diff --git a/.dbeaver/.credentials-config.json.bak b/.dbeaver/.credentials-config.json.bak index 646ae05..5be47bd 100644 Binary files a/.dbeaver/.credentials-config.json.bak and b/.dbeaver/.credentials-config.json.bak differ diff --git a/.dbeaver/.data-sources.json.bak b/.dbeaver/.data-sources.json.bak index a072f73..1ed4cce 100644 --- a/.dbeaver/.data-sources.json.bak +++ b/.dbeaver/.data-sources.json.bak @@ -21,13 +21,17 @@ "name": "aact_db", "save-password": true, "configuration": { - "host": "will-office", + "host": "100.95.169.11", "port": "5432", "database": "aact_db", - "url": "jdbc:postgresql://will-office:5432/aact_db", + "url": "jdbc:postgresql://100.95.169.11:5432/aact_db", "configurationType": "MANUAL", "type": "dev", + "provider-properties": {}, "auth-model": "native" + }, + "custom-properties": { + "resultset.maxrows": "500" } }, "postgres-jdbc-186cd8f479f-6cc3c10c8adc3359": { @@ -42,7 +46,6 @@ "url": "jdbc:postgresql://localhost:54320/postgres", "configurationType": "MANUAL", "type": "dev", - "provider-properties": {}, "auth-model": "native" } } diff --git a/.dbeaver/.project-metadata.json.bak b/.dbeaver/.project-metadata.json.bak index b49a7c8..1334ab3 100644 --- a/.dbeaver/.project-metadata.json.bak +++ b/.dbeaver/.project-metadata.json.bak @@ -1 +1 @@ -{"resources":{"Scripts/DiseaseBurdens_create_table.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"Scripts/GlobalBurdensOfDisease2019Codebook.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"DiseaseBurden"},"development_sql/ASSOICATING NCTIDs to NDCs and Marketing dates.sql":{"default-schema":"public","default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db"}}} \ No newline at end of file +{"resources":{"Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"Scripts/Data_summaries.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"Scripts/DevelopingLinks.sql":{"default-schema":"public","default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db"},"Scripts/DiseaseBurdens_create_table.sql":{"default-schema":"public","default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db"},"Scripts/GlobalBurdensOfDisease2019Codebook.sql":{"default-schema":"DiseaseBurden","default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db"},"Scripts/GroupingTrials.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"Scripts/Script.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"Scripts/TablesAndViews_Public.sql":{"default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db","default-schema":"public"},"development_sql/ASSOICATING NCTIDs to NDCs and Marketing dates.sql":{"default-schema":"public","default-datasource":"postgres-jdbc-186c896a347-2a3d946d2dea4df7","default-catalog":"aact_db"}}} \ No newline at end of file diff --git a/Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql b/Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql index 2046f0c..48994fa 100644 --- a/Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql +++ b/Scripts/ASSOICATING NCTIDs to NDCs and Marketing dates.sql @@ -16,8 +16,8 @@ SELECT bi.nct_id , bi.downcase_mesh_term, rr.tty2 , - rr.rxcui2 as bn_or_in_cui --brand or ingredient - ,count(*) + 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 () @@ -123,4 +123,11 @@ 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 +; + diff --git a/Scripts/Data_summaries.sql b/Scripts/Data_summaries.sql index b063a27..c0e809e 100644 --- a/Scripts/Data_summaries.sql +++ b/Scripts/Data_summaries.sql @@ -17,11 +17,12 @@ 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 + * -- 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(*) @@ -60,5 +61,40 @@ nct_id in (select distinct nct_id from history.trial_snapshots ts) */ 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 +; diff --git a/Scripts/DevelopingLinks.sql b/Scripts/DevelopingLinks.sql index 1aed12f..f09f811 100644 --- a/Scripts/DevelopingLinks.sql +++ b/Scripts/DevelopingLinks.sql @@ -1,3 +1,5 @@ +--TODO: Document and migrate to setup + drop table if exists "DiseaseBurden".trial_to_icd10; drop type if exists "DiseaseBurden".validation_type; diff --git a/Scripts/ExtractingData.sql b/Scripts/ExtractingData.sql new file mode 100644 index 0000000..880ef03 --- /dev/null +++ b/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 +; diff --git a/Scripts/GroupingTrials.sql b/Scripts/GroupingTrials.sql index 6ea338e..c16c95d 100644 --- a/Scripts/GroupingTrials.sql +++ b/Scripts/GroupingTrials.sql @@ -1,6 +1,7 @@ select * from "DiseaseBurden".icd10_to_cause itc ; select * from "DiseaseBurden".cause c ; -select + + select c.id, count(distinct code) @@ -11,22 +12,93 @@ group by c.id order by c.id ; -select count(distinct nct_id) from "DiseaseBurden".trial_to_icd10 tti -where tti.approved = 'accepted'; +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 -select tti.nct_id, tti."condition",itc.cause_text +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' - and - itc.cause_text not in ('Non-communicable diseases','Neoplasms','Mental disorders','Other non-communicable diseases') -group by tti.nct_id , tti."condition" , itc.cause_text order by nct_id -; \ No newline at end of file +; + +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 +; + + diff --git a/Scripts/TablesAndViews_Public.sql b/Scripts/TablesAndViews_Public.sql new file mode 100644 index 0000000..03f2a08 --- /dev/null +++ b/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; + diff --git a/containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql b/containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql index 6d764de..b178a83 100644 --- a/containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql +++ b/containers/AACT_downloader/docker-entrypoint-initdb.d/030_HistoricalSchema.sql @@ -97,6 +97,7 @@ 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, @@ -106,11 +107,21 @@ CREATE TABLE IF NOT EXISTS history.trial_snapshots overall_status history.study_statuses, enrollment integer, enrollment_category history.updatable_catetories, - sponsor character varying(255) COLLATE pg_catalog."default", - responsible_party character varying(255) COLLATE pg_catalog."default", + 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)); \ No newline at end of file diff --git a/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_CAUSE_ICD_CODE_MAP_INFO_SHEET_Y2020M10D15_0(1).PDF