INCATools / INCATools/ontology-access-kit
Add a TSV enricher command that does performant lookup on ontological elements of ids
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
Given:
- a TSV where some specified column is ID, and others are mapped to label, category, ancestor etc
Iterate through TSV in batches performing lookup for missing values, using any supporting backend, using most performant batching for that backend
Example use case: a large SSSOM file with no labels or categories. The client must decide which endpoint is best (e.g. bioportal for broad bio-ontologies, wikidata, lov, a local ontology)
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 repository's existing CLI commands and ontology backend interfaces; the issue names neither files nor tests. Define the TSV column mapping, batching behavior, backend selection, and output expectations before implementation, then verify enrichment on the large SSSOM example.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend-api-design, cli
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100