Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add RxNorm #150

Closed
gaurav opened this issue Jun 7, 2023 · 0 comments · Fixed by #173
Closed

Add RxNorm #150

gaurav opened this issue Jun 7, 2023 · 0 comments · Fixed by #173

Comments

@gaurav
Copy link
Collaborator

gaurav commented Jun 7, 2023

RxNorm is a definitive source for drug information, and so we need to include RXCUIs in cliques.

The general algorithm we should use is:

  1. Include all RxNorm entries, e.g. https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm=204442
  2. Consider them identical to all Ingredient (IN) identifiers -- in this case, RXCUI 5640 "ibuprofen". But note that this does not work with MINs, which work the other way, and tell you which drugs include this one.
  3. Add additional names from RxNorm -- trade names, formulations, etc -- as synonyms of this concept.
  4. Look for additional information in UMLS (e.g. https://uts.nlm.nih.gov/uts/umls/vocabulary/RXNORM/5640) such as trade names, formulations, etc.

This will have the side-benefit of getting rid of a lot of e.g. "Ibuprofen 50MG" entries in NameRes, since they would be cliqued into their ingredients. We could also extract RxNorm-UMLS and RxNorm-MeSH mappings (maybe to other sources as well: ChEBI? UNII?) so that we clique them together with other drugs.

Would close TranslatorSRI/NodeNormalization#127

@gaurav gaurav added this to the Babel September Release milestone Jun 8, 2023
@cbizon cbizon mentioned this issue Jul 27, 2023
gaurav added a commit that referenced this issue Aug 22, 2023
This does basically 2 things -
1. It adds in RXNORM identifiers and creates a Drug compendium
2. It pulls in RXNORM relationships and PUBCHEM RXNORM annotations and creates a drug/chemical conflation

Fixes #150
Fixes #144
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant