ConferenceCall 2023 01 25 - Revision history

Forum: /* Resources */

2023-06-01T16:27:51Z

Resources

← Older revision		Revision as of 16:27, 1 June 2023
Line 220:		Line 220:
	* [https://bit.ly/3kLelTT Presentation Slides]		* [https://bit.ly/3kLelTT Presentation Slides]
	* [https://bit.ly/3wsUHyC Session Video Recording]		* [https://bit.ly/3wsUHyC Session Video Recording]
			* [https://youtu.be/Q04XUNEuQTE Video Recording on YouTube]

	== Previous Meetings ==		== Previous Meetings ==

Forum: /* Agenda */

2023-05-30T20:52:17Z

Agenda

← Older revision		Revision as of 20:52, 30 May 2023
Line 22:		Line 22:

	== Agenda ==		== Agenda ==
	* 12:00 - 12:30 '''~~[[ChrisMungall\|~~Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)''		* 12:00 - 12:30 '''Chris Mungall''' ''The Core Ontology for Biology and Biomedicine (COB)''
	** [https://bit.ly/3kLelTT Slides]		** [https://bit.ly/3kLelTT Slides]
	** [https://bit.ly/3wsUHyC Video Recording]		** [https://bit.ly/3wsUHyC Video Recording]

KenBaclawski: /* Attendees */

2023-01-30T06:48:10Z

Attendees

← Older revision		Revision as of 06:48, 30 January 2023
Line 35:		Line 35:

	== Attendees ==		== Attendees ==
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[AllenBaron\|Allen Baron]]
			* Anthony H
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[ChrisKindermann\|Chris Kindermann]]
			* [[ChrisMungall\|Chris Mungall]]
			* [[ChrisStoeckert\|Chris Stoeckert]]
			* [[ClarePilgrim\|Clare Pilgrim]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato Johnson]]
			* [[ClausWeiland\|Claus Weiland]]
			* [[DamienGoutteGattat\|Damien Goutte-Gattat]]
			* [[DitchTownsend\|Ditch Townsend]]
			* [[DouglasRMiles\|Douglas R Miles]]
			* [[DustinEbert\|Dustin Ebert]]
			* [[EmnaAmdouni\|Emna Amdouni]]
			* [[EvanWallace\|Evan Wallace]]
			* [[FanLi\|Fan Li]]
			* [[FrankLoebe\|Frank Loebe]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[GeorgeHurlburt\|George Hurlburt]]
			* [[GeorgFuellen\|Georg Fuellen]]
			* [[JacquesHilbey\|Jacques Hilbey]]
			* [[JamesOverton\|James Overton]]
			* [[JenniferGiron\|Jennifer C. Girón]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JinjingGuo\|Jinjing Guo]]
			* [[JohnBottoms\|John Bottoms]]
			* [[JohnJudkins\|John Judkins]]
			* [[JuanMulero\|Juan Mulero]]
			* Kai
			* [[KatieMullen\|Katie Mullen]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[KingsleyWiafeKwakye\|Kingsley Wiafe-Kwakye]]
			* [[LeighCarmody\|Leigh Carmody]]
			* [[LynnSchriml\|Lynn Schriml]]
			* [[MarkFox\|Mark Fox]]
			* [[MichaelDeBellis\|Michael DeBellis]]
			* [[MikeBada\|Mike Bada]]
			* [[MikeBennett\|Mike Bennett]]
			* Nico
			* [[PaulFabry\|Paul Fabry]]
			* [[PetrKremen\|Petr Kremen]]
			* [[RamSriram\|Ram D. Sriram]]
			* Randi
			* [[RaviSharma\|Ravi Sharma]]
			* [[RaymondLee\|Raymond Lee]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[SamsonTu\|Samson Tu]]
			* [[SamuelNeaves\|Samuel Neaves]]
			* [[SierraMoxon\|Sierra Moxon]]
			* [[SusanBello\|Susan Bello]]
			* [[SydneyCohen\|Sydney Cohen]]
			* [[ToddSchneider\|Todd Schneider]]
			* [[TomWalpole\|Tom Walpole]]
			* [[TorstenHahmann\|Torsten Hahmann]]
			* [[ValWood\|Val Wood]]
			* [[ViniciusDeSouza\|Vinicius de Souza]]
			* Yousif

	== Discussion ==		== Discussion ==

KenBaclawski: /* Discussion */

2023-01-30T05:34:07Z

Discussion

← Older revision		Revision as of 05:34, 30 January 2023
Line 37:		Line 37:

	== Discussion ==		== Discussion ==
			=== Welcome ===
			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

			=== 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: 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

			=== 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: https://github.com/oborel/obo-relations/blob/master/src/ontology/bfo-classes-minimal.owl

			=== Independent Continuant ===
			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.