b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_CAUSE_ICD_CODE_MAP_INFO_SHEET_Y2020M10D15_0(1).PDF new file mode 100644 index 0000000..a0436f1 Binary files /dev/null and b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_CAUSE_ICD_CODE_MAP_INFO_SHEET_Y2020M10D15_0(1).PDF differ diff --git a/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX similarity index 100% rename from non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX rename to non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_COD_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX diff --git a/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX similarity index 100% rename from non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX rename to non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/IHME_GBD_2019_NONFATAL_CAUSE_ICD_CODE_MAP_Y2020M10D15.XLSX diff --git a/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/source b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Cause list linked to Icd10/source new file mode 100644 index 0000000..40f7017 --- /dev/null +++ b/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 diff --git a/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# b/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# new file mode 100644 index 0000000..c1b880a --- /dev/null +++ b/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; \ No newline at end of file diff --git a/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_ALL_LOCATION_HIERARCHIES_Y2022M06D29.XLSX b/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_ALL_LOCATION_HIERARCHIES_Y2022M06D29.XLSX new file mode 100644 index 0000000..0816887 Binary files /dev/null and b/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_ALL_LOCATION_HIERARCHIES_Y2022M06D29.XLSX differ diff --git a/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.XLSX b/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.XLSX new file mode 100644 index 0000000..d2c94b3 Binary files /dev/null and b/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.XLSX differ diff --git a/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 b/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 new file mode 100644 index 0000000..3cf8b74 --- /dev/null +++ b/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,, diff --git a/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_GBD_HIERARCHIES_INFO_SHEET_Y2022M06D29.PDF b/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_GBD_HIERARCHIES_INFO_SHEET_Y2022M06D29.PDF new file mode 100644 index 0000000..de2cf30 Binary files /dev/null and b/non-db_data_sources/GBD and ICD-10_(2019 version)/GlobalBurdenDisease/Global Burden of Disease Study 2019 (GBD 2019) Cause, REI, and Location 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b/non-db_data_sources/GBD and ICD-10_(2019 version)/WHO ICD-10 (2019)/icd10-2019_categories_with_chapter.psv @@ -0,0 +1,248 @@ +"Level"|"Chapter"|"chapter_code"|"start_code"|"end_code"|"group_name" +1|"I Certain infectious and parasitic diseases "|1|" A00 "|" B99 "|"I Certain infectious and parasitic diseases " +2|"I Certain infectious and parasitic diseases "|1|" A00 "|" A09 "|" Intestinal infectious diseases " +2|"I Certain infectious and parasitic diseases "|1|" A15 "|" A19 "|" Tuberculosis " +2|"I Certain infectious and parasitic diseases "|1|" A20 "|" A28 "|" Certain zoonotic bacterial diseases " +2|"I Certain infectious and parasitic diseases "|1|" A30 "|" A49 "|" Other bacterial diseases " +2|"I Certain infectious and parasitic diseases "|1|" A50 "|" A64 "|" Infections with a predominantly sexual mode of transmission " +2|"I Certain infectious and parasitic diseases "|1|" A65 "|" A69 "|" Other spirochaetal diseases " +2|"I Certain infectious and parasitic diseases "|1|" A70 "|" A74 "|" Other diseases caused by chlamydiae " +2|"I Certain infectious and parasitic diseases "|1|" A75 "|" A79 "|" Rickettsioses " +2|"I Certain infectious and parasitic diseases "|1|" A80 "|" A89 "|" Viral infections of the central nervous system " +2|"I Certain infectious and parasitic diseases "|1|" A92 "|" A99 "|" Arthropod-borne viral fevers and viral haemorrhagic fevers " +2|"I Certain infectious and parasitic diseases "|1|" B00 "|" B09 "|" Viral infections characterized by skin and mucous membrane lesions " +2|"I Certain infectious and parasitic diseases "|1|" B15 "|" B19 "|" Viral hepatitis " +2|"I Certain infectious and parasitic diseases "|1|" B20 "|" B24 "|" Human immunodeficiency virus [HIV] disease " +2|"I Certain infectious and parasitic diseases "|1|" B25 "|" B34 "|" Other viral diseases " +2|"I Certain infectious and parasitic diseases "|1|" B35 "|" B49 "|" Mycoses " +2|"I Certain infectious and parasitic diseases "|1|" B50 "|" B64 "|" Protozoal diseases " +2|"I Certain infectious and parasitic diseases "|1|" B65 "|" B83 "|" Helminthiases " +2|"I Certain infectious and parasitic diseases "|1|" B85 "|" B89 "|" Pediculosis, acariasis and other infestations " +2|"I Certain infectious and parasitic diseases "|1|" B90 "|" B94 "|" Sequelae of infectious and parasitic diseases " +2|"I Certain infectious and parasitic diseases "|1|" B95 "|" B98 "|" Bacterial, viral and other infectious agents " +2|"I Certain infectious and parasitic diseases "|1|" B99 "|" B99 "|" Other infectious diseases " +1|"II Neoplasms "|2|" C00 "|" D48 "|"II Neoplasms " +2|"II Neoplasms "|2|" C00 "|" C14 "|" Malignant neoplasms of lip, oral cavity and pharynx " +2|"II Neoplasms "|2|" C15 "|" C26 "|" Malignant neoplasms of digestive organs " +2|"II Neoplasms "|2|" C30 "|" C39 "|" Malignant neoplasms of respiratory and intrathoracic organs " +2|"II Neoplasms "|2|" C40 "|" C41 "|" Malignant neoplasms of bone and articular cartilage " +2|"II Neoplasms "|2|" C43 "|" C44 "|" Melanoma and other malignant neoplasms of skin " +2|"II Neoplasms "|2|" C45 "|" C49 "|" Malignant neoplasms of mesothelial and soft tissue " +2|"II Neoplasms "|2|" C50 "|" C50 "|" Malignant neoplasm of breast " +2|"II Neoplasms "|2|" C51 "|" C58 "|" Malignant neoplasms of female genital organs " +2|"II Neoplasms "|2|" C60 "|" C63 "|" Malignant neoplasms of male genital organs " +2|"II Neoplasms "|2|" C64 "|" C68 "|" Malignant neoplasms of urinary tract " +2|"II Neoplasms "|2|" C69 "|" C72 "|" Malignant neoplasms of eye, brain and other parts of central nervous