emergent Adverse Events (TEAEs),Baseline through end of treatment (up to 42 months) and follow-up 7 days posttreatment(+ 7 days),,"An adverse event (AE) was as any untoward medical occurrence associated with the use of an investigational medicinal product (IMP), whether or not considered IMP related. A TEAE was an AE that started after trial drug treatment; or if the event was continuous from baseline and was serious, related to IMP, or resulted in death, discontinuation, interruption or reduction of trial therapy. A serious TEAE included any event that resulted in: death, life-threatening, persistent or significant incapacity, substantial disruption of ability to conduct normal life functions, required inpatient hospitalization, prolonged hospitalization, congenital anomaly/birth defect, or other medically significant events as per medical judgment, that jeopardized the participant and that required medical or surgical intervention. A severe TEAE was an inability to work or perform normal daily activity. A summary of serious and all other non-serious TEAEs, regardless of causality, is located in the AE section.",,,,,,
+65742022,NCT02251990,primary,Percentage of Participants Achieving Sustained Virologic Response 12 Weeks After the End of All Study Therapy (SVR12),12 weeks after end of all therapy (Study Week 24),,"Blood was drawn from each participant to assess Hepatitis C Virus ribonucleic acid (HCV RNA) plasma levels using the Roche COBAS® AmpliPrep/COBAS® Taqman HCV Test, v2.0, which had a lower limit of quantification (LLOQ) of 15 IU/mL. SVR12 was defined as HCV RNA below the lower limit of detection (<LLOQ) at 12 weeks after the end of all study therapy. As pre-specified in the protocol, the Deferred Treatment Group was not included in the primary efficacy analysis.",,,,,,
+65742023,NCT02251990,primary,Percentage of Participants Experiencing at Least One Adverse Event (AE) During the DB Treatment Period and First 14 Follow-up Days,DB Treatment period plus first 14 follow-up days (up to 14 weeks),,"An AE is defined as any untoward medical occurrence in a participant administered a pharmaceutical product and which does not necessarily have to have a causal relationship with this treatment. An AE can therefore be any unfavourable and unintended sign, symptom, or disease temporally associated with the use of a medicinal product or protocol-specified procedure, whether or not considered related to the medicinal product or protocol-specified procedure. Any worsening of a pre-existing condition that is temporally associated with the use of the Sponsor's product, is also an AE. The primary safety analysis compared the safety data of the Immediate Treatment Group during the active treatment period to those of the Deferred Treatment Group during the placebo treatment period.",,,,,,
+65742024,NCT02251990,primary,Percentage of Participants That Discontinued From Study Therapy Due to AEs During the DB Treatment Period,DB Treatment period (up to 12 weeks),,"An AE is defined as any untoward medical occurrence in a participant administered a pharmaceutical product and which does not necessarily have to have a causal relationship with this treatment. An AE can therefore be any unfavourable and unintended sign, symptom, or disease temporally associated with the use of a medicinal product or protocol-specified procedure, whether or not considered related to the medicinal product or protocol-specified procedure. Any worsening of a pre-existing condition that is temporally associated with the use of the Sponsor's product, is also an AE. A participant could discontinue from treatment but continue to participate in the study as long as consent was not withdrawn. The primary safety analysis compared the safety data of the Immediate Treatment Group during the active treatment period to those of the Deferred Treatment Group during the placebo treatment period.",,,,,,
+65741679,NCT02256436,primary,Progression-Free Survival (PFS) Per Response Evaluation Criteria in Solid Tumors Version 1.1 (RECIST 1.1) - All Participants,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,"PFS was defined as the time from randomization to the first documented disease progression, or death due to any cause, whichever occurred first. Per RECIST 1.1, progressive disease (PD) was defined as at least a 20% increase in the sum of diameters of target lesions. In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm. Note: The appearance of one or more new lesions was also considered PD. The PFS per RECIST 1.1 was assessed by blinded independent central review (BICR) in all participants up through the primary analysis database cut-off date of 07-Sep-2016.",,,,,,
+65741680,NCT02256436,primary,Overall Survival (OS) - All Participants,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,OS was defined as the time from randomization to death due to any cause. The OS was assessed in all participants up through the primary analysis database cut-off date of 07-Sep-2016.,,,,,,
+65741681,NCT02256436,primary,PFS Per RECIST 1.1 - Participants With Programmed Cell Death-Ligand (PD-L1) Positive Tumors,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,"PFS was defined as the time from randomization to the first documented disease progression, or death due to any cause, whichever occurred first. Per RECIST 1.1, PD was defined as at least a 20% increase in the sum of diameters of target lesions. In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm. Note: The appearance of one or more new lesions was also considered PD. PFS per RECIST 1.1 was assessed by BICR in all participants who had PD-L1 positive tumors (combined positive score [CPS] ≥1%) up through the primary analysis database cut-off date of 07-Sep-2016.",,,,,,
+65741682,NCT02256436,primary,OS - Participants With PD-L1 Positive Tumors,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,"OS was defined as the time from randomization to death due to any cause. For the purposes of this study, participants with PD-L1 CPS ≥1% were considered to have a PD-L1 positive tumor status. OS was assessed in all participants who had PD-L1 positive tumors (CPS ≥1%) up through the primary analysis database cut-off date of 07-Sep-2016.",,,,,,
+65741683,NCT02256436,primary,PFS Per RECIST 1.1 - Participants With Strongly PD-L1 Positive Tumors,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,"PFS was defined as the time from randomization to the first documented disease progression, or death due to any cause, whichever occurred first. Per RECIST 1.1, PD was defined as at least a 20% increase in the sum of diameters of target lesions. In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm. Note: The appearance of one or more new lesions was also considered PD. PFS per RECIST 1.1 was assessed by BICR in all participants who had strongly PD-L1 positive tumors (CPS ≥10%) up through the primary analysis database cut-off date of 07-Sep-2016.",,,,,,
+65741684,NCT02256436,primary,OS - Participants With Strongly PD-L1 Positive Tumors,Through primary analysis database cut-off date of 07-Sep-2016 (Up to approximately 20 months),,"OS was defined as the time from randomization to death due to any cause. For the purposes of this study, participants with a PD-L1 CPS ≥10% were considered to have a strongly PD-L1 positive tumor status. The OS was assessed in all participants who had strongly PD-L1 positive tumors (CPS ≥10%) up through the primary analysis database cut-off date of 07-Sep-2016.",,,,,,
+65741169,NCT02263079,primary,Percentage of Participants With Loss of Hepatitis B Surface Antigen (HBsAg) at 24 Weeks Post-End of Treatment/End of Untreated Observation,24 weeks post-treatment/at the end of untreated observation (Week 80),,This endpoint is defined as loss of HBsAg at 24 weeks post-treatment (follow-up Week 24)/end of untreated observation (Week 80). The percentage of responders (response rate) and 95% CI (using the Clopper-Pearson method) for the response rate are presented for each group.,,,,,,
+65741132,NCT02263508,primary,Phase 1b: Number of Participants With Dose-limiting Toxicities (DLTs),The DLT evaluation period was 6 weeks from the initial administration of pembrolizumab (week 6 to 12).,,"A DLT was defined as any toxicity related to study drug which met any of the following criteria based on Common Terminology Criteria for Adverse Events (CTCAE) version 4.0:
+
+Grade 4 non-hematologic toxicity.
+Grade 3 or higher pneumonitis.
+Grade 3 non-hematologic toxicity lasting > 3 days despite optimal supportive care, excluding grade 3 fatigue.
+Any grade 3 or higher non-hematologic laboratory value if medical intervention was required, or the abnormality lead to hospitalization, or the abnormality persisted for > 1 week.
+Febrile neutropenia grade 3 or grade 4.
+Thrombocytopenia < 25 x 10^9/L if associated with a bleeding event which does not result in hemodynamic instability but required an elective platelet infusion, or a life-threatening bleeding event which resulted in urgent intervention and admission to intensive care unit.
+Grade 5 toxicity (ie, death).
+Any other intolerable toxicity leading to permanent discontinuation of talimogene laherparepvec or pembrolizumab.",,,,,,
+65741133,NCT02263508,primary,Phase 3: Progression Free Survival (PFS) by Blinded Independent Central Review (BICR) Assessed Using Modified RECIST 1.1,"From randomization until the data-cut-off date of 02 March 2020; median (range) time on follow-up was 25.5 (0.6, 44.7) months in the Placebo + Pembrolizumab arm and 25.6 (0.3, 45.8) months in the Talimogene Laherparepvec + Pembrolizumab arm.",,"PFS per modified Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1 is defined as the interval from randomization to the earlier event of progressive disease (PD) per modified RECIST 1.1 or death from any cause.
+
+PD: Increase in size of target lesions from nadir by ≥ 20% and ≥ 5 mm absolute increase above nadir, or the appearance of a new lesion.
+
+Median PFS was calculated using the Kaplan-Meier method. Participants without an event were censored at their last evaluable tumor assessment if available; otherwise on their randomization date.
+
+The primary analysis of PFS was specified to be conducted when 407 PFS events had occurred (data cut-off date 02 March 2020).",,,,,,
+65741134,NCT02263508,primary,Phase 3: Overall Survival,"From randomization until the end of study; median (range) time on follow-up was 34.8 (0.6, 58.3) months in the Placebo + Pembrolizumab arm and 36.8 (0.3, 58.4) months in the Talimogene Laherparepvec + Pembrolizumab arm.",,"Overall survival (OS) is defined as the interval from randomization to death from any cause.
+
+Median overall survival was calculated using the Kaplan-Meier method. Participants without an event were censored at their last known alive date.",,,,,,
+65741096,NCT02264990,primary,Overall Survival (OS) in the Lung Subtype Panel Positive Subgroup,"From randomization up to the data cut-off date of 15 July 2019; median follow-up time was 44.5 and 45.3 months in LSP+ participants for the investigator's choice chemotherapy and veliparib + C/P arms, respectively.",,Overall survival is defined as the time from the date that the participant was randomized to the date of the participant's death. Overall survival was estimated using Kaplan-Meier methodology. Participants still alive at the data cut-off date were censored at the date they were last known to be alive.,,,,,,
+65741091,NCT02265237,primary,"Percentage of Participants in Arms A, B and C With Sustained Virologic Response 12 Weeks Post-treatment (SVR12)",12 weeks after the last actual dose of study drug,,SVR12 was defined as plasma hepatitis C virus ribonucleic acid (HCV RNA) level less than the lower limit of quantification (<LLOQ) 12 weeks after the last dose of study drug.,,,,,,
+65740594,NCT02272725,primary,Acute Kidney Injury,"participants will be followed through the duration of a 50 mile ultramarathon, an expected average of 18 hours",,"The participants experiencing acute kidney injury (diagnosed by an increase in creatinine of greater or equal to 1.5x that of estimated baseline creatinine from age and weight) will be from measured point-of-care blood test of the finish line immediately following the completion of a 50 mile ultramarathon. This outcome measure is a biochemical reading, that may not necessarily be a clinical adverse event.",,,,,,
+65739123,NCT02291549,primary,Nasal Obstruction/Congestion Score,Day 30,,Determined by patients using a daily diary on a scale from 0 (no symptoms) to 3 (severe symptoms) over a period of 7 days prior to the baseline and Day 30 visits. Negative values for change from baseline indicate reduction (improvement) in nasal obstruction/congestion symptoms.,,,,,,
+65739124,NCT02291549,primary,Bilateral Polyp Grade,Day 90,,"Polyp grade was determined by an independent panel of 3 sinus surgeons based on a centralized, blinded videoendoscopy review. Each sinus was graded from 0 (no visible polyps) to 4 (nasal polyps completely obstructing nasal cavity) and then the left and right values were added to obtain a total bilateral polyp grade, ranging from 0 to 8. Negative values for change from baseline indicated reduction (improvement) in bilateral polyp grade.",,,,,,
+65738920,NCT02293902,primary,Percentage of Participants Achieving American College of Rheumatology 20 (ACR20) Response at Week 24,Week 24,,"American College of Rheumatology (ACR) response is a composite rating scale that includes 7 variables: tender joints count (TJC [68 joints]); Swollen joints count (SJC [66 joints]); levels of an acute phase reactant (high sensitivity C-reactive protein [hs-CRP level]); participant's assessment of pain (measured on 0 [no pain]-100 mm [worst pain] visual analog scale [VAS]); participant's global assessment of disease activity (measured on 0 [no arthritis activity]-100 mm [maximal arthritis activity] VAS); physician's global assessment of disease activity (measured on 0 [no arthritis activity]-100 mm [maximal arthritis activity] VAS); participant's assessment of physical function (measured by health assessment questionnaire disability index [HAQ-DI], with scoring range of 0 [better health] - 3 [worst health]). ACR20 response was defined as achieving at least 20% improvement in both TJC and SJC, and at least 20% improvement in at least 3 of the 5 other assessments.",,,,,,
+65738066,NCT02305849,primary,Percentage of Participants With an American College of Rheumatology 20% (ACR20) C-Reactive Protein (CRP) Response at Week 12,Baseline and week 12/Early termination (ET),,"ACR20 response: greater than and equal to (≥) 20 percent (%) improvement in tender and swollen joint count; and ≥ 20% improvement in at least 3 of the following 5 criteria compared with baseline: 1) physician's global assessment of disease activity, 2) participant's assessment of disease activity, 3) participant's assessment of pain, 4) participant's assessment of functional disability via a health assessment questionnaire, and 5) C-reactive protein at each visit.",,,,,,
