update mappings, semantic types (without update to biolink v2) #61
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
add semantic types that we already have in our kps (some are also already in the config file) clinical finding is a semantic type in the multiomics wellness kp api that we could support
Pull Request Test Coverage Report for Build 1044093884
💛 - Coveralls |
|
@colleenXu this PR feels very big to me -- seems to combine several different objectives here. We can discuss on Tuesday whether we want to break this PR into multiple smaller ones, but in the future it would be better to do that anyway I think. |
large changes: - added Transcript, ClinicalFinding (for multiomics wellness kp api) Smaller changes: - fix typos - added mapping fields - SmallMolecule: removed KEGG (not chemical ids), added LINCS / CAS / HMDB (for specific apis that use them) - Drug: added rxcui, ndc, and the chemical stuff - MolecularActivity: changed KEGG to KEGG.REACTION - BiologicalProcess: removed KEGG - CellularComponent: removed MetaCyc, Rhea - Pathway: add GO/SMPDB, change pharmgkb to pharmgkb.pathways - AnatomicalEntity: removed NCIT (not in api) - Cell: removed umls, hpo (couldn't find in the api)
changed clinvar ID to use variation ID (not rcv, which is the record of the variation + its clinical significance). also added another mapping field for hgvs
to match the changes to the src/config and src/common/types files. Also update to link to biothings rather than kevinxin90's repo
update RHEA tests to work based on molecular activity semantic type
change pubchem -> pubchem.compound make CHEMBL7512_DB_IDS writing match the format of the other constants
colleenXu
force-pushed
the
updateMappings
branch
from
7b97527 to
94892bb
Compare
|
Split into 8 PRs...:
|
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.
See the comments in the conversation of most commits for more details.
these fixes should help BTE handle most semantic types in the APIs it ingests
the updated mappings should also help BTE handle the IDs from the APIs/operations it uses