INCATools / INCATools/ontology-access-kit

Home for curify_table, uri_to_curie, curie_to_uri, and irify_table?

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#186 3 comments 1 reaction 0 assignees View on GitHub
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Python
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Merged PRs (30d)
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Description

We frequently use these methods:

- curify_table: all/selected columns with IRIs should be replaced by curies
- irify_table: all/selected columns with curies should be replaced by IRIs
- uri_to_curie: a given uri is converted to a curie
- curie_to_uri: a given curie is converted to a curie

For the latter two we could go straight to bioregistry: https://bioregistry.readthedocs.io/en/latest/api/bioregistry.curie_from_iri.html?highlight=uri_to_curie

Or if we want to keep our dependencies clean implement intermediate utilities in OAK that defer to bioregistry for the implementations?

cc @joeflack4

Contributor guide

Open the contributing guide

Research direction

Start by locating curify_table, irify_table, uri_to_curie, and curie_to_uri in the repository, then review the linked bioregistry API. The issue does not name files or tests and presents multiple dependency and ownership options; done would require a decided home and implementation direction for these utilities.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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