OGMS call July 15th 2020

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Aevermann, Brian

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Jul 14, 2020, 2:55:54 PM7/14/20
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Hello all,

 

We will be having an OGMS development call tomorrow. It will be a focused call, covering the OGMS release detailed in the agenda/notes document in the google drive. Richard is on vacation so he will not be attending.

 

Thanks,

 

Brian Aevermann

 

— 

Brian Aevermann

Bioinformatics Analyst

J. Craig Venter Institute

4120 Capricorn Lane

La Jolla, CA 92037

858-200-1873

 

 

Hello all,

 

The recording on the presentation is now available in the google drive. Its called “OGMS-IDO_COVID_presentation.mp4”.

 

Thanks,


Brian Aeverman

 

 

— 

Brian Aevermann

Bioinformatics Analyst

J. Craig Venter Institute

4120 Capricorn Lane

La Jolla, CA 92037

858-200-1873

 

 

Hello all,

 

We will be having an OGMS call tomorrow at 11 am PDT. The abbreviated agenda is:

 

  1. OGMS release
  2. IDO-COVID-19 ontology presentation
    1. We will be recording this presentation, so if you don’t want your attendance recorded, please change your Webex name to something anonymous
  3. New term requests / issue tracker

 

Detailed agenda available at:

 

Brian Aevermann

Bioinformatics Analyst

J. Craig Venter Institute

4120 Capricorn Lane

La Jolla, CA 92037

858-200-1873

 

 

Hello all,

 

Due to unforeseen personal circumstances, we will not be having an OGMS development call today. I apologize for any inconvenience. If you have any questions or suggestions, please let me know.

 

Thanks,

 

Brian Aevermann

 

 

— 

Brian Aevermann

Bioinformatics Analyst

J. Craig Venter Institute

4120 Capricorn Lane

La Jolla, CA 92037

858-200-1873

 

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Shane Babcock

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Jul 14, 2020, 4:14:38 PM7/14/20
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Hi,

I saw that infectious disorder was again on the agenda. In light of this, I thought that I should inform you that John Beverly and I have been working on proposed revisions to IDO 'infection' and 'infectious disorder' to try to address some worries raised by Werner Ceusters. 

This involved a change (which Barry Smith has expressed some approval for) of the definition of 'infectious disorder' from "An infection that is clinically abnormal" to "A disorder that has infectious agents or infectious structures as parts". (Recall, 'infectious structures' was John's new term to cover viruses, since infectious agents are classified in IDO as organisms and we are no longer classifying viruses as such). 
We would also remove the current OWL equivalence for infectious disorder, which is: 'infection and disorder' (which led to 'infectious disorder' having multiple parentage in IDO). Instead we would turn 'infection' into an equivalence class, and add corresponding axioms to 'infectious disorder' which ensure that the latter is an inferred subclass of the former.

I can provide further details if you would like. Not sure if other IDO people will be at the call, but I plan on being so.

Shane

To view this discussion on the web visit https://groups.google.com/d/msgid/ogms-discuss/A3ADC869-18AE-464C-9CE9-37105CB6AD29%40jcvi.org.

Aevermann, Brian

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Jul 14, 2020, 4:37:16 PM7/14/20
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Hey Shane,

 

Thanks for the update on 'infectious disorder'. I have added this to OGMS as the IDO class, so we will not be taking responsibility for updating the definition in our development. As you mentioned, the current definition at IDO is “An infection that is clinically abnormal”; however, whenever IDO updates their definition we will follow suit.

 

This doesn’t mean we can’t discuss at our call, if people are interested. Just wanted to make it clear that we will follow whatever the IDO group decides.

 

Thanks!

 

b.

 

 

— 

Brian Aevermann

Bioinformatics Analyst

J. Craig Venter Institute

4120 Capricorn Lane

La Jolla, CA 92037

858-200-1873

 

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