Investigate indication linking #13

I know of the following resources:

MeSH
Snowmed
RXnorm

I need to figure out how to

Link Trials to indications
Link Drugs to indications
Group indications

This is going to take a bit.

This issue is to handle a discussion with myself on the topic about what needs to happen.
The actual things I need to do will be handled in other issues.

I know of the following resources: - MeSH - Snowmed - RXnorm I need to figure out how to - Link Trials to indications - Link Drugs to indications - Group indications This is going to take a bit. This issue is to handle a discussion with myself on the topic about what needs to happen. The actual things I need to do will be handled in other issues.

I have a bit more written down in logseq. there is a WHO taxonomy used by other papers.

so, the clinicla trials indications are indexed in mesh terms by the table ctgov.browse_conditions.

so, the clinicla trials indications are indexed in mesh terms by the table `ctgov.browse_conditions`.

I need a way to link spls indications.

I currently have the following data links outlined

  flowchart LR
  
  
  %% Nodes
  spl[(SPLs describe drugs on market)]
  rxnorm[[RxNorm]]
  dom([drugs on market]):::varsOfInterest
  ct[(ClinicalTrials History)]  
  subgraph mesh[Mesh Taxonomy]
    meshd[[MeSH drugs]]
    meshi[[MeSH indications]]
  end
  who[[WHO ATC]]
  
  %% Class definitions
  classDef varsOfInterest fill:#959
  
  meshd <==RxNorm provides an interface to MeSH ==> rxnorm
  spl -.  rxnorm_mapping file .-> rxnorm
  spl -- spl all drug labels --> dom
  ct -. ctgov.browse_interventions .-> meshd
  ct -. ctgov.browse_conditions .-> meshi
  who <==I believe there is an interface==> mesh

I am missing how to link indications to drugs
- there may be the option to do through the WHO ATC. As this provides automatic groups I'd probably go with this.
- Or I can try to group the trials through ctgov.browse_conditions table and group them. I doubt I have the ability to do this well.
- There might be a hybrid approach where you match MeSH terms from trials to WHO ATC and check for poor matches.

I currently have the following data links outlined ``` mermaid flowchart LR %% Nodes spl[(SPLs describe drugs on market)] rxnorm[[RxNorm]] dom([drugs on market]):::varsOfInterest ct[(ClinicalTrials History)] subgraph mesh[Mesh Taxonomy] meshd[[MeSH drugs]] meshi[[MeSH indications]] end who[[WHO ATC]] %% Class definitions classDef varsOfInterest fill:#959 meshd <==RxNorm provides an interface to MeSH ==> rxnorm spl -. rxnorm_mapping file .-> rxnorm spl -- spl all drug labels --> dom ct -. ctgov.browse_interventions .-> meshd ct -. ctgov.browse_conditions .-> meshi who <==I believe there is an interface==> mesh ``` - I am missing how to link indications to drugs - there may be the option to do through the WHO ATC. As this provides automatic groups I'd probably go with this. - Or I can try to group the trials through `ctgov.browse_conditions` table and group them. I doubt I have the ability to do this well. - There might be a hybrid approach where you match MeSH terms from trials to WHO ATC and check for poor matches.

ok, investigated.

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Investigate indication linking #13