bigbio / bigbio/proteomics-sample-metadata

Differentiate between ontology subtree restrictions and non-ontologized strings "of an ontologized type"

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Description

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Strictly speaking the entries in such a column will not be CV terms in the

[EFO_0000542](https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000542)
subtree (since this already a leaf).

This is very different from saying e.g. tumor stage must follow the children of [EFO_0004925](https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0004925). I.e. be one of:
- M0 distant metastasis stage
- M1 distant metastasis stage
- MX distant metastasis stage
- ...

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Research direction

Start by reading the issue text and comparing the linked EFO_0000542 and EFO_0004925 ontology entries. Determine where the project describes ontology subtree restrictions versus non-ontologized strings of an ontologized type; done means the distinction is explicitly documented and the examples are represented consistently.

Written by the indexing model from the issue text.

Assessment

Domain
documentation
Issue type
Documentation
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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