ConferenceCall 2023 02 22 - Revision history

Forum: /* Resources */

2023-06-01T16:29:21Z

Resources

← Older revision		Revision as of 16:29, 1 June 2023
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	== Resources ==		== Resources ==
	* [https://bit.ly/41wx6LZ Video Recording]		* [https://bit.ly/41wx6LZ Video Recording]
			* [https://youtu.be/NV75bAzhzNk Video Recording on YouTube]

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

Gary Berg-Cross: /* Ontology Summit 2023 {{#show:{{PAGENAME}}|?session}} */

2023-04-24T13:42:02Z

Ontology Summit 2023 {{#show:{{PAGENAME}}|?session}}

← Older revision		Revision as of 13:42, 24 April 2023
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	* Ubergraph: A SPARQL endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized		* Ubergraph: A SPARQL endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized
	* Presenter: Jim Balhoff		* Presenter: Jim Balhoff
			* [https://docs.google.com/presentation/d/1RhlZY4Yb_SDHKq3pdqIBmENr6oX7YSNmbk60Jl3JF_0/edit#slide=id.p Slides]
	* [https://bit.ly/41wx6LZ Video Recording]		* [https://bit.ly/41wx6LZ Video Recording]

Forum: /* Discussion */

2023-03-08T16:19:20Z

Discussion

← Older revision		Revision as of 16:19, 8 March 2023
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	== Discussion ==		== Discussion ==
			[12:03] RaviSharma: Hello welcome everyone,

			[12:12] RaviSharma: what is the significance of word Axioms in other ontologies vs just used in other ontologies?

			[12:17] Sue: @Ravi the axioms have formal logic in which the terms from other ontologies are used to define the term in the focus ontology. It is one way to use terms from one ontology in another ontology. Another example of use would be as cross-references.

			[12:17] Mike Bennett: Why equivalent class: Usually one would make the class a subclass both of it's usual (taxonomic) parent and of the restriction. the intersection is implicit

			[12:19] RaviSharma: Jim you showed both ways, which one has less errors? Say in constructing KG.

			[12:20] James Overton: @Mike: We have a standard operation `relax` that converts equivalence axioms to simpler subclass axioms <http://robot.obolibrary.org/relax>. But I think the point stands that querying OWL in SPARQL is hard, and Jim is building toward presenting a more convenient solution.

			[12:23] Tiago Lubiana: Is there a way to differentiate stated/inferred relations in Ubergraph? E.g. one might be interested in retrieving only direct superclasses of a term, but all superclasses in the tree are inferred

			[12:24] James Overton: relation-graph was added to ROBOT 1.9.2 very recently, as part of the <http://robot.obolibrary.org/extract#subset> command.

			[12:24] Chris Mungall: @Tiago - these are distinguishable the named graph the triple belongs to

			[12:28] Alexander Diehl: Is the query language for Ubergraph SPARQL or just SPARQL-like?

			[12:28] Mike Bennett: @James thanks - makes sense.

			[12:29] James Overton: @Alexander: Jim is showing actual SPARQL. He's using a trick to define prefixes for commonly used terms such as `cell` and `has_output`, to make the SPARQL more readable.
			[12:29] James Overton: @Alexander: Jim is showing actual SPARQL. He's using a trick to define prefixes for commonly used terms such as `cell` and `has_output`, to make the SPARQL more readable.

			[12:31] RaviSharma: Jim do these include GO relations mapping all gene pairs?

			[12:32] Chris Mungall: @Ravi - no, this is just the ontology

			[12:33] Asiyah: Is there a list of the 53 ontologies included in the Ubergraph?

			[12:39] Robert Rovetto: what is the visualization tool used for those graph images?

			[12:40] Chris Mungall: https://github.com/INCATools/obographviz

			[12:42] Asiyah Lin - NIAID: Is there a list of 53 ontologies included in the Ubergraph?

			[12:42] Nico Matentzoglu: This query gives you all the phenotypic abnormalities linked to the urine sodium level: https://api.triplydb.com/s/J1QkfjIAw

			[12:43] James Overton: The README has a list of the included ontologies: https://github.com/INCATools/ubergraph

			[12:43] Sierra Moxon: I’ve used this file to determine which ontologies are in Ubergraph https://github.com/INCATools/ubergraph/blob/master/ontologies.txt

			[12:43] Nico Matentzoglu: Or you check Ubergraph: https://api.triplydb.com/s/0TLkJlDcA

			[12:43] James Overton: Sierra's answer seems like a more complete list. Thanks!

			[12:43] Asiyah Lin - NIAID: Thank you both, James and Sierra! and Nico!

			[12:44] RaviSharma: Jim have you checked the lost relations namely other than those that execute SPARQL and those that go in the error file?

			[12:54] RaviSharma: Nico should we not be concentrating on dealing with harmonizing and aligning in terms of levels of depth to achieve better semantic interoperation? Namely by domain overlap handling?

