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

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