+65738067,NCT02305849,primary,Change From Baseline in mTSS at Week 28,Baseline and week 28/ET,,"mTSS was defined as the sum of joint erosion scores graded by assessing erosion severity in 44 joints (16 per hand and 6 per feet) and JSN scores graded by assessing narrowing of joint spaces in 42 joints (15 per hand and 6 per feet). Erosion score was scored from 0 (no erosion) to 5 (complete collapse of bone) and the score for erosion ranges from 0 to 160 in the hands and from 0 to 120 in the feet (the maximum erosion score for a joint in the foot is 10). JSN including subluxation, was scored from 0 (normal) to 4 (complete loss of joint space, bony ankylosis, or luxation), with a maximum JSN score of 168. mTSS scores ranged from 0 (normal) to 448 (worst possible total score). Change from baseline was calculated as score at week 28 (ET) minus score at baseline. An increase in mTSS from baseline represented disease progression and/or joint worsening, no change represented halting of disease progression, and a decrease represented improvement.",,,,,,
+65737977,NCT02307682,primary,Change From Baseline in Best Corrected Visual Acuity (BCVA) (Letters Read) at Week 48 - Study Eye,"Baseline, Week 48",,BCVA (with spectacles or other visual corrective devices) was assessed using Early Treatment Diabetic Retinopathy Study (ETDRS) testing at 4 meters and reported in letters read correctly. Baseline was defined as the last measurement prior to first treatment. An increase (gain) in letters read from the baseline assessment indicates improvement. One eye (study eye) contributed to the analysis.,,,,,,
+65737876,NCT02308163,primary,Percentage of Participants With an American College of Rheumatology 20% (ACR20) C-Reactive Protein (CRP) Response at Week 12,Baseline and Week 12/early termination (ET),,"The ACR20 response required that all criteria from (1) to (3) below be met.
+
+Tender joint count (TJC) : ≥ 20% reduction compared with baseline.
+Swollen joint count (SJC) : ≥ 20% reduction compared with baseline.
+≥ 20% improvement in 3 or more of the following 5 parameters compared with baseline
+
+(3) ≥ 20% improvement in 3 or more of the following 5 parameters compared with baseline: Subject's assessment of pain, Subject's Global Assessment of Arthritis (SGA), Physician's Global Assessment of Arthritis (PGA), Health Assessment Questionnaire - Disability Index (HAQ-DI), C-Reactive Protein (CRP).",,,,,,
+65737433,NCT02313909,primary,Incidence Rate of the Composite Efficacy Outcome (Adjudicated),From randomization until the efficacy cut-off date (median 326 days),,"Components of composite efficacy outcome (adjudicated) includes stroke (ischemic, hemorrhagic, and undefined stroke, TIA with positive neuroimaging) and systemic embolism. Incidence rate estimated as number of participants with incident events divided by cumulative at-risk time, where participant is no longer at risk once an incident event occurred.",,,,,,
+65737434,NCT02313909,primary,Incidence Rate of a Major Bleeding Event According to the International Society on Thrombosis and Haemostasis (ISTH) Criteria (Adjudicated),From randomization until the efficacy cut-off date (median 326 days),,"Major bleeding event (as per ISTH), defined as bleeding event that met at least one of following: fatal bleeding; symptomatic bleeding in a critical area or organ (intraarticular, intramuscular with compartment syndrome, intraocular, intraspinal, pericardial, or retroperitoneal); symptomatic intracranial haemorrhage; clinically overt bleeding associated with a recent decrease in the hemoglobin level of greater than or equal to (>=) 2 grams per decilitre (g/dL) (20 grams per liter [g/L]; 1.24 millimoles per liter [mmol/L]) compared to the most recent hemoglobin value available before the event; clinically overt bleeding leading to transfusion of 2 or more units of packed red blood cells or whole blood. The results were based on classification of events that have been positively adjudicated as major bleeding events. Incidence rate estimated as number of subjects with incident events divided by cumulative at-risk time, where subject is no longer at risk once an incident event occurred.",,,,,,
+65737407,NCT02314117,primary,Progression-free Survival (PFS),Randomization to Radiological Disease Progression or Death from Any Cause (Up to 26 Months),,"PFS time was measured from the date of randomization to the date of radiographic(rgr) documentation of progression(by RECIST v.1.1) or the date of death due to any cause, whichever was earlier.If a participant did not have a complete baseline tumor assessment,then the PFS time was censored at the randomization date.If a participant was not known to have died or have rgr documented progression as of the data cutoff date for the analysis, the PFS time was censored at the last adequate tumor assessment date. If death or progressive disease(PD) occurred after 2 or more consecutive missing rgr visits,censoring occurred at the date of the last rgr visit prior to the missed visits.If death or PD occurred after postdiscontinuation(pdis) systemic anticancer therapy,censoring occurred at the date of last rgr visit prior to the start of pdis systemic anticancer therapy. PD was defined according to RECIST v.1.1.",,,,,,
+66131033,NCT02325466,primary,Mean Change in Low Shear Blood Viscosity,"baseline, week 16",,Compare the effect of aspirin-ticagrelor and ticagrelor monotherapy with aspirin on blood viscosity from week 16 to baseline,,,,,,
+66131034,NCT02325466,primary,Mean Change in High Shear Blood Viscosity,baseline and week 16,,Compare the effect of aspirin-ticagrelor and ticagrelor monotherapy with aspirin on blood viscosity at week 16 to baseline,,,,,,
+65736459,NCT02326272,primary,Proportion of Participants Who Achieve a Psoriasis Activity and Severity Index (PASI75) Response at Week 16,Week 16,,"The PASI75 response assessments are based on at least 75% improvement in the PASI score from Baseline. This is a scoring system that averages the redness, thickness, and scaliness of the psoriatic lesions (on a 0-4 scale) and weights the resulting score by the area of skin involved. Body divided into 4 areas: head, arms, trunk to groin, and legs to top of buttocks. Assignment of an average score for the redness, thickness, and scaling for each of the 4 body areas with a score of 0 (clear) to 4 (very marked). Determining the percentage of skin covered with PSO for each of the body areas and converting to a 0 to 6 scale. Final PASI= average redness, thickness, and scaliness of the psoriatic skin lesions, multiplied by the involved psoriasis area score of the respective section, and weighted by the percentage of the person's affected skin for the respective section. The minimum possible PASI score is 0=no disease, the maximum score is 72=maximal disease.",,,,,,
+65736460,NCT02326272,primary,Proportion of Participants Who Achieve a Physician's Global Assessment (PGA) Clear or Almost Clear (With at Least 2-category Improvement) Response at Week 16,Week 16,,"The Investigator assessed the overall severity of Psoriasis (PSO) using the following 5-point scale: 0=clear, 1=almost clear, 2=mild, 3=moderate, 4=severe.",,,,,,
+65736453,NCT02326298,primary,Proportion of Subjects Who Achieve a Psoriasis Activity and Severity Index (PASI75) Response at Week 16,At Week 16,,"The PASI75 response assessments are based on at least 75% improvement in the PASI score from Baseline. This is a scoring system that averages the redness, thickness, and scaliness of the psoriatic lesions (on a 0-4 scale), and weights the resulting score by the area of skin involved. Body divided into 4 areas: head, arms, trunk to groin, and legs to top of buttocks. Assignment of an average score for the redness, thickness, and scaling for each of the 4 body areas with a score of 0 (clear) to 4 (very marked). Determining the percentage of skin covered with PSO for each of the body areas and converting to a 0 to 6 scale. Final PASI= average redness, thickness, and scaliness of the psoriatic skin lesions, multiplied by the involved psoriasis area score of the respective section, and weighted by the percentage of the person's affected skin for the respective section. The minimum possible PASI score is 0= no disease, the maximum score is 72= maximal disease.",,,,,,
+65736454,NCT02326298,primary,Proportion of Subjects Who Achieve a Physician's Global Assessment (PGA) Clear or Almost Clear (With at Least 2-category Improvement) Response at Week 16,At Week 16,,"The Investigator assessed the overall severity of Psoriasis (PSO) using the following 5-point scale: 0=clear, 1=almost clear, 2=mild, 3=moderate, 4=severe.",,,,,,
+65735593,NCT02340221,primary,Progression-Free Survival (PFS) as Assessed by Investigator Using Response Evaluation Criteria in Solid Tumors (RECIST) Version 1.1 (v1.1) at Primary Analysis,"From randomization until the first occurrence of disease progression or death from any cause, whichever occurs earlier (up to the 15 Oct 2017 data cutoff, approximately 2.5 years)",,"PFS was defined as the time from randomization to disease progression as determined by the investigator with the use of RECIST v1.1 or death due to any cause, whichever occurred earlier. Disease progression was defined as at least a 20% increase in the sum of diameters of target lesions, taking as reference the smallest sum on study, including baseline. In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 millimeters (mm). For non-target lesions, disease progression was defined as unequivocal progression of existing lesions. The appearance of one or more new lesions was also considered progression.",,,,,,
+65735594,NCT02340221,primary,PFS as Assessed by Investigator Using RECIST v1.1 at Final Analysis,"From randomization until the first occurrence of disease progression or death from any cause, whichever occurs earlier (up to approximately 6.2 years)",,"PFS was defined as the time from randomization to disease progression as determined by the investigator with the use of RECIST v1.1 or death due to any cause, whichever occurred earlier. Disease progression was defined as at least a 20% increase in the sum of diameters of target lesions, taking as reference the smallest sum on study, including baseline. In addition to the relative increase of 20%, the sum must also demonstrate an absolute increase of at least 5 mm. For non-target lesions, disease progression was defined as unequivocal progression of existing lesions. The appearance of one or more new lesions was also considered progression.",,,,,,
+65735264,NCT02343458,primary,Change From Baseline in Morning Pre-dose Trough FEV1 at Week 24 of Treatment (US/China Approach),at week 24,,"For the US/China approach, the primary endpoint was the change from baseline in morning pre-dose trough FEV1 at Week 24 of treatment",,,,,,
+65735265,NCT02343458,primary,"Change From Baseline in Morning Pre-dose Trough FEV1 Over Weeks 12-24, Japan Approach",over weeks 12-24,,"Change from baseline in morning pre-dose trough FEV1 over weeks 12-24, Japan approach",,,,,,
+65735266,NCT02343458,primary,"Change From Baseline in Morning Pre-dose Trough FEV1 Over 24 Weeks. Primary Endpoint, EU/SK/TW Approach, Secondary Endpoint US/China Approach.",over 24 weeks,,"Change from baseline in morning pre-dose trough FEV1 over 24 weeks. Primary endpoint, EU/SK/TW approach, Secondary endpoint US/China approach.",,,,,,
+65735069,NCT02346240,primary,Proportion of Subjects Who Achieve a Psoriasis Activity and Severity Index (PASI75) Response at Week 12,Week 12,,"The PASI75 response assessments are based on at least 75% improvement in the PASI score from Baseline. This is a scoring system that averages the redness, thickness, and scaliness of the psoriatic lesions (on a 0-4 scale), and weights the resulting score by the area of skin involved. Body divided into 4 areas: head, arms, trunk to groin, and legs to top of buttocks. Assignment of an average score for the redness, thickness, and scaling for each of the 4 body areas with a score of 0 (clear) to 4 (very marked). Determining the percentage of skin covered with PSO for each of the body areas and converting to a 0 to 6 scale. Final PASI= average redness, thickness, and scaliness of the psoriatic skin lesions, multiplied by the involved psoriasis area score of the respective section, and weighted by the percentage of the person's affected skin for the respective section. The minimum possible PASI score is 0= no disease, the maximum score is 72= maximal disease.",,,,,,
+65735047,NCT02346721,primary,Percentage of Participants With Sustained Virologic Response 12 Weeks After Discontinuation of Therapy (SVR12),Posttreatment Week 12,,SVR12 was defined as HCV RNA < the lower limit of quantitation (LLOQ) 12 weeks following the last dose of study drug.,,,,,,
+65735048,NCT02346721,primary,Percentage of Participants Who Permanently Discontinued Any Study Drug Due to an Adverse Event,Up to 12 weeks,,,,,,,,
+65733078,NCT02370498,primary,Progression-free Survival (PFS) According to Response Criteria in Solid Tumors Version 1.1 (RECIST 1.1) Based on Blinded Independent Central Review (BICR) in Programmed Death-Ligand 1 (PD-L1) Positive Participants,Up to 30 months (through database cut-off date of 26 Oct 2017),,"PFS was defined as the time from randomization to the first documented disease progression per RECIST 1.1 based on BICR, or death due to any cause, whichever occurs first. According to RECIST 1.1, progressive disease (PD) was defined as a 20% relative increase in the sum of diameters (SOD) of target lesions, taking as reference the nadir SOD and an absolute increase of >5 mm in the SOD, or the appearance of new lesions. PFS was analyzed using the Kaplan-Meier method and median PFS (95% confidence interval [CI]) in months was reported for PD-L1 positive participants by treatment group.",,,,,,
+65733079,NCT02370498,primary,Overall Survival (OS) in PD-L1 Positive Participants,Up to 30 months (through database cut-off date of 26 Oct 2017),,OS was defined as the time from randomization to death due to any cause. Participants without documented death at the time of the final analysis were censored at the date of the last follow-up. OS was analyzed using the Kaplan-Meier method and median OS (95% CI) in months was reported for PD-L1 positive participants by treatment group.,,,,,,
+65732884,NCT02373202,primary,Number of Participants With Treatment-Emergent Adverse Events (TEAEs) and Serious Adverse Events (SAEs),Baseline up to Week 58,,Adverse event (AE) was defined as any untoward medical occurrence in a participant who received IMP and did not necessary have to had a causal relationship with treatment. All AEs that occurred from the first dose of the IMP administration up to 6 weeks after last dose of treatment (up to Week 58) were considered as TEAEs. SAEs were AEs resulting in any of the following outcomes or deemed significant for any other reason: death, initial or prolonged inpatient hospitalization, life-threatening experience (immediate risk of dying), persistent or significant disability/incapacity, congenital anomaly or a medically important event. TEAEs included both SAEs and non-SAEs.,,