			Reply from Gary Berg-Cross: Current automation of alignment and harmonization is limited but useful. Some needs to be done manually but in that process we may come to understand what semantic depth means and automate a portion of it.

			[13:00] Asiyah: Is there a way to crowd source people's mappings happened everywhere?

			[13:01] James Overton: @Asiyah: Yes, SSSOM is part of Mapping Commons: https://github.com/mapping-commons

			[13:01] Sierra Moxon: I'm curious if the "confidence score" has a restricted range?

			[13:03] Nico: yes, its basically %

			[13:05] RaviSharma: I asked about a way of controlling the ambiguities as we do while developing software, to which Nico replied that one could filter or selectively map terms from e,g, SnoMed so that two way connections are somewhat possible. The presentations showed to us the improving maturity in ontology integration, KGs and SPARQL use. Thanks to speakers.

			[13:11] Raymond Lee: Thanks!

	== Resources ==		== Resources ==

Forum: /* Attendees */

2023-03-01T17:32:23Z

Attendees

← Older revision		Revision as of 17:32, 1 March 2023
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	* [[GaryBergCross\|Gary Berg-Cross]]		* [[GaryBergCross\|Gary Berg-Cross]]
	* [[GuangrongQin\|Guangrong Qin]]		* [[GuangrongQin\|Guangrong Qin]]
	* [[Hendrick Borgelt\|Hendrick Borgelt]]
	* [[HendrickBorgelt\|Hendrick Borgelt]]		* [[HendrickBorgelt\|Hendrick Borgelt]]
	* [[HenriettHarmse\|Henriett Harmse]]		* [[HenriettHarmse\|Henriett Harmse]]

Forum: /* Attendees */

2023-03-01T17:31:58Z

Attendees

← Older revision		Revision as of 17:31, 1 March 2023
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	* [[RobertRovetto\|Robert Rovetto]]		* [[RobertRovetto\|Robert Rovetto]]
	* [[SabrinaToro\|Sabrina Toro]]		* [[SabrinaToro\|Sabrina Toro]]
	* [[SierraMoxon\|sierra moxon]]
	* [[SierraMoxon\|Sierra Moxon]]		* [[SierraMoxon\|Sierra Moxon]]
	* Sue
	* [[SusanBello\|Susan Bello]]		* [[SusanBello\|Susan Bello]]
	* [[TiagoLubiana\|Tiago Lubiana]]		* [[TiagoLubiana\|Tiago Lubiana]]

Forum: /* Attendees */

2023-03-01T17:29:49Z

Attendees

← Older revision		Revision as of 17:29, 1 March 2023
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	== Attendees ==		== Attendees ==
			* [[AleixPuig\|Aleix Puig]]
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[AsiyahLin\|Asiyah Lin]]
			* [[ChrisKindermann\|Chris Kindermann]]
			* [[ChrisMungall\|Chris Mungall]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato Johnson]]
			* [[DamianGoutteGattat\|Damian Goutte-Gattat]]
			* [[DarrenNatale\|Darren A. Natale]]
			* [[FanLi\|Fan Li]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[GuangrongQin\|Guangrong Qin]]
			* [[Hendrick Borgelt\|Hendrick Borgelt]]
			* [[HendrickBorgelt\|Hendrick Borgelt]]
			* [[HenriettHarmse\|Henriett Harmse]]
			* [[JamesOverton\|James Overton]]
			* [[JanetSinger\|Janet Singer]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JohnJudkins\|John Judkins]]
			* [[KatieMullen\|Katie Mullen]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[Leigh Carmody\|Leigh Carmody]]
			* [[MarciaZeng\|Marcia Zeng]]
			* [[MarkRessler\|Mark Ressler]]
			* [[MikeBennett\|Mike Bennett]]
			* [[NicoMatentzoglu\|Nico Matentzoglu]]
			* [[RamondLec\|Ramond Lec]]
			* [[RaviSharma\|Ravi Sharma]]
			* [[RayStefancsik\|Ray Stefancsik]]
			* [[RobertRovetto\|Robert Rovetto]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[SierraMoxon\|sierra moxon]]
			* [[SierraMoxon\|Sierra Moxon]]
			* Sue
			* [[SusanBello\|Susan Bello]]
			* [[TiagoLubiana\|Tiago Lubiana]]
			* [[WasilaDahdul\|Wasila Dahdul]]
			* [[YaseminBridges\|Yasemin Bridges]]

	== Discussion ==		== Discussion ==

Forum: /* Resources */

2023-02-28T21:42:55Z

Resources

← Older revision		Revision as of 21:42, 28 February 2023
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	== Resources ==		== Resources ==
			* [https://bit.ly/41wx6LZ Video Recording]

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

Forum: /* Agenda */

2023-02-28T21:42:41Z

Agenda

← Older revision		Revision as of 21:42, 28 February 2023
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	* Ubergraph: A SPARQL endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized		* Ubergraph: A SPARQL endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized
	* Presenter: Jim Balhoff		* Presenter: Jim Balhoff
			* [https://bit.ly/41wx6LZ Video Recording]

	== Conference Call Information ==		== Conference Call Information ==

KenBaclawski: Created page with "{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10" |- ! scope="row" | Session | session::Ubergraph |- ! scope="row" | Duration | duration::1 hour |- ! scope="row" rowspan="3" | Date/Time | has date::22 Feb 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}}|?ses..."

