Request to Update definition of 'infectious disorder'

[PhiBabs935]

In the Infectious Disease Ontology, we recently updated the definition for 'infectious disorder'.

We now define the term as follows: "Disorder that is part of an organism whose extended organism has some infectious pathogen as part, which participates in the formation of the disorder."

[Edit: 9/16: it was incorrect to redefine infectious disorder, and infection, as parts of the organism. Should read: "Disorder that is part of an extended organism that has some infectious pathogen as part, which participates in the formation of the disorder."
Looking back, I noticed that here: http://ontology.buffalo.edu/ido/Dispositions_and_IDO.pdf (Cowell L, Goldfain A, Smith B) it is explicitly said that an infection is not part of the organism. I think that this was part of the rationale for introducing the extended organism class. But I would need further input here from those who originally contributed to the term's creation, as I wasn't working on this stuff back then.]

Note, 'infectious pathogen' is shorthand for 'infectious agent (organism with infectious disposition) or infectious structure (our new term for viruses, and other infectious entities such as prions, that are non-organisms).

This is a defined class in IDO, but the OWL definition refers to other IDO terms that are not in OGMS.

The term is now an inferred subclass of 'infection', (the previous definition had led to problems).

[cmungall]

Have you tested this definition with domain experts? It seems a little abstruse? How is someone reading the textual definition expected to know how to interpret "organism whose extended organism"

Is this circumlocution even necessary?

[PhiBabs935]

Perhaps not. In OGMS disorder is already defined as a material entity part of an extended organism.

I don't fully understand the worry though about the locution. Extended organism is clearly defined in OGMS.

[cmungall]

Thanks, I guess my comment more applies to the root OGMS class and this is more a comment on OGMS as a whole rather than your own contribution which is consistent with the overall framework. However, the use of extended organism for infectious disease seems particularly strange. When is an infection located in an extended organism but not located in the organism itself?

I don't fully understand the worry though about the locution. Extended organism is clearly defined in OGMS.

OK, so let's say a user ends up at

https://www.ebi.ac.uk/ols/ontologies/ogms/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000045

or

http://bioportal.bioontology.org/ontologies/OGMS/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOGMS_0000045&jump_to_nav=true

or the ontobee page or any other browser

Assuming that the user is not a member of the small community of ontologists trained in OGMS, assume they are confused by the definition and in particular the term 'extended organism' which is not part of normal scientific discourse in their field. How does the user go about finding more information?

is the user expected to copy and paste substrings they don't understand in a definition into the search interface of the browser? What if the context is another ontology in which the OGMS class is imported? Extended organism wouldn't be auto-included by SLME or MIREOT, so if the user searched for the term within the ontology they wouldn't find it.

I think it might help OGMS to have a more product oriented mentality. The end product is not some philosophical theories (which may be in themselves quite nice) but is instead a concerete information product that is used (or mis-used) in some kind of context.

Extended organism is clearly defined in OGMS.

I would beg to differ here.

An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism

What does it mean to overlap with an organism? Of course, being in the minority of people who know mereology, I know what this means in the strict sense. But what are some actual examples of things things that overlap with organisms that are not themselves part of that organism? (bonus points for saying why this is relevant for disease). I consider myself reasonably well versed in the history of OGMS, BFO, mereology, with expertise in representing diseases using ontologies, yet I am totally bamboozled by why this is all here or relevant. I'm not sure what an average user would think.

The definition provenance for extended organism links to a google code discussion that is not particularly helpful.

[PhiBabs935]

Alright, I see. You are right that the term would not be clear to domain experts. I will have to think about this stuff some more. Thanks for this Chris.