			=== SKOS ===
			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

			=== Qualities ===
			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.

			=== Acknowledgments ===
			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!

	== Resources ==		== Resources ==

KenBaclawski: /* Resources */

2023-01-26T00:56:43Z

Resources

← Older revision		Revision as of 00:56, 26 January 2023
Line 39:		Line 39:

	== Resources ==		== Resources ==
			* [https://bit.ly/3kLelTT Presentation Slides]
	* [https://bit.ly/3wsUHyC Session Video Recording]		* [https://bit.ly/3wsUHyC Session Video Recording]

KenBaclawski: /* Agenda */

2023-01-26T00:56:20Z

Agenda

← Older revision		Revision as of 00:56, 26 January 2023
Line 22:		Line 22:

	== Agenda ==		== Agenda ==
	* 12:00 - 12:30 '''[[ChrisMungall\|Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)'' [https://bit.ly/3wsUHyC Video Recording]		* 12:00 - 12:30 '''[[ChrisMungall\|Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)''
			** [https://bit.ly/3kLelTT Slides]
			** [https://bit.ly/3wsUHyC Video Recording]
	* 12:30 - 13:00 Discussion		* 12:30 - 13:00 Discussion

KenBaclawski: /* Resources */

2023-01-25T19:24:29Z

Resources

← Older revision		Revision as of 19:24, 25 January 2023
Line 37:		Line 37:

	== Resources ==		== Resources ==
			* [https://bit.ly/3wsUHyC Session Video Recording]

	== Previous Meetings ==		== Previous Meetings ==

KenBaclawski: /* Agenda */

2023-01-25T19:24:04Z

Agenda

← Older revision		Revision as of 19:24, 25 January 2023
Line 22:		Line 22:

	== Agenda ==		== Agenda ==
	* 12:00 - 12:30 '''[[ChrisMungall\|Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)''		* 12:00 - 12:30 '''[[ChrisMungall\|Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)'' [https://bit.ly/3wsUHyC Video Recording]
	* 12:30 - 13:00 Discussion		* 12:30 - 13:00 Discussion

KenBaclawski at 18:54, 15 December 2022

2022-12-15T18:54:24Z

← Older revision		Revision as of 18:54, 15 December 2022
Line 22:		Line 22:

	== Agenda ==		== Agenda ==
	* 12:00 - 12:30 [[ChrisMungall\|Chris Mungall]] The Core Ontology for Biology and Biomedicine (COB)		* 12:00 - 12:30 '''[[ChrisMungall\|Chris Mungall]]''' ''The Core Ontology for Biology and Biomedicine (COB)''
	* 12:30 - 13:00 Discussion		* 12:30 - 13:00 Discussion

KenBaclawski: Created page with "{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10" |- ! scope="row" | Session | session::COB |- ! scope="row" | Duration | duration::1 hour |- ! scope="row" rowspan="3" | Date/Time | has date::25 Jan 2023 17:00 GMT |- | 9:00am PST/12:00pm EST |- | 5:00pm GMT/6:00pm CST |- ! scope="row" | Convener | Gary Berg-Cross |} = Ontology Summit 2023 {{#show:{{PAGENAME}}|?session}}..."

2022-12-15T18:53:44Z

Created page with "{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10" |- ! scope="row" | Session | session::COB |- ! scope="row" | Duration | duration::1 hour |- ! scope="row" rowspan="3" | Date/Time | has date::25 Jan 2023 17:00 GMT |- | 9:00am PST/12:00pm EST |- | 5:00pm GMT/6:00pm CST |- ! scope="row" | Convener | Gary Berg-Cross |} = Ontology Summit 2023 {{#show:{{PAGENAME}}|?session}}..."

