INCATools / INCATools/ontology-access-kit
annotator should provide finer-grained model of match type
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
May apply to OLS more than BioPortal
Consider annotating 'E. coil' against the [NCBI Taxonomy](https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCBITaxon_562&lang=en&viewMode=All&siblings=false). That's not just a synonym for NCBITaxon:562, 'Escherichia coli', it's an _exact synonym_.
Actually, NCBITaxon looks broken in BioPortal right now: https://bioportal.bioontology.org/ontologies/NCBITAXON/?p=summary
But BioPortal does similar modeling of synonyms for [acetic acid](https://bioportal.bioontology.org/ontologies/CHEBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_15366)
Contributor guide
Research direction
Start by locating the annotator entry point and its existing match-type model. Use the E. coli/NCBI Taxonomy and acetic acid/CHEBI examples in the issue to understand the expected distinction, then verify that exact synonyms receive a finer-grained match type. No file or test is named, and the issue has had no recent activity.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100