system " +2|"II Neoplasms "|2|" C73 "|" C75 "|" Malignant neoplasms of thyroid and other endocrine glands " +2|"II Neoplasms "|2|" C76 "|" C80 "|" Malignant neoplasms of ill-defined, secondary and unspecified sites " +2|"II Neoplasms "|2|" C81 "|" C96 "|" Malignant neoplasms, stated or presumed to be primary, of lymphoid, haematopoietic and related tissue " +2|"II Neoplasms "|2|" C97 "|" C97 "|" Malignant neoplasms of independent (primary) multiple sites " +2|"II Neoplasms "|2|" D00 "|" D09 "|" In situ neoplasms " +2|"II Neoplasms "|2|" D10 "|" D36 "|" Benign neoplasms " +2|"II Neoplasms "|2|" D37 "|" D48 "|" Neoplasms of uncertain or unknown behaviour " +1|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D50 "|" D89 "|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D50 "|" D53 "|" Nutritional anaemias " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D55 "|" D59 "|" Haemolytic anaemias " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D60 "|" D64 "|" Aplastic and other anaemias " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D65 "|" D69 "|" Coagulation defects, purpura and other haemorrhagic conditions " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D70 "|" D77 "|" Other diseases of blood and blood-forming organs " +2|"III Diseases of the blood and blood-forming organs and certain disorders involving the immune mechanism "|3|" D80 "|" D89 "|" Certain disorders involving the immune mechanism " +1|"IV Endocrine, nutritional and metabolic diseases "|4|" E00 "|" E90 "|"IV Endocrine, nutritional and metabolic diseases " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E00 "|" E07 "|" Disorders of thyroid gland " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E10 "|" E14 "|" Diabetes mellitus " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E15 "|" E16 "|" Other disorders of glucose regulation and pancreatic internal secretion " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E20 "|" E35 "|" Disorders of other endocrine glands " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E40 "|" E46 "|" Malnutrition " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E50 "|" E64 "|" Other nutritional deficiencies " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E65 "|" E68 "|" Obesity and other hyperalimentation " +2|"IV Endocrine, nutritional and metabolic diseases "|4|" E70 "|" E90 "|" Metabolic disorders " +1|"V Mental and behavioural disorders "|5|" F00 "|" F99 "|"V Mental and behavioural disorders " +2|"V Mental and behavioural disorders "|5|" F00 "|" F09 "|" Organic, including symptomatic, mental disorders " +2|"V Mental and behavioural disorders "|5|" F10 "|" F19 "|" Mental and behavioural disorders due to psychoactive substance use " +2|"V Mental and behavioural disorders "|5|" F20 "|" F29 "|" Schizophrenia, schizotypal and delusional disorders " +2|"V Mental and behavioural disorders "|5|" F30 "|" F39 "|" Mood [affective] disorders " +2|"V Mental and behavioural disorders "|5|" F40 "|" F48 "|" Neurotic, stress-related and somatoform disorders " +2|"V Mental and behavioural disorders "|5|" F50 "|" F59 "|" Behavioural syndromes associated with physiological disturbances and physical factors " +2|"V Mental and behavioural disorders "|5|" F60 "|" F69 "|" Disorders of adult personality and behaviour " +2|"V Mental and behavioural disorders "|5|" F70 "|" F79 "|" Mental retardation " +2|"V Mental and behavioural disorders "|5|" F80 "|" F89 "|" Disorders of psychological development " +2|"V Mental and behavioural disorders "|5|" F90 "|" F98 "|" Behavioural and emotional disorders with onset usually occurring in childhood and adolescence " +2|"V Mental and behavioural disorders "|5|" F99 "|" F99 "|" Unspecified mental disorder " +1|"VI Diseases of the nervous system "|6|" G00 "|" G99 "|"VI Diseases of the nervous system " +2|"VI Diseases of the nervous system "|6|" G00 "|" G09 "|" Inflammatory diseases of the central nervous system " +2|"VI Diseases of the nervous system "|6|" G10 "|" G14 "|" Systemic atrophies primarily affecting the central nervous system " +2|"VI Diseases of the nervous system "|6|" G20 "|" G26 "|" Extrapyramidal and movement disorders " +2|"VI Diseases of the nervous system "|6|" G30 "|" G32 "|" Other degenerative diseases of the nervous system " +2|"VI Diseases of the nervous system "|6|" G35 "|" G37 "|" Demyelinating diseases of the central nervous system " +2|"VI Diseases of the nervous system "|6|" G40 "|" G47 "|" Episodic and paroxysmal disorders " +2|"VI Diseases of the nervous system "|6|" G50 "|" G59 "|" Nerve, nerve root and plexus disorders " +2|"VI Diseases of the nervous system "|6|" G60 "|" G64 "|" Polyneuropathies and other disorders of the peripheral nervous system " +2|"VI Diseases of the nervous system "|6|" G70 "|" G73 "|" Diseases of myoneural junction and muscle " +2|"VI Diseases of the nervous system "|6|" G80 "|" G83 "|" Cerebral palsy and other paralytic syndromes " +2|"VI Diseases of the nervous system "|6|" G90 "|" G99 "|" Other disorders of the nervous system " +1|"VII Diseases of the eye and adnexa "|7|" H00 "|" H59 "|"VII Diseases of the eye and adnexa " +2|"VII Diseases of the eye and adnexa "|7|" H00 "|" H06 "|" Disorders of eyelid, lacrimal system and orbit " +2|"VII Diseases of the eye and adnexa "|7|" H10 "|" H13 "|" Disorders of conjunctiva " +2|"VII Diseases of the eye and adnexa "|7|" H15 "|" H22 "|" Disorders of sclera, cornea, iris and ciliary body " +2|"VII Diseases of the eye and adnexa "|7|" H25 "|" H28 "|" Disorders of lens " +2|"VII Diseases of the eye and adnexa "|7|" H30 "|" H36 "|" Disorders of choroid and retina " +2|"VII Diseases of the eye and adnexa "|7|" H40 "|" H42 "|" Glaucoma " +2|"VII Diseases of the eye and adnexa "|7|" H43 "|" H45 "|" Disorders of vitreous body and globe " +2|"VII Diseases of the eye and adnexa "|7|" H46 "|" H48 "|" Disorders of optic nerve and visual pathways " +2|"VII Diseases of the eye and adnexa "|7|" H49 "|" H52 "|" Disorders of ocular muscles, binocular movement, accommodation and refraction " +2|"VII Diseases of the eye and adnexa "|7|" H53 "|" H54 "|" Visual disturbances and blindness " +2|"VII Diseases of the eye and adnexa "|7|" H55 "|" H59 "|" Other disorders of eye and adnexa " +1|"VIII Diseases of the ear and mastoid process "|8|" H60 "|" H95 "|"VIII Diseases of the