Python wrapper to different clients to determine how a particular term is used.

Overview

ontology_term_usage

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

Demo server (NOT STABLE):

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 -s

Caveats

It 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

API

To run the API locally:

make app

Deployment on AWS via serverless:

Follow

https://adem.sh/blog/tutorial-fastapi-aws-lambda-serverless

for serverless/lambda deployment

Type

make deploy

Future plans

It may be better to wrap this into a generic obolibrary python package

Owner
Chris Mungall
Computer Research Scientist at Berkeley Lab. Interests: AI / Ontologies / Bioinformatics. Projects: GO, Monarch, Alliance, OBOFoundry, NMDC
Chris Mungall
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