+65732885,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Vital Signs Abnormalities,Baseline up to Week 58,,"Criteria for potentially clinically significant vital sign abnormalities:
+
+Systolic blood pressure (SBP) supine: <=95 mmHg and decrease from baseline (DFB) >=20 mmHg; >=160 mmHg and increase from baseline (IFB) >=20 mmHg
+Diastolic blood pressure (DBP) supine: <=45 mmHg and DFB >=10 mmHg; >=110 mmHg and IFB ≥10 mmHg
+SBP (Orthostatic): <=-20 mmHg
+DBP (Orthostatic): <=-10 mmHg
+Heart rate (HR) supine: <=50 beats per minute (bpm) and DFB >=20 bpm; >=120 bpm and IFB >=20 bpm
+Weight: >=5% DFB; >=5% IFB",,,,,,
+65732886,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Electrocardiogram (ECG) Abnormalities,Baseline up to Week 58,,"Criteria for potentially clinically significant ECG abnormalities:
+
+PR Interval: >200 milliseconds (ms); >200 ms and IFB >=25%; >220 ms; >220 ms and IFB >=25%; >240 ms; >240 ms and IFB >=25%
+QRS Interval: >110 ms; >110 ms and IFB >=25%; >120 ms; >120 ms and IFB >=25%
+QT Interval: >500 ms
+QTc Bazett (QTc B): >450 ms; >480 ms; >500 ms; IFB >30 and <=60 ms, IFB >60 ms
+QTc Fridericia (QTc F): >450 ms; >480 ms; >500 ms; IFB >30 and <=60 ms; IFB >60 ms",,,,,,
+65732887,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Laboratory Abnormalities: Hematological Parameters,Baseline up to Week 58,,"Criteria for potentially clinically significant abnormalities:
+
+Hemoglobin: <=115 g/L (Male[M]) or <=95 g/L (Female[F]); >=185 g/L (M) or >=165 g/L (F); DFB >=20 g/L
+Hematocrit: <=0.37 v/v (M) or <=0.32 v/v (F); >=0.55 v/v (M) or >=0.5 v/v (F)
+Red blood cells (RBC): >=6 Tera/L
+Platelets: <50 Giga/L; >=50 and <100 Giga/L; >=700 Giga/L
+White blood cells (WBC): <3.0 Giga/L (Non-Black [NB]) or <2.0 Giga/L (Black [B]); >=16.0 Giga/L
+Neutrophils: <1.5 Giga/L (NB) or <1.0 Giga/L (B); <1.0 Giga/L
+Lymphocytes: <0.5 Giga/L; >=0.5 Giga/L and <lower limit of normal (LLN); >4.0 Giga/L
+Monocytes: >0.7 Giga/L
+Basophils: >0.1 Giga/L
+Eosinophils: >0.5 Giga/L or >upper limit of normal (ULN) (if ULN >=0.5 Giga/L)",,,,,,
+65732888,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Laboratory Abnormalities: Metabolic Parameters,Baseline up to Week 58,,"Criteria for potentially clinically significant abnormalities:
+
+Glucose: <=3.9 mmol/L and <LLN; >=11.1 mmol/L (unfasted [unfas]) or >=7 mmol/L (fasted [fas])
+Hemoglobin A1c (HbA1c): >8%
+Total cholesterol: >=6.2 mmol/L; >=7.74 mmol/L
+LDL cholesterol: >=4.1 mmol/L; >=4.9 mmol/L
+Triglycerides: >=4.6 mmol/L; >=5.6 mmol/L",,,,,,
+65732889,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Laboratory Abnormalities: Electrolytes,Baseline up to Week 58,,"Criteria for potentially clinically significant abnormalities:
+
+Sodium: <=129 mmol/L; >=160 mmol/L
+Potassium: <3 mmol/L; >=5.5 mmol/L
+Chloride: <80 mmol/L; >115 mmol/L",,,,,,
+65732890,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Laboratory Abnormalities: Renal Function Parameters,Baseline up to Week 58,,"Criteria for potentially clinically significant abnormalities:
+
+Creatinine: >=150 micromol/L (adults); >=30% change from baseline, >=100% change from baseline
+Creatinine clearance: <15 mL/min; >=15 to <30 mL/min; >=30 to <60 mL/min; >=60 to <90 mL/min
+Blood urea nitrogen: >=17 mmol/L
+Uric acid: <120 micromol/L; >408 micromol/L",,,,,,
+65732891,NCT02373202,primary,Number of Participants With Potentially Clinically Significant Laboratory Abnormalities: Liver Function Parameters,Baseline up to Week 58,,"Criteria for potentially clinically significant abnormalities:
+
+Alanine Aminotransferase (ALT): >1 ULN and <=1.5 ULN; >1.5 ULN and <=3 ULN; >3 ULN and <=5 ULN; >5 ULN and <=10 ULN; >10 ULN and <=20 ULN; >20 ULN
+Aspartate aminotransferase (AST): >1 ULN and <=1.5 ULN; >1.5 ULN and <=3 ULN; >3 ULN and <=5 ULN; >5 ULN and <=10 ULN; >10 ULN and <=20 ULN; >20 ULN
+Alkaline phosphatase: >1.5 ULN
+Total bilirubin (TBILI): >1.5 ULN; >2 ULN
+Conjugated bilirubin(CBILI): >1.5 ULN
+Unconjugated bilirubin: >1.5 ULN
+ALT >3 ULN and TBILI >2 ULN
+CBILI >35% TBILI and TBILI >1.5 ULN
+Albumin: <=25 g/L",,,,,,
+65732795,NCT02375971,primary,Percentage of Participants With Absence of Active ROP and Absence of Unfavorable Structural Outcomes in Both Eyes at Week 24,Week 24,,"To achieve this outcome, patients must fulfill all the following criteria, 1) survival, 2) no intervention with a second modality for ROP, 3) absence of active ROP and 4) absence of unfavorable structural outcome. Retinopathy of prematurity (ROP) is a pathologic process that occurs in the incompletely vascularized, developing retina of low birth-weight preterm neonates.",,,,,,
+66130931,NCT02381652,primary,Number of Treatment-Emergent Adverse Events: Cingal 13-02 vs. Cingal 13-01,Baseline through 6 weeks post-injection,,"The primary outcome measure will compare safety results (all adverse events, whether related to the study injection or not) for Cingal 13-01 and Cingal 13-02.",,,,,,
+65731360,NCT02396316,primary,Change in Intraocular Pressure (IOP) From Baseline to Pre-dose at Week 1,From baseline to pre-dose at Week 1,,It compared the change in IOP from baseline to pre-dose at Week 1 between the aflibercept group vs the sham group.,,,,,,
+65730311,NCT02410772,primary,"TB Disease-free Survival at 12M After Study Treatment Assignment Among Participants in Control Regimen, Regimen1 (2HRZE/4HR) to Experimental Regimens, Regimen3 (2HPZM/2HPM) and Regimen2 (2HPZ/2HP) (Modified Intent to Treat [MITT] Population)",Twelve months after treatment assignment,,"To evaluate the efficacy of a rifapentine-containing regimen to determine whether the single substitution of rifapentine for rifampin makes it possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis To evaluate the efficacy of a rifapentine-containing regimen that in addition substitutes moxifloxacin for ethambutol and continues moxifloxacin during the continuation phase, to determine whether it is possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis A primary outcome status of ""favorable"", ""unfavorable"", or ""not assessable"" was assigned. For detailed definitions of outcomes please refer to: Dorman SE, at al. N Engl J Med. 2021 May 6;384(18):1705-1718.",,,,,,
+65730312,NCT02410772,primary,"TB Disease-free Survival at 12M After Study Treatment Assignment Among Participants in Control Regimen, Regimen1 (2HRZE/4HR) to Experimental Regimens, Regimen3 (2HPZM/2HPM) and Regimen2 (2HPZ/2HP) (Assessable Population)",Twelve months after treatment assignment,,"To evaluate the efficacy of a rifapentine-containing regimen to determine whether the single substitution of rifapentine for rifampin makes it possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis
+To evaluate the efficacy of a rifapentine-containing regimen that in addition substitutes moxifloxacin for ethambutol and continues moxifloxacin during the continuation phase, to determine whether it is possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis A primary outcome status of ""favorable"", ""unfavorable"", or ""not assessable"" was assigned. For detailed definitions of outcomes please refer to: Dorman SE, at al. N Engl J Med. 2021 May 6;384(18):1705-1718.",,,,,,
+65730313,NCT02410772,primary,"Percentage Participants With Grade 3 or Higher Adverse Events During Study Drug Treatment in Control Regimen (Regimen 1 2HRZE/4HR) Compared to Experimental Regimens, Regimen 3 (2HPZM/2HPM) and Regimen 2 (2HPZ/2HP) (Safety Analysis Population)",Four months and up to 14 days after last does of after study treatment (Regimen 2 and 3) or Six months and up to 14 days after last does of after study treatment (Regimen 1),,"To evaluate the Safety of a rifapentine-containing regimen to determine whether the single substitution of rifapentine for rifampin makes it possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis
+To evaluate the Safety of a rifapentine-containing regimen that in addition substitutes moxifloxacin for ethambutol and continues moxifloxacin during the continuation phase, to determine whether it is possible to reduce to seventeen weeks the duration of treatment for drug-susceptible pulmonary tuberculosis Grade 3 or higher Adverse Events are collected by Clinical sites in systematic way through the laboratory tests and physical exam during regular study follow up visits and also in a non-systematic way when it was self-reported by participants during the study visits. The events are graded by site investigators per Common Terminology Criteria for Adverse Events (CTCAE V4.03",,,,,,
+64226215,NCT02425644,primary,Annualized Confirmed Relapse Rate,From randomization to end of study (Week 108),,"Relapse: occurrence of acute episode of one or more new symptoms or worsened symptoms of Multiple sclerosis (MS), not associated with fever/infection and lasting 24 hours after stable 30 days period. Confirmed relapse: increase from baseline at least 0.5 point Expanded Disability Status Scale (EDSS) score or increase of one point in one, two or three Functional Systems (FS), excluding bowel/bladder and cerebral/mental FS. EDSS and FS scores are based on neurological examination for assessing its impairment in MS. Among eight FS, seven are ordinal clinical rating scales ranging from 0-5 or 6 with higher scale indicates overall functional impairment assessing Visual,Brain Stem,Pyramidal,Cerebellar,Sensory, Bowel/Bladder and Cerebral functions. Rating individual FS scores is used to rate EDSS in conjunction with observations and information concerning gait and use of assistance. EDSS is ordinal clinical rating scale ranging from 0 (normal neurological examination) to 10(death due to MS).",,,,,,
+65728673,NCT02434328,primary,Change From Baseline in Best Corrected Visual Acuity (BCVA) (Letters Read) at Week 48 - Study Eye,"Baseline, Week 48",,BCVA (with spectacles or other visual corrective devices) was assessed using Early Treatment Diabetic Retinopathy Study (ETDRS) testing at 4 meters and reported in letters read correctly. Baseline was defined as the last measurement prior to first treatment. An increase (gain) in letters read from the baseline assessment indicates improvement. One eye (study eye) contributed to the analysis.,,,,,,
+65728403,NCT02437162,primary,Percentage of Participants Who Achieved an Assessment of Spondyloarthritis International Society (ASAS) 40 Response at Week 24,Week 24,,"ASAS 40 defined as improvement from baseline of greater than or equal to (>=) 40 percent (%) and absolute improvement from baseline of at least 2 on 0 to 10 centimeter (cm) scale in at least 3 of following 4 domains: Patient's global assessment (0 to 10cm; 0=very well,10=very poor),total back pain (0 to 10cm; 0=no pain,10=most severe pain), BASFI (self-assessment represented as mean (0 to 10 cm; 0=easy to 10=impossible) of 10 questions, 8 of which relate to participant's functional anatomy and 2 relate to participant's ability to cope with everyday life), Inflammation(0 to 10cm;0=none,10=very severe); no worsening at all from baseline in remaining domain. ASAS40 response based on imputed data using treatment failure(consider non-responders at and after treatment failure),early escape rules(consider non-responder at Week 20 and 24),non-responder[NRI] (missing responses at post baseline visit imputed as non-responder).",,,,,,
+65726374,NCT02462486,primary,Percentage of Participants With Stable Vision at Week 52,Baseline to Week 52,,"Stable vision was defined as vision loss of fewer than 15 letters in Best-corrected Visual Acuity (BCVA) from baseline. BCVA is measured using an eye chart and is reported as the number of letters read correctly using the ETDRS Scale (ranging from 0 to 100 letters) in the study eye. The lower the number of letters read correctly on the eye chart, the worse the vision (or visual acuity). An increase in the number of letters read correctly means that vision has improved. The percentage of participants with a BCVA loss of fewer than 15 letters are reported. Study eye was defined as the eye that meets the entry criteria. If both the eyes met all of the entry criteria, the eye with worse BCVA at baseline (Day 1) was selected. If BCVA values for both eyes were identical then participant had to select the non-dominant eye, or else right eye was selected as study eye.",,,,,,
+65726321,NCT02462928,primary,Percentage of Participants With Stable Vision at Week 52,Baseline to Week 52,,"Stable vision was defined as a loss of fewer than 15 letters in BCVA compared to baseline. BCVA was measured using an eye chart and reported as the number of letters read correctly using the Early Treatment of Diabetic Retinopathy Study (ETDRS) Scale (ranging from 0 to 100 letters) in the study eye. The lower the number of letters read correctly on the eye chart, the worse the vision (or visual acuity). An increase in the number of letters read correctly means that vision has improved. The percentage of participants with a BCVA loss of fewer than 15 letters are reported. The study eye is defined as the eye that meets the entry criteria. If both eyes met the entry criteria, the eye with the worse BCVA at baseline (Day 1) was selected as the study eye. If both eyes had same BCVA values at baseline (Day 1), then the participant had to select their non-dominant eye for treatment, or else the right eye was selected as the study eye.",,,,,,
+65725831,NCT02472886,primary,Percentage of Participants With Sustained Virologic Response 12 Weeks After Discontinuation of Therapy (SVR12),Posttreatment Week 12,,SVR12 was defined as HCV RNA < the lower limit of quantitation (LLOQ) 12 weeks following the last dose of study drug.,,,,,,
+65725832,NCT02472886,primary,Percentage of Participants Who Discontinued Study Drug Due to Any Adverse Event (AE),Up to 12 weeks,,,,,,,,
+65719724,NCT02540954,primary,Mean Change in Early Treatment Diabetic Retinopathy Study (ETDRS) Best-corrected Visual Acuity (BCVA) Letter Score for the Study Eye,From baseline to Week 52,,"Visual function was assessed with the procedure from the ETDRS adapted for the Age Related Eye Disease Study using charts with 70 letters at a starting distance of 4 meters. Charts are organized in 14 lines of decreasing size with 5 letters each. Participants reading up to 19 letters at 4 meters were tested at 1 meter to read the first 6 lines. The score equals the sum of letters read at 1 meter and 4 meters. If more than 19 letters are read at 4 meters the score equals the number of letters read plus 30. The score range is 0 to 100, and a higher score represents better visual function.",,,,,,