ear and mastoid process " +2|"VIII Diseases of the ear and mastoid process "|8|" H60 "|" H62 "|" Diseases of external ear " +2|"VIII Diseases of the ear and mastoid process "|8|" H65 "|" H75 "|" Diseases of middle ear and mastoid " +2|"VIII Diseases of the ear and mastoid process "|8|" H80 "|" H83 "|" Diseases of inner ear " +2|"VIII Diseases of the ear and mastoid process "|8|" H90 "|" H95 "|" Other disorders of ear " +1|"IX Diseases of the circulatory system "|9|" I00 "|" I99 "|"IX Diseases of the circulatory system " +2|"IX Diseases of the circulatory system "|9|" I00 "|" I02 "|" Acute rheumatic fever " +2|"IX Diseases of the circulatory system "|9|" I05 "|" I09 "|" Chronic rheumatic heart diseases " +2|"IX Diseases of the circulatory system "|9|" I10 "|" I15 "|" Hypertensive diseases " +2|"IX Diseases of the circulatory system "|9|" I20 "|" I25 "|" Ischaemic heart diseases " +2|"IX Diseases of the circulatory system "|9|" I26 "|" I28 "|" Pulmonary heart disease and diseases of pulmonary circulation " +2|"IX Diseases of the circulatory system "|9|" I30 "|" I52 "|" Other forms of heart disease " +2|"IX Diseases of the circulatory system "|9|" I60 "|" I69 "|" Cerebrovascular diseases " +2|"IX Diseases of the circulatory system "|9|" I70 "|" I79 "|" Diseases of arteries, arterioles and capillaries " +2|"IX Diseases of the circulatory system "|9|" I80 "|" I89 "|" Diseases of veins, lymphatic vessels and lymph nodes, not elsewhere classified " +2|"IX Diseases of the circulatory system "|9|" I95 "|" I99 "|" Other and unspecified disorders of the circulatory system " +1|"X Diseases of the respiratory system "|10|" J00 "|" J99 "|"X Diseases of the respiratory system " +2|"X Diseases of the respiratory system "|10|" J00 "|" J06 "|" Acute upper respiratory infections " +2|"X Diseases of the respiratory system "|10|" J09 "|" J18 "|" Influenza and pneumonia " +2|"X Diseases of the respiratory system "|10|" J20 "|" J22 "|" Other acute lower respiratory infections " +2|"X Diseases of the respiratory system "|10|" J30 "|" J39 "|" Other diseases of upper respiratory tract " +2|"X Diseases of the respiratory system "|10|" J40 "|" J47 "|" Chronic lower respiratory diseases " +2|"X Diseases of the respiratory system "|10|" J60 "|" J70 "|" Lung diseases due to external agents " +2|"X Diseases of the respiratory system "|10|" J80 "|" J84 "|" Other respiratory diseases principally affecting the interstitium " +2|"X Diseases of the respiratory system "|10|" J85 "|" J86 "|" Suppurative and necrotic conditions of lower respiratory tract " +2|"X Diseases of the respiratory system "|10|" J90 "|" J94 "|" Other diseases of pleura " +2|"X Diseases of the respiratory system "|10|" J95 "|" J99 "|" Other diseases of the respiratory system " +1|"XI Diseases of the digestive system "|11|" K00 "|" K93 "|"XI Diseases of the digestive system " +2|"XI Diseases of the digestive system "|11|" K00 "|" K14 "|" Diseases of oral cavity, salivary glands and jaws " +2|"XI Diseases of the digestive system "|11|" K20 "|" K31 "|" Diseases of oesophagus, stomach and duodenum " +2|"XI Diseases of the digestive system "|11|" K35 "|" K38 "|" Diseases of appendix " +2|"XI Diseases of the digestive system "|11|" K40 "|" K46 "|" Hernia " +2|"XI Diseases of the digestive system "|11|" K50 "|" K52 "|" Noninfective enteritis and colitis " +2|"XI Diseases of the digestive system "|11|" K55 "|" K64 "|" Other diseases of intestines " +2|"XI Diseases of the digestive system "|11|" K65 "|" K67 "|" Diseases of peritoneum " +2|"XI Diseases of the digestive system "|11|" K70 "|" K77 "|" Diseases of liver " +2|"XI Diseases of the digestive system "|11|" K80 "|" K87 "|" Disorders of gallbladder, biliary tract and pancreas " +2|"XI Diseases of the digestive system "|11|" K90 "|" K93 "|" Other diseases of the digestive system " +1|"XII Diseases of the skin and subcutaneous tissue "|12|" L00 "|" L99 "|"XII Diseases of the skin and subcutaneous tissue " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L00 "|" L08 "|" Infections of the skin and subcutaneous tissue " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L10 "|" L14 "|" Bullous disorders " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L20 "|" L30 "|" Dermatitis and eczema " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L40 "|" L45 "|" Papulosquamous disorders " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L50 "|" L54 "|" Urticaria and erythema " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L55 "|" L59 "|" Radiation-related disorders of the skin and subcutaneous tissue " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L60 "|" L75 "|" Disorders of skin appendages " +2|"XII Diseases of the skin and subcutaneous tissue "|12|" L80 "|" L99 "|" Other disorders of the skin and subcutaneous tissue " +1|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M00 "|" M99 "|"XIII Diseases of the musculoskeletal system and connective tissue " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M00 "|" M25 "|" Arthropathies " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M30 "|" M36 "|" Systemic connective tissue disorders " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M40 "|" M54 "|" Dorsopathies " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M60 "|" M79 "|" Soft tissue disorders " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M80 "|" M94 "|" Osteopathies and chondropathies " +2|"XIII Diseases of the musculoskeletal system and connective tissue "|13|" M95 "|" M99 "|" Other disorders of the musculoskeletal system and connective tissue " +1|"XIV Diseases of the genitourinary system "|14|" N00 "|" N99 "|"XIV Diseases of the genitourinary system " +2|"XIV Diseases of the genitourinary system "|14|" N00 "|" N08 "|" Glomerular diseases " +2|"XIV Diseases of the genitourinary system "|14|" N10 "|" N16 "|" Renal tubulo-interstitial diseases " +2|"XIV Diseases of the genitourinary system "|14|" N17 "|" N19 "|" Renal failure " +2|"XIV Diseases of the genitourinary system "|14|" N20 "|" N23 "|" Urolithiasis " +2|"XIV Diseases of the genitourinary system "|14|" N25 "|" N29 "|" Other disorders of kidney and ureter " +2|"XIV Diseases of the genitourinary system "|14|" N30 "|" N39 "|" Other diseases of urinary system " +2|"XIV Diseases of the genitourinary system "|14|" N40 "|" N51 "|" Diseases