2022-12-15T19:01:00Z

Created page with "{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10" |- ! scope="row" | Session | session::Ubergraph |- ! scope="row" | Duration | duration::1 hour |- ! scope="row" rowspan="3" | Date/Time | has date::22 Feb 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}}|?ses..."

New page

{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10"
|-
! scope="row" | Session
| [[session::Ubergraph]]
|-
! scope="row" | Duration
| [[duration::1 hour]]
|-
! scope="row" rowspan="3" | Date/Time
| [[has date::22 Feb 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 ==
* Ubergraph: A SPARQL endpoint with many OBO ontologies loaded and pre-reasoned with simple triples materialized
* Presenter: Jim Balhoff

== Conference Call Information ==
* Date: '''Wednesday, 22 Feb 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=02&day=22&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_02_22]]
|?|?Session|mainlabel=-|order=desc|limit=3}}

== Next Meetings ==
{{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2023_02_22]]
|?|?Session|mainlabel=-|order=asc|limit=3}}

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

← Older revision		Revision as of 17:32, 1 March 2023
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	* [[GaryBergCross\|Gary Berg-Cross]]		* [[GaryBergCross\|Gary Berg-Cross]]
	* [[GuangrongQin\|Guangrong Qin]]		* [[GuangrongQin\|Guangrong Qin]]
	* [[Hendrick Borgelt\|Hendrick Borgelt]]
	* [[HendrickBorgelt\|Hendrick Borgelt]]		* [[HendrickBorgelt\|Hendrick Borgelt]]
	* [[HenriettHarmse\|Henriett Harmse]]		* [[HenriettHarmse\|Henriett Harmse]]

← Older revision		Revision as of 17:31, 1 March 2023
Line 67:		Line 67:
	* [[RobertRovetto\|Robert Rovetto]]		* [[RobertRovetto\|Robert Rovetto]]
	* [[SabrinaToro\|Sabrina Toro]]		* [[SabrinaToro\|Sabrina Toro]]
	* [[SierraMoxon\|sierra moxon]]
	* [[SierraMoxon\|Sierra Moxon]]		* [[SierraMoxon\|Sierra Moxon]]
	* Sue
	* [[SusanBello\|Susan Bello]]		* [[SusanBello\|Susan Bello]]
	* [[TiagoLubiana\|Tiago Lubiana]]		* [[TiagoLubiana\|Tiago Lubiana]]

← Older revision		Revision as of 17:29, 1 March 2023
Line 34:		Line 34:

	== Attendees ==		== Attendees ==
			* [[AleixPuig\|Aleix Puig]]
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[AsiyahLin\|Asiyah Lin]]
			* [[ChrisKindermann\|Chris Kindermann]]
			* [[ChrisMungall\|Chris Mungall]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato Johnson]]
			* [[DamianGoutteGattat\|Damian Goutte-Gattat]]
			* [[DarrenNatale\|Darren A. Natale]]
			* [[FanLi\|Fan Li]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[GuangrongQin\|Guangrong Qin]]
			* [[Hendrick Borgelt\|Hendrick Borgelt]]
			* [[HendrickBorgelt\|Hendrick Borgelt]]
			* [[HenriettHarmse\|Henriett Harmse]]
			* [[JamesOverton\|James Overton]]
			* [[JanetSinger\|Janet Singer]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JohnJudkins\|John Judkins]]
			* [[KatieMullen\|Katie Mullen]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[Leigh Carmody\|Leigh Carmody]]
			* [[MarciaZeng\|Marcia Zeng]]
			* [[MarkRessler\|Mark Ressler]]
			* [[MikeBennett\|Mike Bennett]]
			* [[NicoMatentzoglu\|Nico Matentzoglu]]
			* [[RamondLec\|Ramond Lec]]
			* [[RaviSharma\|Ravi Sharma]]
			* [[RayStefancsik\|Ray Stefancsik]]
			* [[RobertRovetto\|Robert Rovetto]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[SierraMoxon\|sierra moxon]]
			* [[SierraMoxon\|Sierra Moxon]]
			* Sue
			* [[SusanBello\|Susan Bello]]
			* [[TiagoLubiana\|Tiago Lubiana]]
			* [[WasilaDahdul\|Wasila Dahdul]]
			* [[YaseminBridges\|Yasemin Bridges]]

	== Discussion ==		== Discussion ==