INCATools / INCATools/ontology-access-kit

High-level interface via the Bioregistry

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#74 2 comments 0 reactions 0 assignees View on GitHub
design
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

Open the contributing 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

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