Make template definition for Unusual X infection

[pnrobinson]

See https://www.ncbi.nlm.nih.gov/pubmed/22052638

[LCCarmody]

Not sure if this should be added. There was a request at the hackathon (https://github.com/obophenotype/human-phenotype-ontology/issues/4004) for this term as a phenotype. It is a phenotype in OMIM: 618131, OMIM:243700 and others. Should it also be a MONDO term?

[pnrobinson]

This is an important phenotype for many immunological diseases. I do not think that the specific subterms are usually called Unusual X infection though

[LCCarmody]

That makes sense. I am happy to add it. I assume Molluscum contagiosum should be under 'Opportunistic infections'. But I think there needs to be a bit more added to the hierarchy, since it doesn't fit under 'Severe viral infections' or 'Disseminated viral infections'. Should another term be added as 'Opportunistic viral infections' as parent of all 3?

If this looks okay, I will add it and close #4004

Opportunistic infections

Opportunistic viral infections

Molluscum contagiosum Dissemeniated viral infections Severe viral infections

[pnrobinson]

Suggested definition: A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystisjirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to antibiotic treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. PMID:22052638

[pnrobinson]

I have added this term and rearranged the top level. We should use the definition as a template for any lower level terms such as Unusual infection.

[cmungall]

Does this term violate the TPR as we move to common disease?

"A type of infection that is regarded as a sign of a pathological susceptibility to infection."

E.g

https://www.ebi.ac.uk/ols/ontologies/hp/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0031700

[pnrobinson]

This is being modelled as an unusual infection. These terms are basically a history of an unusual infection and are not modelling the disease itself, which will go in Mondo and which in the future we need to explicitly link to. Perhaps it would be better to relable the term "Opportunistic parasitic infection" -- is that what you are referring to @cmungall ?

[pnrobinson]

I think we now have a good structure in this area, closing.