|Date/Time||25 Jan 2023 17:00 GMT|
|9:00am PST/12:00pm EST|
|5:00pm GMT/6:00pm CST|
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
- ref: World Clock
- Expected Call Duration: 1 hour
- Video Conference URL
- Conference ID: 837 8041 8377
- Passcode: 323309
- Chat Room
The unabbreviated URLs are:
- Conference URL: https://us02web.zoom.us/j/83780418377?pwd=MlRFTHJQclRBd3RhYVl3aG1rTHJOQT09
- Chat room: http://webconf.soaphub.org/conf/room/ontology_summit_2023
- Alexander Diehl
- Alex Shkotin
- Allen Baron
- Anthony H
- Arwa Ibrahim
- Chris Kindermann
- Chris Mungall
- Chris Stoeckert
- Clare Pilgrim
- Claudia Sanchez-Beato Johnson
- Claus Weiland
- Damien Goutte-Gattat
- Ditch Townsend
- Douglas R Miles
- Dustin Ebert
- Emna Amdouni
- Evan Wallace
- Fan Li
- Frank Loebe
- Gary Berg-Cross
- George Hurlburt
- Georg Fuellen
- Jacques Hilbey
- James Overton
- Jennifer C. Girón
- Jie Zheng
- Jim Balhoff
- Jinjing Guo
- John Bottoms
- John Judkins
- Juan Mulero
- Katie Mullen
- Ken Baclawski
- Kingsley Wiafe-Kwakye
- Leigh Carmody
- Lynn Schriml
- Mark Fox
- Michael DeBellis
- Mike Bada
- Mike Bennett
- Paul Fabry
- Petr Kremen
- Ram D. Sriram
- Ravi Sharma
- Raymond Lee
- Sabrina Toro
- Samson Tu
- Samuel Neaves
- Sierra Moxon
- Susan Bello
- Sydney Cohen
- Todd Schneider
- Tom Walpole
- Torsten Hahmann
- Val Wood
- Vinicius de Souza
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 - https://www.iso.org/standard/71954.html
Michael DeBellis: Thanks for the link Sydney
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: http://obofoundry.org/COB/obo-bridge/
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
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: https://github.com/oborel/obo-relations/blob/master/src/ontology/bfo-classes-minimal.owl
RaviSharma: what would be example of independant continuant?
James Overton: BFO 'independent continuant' http://purl.obolibrary.org/obo/BFO_0000004 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 https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-2-S2-S6
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!
|ConferenceCall 2023 01 18||Launch|
|ConferenceCall 2022 12 14||Planning|
|ConferenceCall 2022 12 07||Data Principles|
|... further results|
|ConferenceCall 2023 02 01||ROBOT|
|ConferenceCall 2023 02 08||ODK|
|ConferenceCall 2023 02 15||OBO Dashboards|
|... further results|