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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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Infectology / infectious disease #57

Closed allysonlister closed 3 years ago

allysonlister commented 4 years ago

Hi Ally, I can confirm we said 'Infectious Disease Medicine' for the SRAO term, and then we chose 'Infectology' for DRAO.

Originally posted by @Drosophilic in https://github.com/FAIRsharing/subject-ontology/issues/49#issuecomment-626703517

allysonlister commented 4 years ago

Label

Recommendation: infectious disease

Reasoning: https://github.com/FAIRsharing/subject-ontology/issues/49 states that we agreed on Infectology, but I'm starting to think this doesn't sound appropriate for DRAO. I'd like to follow other DRAO classes such as 'cardiovascular disease' and call this class 'infectious disease', which still remains sufficiently different from the SRAO term 'Infectious Disease Medicine' as described in https://github.com/FAIRsharing/subject-ontology/issues/49#issuecomment-626703517. What are your thoughts?

IRI

Recommendation: EFO: http://www.ebi.ac.uk/efo/EFO_0005741

Reasoning: EFO, OBI and IDO have infectious disease as a child term of disease; IDO uses the OGMS disease term (as we do) and OBI and EFO each use their own IRI for their disease term, but the structure is the same. Although all classes would be appropriate, as we are already using many EFO terms for various children of the disease class, and EFO has the best definition and equivalentTo cross references to other ontologies, I would go with EFO.

Definition

Use EFO's: A disorder resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact.

Hierarchy

Recommendation: child of disease

Reasoning: We already have 'Infection' from OBI ("the detrimental process in which an infectious agent colonizes or replicates in a host environment") as part of the process hierarchy in DRAO, however this is a process and not the 'disease' hierarchy we were talking about earlier in https://github.com/FAIRsharing/subject-ontology/issues/49. Therefore I think we're justified in having this new term for the concept of the diseases (which are classed in DRAO within the disposition hierarchy): disposition

(@Drosophilic thought about perhaps having this as a child of disease -> human disease, but as infectious diseases are broader than just humans, placing it as a child of disease might be more suitable.)

What do you think, @Drosophilic and @delphinedauga? Thanks!

delphinedauga commented 4 years ago

Agree !

Drosophilic commented 3 years ago

Agreed!

allysonlister commented 3 years ago

Please note that this is a completely new term, and therefore will not need a mapping added at development/refactored-IRIs-current.txt