of male genital organs " +2|"XIV Diseases of the genitourinary system "|14|" N60 "|" N64 "|" Disorders of breast " +2|"XIV Diseases of the genitourinary system "|14|" N70 "|" N77 "|" Inflammatory diseases of female pelvic organs " +2|"XIV Diseases of the genitourinary system "|14|" N80 "|" N98 "|" Noninflammatory disorders of female genital tract " +2|"XIV Diseases of the genitourinary system "|14|" N99 "|" N99 "|" Other disorders of the genitourinary system " +1|"XV Pregnancy, childbirth and the puerperium "|15|" O00 "|" O99 "|"XV Pregnancy, childbirth and the puerperium " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O00 "|" O08 "|" Pregnancy with abortive outcome " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O10 "|" O16 "|" Oedema, proteinuria and hypertensive disorders in pregnancy, childbirth and the puerperium " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O20 "|" O29 "|" Other maternal disorders predominantly related to pregnancy " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O30 "|" O48 "|" Maternal care related to the fetus and amniotic cavity and possible delivery problems " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O60 "|" O75 "|" Complications of labour and delivery " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O80 "|" O84 "|" Delivery " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O85 "|" O92 "|" Complications predominantly related to the puerperium " +2|"XV Pregnancy, childbirth and the puerperium "|15|" O94 "|" O99 "|" Other obstetric conditions, not elsewhere classified " +1|"XVI Certain conditions originating in the perinatal period "|16|" P00 "|" P96 "|"XVI Certain conditions originating in the perinatal period " +2|"XVI Certain conditions originating in the perinatal period "|16|" P00 "|" P04 "|" Fetus and newborn affected by maternal factors and by complications of pregnancy, labour and delivery " +2|"XVI Certain conditions originating in the perinatal period "|16|" P05 "|" P08 "|" Disorders related to length of gestation and fetal growth " +2|"XVI Certain conditions originating in the perinatal period "|16|" P10 "|" P15 "|" Birth trauma " +2|"XVI Certain conditions originating in the perinatal period "|16|" P20 "|" P29 "|" Respiratory and cardiovascular disorders specific to the perinatal period " +2|"XVI Certain conditions originating in the perinatal period "|16|" P35 "|" P39 "|" Infections specific to the perinatal period " +2|"XVI Certain conditions originating in the perinatal period "|16|" P50 "|" P61 "|" Haemorrhagic and haematological disorders of fetus and newborn " +2|"XVI Certain conditions originating in the perinatal period "|16|" P70 "|" P74 "|" Transitory endocrine and metabolic disorders specific to fetus and newborn " +2|"XVI Certain conditions originating in the perinatal period "|16|" P75 "|" P78 "|" Digestive system disorders of fetus and newborn " +2|"XVI Certain conditions originating in the perinatal period "|16|" P80 "|" P83 "|" Conditions involving the integument and temperature regulation of fetus and newborn " +2|"XVI Certain conditions originating in the perinatal period "|16|" P90 "|" P96 "|" Other disorders originating in the perinatal period " +1|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q00 "|" Q99 "|"XVII Congenital malformations, deformations and chromosomal abnormalities " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q00 "|" Q07 "|" Congenital malformations of the nervous system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q10 "|" Q18 "|" Congenital malformations of eye, ear, face and neck " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q20 "|" Q28 "|" Congenital malformations of the circulatory system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q30 "|" Q34 "|" Congenital malformations of the respiratory system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q35 "|" Q37 "|" Cleft lip and cleft palate " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q38 "|" Q45 "|" Other congenital malformations of the digestive system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q50 "|" Q56 "|" Congenital malformations of genital organs " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q60 "|" Q64 "|" Congenital malformations of the urinary system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q65 "|" Q79 "|" Congenital malformations and deformations of the musculoskeletal system " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q80 "|" Q89 "|" Other congenital malformations " +2|"XVII Congenital malformations, deformations and chromosomal abnormalities "|17|" Q90 "|" Q99 "|" Chromosomal abnormalities, not elsewhere classified " +1|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R00 "|" R99 "|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R00 "|" R09 "|" Symptoms and signs involving the circulatory and respiratory systems " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R10 "|" R19 "|" Symptoms and signs involving the digestive system and abdomen " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R20 "|" R23 "|" Symptoms and signs involving the skin and subcutaneous tissue " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R25 "|" R29 "|" Symptoms and signs involving the nervous and musculoskeletal systems " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R30 "|" R39 "|" Symptoms and signs involving the urinary system " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R40 "|" R46 "|" Symptoms and signs involving cognition, perception, emotional state and behaviour " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R47 "|" R49 "|" Symptoms and signs involving speech and voice " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R50 "|" R69 "|" General symptoms and signs " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R70 "|" R79 "|" Abnormal findings on examination of blood, without diagnosis " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R80 "|" R82 "|" Abnormal findings on examination of urine, without diagnosis " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R83 "|" R89 "|" Abnormal findings on examination of other body fluids, substances and tissues, without diagnosis " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R90 "|" R94 "|" Abnormal findings on diagnostic imaging and in function studies, without