IDO/OGMS & infectious disorder

[Shane Babcock]

Hi all,

This is Shane Babcock, one of the co-authors for the new preprint paper on the Infectious Disease Ontology (https://osf.io/az6u5/) mentioned during today's OGMS meeting.

Today at the meeting, it was noted that OGMS would be adding the term infectious disorder and so work had to be done to ensure consistency with IDO here.

This is actually perfect timing, I believe, as recently IDO:infectious disorder is a term that has raised some issues, along with some issues concerning the definition of infection in IDO. Please note that the definition of infection has been slightly adjusted from how it appears in the most recent Bioportal upload. 

Werner Ceusters has provided some thorough comments on the paper, in particular raising pressing objections concerning the definitions of infection and infectious disorder, and their relationship. I was hoping the OGMS community might have some insight on how we might address these issues moving forward. The relationship between these classes in IDO hinges on the idea that there can be cases of infections that are not clinically abnormal. According to IDO, infectious disorders are those infections that are abnormal.

Attached is a short excerpt from the IDO paper, specifically the section on extending IDO from OGMS. Werner's comments are included, and in particular I highlighted in yellow comments related to infection/infectious disorder. He also raises some worries about the OGMS term extended organism, which I highlight.

If there are any other errors, or things that need to be fixed, feel free to let me know.

Shane