ga4gh / ga4gh/experiments-metadata
Some fields should suggest a subset of a given ontology
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Description
From @sveinugu:
Since e.g. not all terms in the OBI ontology describe experiment assays, it might be an idea to specify that for the “assay_type” field, all terms should have the “assay” concept as an ancestor: (https://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000070)
And similarly for other fields specifying terms. We did this in the FAIRtracks model, e.g.[ https://github.com/fairtracks/fairtracks_standard/blob/master/docs/fairtracks_experiment-properties-experimental-technique.md#term_id](https://github.com/fairtracks/fairtracks_standard/blob/master/docs/fairtracks_experiment-properties-experimental-technique.md#term_id) (Here we used the more generic concept “planned process” as the ancestor for a more generic field “experimental technique”:[ https://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000011](https://bioportal.bioontology.org/ontologies/OBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000011))
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Research direction
Start by reviewing the issue's OBI BioPortal links and the referenced FAIRtracks experimental-technique documentation. Identify which metadata fields specify ontology terms and determine the expected ancestor constraints; the work is done when the applicable fields and their ontology subsets are explicitly defined in the standard.
Written by the indexing model from the issue text.
Assessment
- Domain
- data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100