Ontolog Forum

Session COB
Duration 1 hour
Date/Time 25 Jan 2023 17:00 GMT
9:00am PST/12:00pm EST
5:00pm GMT/6:00pm CST
Convener Gary Berg-Cross

Ontology Summit 2023 COB

Helping scientific researchers make better use of ontologies


  • 12:00 - 12:30 Chris Mungall The Core Ontology for Biology and Biomedicine (COB)
  • 12:30 - 13:00 Discussion

Conference Call Information

  • Date: Wednesday, 25 Jan 2023
  • Start Time: 9:00am PST / 12:00pm EST / 6:00pm CST / 5:00pm GMT / 1700 UTC
  • Expected Call Duration: 1 hour
  • Video Conference URL
    • Conference ID: 837 8041 8377
    • Passcode: 323309
  • Chat Room

The unabbreviated URLs are:




RaviSharma: Welcome Everyone. Welcome to Chris Mungall.

Upper Model Requirements

Michael DeBellis: Perhaps this will be answered in the talk but has anyone defined the requirements and use cases for an Upper Model?

Sydney Cohen: If you're talking generally about top-level ontologies, there's this ISO/IEC standard -

Michael DeBellis: Thanks for the link Sydney

COB Requirements

Kai: Question from Damion Dooley and myself:

Should I assume that if I see a COB term and its COB id that originates from another OBO ontology term, that in adopting COB in an ontology, I can/should switch to the COB id? I understand that the SSSOM mapping file must indicate equivalency between the two.

And is this true too of properties? For example "is specified input of" is COB_0000027, and SSSOM file makes equivalency to OBI_0000295. I was puzzled because I thought COB would still stay away from minting common properties, instead leaving that to RO's domain.

James Overton: I'm sure Chris will talk about some of the things we need COB to do, but we do not have a formalized set of requirements and use cases for COB.

James Overton: This should (partially?) address Kai and Damion's question:

ToddSchneider: Do you develop requirements when there is disagreements about representations?

James Overton: Collecting requirements is a good approach to building community consensus. I would say that we're doing that more and more as try to align on design patterns.

Gary BC: Bio has some deceptively simple granular levels from systems, to organs to cells to molecules. But there may be an interesting connection to the more complex material/materials that Torsten mentioned.

James Overton: Keep in mind that the OBO community works at different scales. Projects may work in different ways, including gatherings fprmal requirements, and may have a long history of doing so. Strong coordination at the OBO Community level is relatively more recent, and driven by improvements to our tools and infastructure.

Gary BC: Torsten and others have found value in using common logic, rather than the more restritic DL/OWL for some of their models.

TorstenHahmann: I agree with Gary, sometimes it is easier to use first-order logic or Common Logic to delay dealing with some of the engineering problems

BFO Version

ToddSchneider: Which version of BFO is being used currently? The ISO version?

James Overton: RO uses a subset of BFO classes from BFO 1.1, defined here:

Independent Continuant

RaviSharma: what would be example of independant continuant?

James Overton: BFO 'independent continuant' That link should show a number of examples.

RaviSharma: I saw examples of independent continuant but at high level as process!

James Overton: 'independent continuant' example of usage: an organism; a leg; a molecule; the bottom right portion of a human torso; a heart; an atom; a chair; the interior of your mouth; a spatial region; an orchestra.


Michael DeBellis: Have you considered using SKOS for some of the mapping? E.g., the two definitions of atom may be a skos:closeMatch.. almost synonyms but not quite

James Overton: Yes, skos:closeMatch is used for some of the links in that obo-bridge document.

has participant vs occurs in

John Judkins: When should we use 'has participant' and when should we use 'occurs in' to link a continuant to a process?

James Overton: @John: Roughly, P 'occurs in' C requires that the process P takes place completely "inside" the continuant C, while P 'has participant' C does not require that.

Schulz Conflation Model

Michael DeBellis: Does anyone have alink to the Schulz conflation model paper?

James Overton: The Stefan Schulz paper Chris mentioned

Michael DeBellis: Thanks James


ToddSchneider: Are Qualities related to Units of Measure?

ToddSchneider: Was an ontology of Qualities developed?

Alignment with COB

Nico: A question I keep being asked: how do we “align with COB”? Practically.

Nico: So basically, instead of importing BFO directly we import COB! Thanks Chris

Chris Mungall: I agree.

Kai: I also agree.

Nico: But there are reservations on this, and it’s hard to coordinate

Nico: It basically means we have to allow cob classes without fixed bfo alignment!

Nico: Relevant: OBO Foundry is debating to require COB alignment moving forward!

Phenotype/Disease Integration into COB

RaviSharma: Are phenotype parameters totally independent of genetic changes?

Petr Kremen: Are there any plans/roadmap for the phenotype/disease integration into COB? Its about agreeing to Schulz conflation. If we can, we can do phenotype disease in less than a day!

Michael DeBellis: In general Phenotype = Genotype + Environment

Mike Bennett: Presumably in most cases a phenotype arises through the expression of some combination of genes interacting i.e. emergent?

So that would make Phenotype a Generically Dependent Continuant in BFO?

Alexander Diehl: The word phenotype is a conflation of descriptions of material entities and descriptions of processes and how these things may vary

I have argued for treating phenotypes as information artifacts that are about an organism, though the phenotype ontology folks generally reject this approach

Petr Kremen: Yeah, I expect st. like that - I was more curious about whether there is any driving force/project/activity that tries to drive it

Nico: The uPheno effort is pushing for it, but we could do with pressure

Petr Kremen: Thanks Nico and Chris for info, will check.


Michael DeBellis: Thanks Chris, really interesting

Tom Walpole: Good Stuff - Thank You

Petr Kremen: Thanks Chris, great job!

Ravi Sharma: Thanks chris and torsten and James and Gary and Ken.

Nico: Awesome talk thanks Chris!

Paul Fabry: Great talk. Thank you!

Jacques Hilbey: Thanks!


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