llm-extractor/prompt_nuextractor

@@ -0,0 +1,19 @@
+### Template:
+{
+    "longest_observation_scalar": "",
+    "longest_observation_unit": "",
+}
+### Examples:
+
+
+### Text:
+
+{ "longest_observation_scalar": 3, "longest_observation_unit": "weeks" }
+{ "longest_observation_scalar": 4,   "longest_observation_unit": "months"}
+{ "longest_observation_scalar": 14,   "longest_observation_unit": "months"}
+{ "longest_observation_scalar": 48,   "longest_observation_unit": "weeks"}
+{ "longest_observation_scalar": 14,   "longest_observation_unit": "months"}
+{ "longest_observation_scalar": null, "longest_observation_unit": null }
+{ "longest_observation_scalar": null, "longest_observation_unit": null }
+
+"""

logs.org

@@ -0,0 +1,140 @@
+* Plan/Todo [2025-01-06]
+Goal is to update the main images with more details, i.e. adding means
+etc.
+
+- get aact_db back up
+- attach it to a "research" network
+- restart rocker, attaching it to the same research network.
+
+** NOTES
+
+aact_db-restored-2024-11-27 didn't successfully restore. It is missing
+all the important stuff.
+
+Figured out why the restore was failing. My code to restore had a faulty
+check to see if the DB was up and ready. Fixed that now.
+
+Waiting for restore (manually triggered) to start. Then I should have
+access to the table as needed.
+
+It seems like I'm missing some data within a schema, specifically the
+Formularies and their associated views.
+
+My options are:
+
+- search around for documentation or other stuff
+- try to rebuild
+
+my suspision is that I forgot to back it up. I think it is probably
+worth looking for. - So I've been looking through my copy of
+ClinicalTrialsDataProcessing, and have not found anything referencing
+it. The formularies data is required for my analysis though. If I
+remember correctly, I manually uploaded the USP datasets in DBeaver,
+then created any views etc.
+
+I think that I'll have to recreate it. This is going to be hard because
+I'm not sure what it did. At least I created mildly informative table
+names.
+
+The tables/views I've identified are: -
+=Formularies.nct_to_brands_through_uspdc=
+
+It looks like I need to - import usp-dc dataset - link those drugs to
+usp data - create a view that links those automatically - back it up. -
+double check the data I get from the request.
+
+The links will be through RXCUIs, and grouped on =USP Class= In effect,
+for a given RXCUI, I want to get the list of RXCUI's which have the same
+USP-DC class, and then be able to link back to brands.
+
+This should have the following links: - RXCUI -> USP-DC category/class
+pair - USP-DC category/class pair -> RXCUIs - RXUCIs -> competitors
+
+Do I want to combine the USP-DC and UPS-MMG datasets? No, there is
+enough difference in them that I don't want to have to handle it that
+way.
+
+I've been working on this in scripts/ConfiguringFormularies.sql
+
+So what I've managed to do so far is export tables, backup the data.
+
+I've got a version that connects trials to brand names, but there may be
+more details to the connection than I thought. I'd like to check if I
+need to filter anything or check if there are other ingredients etc that
+I need to include. */I probably need to write some descriptions of all
+the tables and views to put everything together. An ai would probably be
+helpful in doing this./*
+
+
+** Code snippets
+#+begin_example
+podman run \
+ -e POSTGRES_PASSWORD="${POSTGRES_PASSWORD}" \
+ -e POSTGRES_USER="${POSTGRES_USER}" \
+ -e POSTGRES_DB="${POSTGRES_DB}" \
+ --name "${CONTAINER_NAME}" \
+ --detach \
+ --network research-network \
+ --shm-size=512mb \
+ --volume ./backup/:/backup/ \
+ -p 5432:5432\
+ postgres:14-alpine
+#+end_example
+
+#+begin_example
+function check_postgres {
+podman exec -i "${POSTGRES_DB}" psql -h localhost -U "${POSTGRES_USER}" -d "${POSTGRES_DB}" -c '\q' > /dev/null 2>&1    
+}
+#+end_example
+
+** Notes at end of day
+- was reasonably productive in getting stuff unblocked for finishing
+  JMP, which i'll need to do before I leave town next week.
+
+
+** What I've got to do tomorrow
+I've got a version that connects trials to brand names, but there may be
+more details to the connection than I thought. I'd like to check if I
+need to filter anything or check if there are other ingredients etc that
+I need to include. */I probably need to write some descriptions of all
+the tables and views to put everything together. An ai would probably be
+helpful in doing this./* At the end of it all, I should be able to get a
+count of competing drugs per trial.
+
+Once that is done, I can relink aact_db and rocker, then rerun my
+analysis. Then I can adjust the images that I need for my JMP.
+* [2025-01-07 Tue 12:01] notes
+
+  So what I've got to do is 
+
+** DONE  Investigate what compounds are showing up in my current list
+    if that is what I want, then I'll be able proceed with redoing my images
+   if not, then I'll have to work on adjusting the views etc that I have.
+
+   I've looked through it and it seems to correct.
+
+*** [[/mnt/will/large_data/Research_large_data/ClinicalTrialsDataProcessing/Scripts/ConfiguringFormularies.sql][ConfiguringFormularies.sql:81]] [2025-01-07 Tue 13:24] 
+  I've tweaked these three views to make them clearer.
+  I also renamed the view of interest to ="Formularies".nct_to_brand_counts_through_uspdc= to better represent what it does.
+
+
+** DONE Rerun the analysis
+   CLOSED: [2025-01-07 Tue 16:39]
+    So it looks like I'll need to 
+    1. take a backup of aact_db
+    2. restore from backup, putting the container in the research network
+    3. then rerun the analysis.
+
+      Ok, I'm pushing the backup and can get started on restoring from backup.
+      Backup is restoring. As I recall, this takes 40 minutes.
+   
+      had some mild tweaks to match the new results
+   it now runs
+
+** DONE Add more details to images
+   CLOSED: [2025-01-13 Mon 10:26]
+    The details I want to add include:
+
+    - [x] sample sizes for breakdowns
+    - [x] box and whisker plot along the bottom of the large values
+   [[https://claude.ai/chat/0e6b6368-130e-4aa8-aa16-97b6c937bba4]] has details

non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/source

@@ -0,0 +1 @@
+https://doi.org/10.6069/GHCW-8955

non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Global Burden of Disease Study 2019 (GBD 2019) Cause, REI, and Location Hierarchies/.~lock.IHME_GBD_2019_CAUSE_HIERARCHY_Y2020M11D25.csv#

@@ -0,0 +1 @@
+,dad,home-pc,03.04.2023 15:13,file:///home/dad/.config/libreoffice/4;

non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Global Burden of Disease Study 2019 (GBD 2019) Cause, REI, and Location Hierarchies/IHME_GBD_2019_CAUSE_HIERARCHY_Y2020M11D25.csv