diagnosis " +2|"XVIII Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified "|18|" R95 "|" R99 "|" Ill-defined and unknown causes of mortality " +1|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S00 "|" T98 "|"XIX Injury, poisoning and certain other consequences of external causes " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S00 "|" S09 "|" Injuries to the head " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S10 "|" S19 "|" Injuries to the neck " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S20 "|" S29 "|" Injuries to the thorax " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S30 "|" S39 "|" Injuries to the abdomen, lower back, lumbar spine and pelvis " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S40 "|" S49 "|" Injuries to the shoulder and upper arm " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S50 "|" S59 "|" Injuries to the elbow and forearm " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S60 "|" S69 "|" Injuries to the wrist and hand " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S70 "|" S79 "|" Injuries to the hip and thigh " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S80 "|" S89 "|" Injuries to the knee and lower leg " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" S90 "|" S99 "|" Injuries to the ankle and foot " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T00 "|" T07 "|" Injuries involving multiple body regions " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T08 "|" T14 "|" Injuries to unspecified part of trunk, limb or body region " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T15 "|" T19 "|" Effects of foreign body entering through natural orifice " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T20 "|" T32 "|" Burns and corrosions " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T33 "|" T35 "|" Frostbite " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T36 "|" T50 "|" Poisoning by drugs, medicaments and biological substances " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T51 "|" T65 "|" Toxic effects of substances chiefly nonmedicinal as to source " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T66 "|" T78 "|" Other and unspecified effects of external causes " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T79 "|" T79 "|" Certain early complications of trauma " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T80 "|" T88 "|" Complications of surgical and medical care, not elsewhere classified " +2|"XIX Injury, poisoning and certain other consequences of external causes "|19|" T90 "|" T98 "|" Sequelae of injuries, of poisoning and of other consequences of external causes " +1|"XX External causes of morbidity and mortality "|20|" V01 "|" Y98 "|"XX External causes of morbidity and mortality " +2|"XX External causes of morbidity and mortality "|20|" V01 "|" X59 "|" Accidents " +2|"XX External causes of morbidity and mortality "|20|" X60 "|" X84 "|" Intentional self-harm " +2|"XX External causes of morbidity and mortality "|20|" X85 "|" Y09 "|" Assault " +2|"XX External causes of morbidity and mortality "|20|" Y10 "|" Y34 "|" Event of undetermined intent " +2|"XX External causes of morbidity and mortality "|20|" Y35 "|" Y36 "|" Legal intervention and operations of war " +2|"XX External causes of morbidity and mortality "|20|" Y40 "|" Y84 "|" Complications of medical and surgical care " +2|"XX External causes of morbidity and mortality "|20|" Y85 "|" Y89 "|" Sequelae of external causes of morbidity and mortality " +2|"XX External causes of morbidity and mortality "|20|" Y90 "|" Y98 "|" Supplementary factors related to causes of morbidity and mortality classified elsewhere " +1|"XXI Factors influencing health status and contact with health services "|21|" Z00 "|" Z99 "|"XXI Factors influencing health status and contact with health services " +2|"XXI Factors influencing health status and contact with health services "|21|" Z00 "|" Z13 "|" Persons encountering health services for examination and investigation " +2|"XXI Factors influencing health status and contact with health services "|21|" Z20 "|" Z29 "|" Persons with potential health hazards related to communicable diseases " +2|"XXI Factors influencing health status and contact with health services "|21|" Z30 "|" Z39 "|" Persons encountering health services in circumstances related to reproduction " +2|"XXI Factors influencing health status and contact with health services "|21|" Z40 "|" Z54 "|" Persons encountering health services for specific procedures and health care " +2|"XXI Factors influencing health status and contact with health services "|21|" Z55 "|" Z65 "|" Persons with potential health hazards related to socioeconomic and psychosocial circumstances " +2|"XXI Factors influencing health status and contact with health services "|21|" Z70 "|" Z76 "|" Persons encountering health services in other circumstances " +2|"XXI Factors influencing health status and contact with health services "|21|" Z80 "|" Z99 "|" Persons with potential health hazards related to family and personal history and certain conditions influencing health status " +1|"XXII Codes for special purposes "|22|" U00 "|" U85 "|"XXII Codes for special purposes " +2|"XXII Codes for special purposes "|22|" U00 "|" U49 "|" Provisional assignment of new diseases of uncertain etiology or emergency use " +2|"XXII Codes for special purposes "|22|" U82 "|" U85 "|" Resistance to antimicrobial and antineoplastic drugs " diff --git a/non-db_data_sources/GBD and ICD-10_(2019 version)/WHO ICD-10 (2019)/icd10_categories.txt b/non-db_data_sources/GBD and ICD-10_(2019 version)/WHO ICD-10 (2019)/icd10_categories.txt new file mode 100644 index 0000000..9569dfa --- /dev/null +++ b/non-db_data_sources/GBD and ICD-10_(2019 version)/WHO ICD-10 (2019)/icd10_categories.txt @@ -0,0 +1,225 @@ +A00 | A09 | Intestinal infectious diseases +A15 | A19 | Tuberculosis +A20 | A28 | Certain zoonotic bacterial diseases +A30 | A49 | Other bacterial diseases +A50 | A64 | Infections with a predominantly sexual mode of transmission +A65 | A69 | Other spirochaetal diseases +A70 | A74 | Other diseases caused by chlamydiae +A75 | A79 | Rickettsioses +A80 | A89 | Viral infections of the central nervous system +A92 | A99 | Arthropod-borne viral fevers and viral haemorrhagic fevers +B00 | B09 | Viral infections characterized by skin and mucous membrane lesions +B15 | B19 | Viral hepatitis +B20 | B24 | Human immunodeficiency virus [HIV] disease +B25 | B34 | Other viral diseases +B35 | B49 | Mycoses +B50 | B64 | Protozoal diseases +B65 | B83 | Helminthiases +B85 | B89 | Pediculosis, acariasis and other infestations +B90 | B94 | Sequelae of infectious and parasitic diseases +B95 | B98 | Bacterial, viral and other infectious agents +B99 | B99 | Other infectious diseases +C00 | C14 | Malignant neoplasms of lip, oral cavity and pharynx +C15 | C26 | Malignant neoplasms of digestive organs +C30 | C39 | Malignant neoplasms of respiratory and intrathoracic organs +C40 | C41 | Malignant neoplasms of bone and articular cartilage +C43 | C44 | Melanoma and other malignant neoplasms of skin +C45 | C49 | Malignant neoplasms of mesothelial and soft tissue +C50 | C50 | Malignant neoplasm of breast +C51 | C58 | Malignant neoplasms of female genital organs +C60 | C63 | Malignant neoplasms of male genital organs +C64 | C68 | Malignant neoplasms of urinary tract +C69 | C72 | Malignant neoplasms of eye, brain and other parts of central nervous system +C73 | C75 | Malignant neoplasms of thyroid and other endocrine glands +C76 | C80 | Malignant neoplasms of ill-defined, secondary and unspecified sites +C81 | C96 | Malignant neoplasms, stated or presumed to be primary, of lymphoid, haematopoietic and related tissue +C97 | C97 | Malignant neoplasms of independent (primary) multiple sites +D00 | D09 | In situ neoplasms +D10 | D36 | Benign neoplasms +D37 | D48 | Neoplasms of uncertain or unknown behaviour +D50 | D53 | Nutritional anaemias +D55 | D59 | Haemolytic anaemias +D60 | D64 | Aplastic and other anaemias +D65 | D69 | Coagulation defects, purpura and other haemorrhagic conditions +D70 | D77 | Other diseases of blood and blood-forming organs +D80 | D89 | Certain disorders involving the immune mechanism +E00 | E07 | Disorders of thyroid gland +E10 | E14 | Diabetes mellitus +E15 | E16 | Other disorders of glucose regulation and pancreatic internal secretion +E20 | E35 | Disorders of other endocrine glands +E40 | E46 | Malnutrition +E50 | E64 | Other nutritional deficiencies +E65 | E68 | Obesity and other hyperalimentation +E70 | E90 | Metabolic disorders +F00 | F09 | Organic, including symptomatic, mental disorders +F10 | F19 | Mental and behavioural disorders due to psychoactive substance use +F20 | F29 | Schizophrenia, schizotypal and delusional disorders +F30 | F39 | Mood [affective] disorders +F40 | F48 | Neurotic, stress-related and somatoform disorders +F50 | F59 | Behavioural syndromes associated with physiological disturbances and physical factors +F60 | F69 | Disorders of adult personality and behaviour +F70 | F79 | Mental retardation +F80 | F89 | Disorders of psychological development +F90 | F98 | Behavioural and emotional disorders with onset usually occurring in childhood and adolescence +F99 | F99 | Unspecified mental disorder +G00 | G09 | Inflammatory diseases of the central nervous system +G10 | G14 | Systemic atrophies primarily affecting the central nervous system +G20 | G26 | Extrapyramidal and movement disorders +G30 | G32 | Other degenerative diseases of the nervous system +G35 | G37 | Demyelinating diseases of the central nervous system +G40 | G47 | Episodic and paroxysmal disorders +G50 | G59 | Nerve, nerve root and plexus disorders +G60 | G64 | Polyneuropathies and other disorders of the peripheral nervous system +G70 | G73 | Diseases of myoneural junction and muscle +G80 | G83 | Cerebral palsy and other paralytic syndromes +G90 | G99 | Other disorders of the nervous system +H00 | H06 | Disorders of eyelid, lacrimal system and orbit +H10 | H13 | Disorders of conjunctiva +H15 | H22 | Disorders of sclera, cornea, iris and ciliary body +H25 | H28 | Disorders of lens +H30 | H36 | Disorders of choroid and retina +H40 | H42 | Glaucoma +H43 | H45 | Disorders of vitreous body and globe +H46 | H48 | Disorders of optic nerve and visual pathways +H49 | H52 | Disorders of ocular muscles, binocular movement, accommodation and refraction +H53 | H54 | Visual disturbances and blindness +H55 | H59 | Other disorders of eye and adnexa +H60 | H62 | Diseases of external ear +H65 | H75 | Diseases of middle ear and mastoid +H80 | H83 | Diseases of inner ear +H90 | H95 | Other disorders of ear +I00 | I02 | Acute rheumatic fever +I05 | I09 | Chronic rheumatic heart diseases +I10 | I15 | Hypertensive diseases +I20 | I25 | Ischaemic heart diseases +I26 | I28 | Pulmonary heart disease and diseases of pulmonary circulation +I30 | I52 | Other forms of heart disease +I60 | I69 | Cerebrovascular diseases +I70 | I79 | Diseases of arteries, arterioles and capillaries +I80 | I89 | Diseases of veins, lymphatic vessels and lymph nodes, not elsewhere classified +I95 | I99 | Other and unspecified disorders of the circulatory system +J00 | J06 | Acute upper respiratory infections +J09 | J18 | Influenza and pneumonia +J20 | J22 | Other acute lower respiratory infections +J30 | J39 | Other diseases of upper respiratory tract +J40 | J47 | Chronic lower respiratory diseases +J60 | J70 | Lung diseases due to external agents +J80 | J84 | Other respiratory diseases principally affecting the interstitium +J85 | J86 | Suppurative and necrotic conditions of lower respiratory tract +J90 | J94 | Other diseases of pleura +J95 | J99 | Other diseases of the respiratory system +K00 | K14 | Diseases of oral cavity, salivary glands and jaws +K20 | K31 | Diseases of oesophagus, stomach and duodenum +K35 | K38 | Diseases of appendix +K40 | K46 | Hernia +K50 | K52 | Noninfective enteritis and colitis +K55 | K64 | Other diseases of intestines +K65 | K67 | Diseases of peritoneum +K70 | K77 | Diseases of liver +K80 | K87 | Disorders of gallbladder, biliary tract and pancreas +K90 | K93 | Other diseases of the digestive system +L00 | L08 | Infections of the skin and subcutaneous tissue +L10 | L14 | Bullous disorders +L20 | L30 | Dermatitis and eczema +L40 | L45 | Papulosquamous disorders +L50 | L54 | Urticaria and erythema +L55 | L59 | Radiation-related disorders of the skin and subcutaneous tissue +L60 | L75 | Disorders of skin appendages +L80 | L99 | Other disorders of the skin and subcutaneous tissue +M00 | M25 | Arthropathies +M30 | M36 | Systemic connective tissue