Add UMLS IDs to taxon #60
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This allows bmt to choose the Biolink model it is designed to work with.
These are prefixes not mentioned in the Biolink model that we would like to incorporate into the compendium anyway.
No longer needed, since UMLS has now been added to OrganismTaxon.
cbizon
approved these changes
Sep 30, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
We identified many UMLS IDs that correspond to taxa but aren't currently imported in TranslatorSRI/NodeNormalization#119 (comment). This PR updates the taxon compendia to include taxa from UMLS. Since Biolink Model v3.0.2 doesn't include UMLS as an identifier prefix for OrganismTaxon, this PR adds an
extra_prefixesargument towrite_compendium()to addUMLSto that list, sinceUMLSwas added to the Biolink Model OrganismTaxon class (biolink/biolink-model#1084), we don't actually use this functionality here. But I'm leaving it in since we might need it in the future.