@@ -0,0 +1,365 @@
+Cause ID,Cause Name,Parent ID,Parent Name,Level,Cause Outline,Sort Order,YLL Only,YLD Only
+294,All causes,294,All causes,0,Total,1,,
+295,"Communicable, maternal, neonatal, and nutritional diseases",294,All causes,1,A,2,,
+955,HIV/AIDS and sexually transmitted infections,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.1,3,,
+298,HIV/AIDS,955,HIV/AIDS and sexually transmitted infections,3,A.1.1,4,,
+948,HIV/AIDS - Drug-susceptible Tuberculosis,298,HIV/AIDS,4,A.1.1.1,5,,
+949,HIV/AIDS - Multidrug-resistant Tuberculosis without extensive drug resistance,298,HIV/AIDS,4,A.1.1.2,6,,
+950,HIV/AIDS - Extensively drug-resistant Tuberculosis,298,HIV/AIDS,4,A.1.1.3,7,,
+300,HIV/AIDS resulting in other diseases,298,HIV/AIDS,4,A.1.1.4,8,,
+393,Sexually transmitted infections excluding HIV,955,HIV/AIDS and sexually transmitted infections,3,A.1.2,9,,
+394,Syphilis,393,Sexually transmitted infections excluding HIV,4,A.1.2.1,10,,
+395,Chlamydial infection,393,Sexually transmitted infections excluding HIV,4,A.1.2.2,11,,
+396,Gonococcal infection,393,Sexually transmitted infections excluding HIV,4,A.1.2.3,12,,
+397,Trichomoniasis,393,Sexually transmitted infections excluding HIV,4,A.1.2.4,13,,X
+398,Genital herpes,393,Sexually transmitted infections excluding HIV,4,A.1.2.5,14,,X
+399,Other sexually transmitted infections,393,Sexually transmitted infections excluding HIV,4,A.1.2.6,15,,
+956,Respiratory infections and tuberculosis,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.2,16,,
+297,Tuberculosis,956,Respiratory infections and tuberculosis,3,A.2.1,17,,
+954,Latent tuberculosis infection,297,Tuberculosis,4,A.2.1.1,18,,X
+934,Drug-susceptible tuberculosis,297,Tuberculosis,4,A.2.1.2,19,,
+946,Multidrug-resistant tuberculosis without extensive drug resistance,297,Tuberculosis,4,A.2.1.3,20,,
+947,Extensively drug-resistant tuberculosis,297,Tuberculosis,4,A.2.1.4,21,,
+322,Lower respiratory infections,956,Respiratory infections and tuberculosis,3,A.2.2,22,,
+328,Upper respiratory infections,956,Respiratory infections and tuberculosis,3,A.2.3,23,,
+329,Otitis media,956,Respiratory infections and tuberculosis,3,A.2.4,24,,
+957,Enteric infections,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.3,25,,
+302,Diarrheal diseases,957,Enteric infections,3,A.3.1,26,,
+958,Typhoid and paratyphoid,957,Enteric infections,3,A.3.2,27,,
+319,Typhoid fever,958,Typhoid and paratyphoid,4,A.3.2.1,28,,
+320,Paratyphoid fever,958,Typhoid and paratyphoid,4,A.3.2.2,29,,
+959,Invasive Non-typhoidal Salmonella (iNTS),957,Enteric infections,3,A.3.3,30,,
+321,Other intestinal infectious diseases,957,Enteric infections,3,A.3.4,31,,
+344,Neglected tropical diseases and malaria,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.4,32,,
+345,Malaria,344,Neglected tropical diseases and malaria,3,A.4.1,33,,
+346,Chagas disease,344,Neglected tropical diseases and malaria,3,A.4.2,34,,
+347,Leishmaniasis,344,Neglected tropical diseases and malaria,3,A.4.3,35,,
+348,Visceral leishmaniasis,347,Leishmaniasis,4,A.4.3.1,36,,
+349,Cutaneous and mucocutaneous leishmaniasis,347,Leishmaniasis,4,A.4.3.2,37,,X
+350,African trypanosomiasis,344,Neglected tropical diseases and malaria,3,A.4.4,38,,
+351,Schistosomiasis,344,Neglected tropical diseases and malaria,3,A.4.5,39,,
+352,Cysticercosis,344,Neglected tropical diseases and malaria,3,A.4.6,40,,
+353,Cystic echinococcosis,344,Neglected tropical diseases and malaria,3,A.4.7,41,,
+354,Lymphatic filariasis,344,Neglected tropical diseases and malaria,3,A.4.8,42,,X
+355,Onchocerciasis,344,Neglected tropical diseases and malaria,3,A.4.9,43,,X
+356,Trachoma,344,Neglected tropical diseases and malaria,3,A.4.10,44,,X
+357,Dengue,344,Neglected tropical diseases and malaria,3,A.4.11,45,,
+358,Yellow fever,344,Neglected tropical diseases and malaria,3,A.4.12,46,,
+359,Rabies,344,Neglected tropical diseases and malaria,3,A.4.13,47,,
+360,Intestinal nematode infections,344,Neglected tropical diseases and malaria,3,A.4.14,48,,
+361,Ascariasis,360,Intestinal nematode infections,4,A.4.14.1,49,,
+362,Trichuriasis,360,Intestinal nematode infections,4,A.4.14.2,50,,X
+363,Hookworm disease,360,Intestinal nematode infections,4,A.4.14.3,51,,X
+364,Food-borne trematodiases,344,Neglected tropical diseases and malaria,3,A.4.15,52,,X
+405,Leprosy,344,Neglected tropical diseases and malaria,3,A.4.16,53,,X
+843,Ebola,344,Neglected tropical diseases and malaria,3,A.4.17,54,,
+935,Zika virus,344,Neglected tropical diseases and malaria,3,A.4.18,55,,
+936,Guinea worm disease,344,Neglected tropical diseases and malaria,3,A.4.19,56,,X
+365,Other neglected tropical diseases,344,Neglected tropical diseases and malaria,3,A.4.20,57,,
+961,Other infectious diseases,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.5,58,,
+332,Meningitis,961,Other infectious diseases,3,A.5.1,59,,
+337,Encephalitis,961,Other infectious diseases,3,A.5.2,60,,
+338,Diphtheria,961,Other infectious diseases,3,A.5.3,61,,
+339,Whooping cough,961,Other infectious diseases,3,A.5.4,62,,
+340,Tetanus,961,Other infectious diseases,3,A.5.5,63,,
+341,Measles,961,Other infectious diseases,3,A.5.6,64,,
+342,Varicella and herpes zoster,961,Other infectious diseases,3,A.5.7,65,,
+400,Acute hepatitis,961,Other infectious diseases,3,A.5.8,66,,
+401,Acute hepatitis A,400,Acute hepatitis,4,A.5.8.1,67,,
+402,Acute hepatitis B,400,Acute hepatitis,4,A.5.8.2,68,,
+403,Acute hepatitis C,400,Acute hepatitis,4,A.5.8.3,69,,
+404,Acute hepatitis E,400,Acute hepatitis,4,A.5.8.4,70,,
+408,Other unspecified infectious diseases,961,Other infectious diseases,3,A.5.9,71,,
+962,Maternal and neonatal disorders,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.6,72,,
+366,Maternal disorders,962,Maternal and neonatal disorders,3,A.6.1,73,,
+367,Maternal hemorrhage,366,Maternal disorders,4,A.6.1.1,74,,
+368,Maternal sepsis and other maternal infections,366,Maternal disorders,4,A.6.1.2,75,,
+369,Maternal hypertensive disorders,366,Maternal disorders,4,A.6.1.3,76,,
+370,Maternal obstructed labor and uterine rupture,366,Maternal disorders,4,A.6.1.4,77,,
+995,Maternal abortion and miscarriage,366,Maternal disorders,4,A.6.1.5,78,,
+374,Ectopic pregnancy,366,Maternal disorders,4,A.6.1.6,79,,
+375,Indirect maternal deaths,366,Maternal disorders,4,A.6.1.7,80,X,
+376,Late maternal deaths,366,Maternal disorders,4,A.6.1.8,81,X,
+741,Maternal deaths aggravated by HIV/AIDS,366,Maternal disorders,4,A.6.1.9,82,X,
+379,Other maternal disorders,366,Maternal disorders,4,A.6.1.10,83,,
+380,Neonatal disorders,962,Maternal and neonatal disorders,3,A.6.2,84,,
+381,Neonatal preterm birth,380,Neonatal disorders,4,A.6.2.1,85,,
+382,Neonatal encephalopathy due to birth asphyxia and trauma,380,Neonatal disorders,4,A.6.2.2,86,,
+383,Neonatal sepsis and other neonatal infections,380,Neonatal disorders,4,A.6.2.3,87,,
+384,Hemolytic disease and other neonatal jaundice,380,Neonatal disorders,4,A.6.2.4,88,,
+385,Other neonatal disorders,380,Neonatal disorders,4,A.6.2.5,89,,
+386,Nutritional deficiencies,295,"Communicable, maternal, neonatal, and nutritional diseases",2,A.7,90,,
+387,Protein-energy malnutrition,386,Nutritional deficiencies,3,A.7.1,91,,
+388,Iodine deficiency,386,Nutritional deficiencies,3,A.7.2,92,,X
+389,Vitamin A deficiency,386,Nutritional deficiencies,3,A.7.3,93,,X
+390,Dietary iron deficiency,386,Nutritional deficiencies,3,A.7.4,94,,X
+391,Other nutritional deficiencies,386,Nutritional deficiencies,3,A.7.5,95,,
+409,Non-communicable diseases,294,All causes,1,B,96,,
+410,Neoplasms,409,Non-communicable diseases,2,B.1,97,,
+444,Lip and oral cavity cancer,410,Neoplasms,3,B.1.1,98,,
+447,Nasopharynx cancer,410,Neoplasms,3,B.1.2,99,,
+450,Other pharynx cancer,410,Neoplasms,3,B.1.3,100,,
+411,Esophageal cancer,410,Neoplasms,3,B.1.4,101,,
+414,Stomach cancer,410,Neoplasms,3,B.1.5,102,,
+441,Colon and rectum cancer,410,Neoplasms,3,B.1.6,103,,
+417,Liver cancer,410,Neoplasms,3,B.1.7,104,,
+418,Liver cancer due to hepatitis B,417,Liver cancer,4,B.1.7.1,105,,
+419,Liver cancer due to hepatitis C,417,Liver cancer,4,B.1.7.2,106,,
+420,Liver cancer due to alcohol use,417,Liver cancer,4,B.1.7.3,107,,
+996,Liver cancer due to NASH,417,Liver cancer,4,B.1.7.4,108,,
+1021,Liver cancer due to other causes,417,Liver cancer,4,B.1.7.5,109,,
+453,Gallbladder and biliary tract cancer,410,Neoplasms,3,B.1.8,110,,
+456,Pancreatic cancer,410,Neoplasms,3,B.1.9,111,,
+423,Larynx cancer,410,Neoplasms,3,B.1.10,112,,
+426,"Tracheal, bronchus, and lung cancer",410,Neoplasms,3,B.1.11,113,,
+459,Malignant skin melanoma,410,Neoplasms,3,B.1.12,114,,
+462,Non-melanoma skin cancer,410,Neoplasms,3,B.1.13,115,,
+849,Non-melanoma skin cancer (squamous-cell carcinoma),462,Non-melanoma skin cancer,4,B.1.13.1,116,,
+850,Non-melanoma skin cancer (basal-cell carcinoma),462,Non-melanoma skin cancer,4,B.1.13.2,117,,X
+429,Breast cancer,410,Neoplasms,3,B.1.14,118,,
+432,Cervical cancer,410,Neoplasms,3,B.1.15,119,,
+435,Uterine cancer,410,Neoplasms,3,B.1.16,120,,
+465,Ovarian cancer,410,Neoplasms,3,B.1.17,121,,
+438,Prostate cancer,410,Neoplasms,3,B.1.18,122,,
+468,Testicular cancer,410,Neoplasms,3,B.1.19,123,,
+471,Kidney cancer,410,Neoplasms,3,B.1.20,124,,
+474,Bladder cancer,410,Neoplasms,3,B.1.21,125,,
+477,Brain and central nervous system cancer,410,Neoplasms,3,B.1.22,126,,
+480,Thyroid cancer,410,Neoplasms,3,B.1.23,127,,
+483,Mesothelioma,410,Neoplasms,3,B.1.24,128,,
+484,Hodgkin lymphoma,410,Neoplasms,3,B.1.25,129,,
+485,Non-Hodgkin lymphoma,410,Neoplasms,3,B.1.26,130,,
+486,Multiple myeloma,410,Neoplasms,3,B.1.27,131,,
+487,Leukemia,410,Neoplasms,3,B.1.28,132,,
+845,Acute lymphoid leukemia,487,Leukemia,4,B.1.28.1,133,,
+846,Chronic lymphoid leukemia,487,Leukemia,4,B.1.28.2,134,,
+847,Acute myeloid leukemia,487,Leukemia,4,B.1.28.3,135,,
+848,Chronic myeloid leukemia,487,Leukemia,4,B.1.28.4,136,,
+943,Other leukemia,487,Leukemia,4,B.1.28.5,137,,
+1022,Other malignant neoplasms,410,Neoplasms,3,B.1.29,138,,
+490,Other neoplasms,410,Neoplasms,3,B.1.30,139,,
+964,"Myelodysplastic, myeloproliferative, and other hematopoietic neoplasms",490,Other neoplasms,4,B.1.30.1,140,,
+965,Benign and in situ intestinal neoplasms,490,Other neoplasms,4,B.1.30.2,141,,X
+966,Benign and in situ cervical and uterine neoplasms,490,Other neoplasms,4,B.1.30.3,142,,X
+967,Other benign and in situ neoplasms,490,Other neoplasms,4,B.1.30.4,143,,X
+491,Cardiovascular diseases,409,Non-communicable diseases,2,B.2,144,,
+492,Rheumatic heart disease,491,Cardiovascular diseases,3,B.2.1,145,,
+493,Ischemic heart disease,491,Cardiovascular diseases,3,B.2.2,146,,
+494,Stroke,491,Cardiovascular diseases,3,B.2.3,147,,
+495,Ischemic stroke,494,Stroke,4,B.2.3.1,148,,
+496,Intracerebral hemorrhage,494,Stroke,4,B.2.3.2,149,,
+497,Subarachnoid hemorrhage,494,Stroke,4,B.2.3.3,150,,
+498,Hypertensive heart disease,491,Cardiovascular diseases,3,B.2.4,151,,
+504,Non-rheumatic valvular heart disease,491,Cardiovascular diseases,3,B.2.5,152,,
+968,Non-rheumatic calcific aortic valve disease,504,Non-rheumatic valvular heart disease,4,B.2.5.1,153,,
+969,Non-rheumatic degenerative mitral valve disease,504,Non-rheumatic valvular heart disease,4,B.2.5.2,154,,
+970,Other non-rheumatic valve diseases,504,Non-rheumatic valvular heart disease,4,B.2.5.3,155,,
+499,Cardiomyopathy and myocarditis,491,Cardiovascular diseases,3,B.2.6,156,,
+942,Myocarditis,499,Cardiomyopathy and myocarditis,4,B.2.6.1,157,,
+938,Alcoholic cardiomyopathy,499,Cardiomyopathy and myocarditis,4,B.2.6.2,158,,
+944,Other cardiomyopathy,499,Cardiomyopathy and myocarditis,4,B.2.6.3,159,,
+500,Atrial fibrillation and flutter,491,Cardiovascular diseases,3,B.2.8,160,,
+501,Aortic aneurysm,491,Cardiovascular diseases,3,B.2.9,161,X,
+502,Peripheral artery disease,491,Cardiovascular diseases,3,B.2.10,162,,
+503,Endocarditis,491,Cardiovascular diseases,3,B.2.11,163,,
+1023,Other cardiovascular and circulatory diseases,491,Cardiovascular diseases,3,B.2.12,164,,
+508,Chronic respiratory diseases,409,Non-communicable diseases,2,B.3,165,,
+509,Chronic obstructive pulmonary disease,508,Chronic respiratory diseases,3,B.3.1,166,,
+510,Pneumoconiosis,508,Chronic respiratory diseases,3,B.3.2,167,,
+511,Silicosis,510,Pneumoconiosis,4,B.3.2.1,168,,
+512,Asbestosis,510,Pneumoconiosis,4,B.3.2.2,169,,
+513,Coal workers pneumoconiosis,510,Pneumoconiosis,4,B.3.2.3,170,,
+514,Other pneumoconiosis,510,Pneumoconiosis,4,B.3.2.4,171,,
+515,Asthma,508,Chronic respiratory diseases,3,B.3.3,172,,
+516,Interstitial lung disease and pulmonary sarcoidosis,508,Chronic respiratory diseases,3,B.3.4,173,,
+520,Other chronic respiratory diseases,508,Chronic respiratory diseases,3,B.3.5,174,,
+526,Digestive diseases,409,Non-communicable diseases,2,B.4,175,,
+521,Cirrhosis and other chronic liver diseases,526,Digestive diseases,3,B.4.1,176,,
+522,Cirrhosis and other chronic liver diseases due to hepatitis B,521,Cirrhosis and other chronic liver diseases,4,B.4.1.1,177,,
+523,Cirrhosis and other chronic liver diseases due to hepatitis C,521,Cirrhosis and other chronic liver diseases,4,B.4.1.2,178,,
+524,Cirrhosis and other chronic liver diseases due to alcohol use,521,Cirrhosis and other chronic liver diseases,4,B.4.1.3,179,,
+971,Cirrhosis and other chronic liver diseases due to NAFLD,521,Cirrhosis and other chronic liver diseases,4,B.4.1.4,180,,
+525,Cirrhosis and other chronic liver diseases due to other causes,521,Cirrhosis and other chronic liver diseases,4,B.4.1.5,181,,
+992,Upper digestive system diseases,526,Digestive diseases,3,B.4.2,182,,
+527,Peptic ulcer disease,992,Upper digestive system diseases,4,B.4.2.1,183,,
+528,Gastritis and duodenitis,992,Upper digestive system diseases,4,B.4.2.2,184,,
+536,Gastroesophageal reflux disease,992,Upper digestive system diseases,4,B.4.2.3,185,,X
+529,Appendicitis,526,Digestive diseases,3,B.4.3,186,,
+530,Paralytic ileus and intestinal obstruction,526,Digestive diseases,3,B.4.4,187,,
+531,"Inguinal, femoral, and abdominal hernia",526,Digestive diseases,3,B.4.5,188,,
+532,Inflammatory bowel disease,526,Digestive diseases,3,B.4.6,189,,
+533,Vascular intestinal disorders,526,Digestive diseases,3,B.4.7,190,,
+534,Gallbladder and biliary diseases,526,Digestive diseases,3,B.4.8,191,,
+535,Pancreatitis,526,Digestive diseases,3,B.4.9,192,,
+541,Other digestive diseases,526,Digestive diseases,3,B.4.10,193,,
+542,Neurological disorders,409,Non-communicable diseases,2,B.5,194,,
+543,Alzheimer's disease and other dementias,542,Neurological disorders,3,B.5.1,195,,
+544,Parkinson's disease,542,Neurological disorders,3,B.5.2,196,,
+545,Idiopathic epilepsy,542,Neurological disorders,3,B.5.3,197,,
+546,Multiple sclerosis,542,Neurological disorders,3,B.5.4,198,,
+554,Motor neuron disease,542,Neurological disorders,3,B.5.5,199,,
+972,Headache disorders,542,Neurological disorders,3,B.5.6,200,,X
+547,Migraine,972,Headache disorders,4,B.5.6.1,201,,X
+548,Tension-type headache,972,Headache disorders,4,B.5.6.2,202,,X
+557,Other neurological disorders,542,Neurological disorders,3,B.5.7,203,,
+558,Mental disorders,409,Non-communicable diseases,2,B.6,204,,
+559,Schizophrenia,558,Mental disorders,3,B.6.1,205,,X
+567,Depressive disorders,558,Mental disorders,3,B.6.2,206,,X
+568,Major depressive disorder,567,Depressive disorders,4,B.6.2.1,207,,X
+569,Dysthymia,567,Depressive disorders,4,B.6.2.2,208,,X
+570,Bipolar disorder,558,Mental disorders,3,B.6.3,209,,X
+571,Anxiety disorders,558,Mental disorders,3,B.6.4,210,,X
+572,Eating disorders,558,Mental disorders,3,B.6.5,211,,
+573,Anorexia nervosa,572,Eating disorders,4,B.6.5.1,212,,
+574,Bulimia nervosa,572,Eating disorders,4,B.6.5.2,213,,
+575,Autism spectrum disorders,558,Mental disorders,3,B.6.6,214,,X
+578,Attention-deficit/hyperactivity disorder,558,Mental disorders,3,B.6.7,215,,X
+579,Conduct disorder,558,Mental disorders,3,B.6.8,216,,X
+582,Idiopathic developmental intellectual disability,558,Mental disorders,3,B.6.9,217,,X
+585,Other mental disorders,558,Mental disorders,3,B.6.10,218,,X
+973,Substance use disorders,409,Non-communicable diseases,2,B.7,219,,
+560,Alcohol use disorders,973,Substance use disorders,3,B.7.1,220,,
+561,Drug use disorders,973,Substance use disorders,3,B.7.2,221,,
+562,Opioid use disorders,561,Drug use disorders,4,B.7.2.1,222,,
+563,Cocaine use disorders,561,Drug use disorders,4,B.7.2.2,223,,
+564,Amphetamine use disorders,561,Drug use disorders,4,B.7.2.3,224,,
+565,Cannabis use disorders,561,Drug use disorders,4,B.7.2.4,225,,X
+566,Other drug use disorders,561,Drug use disorders,4,B.7.2.5,226,,
+974,Diabetes and kidney diseases,409,Non-communicable diseases,2,B.8,227,,
+587,Diabetes mellitus,974,Diabetes and kidney diseases,3,B.8.1,228,,
+975,Diabetes mellitus type 1,587,Diabetes mellitus,4,B.8.1.1,229,,
+976,Diabetes mellitus type 2,587,Diabetes mellitus,4,B.8.1.2,230,,
+589,Chronic kidney disease,974,Diabetes and kidney diseases,3,B.8.2,231,,
+997,Chronic kidney disease due to diabetes mellitus type 1,589,Chronic kidney disease,4,B.8.2.1,232,,
+998,Chronic kidney disease due to diabetes mellitus type 2,589,Chronic kidney disease,4,B.8.2.2,233,,
+591,Chronic kidney disease due to hypertension,589,Chronic kidney disease,4,B.8.2.3,234,,
+592,Chronic kidney disease due to glomerulonephritis,589,Chronic kidney disease,4,B.8.2.4,235,,
+593,Chronic kidney disease due to other and unspecified causes,589,Chronic kidney disease,4,B.8.2.5,236,,
+588,Acute glomerulonephritis,974,Diabetes and kidney diseases,3,B.8.3,237,,
+653,Skin and subcutaneous diseases,409,Non-communicable diseases,2,B.9,238,,
+654,Dermatitis,653,Skin and subcutaneous diseases,3,B.9.1,239,,X
+977,Atopic dermatitis,654,Dermatitis,4,B.9.1.1,240,,X
+978,Contact dermatitis,654,Dermatitis,4,B.9.1.2,241,,X
+979,Seborrhoeic dermatitis,654,Dermatitis,4,B.9.1.3,242,,X