disorders +M40 | M54 | Dorsopathies +M60 | M79 | Soft tissue disorders +M80 | M94 | Osteopathies and chondropathies +M95 | M99 | Other disorders of the musculoskeletal system and connective tissue +N00 | N08 | Glomerular diseases +N10 | N16 | Renal tubulo-interstitial diseases +N17 | N19 | Renal failure +N20 | N23 | Urolithiasis +N25 | N29 | Other disorders of kidney and ureter +N30 | N39 | Other diseases of urinary system +N40 | N51 | Diseases of male genital organs +N60 | N64 | Disorders of breast +N70 | N77 | Inflammatory diseases of female pelvic organs +N80 | N98 | Noninflammatory disorders of female genital tract +N99 | N99 | Other disorders of the genitourinary system +O00 | O08 | Pregnancy with abortive outcome +O10 | O16 | Oedema, proteinuria and hypertensive disorders in pregnancy, childbirth and the puerperium +O20 | O29 | Other maternal disorders predominantly related to pregnancy +O30 | O48 | Maternal care related to the fetus and amniotic cavity and possible delivery problems +O60 | O75 | Complications of labour and delivery +O80 | O84 | Delivery +O85 | O92 | Complications predominantly related to the puerperium +O94 | O99 | Other obstetric conditions, not elsewhere classified +P00 | P04 | Fetus and newborn affected by maternal factors and by complications of pregnancy, labour and delivery +P05 | P08 | Disorders related to length of gestation and fetal growth +P10 | P15 | Birth trauma +P20 | P29 | Respiratory and cardiovascular disorders specific to the perinatal period +P35 | P39 | Infections specific to the perinatal period +P50 | P61 | Haemorrhagic and haematological disorders of fetus and newborn +P70 | P74 | Transitory endocrine and metabolic disorders specific to fetus and newborn +P75 | P78 | Digestive system disorders of fetus and newborn +P80 | P83 | Conditions involving the integument and temperature regulation of fetus and newborn +P90 | P96 | Other disorders originating in the perinatal period +Q00 | Q07 | Congenital malformations of the nervous system +Q10 | Q18 | Congenital malformations of eye, ear, face and neck +Q20 | Q28 | Congenital malformations of the circulatory system +Q30 | Q34 | Congenital malformations of the respiratory system +Q35 | Q37 | Cleft lip and cleft palate +Q38 | Q45 | Other congenital malformations of the digestive system +Q50 | Q56 | Congenital malformations of genital organs +Q60 | Q64 | Congenital malformations of the urinary system +Q65 | Q79 | Congenital malformations and deformations of the musculoskeletal system +Q80 | Q89 | Other congenital malformations +Q90 | Q99 | Chromosomal abnormalities, not elsewhere classified +R00 | R09 | Symptoms and signs involving the circulatory and respiratory systems +R10 | R19 | Symptoms and signs involving the digestive system and abdomen +R20 | R23 | Symptoms and signs involving the skin and subcutaneous tissue +R25 | R29 | Symptoms and signs involving the nervous and musculoskeletal systems +R30 | R39 | Symptoms and signs involving the urinary system +R40 | R46 | Symptoms and signs involving cognition, perception, emotional state and behaviour +R47 | R49 | Symptoms and signs involving speech and voice +R50 | R69 | General symptoms and signs +R70 | R79 | Abnormal findings on examination of blood, without diagnosis +R80 | R82 | Abnormal findings on examination of urine, without diagnosis +R83 | R89 | Abnormal findings on examination of other body fluids, substances and tissues, without diagnosis +R90 | R94 | Abnormal findings on diagnostic imaging and in function studies, without diagnosis +R95 | R99 | Ill-defined and unknown causes of mortality +S00 | S09 | Injuries to the head +S10 | S19 | Injuries to the neck +S20 | S29 | Injuries to the thorax +S30 | S39 | Injuries to the abdomen, lower back, lumbar spine and pelvis +S40 | S49 | Injuries to the shoulder and upper arm +S50 | S59 | Injuries to the elbow and forearm +S60 | S69 | Injuries to the wrist and hand +S70 | S79 | Injuries to the hip and thigh +S80 | S89 | Injuries to the knee and lower leg +S90 | S99 | Injuries to the ankle and foot +T00 | T07 | Injuries involving multiple body regions +T08 | T14 | Injuries to unspecified part of trunk, limb or body region +T15 | T19 | Effects of foreign body entering through natural orifice +T20 | T32 | Burns and corrosions +T33 | T35 | Frostbite +T36 | T50 | Poisoning by drugs, medicaments and biological substances +T51 | T65 | Toxic effects of substances chiefly nonmedicinal as to source +T66 | T78 | Other and unspecified effects of external causes +T79 | T79 | Certain early complications of trauma +T80 | T88 | Complications of surgical and medical care, not elsewhere classified +T90 | T98 | Sequelae of injuries, of poisoning and of other consequences of external causes +V01 | X59 | Accidents +X60 | X84 | Intentional self-harm +X85 | Y09 | Assault +Y10 | Y34 | Event of undetermined intent +Y35 | Y36 | Legal intervention and operations of war +Y40 | Y84 | Complications of medical and surgical care +Y85 | Y89 | Sequelae of external causes of morbidity and mortality +Y90 | Y98 | Supplementary factors related to causes of morbidity and mortality classified elsewhere +Z00 | Z13 | Persons encountering health services for examination and investigation +Z20 | Z29 | Persons with potential health hazards related to communicable diseases +Z30 | Z39 | Persons encountering health services in circumstances related to reproduction +Z40 | Z54 | Persons encountering health services for specific procedures and health care +Z55 | Z65 | Persons with potential health hazards related to socioeconomic and psychosocial circumstances +Z70 | Z76 | Persons encountering health services in other circumstances +Z80 | Z99 | Persons with potential health hazards related to family and personal history and certain conditions influencing health status +U00 | U49 | Provisional assignment of new diseases of uncertain etiology or emergency use +U82 | U85 | Resistance to antimicrobial and antineoplastic drugs diff --git a/scripts/umls_requests.py b/scripts/umls_requests.py index 8652a83..9ea1afa 100644 --- a/scripts/umls_requests.py +++ b/scripts/umls_requests.py @@ -40,7 +40,25 @@ with postgres_conn() as pconn, pconn.cursor(cursor_factory=extras.DictCursor) as order by nct_id ; """ - pcurse.execute(sql) + 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 = []