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FAIRsharing / domain-ontology

A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 50 publicly-available ontologies.
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Modification: Infection to be made visible to FAIRsharing users #72

Closed allysonlister closed 3 years ago

allysonlister commented 3 years ago

What are you changing?

Add the inSubset=FAIRsharing annotation property to http://purl.obolibrary.org/obo/IDO_0000586 (Infection).

Why are you suggesting this change?

It is currently being used to curate records in FAIRsharing, and therefore needs to have this property set.

Mapping

No changes will need to be made to the hierarchy, IRIs or to any other properties of the class.

allysonlister commented 3 years ago

As shown by the robot diff below, the modifications made to DRAO are only those mentioned in this ticket:

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

infection http://purl.obolibrary.org/obo/IDO_0000586

Added

allysonlister commented 3 years ago

Why am I revisiting Infection?

There is a twist here - I didn't realize, due to the way the original OBI label is, that we had Infection in two places in DRAO:

It is the OBI term that was visible prior to this ticket being made. Therefore we need to decide which term and hierarchy to retain, and update DRAO to reflect that. After this point, we need to tidy up https://fairsharing.org/collection/COVID19Resources, which is the only record in FAIRsharing with this problem.

Below are the two locations (highlighted) of the two infection terms in the current DRAO hierarchy.

infection

Why are you suggesting this change?

As this is an automatically-generated hierarchy, it is inevitable that these kinds of concept duplications will occur, and should be resolved as they are discovered.

Mapping

I suggest the following:

Old IRI New IRI Note
http://purl.obolibrary.org/obo/IDO_0000586 http://purl.obolibrary.org/obo/OBI_1110021 The IDO term is not required, as we already have an OBI equivalent already in use.

Hierarchy

Recommendation: I suggest that we align with OBI, and put the child of IDO Infection under the OBI Infection

Reasoning: I prefer the placement of the OBI term.

Please could @delphinedauga and @Drosophilic provide comments / confirm they're happy with these suggested changes. Thanks!

delphinedauga commented 3 years ago

Thanks @allysonlister , I agree with your suggestion :)

Drosophilic commented 3 years ago

I agree @allysonlister, all sounds good!

allysonlister commented 3 years ago

Updates to DRAO have resulted in the following changes, consistent with the work required for this ticket.

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

hospital-acquired infection http://purl.obolibrary.org/obo/IDO_0000630

Removed

Added

infection http://purl.obolibrary.org/obo/IDO_0000586

Removed