New page

{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10"
|-
! scope="row" | Session
| [[session::COB]]
|-
! scope="row" | Duration
| [[duration::1 hour]]
|-
! scope="row" rowspan="3" | Date/Time
| [[has date::25 Jan 2023 17:00 GMT]]
|-
| 9:00am PST/12:00pm EST
|-
| 5:00pm GMT/6:00pm CST
|-
! scope="row" | Convener
| [[convener::GaryBergCross|Gary Berg-Cross]]
|}

= [[OntologySummit2023|Ontology Summit 2023]] {{#show:{{PAGENAME}}|?session}} =
{{:OntologySummit2023/Description}}

== Agenda ==
* 12:00 - 12:30 [[ChrisMungall|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: [http://www.timeanddate.com/worldclock/fixedtime.html?month=01&day=25&year=2023&hour=12&min=00&sec=0&p1=179 World Clock]
* Expected Call Duration: 1 hour
{{:OntologySummit2023/ConferenceCallInformation}}

== Attendees ==

== Discussion ==

== Resources ==

== Previous Meetings ==
{{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2023_01_25]]
|?|?Session|mainlabel=-|order=desc|limit=3}}

== Next Meetings ==
{{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2023_01_25]]
|?|?Session|mainlabel=-|order=asc|limit=3}}

[[Category:OntologySummit2023]]
[[Category:Icom_conf_Conference]]
[[Category:Occurrence| ]]

← Older revision		Revision as of 06:48, 30 January 2023
Line 35:		Line 35:

	== Attendees ==		== Attendees ==
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[AllenBaron\|Allen Baron]]
			* Anthony H
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[ChrisKindermann\|Chris Kindermann]]
			* [[ChrisMungall\|Chris Mungall]]
			* [[ChrisStoeckert\|Chris Stoeckert]]
			* [[ClarePilgrim\|Clare Pilgrim]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato Johnson]]
			* [[ClausWeiland\|Claus Weiland]]
			* [[DamienGoutteGattat\|Damien Goutte-Gattat]]
			* [[DitchTownsend\|Ditch Townsend]]
			* [[DouglasRMiles\|Douglas R Miles]]
			* [[DustinEbert\|Dustin Ebert]]
			* [[EmnaAmdouni\|Emna Amdouni]]
			* [[EvanWallace\|Evan Wallace]]
			* [[FanLi\|Fan Li]]
			* [[FrankLoebe\|Frank Loebe]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[GeorgeHurlburt\|George Hurlburt]]
			* [[GeorgFuellen\|Georg Fuellen]]
			* [[JacquesHilbey\|Jacques Hilbey]]
			* [[JamesOverton\|James Overton]]
			* [[JenniferGiron\|Jennifer C. Girón]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JinjingGuo\|Jinjing Guo]]
			* [[JohnBottoms\|John Bottoms]]
			* [[JohnJudkins\|John Judkins]]
			* [[JuanMulero\|Juan Mulero]]
			* Kai
			* [[KatieMullen\|Katie Mullen]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[KingsleyWiafeKwakye\|Kingsley Wiafe-Kwakye]]
			* [[LeighCarmody\|Leigh Carmody]]
			* [[LynnSchriml\|Lynn Schriml]]
			* [[MarkFox\|Mark Fox]]
			* [[MichaelDeBellis\|Michael DeBellis]]
			* [[MikeBada\|Mike Bada]]
			* [[MikeBennett\|Mike Bennett]]
			* Nico
			* [[PaulFabry\|Paul Fabry]]
			* [[PetrKremen\|Petr Kremen]]
			* [[RamSriram\|Ram D. Sriram]]
			* Randi
			* [[RaviSharma\|Ravi Sharma]]
			* [[RaymondLee\|Raymond Lee]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[SamsonTu\|Samson Tu]]
			* [[SamuelNeaves\|Samuel Neaves]]
			* [[SierraMoxon\|Sierra Moxon]]
			* [[SusanBello\|Susan Bello]]
			* [[SydneyCohen\|Sydney Cohen]]
			* [[ToddSchneider\|Todd Schneider]]
			* [[TomWalpole\|Tom Walpole]]
			* [[TorstenHahmann\|Torsten Hahmann]]
			* [[ValWood\|Val Wood]]
			* [[ViniciusDeSouza\|Vinicius de Souza]]
			* Yousif

	== Discussion ==		== Discussion ==