+655,Psoriasis,653,Skin and subcutaneous diseases,3,B.9.2,243,,X
+980,Bacterial skin diseases,653,Skin and subcutaneous diseases,3,B.9.3,244,,
+656,Cellulitis,980,Bacterial skin diseases,4,B.9.3.1,245,,
+657,Pyoderma,980,Bacterial skin diseases,4,B.9.3.2,246,,
+658,Scabies,653,Skin and subcutaneous diseases,3,B.9.4,247,,X
+659,Fungal skin diseases,653,Skin and subcutaneous diseases,3,B.9.5,248,,X
+660,Viral skin diseases,653,Skin and subcutaneous diseases,3,B.9.6,249,,X
+661,Acne vulgaris,653,Skin and subcutaneous diseases,3,B.9.7,250,,X
+662,Alopecia areata,653,Skin and subcutaneous diseases,3,B.9.8,251,,X
+663,Pruritus,653,Skin and subcutaneous diseases,3,B.9.9,252,,X
+664,Urticaria,653,Skin and subcutaneous diseases,3,B.9.10,253,,X
+665,Decubitus ulcer,653,Skin and subcutaneous diseases,3,B.9.11,254,,
+668,Other skin and subcutaneous diseases,653,Skin and subcutaneous diseases,3,B.9.12,255,,
+669,Sense organ diseases,409,Non-communicable diseases,2,B.10,256,,X
+981,Blindness and vision loss,669,Sense organ diseases,3,B.10.1,257,,X
+670,Glaucoma,981,Blindness and vision loss,4,B.10.1.1,258,,X
+671,Cataract,981,Blindness and vision loss,4,B.10.1.2,259,,X
+672,Age-related macular degeneration,981,Blindness and vision loss,4,B.10.1.3,260,,X
+999,Refraction disorders,981,Blindness and vision loss,4,B.10.1.4,261,,X
+1000,Near vision loss,981,Blindness and vision loss,4,B.10.1.5,262,,X
+675,Other vision loss,981,Blindness and vision loss,4,B.10.1.6,263,,X
+674,Age-related and other hearing loss,669,Sense organ diseases,3,B.10.2,264,,X
+679,Other sense organ diseases,669,Sense organ diseases,3,B.10.3,265,,X
+626,Musculoskeletal disorders,409,Non-communicable diseases,2,B.11,266,,
+627,Rheumatoid arthritis,626,Musculoskeletal disorders,3,B.11.1,267,,
+628,Osteoarthritis,626,Musculoskeletal disorders,3,B.11.2,268,,X
+1014,Osteoarthritis hip,628,Osteoarthritis,4,B.11.2.1,269,,X
+1015,Osteoarthritis knee,628,Osteoarthritis,4,B.11.2.2,270,,X
+1016,Osteoarthritis hand,628,Osteoarthritis,4,B.11.2.3,271,,X
+1017,Osteoarthritis other,628,Osteoarthritis,4,B.11.2.4,272,,X
+630,Low back pain,626,Musculoskeletal disorders,3,B.11.3,273,,X
+631,Neck pain,626,Musculoskeletal disorders,3,B.11.4,274,,X
+632,Gout,626,Musculoskeletal disorders,3,B.11.5,275,,X
+639,Other musculoskeletal disorders,626,Musculoskeletal disorders,3,B.11.6,276,,
+640,Other non-communicable diseases,409,Non-communicable diseases,2,B.12,277,,
+641,Congenital birth defects,640,Other non-communicable diseases,3,B.12.1,278,,
+642,Neural tube defects,641,Congenital birth defects,4,B.12.1.1,279,,
+643,Congenital heart anomalies,641,Congenital birth defects,4,B.12.1.2,280,,
+644,Orofacial clefts,641,Congenital birth defects,4,B.12.1.3,281,,
+645,Down syndrome,641,Congenital birth defects,4,B.12.1.4,282,,
+646,Turner syndrome,641,Congenital birth defects,4,B.12.1.5,283,,X
+647,Klinefelter syndrome,641,Congenital birth defects,4,B.12.1.6,284,,X
+648,Other chromosomal abnormalities,641,Congenital birth defects,4,B.12.1.7,285,,
+649,Congenital musculoskeletal and limb anomalies,641,Congenital birth defects,4,B.12.1.8,286,,
+650,Urogenital congenital anomalies,641,Congenital birth defects,4,B.12.1.9,287,,
+651,Digestive congenital anomalies,641,Congenital birth defects,4,B.12.1.10,288,,
+652,Other congenital birth defects,641,Congenital birth defects,4,B.12.1.11,289,,
+594,Urinary diseases and male infertility,640,Other non-communicable diseases,3,B.12.2,290,,
+595,Urinary tract infections and interstitial nephritis,594,Urinary diseases and male infertility,4,B.12.2.1,291,,
+596,Urolithiasis,594,Urinary diseases and male infertility,4,B.12.2.2,292,,
+597,Benign prostatic hyperplasia,594,Urinary diseases and male infertility,4,B.12.2.3,293,,X
+598,Male infertility,594,Urinary diseases and male infertility,4,B.12.2.4,294,,X
+602,Other urinary diseases,594,Urinary diseases and male infertility,4,B.12.2.5,295,,
+603,Gynecological diseases,640,Other non-communicable diseases,3,B.12.3,296,,
+604,Uterine fibroids,603,Gynecological diseases,4,B.12.3.1,297,,
+605,Polycystic ovarian syndrome,603,Gynecological diseases,4,B.12.3.2,298,,X
+606,Female infertility,603,Gynecological diseases,4,B.12.3.3,299,,X
+607,Endometriosis,603,Gynecological diseases,4,B.12.3.4,300,,
+608,Genital prolapse,603,Gynecological diseases,4,B.12.3.5,301,,
+609,Premenstrual syndrome,603,Gynecological diseases,4,B.12.3.6,302,,X
+612,Other gynecological diseases,603,Gynecological diseases,4,B.12.3.7,303,,
+613,Hemoglobinopathies and hemolytic anemias,640,Other non-communicable diseases,3,B.12.4,304,,
+614,Thalassemias,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.1,305,,
+837,Thalassemias trait,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.2,306,,X
+615,Sickle cell disorders,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.3,307,,
+838,Sickle cell trait,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.4,308,,X
+616,G6PD deficiency,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.5,309,,
+839,G6PD trait,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.6,310,,X
+618,Other hemoglobinopathies and hemolytic anemias,613,Hemoglobinopathies and hemolytic anemias,4,B.12.4.7,311,,
+619,"Endocrine, metabolic, blood, and immune disorders",640,Other non-communicable diseases,3,B.12.5,312,,
+680,Oral disorders,640,Other non-communicable diseases,3,B.12.6,313,,X
+681,Caries of deciduous teeth,680,Oral disorders,4,B.12.6.1,314,,X
+682,Caries of permanent teeth,680,Oral disorders,4,B.12.6.2,315,,X
+683,Periodontal diseases,680,Oral disorders,4,B.12.6.3,316,,X
+684,Edentulism,680,Oral disorders,4,B.12.6.4,317,,X
+685,Other oral disorders,680,Oral disorders,4,B.12.6.5,318,,X
+686,Sudden infant death syndrome,640,Other non-communicable diseases,3,B.12.7,319,X,
+687,Injuries,294,All causes,1,C,320,,
+688,Transport injuries,687,Injuries,2,C.1,321,,
+689,Road injuries,688,Transport injuries,3,C.1.1,322,,
+690,Pedestrian road injuries,689,Road injuries,4,C.1.1.1,323,,
+691,Cyclist road injuries,689,Road injuries,4,C.1.1.2,324,,
+692,Motorcyclist road injuries,689,Road injuries,4,C.1.1.3,325,,
+693,Motor vehicle road injuries,689,Road injuries,4,C.1.1.4,326,,
+694,Other road injuries,689,Road injuries,4,C.1.1.5,327,,
+695,Other transport injuries,688,Transport injuries,3,C.1.2,328,,
+696,Unintentional injuries,687,Injuries,2,C.2,329,,
+697,Falls,696,Unintentional injuries,3,C.2.1,330,,
+698,Drowning,696,Unintentional injuries,3,C.2.2,331,,
+699,"Fire, heat, and hot substances",696,Unintentional injuries,3,C.2.3,332,,
+700,Poisonings,696,Unintentional injuries,3,C.2.4,333,,
+701,Poisoning by carbon monoxide,700,Poisonings,4,C.2.4.1,334,,
+703,Poisoning by other means,700,Poisonings,4,C.2.4.2,335,,
+704,Exposure to mechanical forces,696,Unintentional injuries,3,C.2.5,336,,
+705,Unintentional firearm injuries,704,Exposure to mechanical forces,4,C.2.5.1,337,,
+707,Other exposure to mechanical forces,704,Exposure to mechanical forces,4,C.2.5.2,338,,
+708,Adverse effects of medical treatment,696,Unintentional injuries,3,C.2.6,339,,
+709,Animal contact,696,Unintentional injuries,3,C.2.7,340,,
+710,Venomous animal contact,709,Animal contact,4,C.2.7.1,341,,
+711,Non-venomous animal contact,709,Animal contact,4,C.2.7.2,342,,
+712,Foreign body,696,Unintentional injuries,3,C.2.8,343,,
+713,Pulmonary aspiration and foreign body in airway,712,Foreign body,4,C.2.8.1,344,,
+714,Foreign body in eyes,712,Foreign body,4,C.2.8.2,345,,X
+715,Foreign body in other body part,712,Foreign body,4,C.2.8.3,346,,
+842,Environmental heat and cold exposure,696,Unintentional injuries,3,C.2.9,347,,
+729,Exposure to forces of nature,696,Unintentional injuries,3,C.2.10,348,,
+716,Other unintentional injuries,696,Unintentional injuries,3,C.2.11,349,,
+717,Self-harm and interpersonal violence,687,Injuries,2,C.3,350,,
+718,Self-harm,717,Self-harm and interpersonal violence,3,C.3.1,351,,
+721,Self-harm by firearm,718,Self-harm,4,C.3.1.1,352,,
+723,Self-harm by other specified means,718,Self-harm,4,C.3.1.2,353,,
+724,Interpersonal violence,717,Self-harm and interpersonal violence,3,C.3.2,354,,
+725,Physical violence by firearm,724,Interpersonal violence,4,C.3.2.1,355,,
+726,Physical violence by sharp object,724,Interpersonal violence,4,C.3.2.2,356,,
+941,Sexual violence,724,Interpersonal violence,4,C.3.2.3,357,,X
+727,Physical violence by other means,724,Interpersonal violence,4,C.3.2.4,358,,
+945,Conflict and terrorism,717,Self-harm and interpersonal violence,3,C.3.3,359,,
+854,Executions and police conflict,717,Self-harm and interpersonal violence,3,C.3.4,360,,
+1029,Total cancers,294,All causes,1,D,361,,
+1026,Total burden related to hepatitis B,294,All causes,1,E,362,,
+1027,Total burden related to hepatitis C,294,All causes,1,F,363,,
+1028,Total burden related to Non-alcoholic fatty liver disease (NAFLD),294,All causes,1,G,364,,

