INCATools / INCATools/ontology-access-kit
Pass `prefix_map` to implementation objects?
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- Dominant language
- Python
- Stars
- 198
- Forks
- 35
- Avg merge
- 3d 4h
- Merged PRs (30d)
- 1
Description
Overview
This should be relevant in situations where (a) I want to consistently only CURIES back from .entities() (assuming all the term URI stems are contained in my prefix_map) and (b) when I want to get all of the terms 'owned' by the ontology.
I'm so far mostly using ProntoImplementation and SqlImplementation, but I don't see a way to pass prefix_map to either of these on object initialization (or to the methods I'm interested in).
Additional thoughts
If we pass prefix_map, we can then further pass it to curies.
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 ProntoImplementation and SqlImplementation entry points, especially object initialization and the .entities() methods. Trace how prefix_map could reach the curies integration, then define the supported API and verify that CURIE-only results and ontology-owned-term lookups behave as intended.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, sql
- Domain
- api, backend-api-design, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 32/100