Wikidata:Property proposal/Experimental Factor Ontology ID
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Experimental Factor Ontology ID[edit]
Originally proposed at Wikidata:Property proposal/Natural science
| Description | The identifer for an experimental factor in the Experimental Factor Ontology |
|---|---|
| Represents | Experimental Factor Ontology (Q16251642) |
| Data type | External identifier |
| Example 1 | acne (Q79928)→0003894 |
| Example 2 | disease (Q12136)→0000408 |
| Example 3 | Chagas disease (Q649558)→0008559 |
| Source | https://www.ebi.ac.uk/efo/ |
| Planned use | Create a Mix'n'Match catalog; semi-automatically add IDs to Wikidata via ontology cross references |
| Expected completeness | eventually complete (Q21873974) |
| Formatter URL | http://www.ebi.ac.uk/efo/EFO_$1 |
| See also | Gene Ontology ID (P686), Cell Ontology ID (P7963) |
| Single-value constraint | yes |
| Distinct-values constraint | yes |
Motivation[edit]
The Experimental factor ontology, EFO, is a well-recognized ontology, providing concepts used in a wide variety of resources in EMBL-EBI. I am exploring the reconciliation of some CC0 data in the Open Targets platform to Wikidata, and some of the concepts are represented in EFO. It would be great to have curated mappings to EFO on Wikidata, both generally and for this particular application. TiagoLubiana (talk) 22:16, 4 August 2023 (UTC)
Discussion[edit]
Support I support this, EFO is an important and well-regarded ontology. However, the local unique identifiers should explicitly not include the EFO_ at the beginning of local unique identifiers. Cthoyt (talk) 01:51, 5 August 2023 (UTC)
- @Cthoyt: Thanks! I've changed the proposal to put "EFO_" in the formatter url. TiagoLubiana (talk) 15:26, 5 August 2023 (UTC)
Weak support I am still not sure Wikidata is the place to store ontology mappings. Please add the regular expression, accommodating Cthoyt's point. What qualifiers would you suggest to explain why they were matched? Are you going to monitor ontological conflicts in Wikidata resulting from adding the identifier? How does this work for other ontologies, like ChEBI ID (P683)? But I don't want to make this property proposal responsible for that, so the weak support. Egon Willighagen (talk) 05:00, 5 August 2023 (UTC)
- @Egon Willighagen: Thanks! I've added the regex; for xref-based mappings I've used heuristics like inferred by common HGNC mappings on source and on Wikidata (Q119459343), but I agree with you. While I think there are better approaces for mapping, like SSSOM, I believe Wikidata provides good infrastructure for a first pass on mappings, if for nothing else, for display of the resources on Wikipedia pages. TiagoLubiana (talk) 15:26, 5 August 2023 (UTC)
- @TiagoLubiana, Cthoyt, Egon Willighagen:
Done Mahir256 (talk) 18:54, 14 August 2023 (UTC)