non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Global Burden of Disease Study 2019 (GBD 2019) Cause, REI, and Location Hierarchies/source

@@ -0,0 +1 @@
+https://doi.org/10.6069/Q0YC-CR46

non-db_data_sources/GBD and ICD-10_(2019 version)/ICD10-to-GDB_expander.py

@@ -0,0 +1,103 @@
+import pandas as pd
+import numpy as np
+import itertools
+
+
+
+IHME_COD_FILEPATH = "./GlobalBurdenDisease/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX"
+IHME_NONFATAL_FILEPATH = "./GlobalBurdenDisease/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX"
+ICD10CM_ORDER_FILEPATH = "./icd10_combined-who-cms.psv"
+
+def justify(string):
+    '''
+    The purpose of this is to transform codes such as A00 and A000
+    into a normalized, sortable format e.g. 'A00----' and 'A000---'
+    '''
+    return string.ljust(7,"-")
+
+
+class CodeRange():
+    def __init__(self,cause,code_book,codes):
+        self.cause = cause
+        self.code_book = code_book
+        self.code_list = []
+
+        codes = "" if type(codes) is float else codes #normalize codes to string...
+        codes = [x.strip().replace('.','').split('-') for x in codes.split(",")]
+        
+        for rng in codes:
+
+            if rng[0] is None:
+                raise Exception("Listed ICD10 Code (Begin:{}) is not in codebook".format(rng), rng)
+
+            #lookup codes
+            if len(rng) == 1:
+                begin = justify(rng[0])
+                if self.code_book.get(begin) is None:
+                    continue
+                else:
+                    self.code_list.append(begin)
+            else:
+                begin = justify(rng[0])
+                end = justify(rng[1])
+                begin_bitmask = [x >= begin for x in list(self.code_book)]
+                end_bitmask = [x <= end for x in list(self.code_book)]
+
+                bitmask = [x and y for x,y in zip(begin_bitmask,end_bitmask)]
+                
+                self.code_list.extend(list(itertools.compress(list(self.code_book),bitmask)))
+
+
+
+    def __str__(self):
+        txt = ''
+        for item in self.code_list:
+            txt += "{} | {}\n".format(item, self.cause)
+
+        return txt
+
+#READ in ICD10CM codes
+
+icd10_codes = {}
+
+
+with open(ICD10CM_ORDER_FILEPATH,"r") as icd_fh:
+    for idx,line in enumerate(icd_fh.readlines()):
+        #read info
+        code, descr, source = line.split("|")
+        #cleanup info
+        code = justify(code.strip())
+        descr = descr.strip()
+        source = source.strip()
+
+        #Store in code dict
+        icd10_codes[code] = (idx,descr, source)
+
+
+
+cod = pd.read_excel(IHME_COD_FILEPATH,header=1)
+
+with open("COD_cause2code.psv", "w") as outfh:
+    itt = 0
+    for row in cod.itertuples():
+        cause = row[1]
+        codes = row[2]
+        
+        c = CodeRange(cause,icd10_codes,codes)
+
+        outfh.write(c.__str__())
+
+
+
+
+nonfatal = pd.read_excel(IHME_NONFATAL_FILEPATH,header=1)
+with open("NONFATAL_cause2code.psv", "w") as outfh:
+    itt = 0
+    for row in nonfatal.itertuples():
+        cause = row[2]
+        codes= row[3]
+        c = CodeRange(cause,icd10_codes,codes)
+
+        outfh.write(c.__str__())
+
+

non-db_data_sources/GBD and ICD-10_(2019 version)/WHO ICD-10 (2019)/.~lock.icd10-2019_categories_with_chapter.psv#

@@ -0,0 +1 @@
+,dad,home-pc,06.04.2023 22:41,file:///home/dad/.config/libreoffice/4;