INCATools / INCATools/ontology-access-kit
High-level interface via the Bioregistry
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
The `bioontologies` package has a very high-level interface for getting OBO graphs by prefix, since it can automatically look up the appropriate IRIs via its mappings to OBO Foundry.
```
import bioontologies
parse_results = bioontologies.get_obograph_by_prefix("go")
go_graph_document = parse_results.graph_document
```
This could be extended to OAK and also let you choose if you want the OWL, OBO, or OBO Graph JSON artifact to get consumed
Contributor guide
Research direction
Start with the existing bioontologies.get_obograph_by_prefix("go") interface and review how it resolves prefixes through OBO Foundry mappings. Then determine how OAK should expose the equivalent high-level interface and allow selecting OWL, OBO, or OBO Graph JSON artifacts; done means the supported artifact choices and interface behavior are defined and implemented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100