Python wrapper to different clients to determine how a particular term is used.
One use case is for ontology developers who want to obsolete a term but need to know how it is used.
For example, if GO wanted to obsolete "apoptosis", GO editors could query for GO:0006915 and see which ontologies use it.
For more context see:
Demo server (NOT STABLE):
- https://v61vbincq3.execute-api.us-east-1.amazonaws.com/staging/docs
- https://v61vbincq3.execute-api.us-east-1.amazonaws.com/staging/usage/GO:0006915
Services wrapped:
- ontobee
- ubergraph (subset of OBO)
- go (for annotations and go-cams)
- uniprot sparql endpoint (for annotations)
Planned:
- bioportal
For more details, see inline docs and tests
No CLI yet. We will implement using click
Demo:
poetry run pytest -sIt is actually quite hard to determine whether a term is used. Many ontologies do not put their "complete" versions forward as the main URL that is loaded into services like OLS, Ontobee, Bioportal, in particular, the inter-ontology axioms this tool queries may be missing.
Ubergraph gets around this partially by having its own configuration that may load additional axioms - but ubergraph may not have all of obo
To run the API locally:
make app- Docs: http://127.0.0.1:8000/docs
- Find usages: http://127.0.0.1:8000/usage/GO:0007588
Deployment on AWS via serverless:
Follow
https://adem.sh/blog/tutorial-fastapi-aws-lambda-serverless
for serverless/lambda deployment
Type
make deploy- It may be better to wrap this into a generic obolibrary python package