INCATools / INCATools/ontology-development-kit

Automate mapping of deprecated terms in use

Open
#499 3 comments 0 reactions 1 assignee Claimed by @anitacaron View on GitHub
enhancement tech
Dominant language
Dockerfile
Stars
375
Forks
69
Avg merge
3d 5h
Merged PRs (30d)
7

Description

This is, IMO, a major missing component of the ODK

* MVP - generate a report of mappings for obsoleted terms every time imports are updated. We already have suitable SPARQL for finding mappings `src/sparql/obsoletes.sparql`.
* This should be extended to:
* Report label and comments on obsoleted term if present
* Report label of mapped term
* Report if ID of obsolete term is the value of an OboInOWL#alt_id axiom (this indicates obsoletion was due to OBO merge.
* Potential problems:
* lack of range restrictions or checks on the value of replaced_by & consider axioms could cause problems for mapping to term referred to. We need to support the following possibilities:
* OBO curie - type string
* IRI (typed)
* short_form ID (?)
* Too complex to support all of above in SPARQL?

* Complete functionality
* ODK option to auto-update editors file & template tsvs for every obsolete term for which there is a *single* replacement mapped via 'replaced_by'. Automated update should be accompanied by a report of all mappings.

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.