re-engineering request on health surveillance hierarchy from IDO team

[linikujp]

IDOBRU surveillance hierarchy re-engineering -- (quoted from Shane Babcock's email. "You" is Asiyah Yu Lin, and "I" or "me" is Shane, "we" means Shane Babcock and Barry Smith)

The following is a suggested reengineering, me and Barry Smith worked that appears in the most recent draft of the new IDO paper. This is designed to fix the issue you and I previously talked about (see your comment in the margin) where the current IDOBRU hierarchy falsely implies that infectious disease surveillance only includes surveillance of human infectious disease. I was hoping that we could work together to make something like the suggested changes below. That way a new version of IDOBRU could be uploaded to bioportal before sometime before the new IDO paper is published. (Optionally, we could also address some other small issues I raised in a supplementary material document. I have imported that discussion here below. Since you created IDOBRU, your feedback on that would be appreciated. Though, the suggested movement of some terms up to OBI might take more work as it will involve others)

---

“The following is an example of a hierarchy of surveillance related terms, all of which (below OBI:planned process) were created for IDOBRU:

All of the terms from human disease surveillance and animal disease surveillance up will be ported to an external ontology such as OBI. Animal infectious disease surveillance and human infectious disease surveillance will be promoted to IDO Core and then imported from there to IDOBRU.”

[linikujp]

Suggest to use "public health surveillance" rather than "health surveillance"

[linikujp]

1. Better to not including the disease surveillance under biosurveillance, as the biosurveillance is a term almost used exclusively for bioterrorism threats surveillance. Please see: https://en.wikipedia.org/wiki/Biosurveillance; https://www.dhs.gov/science-and-technology/biosurveillance.

2. need to reconsider the disease surveillance as a term or not. better to directly use infectious disease surveillance and move up to OBI.

3. We do not have a animal brucellosis term, and human is a subclass of animal. So I don't agree the hierarchies here. Suggest to use veterinary brucellosis instead of animal brucellosis if we need to seperate human disease and veterinary disease.

4. My suggested hierarchy is

[PhiBabs935]

The following epidemiology terms were created earlier on for IDOBRU because IDO Core didn't have the relevant terms. -infectious disease endemic site (parent of brucellosis endemic site) -infectious disease free site (parent of brucellosis free site) -infectious disease non-endemic site (parent of brucellosis non-endemic site) -infectious disease re-emergence site (parent of brucellosis re-emergence site)

As discussed in the new new paper (https://osf.io/az6u5/) we should move these infectious disease site terms up to IDO, and then import them from there to serve as the parents for the brucellosis specific terms. -The same should (perhaps) be done for similar terms, such as: -'reemerging infectious disease'

I will look more carefully later for more examples.

Was there anything else you wanted me to add to the issues tracker that I mentioned previously?

[linikujp]

Will keep the biosurveillance to be the mother class of infectious disease surveillance, due to this https://www.sciencedirect.com/topics/medicine-and-dentistry/biosurveillance https://www.ncbi.nlm.nih.gov/books/NBK189584/

There maybe a need for term of bioterrorism surveillance. I'll add it into IDOBRU and later will transfer to appropriate place.

This is current hirearchy:

[PhiBabs935]

Alright, sounds good. In the IDO paper (for the sake of simplicity) I may just show the hierarchy partially (starting at infectious disease surveillance and mentioning that the super-classes above it have been omitted). The main point is to mention it in order to talk about infectious disease surveillance being moved to IDO Core.

I can always add more detailed discussion, and the full hierarchy, in the supplementary document on the re-engineering of the IDO extensions.

[yongqunh]

Good discussion. These terms are important terms and worth transferring. Thanks.

[linikujp]

Meeting on 05/19/2020 with John B., Shane B. Oliver H. and Asiyah L. Will post to IDO issue the list of terms that are not IDOBRU specific for IDO's backlog.