INCATools / INCATools/ontology-access-kit
Add lint checks for casing in ontology term labels and synonyms
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- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
Arguably this doesn't belong in OAK but should go in robot as it's more tied to ontology development, but this would be easy to fold in
The input would be an ontology, the output would be a kgcl file (kgcl syntax or yaml/json) e.g
- "rename 'parkinsons disease' to 'Parkinson disease'"
- "change synonym 'HYPERFOOEMIA' to 'hyperfooemia' for MONDO:1234567'
The rules could be custom for each ontology. E.g HPO uses first letter upper case. NCIT uses title case.
There needs to be some fuzziness as there are many proper name - non-proper name clashes. I attempted to mine these here:
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing the OAK-versus-robot scope described in the issue and the linked capital-offence project. Define how an ontology becomes KGCL syntax or YAML/JSON output, then clarify configurable casing rules for HPO and NCIT and the required fuzziness for proper-name clashes; done means those decisions are documented and testable.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- tooling
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100