reclassify infectious disease terms

monarch-initiative / mondo

Mondo Disease Ontology

http://obofoundry.org/ontology/mondo

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reclassify infectious disease terms #3142

Closed nicolevasilevsky closed 3 years ago

nicolevasilevsky commented 3 years ago

Per the Mondo developers call on 06/11, we propose to treat parasite as a synonym of eukaryote

[ ] to do: add parasite logical axiom w/ eukaryote

Question: can anyone think of a eukaryotic infectious disease that is not a parasitic disease?

Question: Should we put fungal infectious disease under parasitic infectious disease?

[ ] to do: classify all children of infectious disease as a child of bacterial infectious disease, viral infectious disease or parasitic infectious disease?

cc @cmungall @mellybelly @pnrobinson @sabrinatoro

pnrobinson commented 3 years ago

Fungi are eukaryotes but are not considered parasites. Fungi are opportunistic

maglott commented 3 years ago

Shouldn't synonyms be reciprocal? Not all eukaryotes are parasites. Amoebae are also eukaryotes, and they are not fungi

what does "classify all children of infectious disease as a child of bacteria, virus or parasite/eukaryote" mean? Seems odd to classify any disorder as a child of an organism.

nicolevasilevsky commented 3 years ago

@maglott I meant: bacterial infectious disease, viral infectious disease or parasitic infectious disease. Yes, not as children of organisms, that would be odd! :)

maglott commented 3 years ago

And going back to the original question... if we think of parasites as describes in https://en.wikipedia.org/wiki/Parasitism, I don't think all fungal infections are categorized as parasitic. For example, https://www.ncbi.nlm.nih.gov/mesh/68002177 is not treed under parasitic diseases. https://www.ncbi.nlm.nih.gov/mesh/68010272

pnrobinson commented 3 years ago

fungal infections are not considered to be parasitic infections

nicolevasilevsky commented 3 years ago

Thanks for your feedback @pnrobinson and @maglott

The next open question is:

how to better define parasitic infection (textually and can it be defined logically?) Ask experts from https://veupathdb.org/veupathdb/app

pnrobinson commented 3 years ago

Isn't there an ontology term for parasite that we can refer to? The definition could be simply an disease caused by infection by a parasite.

cmungall commented 3 years ago

@pnrobinson

fungal infections are not considered to be parasitic infections

is this true for all fungal infections, or just some?

currently many sources treat for example Cryptosporidium infection as parasitic e.g

are these formally wrong?

If it is the case that some fungal infections are parasitic infections, what is the differentia?

Our current def is from NCIT:

A successful invasion of a host by an organism that uses the host for food and shelter

As @nicolevasilevsky says we need a more precise definition here

cmungall commented 3 years ago

Isn't there an ontology term for parasite that we can refer to? https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0002444

But it lacks a definition. Someone contact the Term Editor and bug them.

oh hold on...

nicolevasilevsky commented 3 years ago

oh hold on...

haha

cmungall commented 3 years ago

http://purl.obolibrary.org/obo/IDO_0000403

A symbiont role borne by an organism in virtue of the fact that it derives a growth, survival, or fitness advantage from symbiosis while the other symbiont's growth, survival, or fitness is reduced.

Where symbiosis is An interaction between two organisms living together in more or less intimate association

Well it's a bit more precise than the current mondo definition but still hard to apply operationally.

derives a growth, survival, or fitness advantage from symbiosis: fits all fungal infections
the other symbiont's growth, survival, or fitness is reduced: fits many fungal infections, not just Cryptosporidium
living together in more or less intimate association: ?? who knows. I don't know what it means to be intimate with a fungus that is infecting me, and why I would be more intimate with Cryptosporidium than other fungi

pnrobinson commented 3 years ago

I am not up to date on this but is it certain that cryptosporidium is a fungus? https://www.cdc.gov/parasites/crypto/index.html

An important difference is that funguses can live without a human host and are opportunistic infectious agents.

The word parasite can be interpreted as a role or as a characteristic of phyla, e.g. the phylum of cryptosporidium, The Apicomplexa (also called Apicomplexia) are a large phylum of parasitic alveolates. https://en.wikipedia.org/wiki/Apicomplexa

I think for mondo we do not want to include the "role" of being a parasite, but rather want to use the biological definitions.

nicolevasilevsky commented 3 years ago

cryptosporidium was a mistake, it's a parasitic disease. :)