ConferenceCall 2023 02 08 - Revision history

Forum: /* Resources */

2023-06-01T16:28:38Z

Resources

← Older revision		Revision as of 16:28, 1 June 2023
Line 157:		Line 157:
	* [https://bit.ly/3YDzVIJ Video Recording]		* [https://bit.ly/3YDzVIJ Video Recording]
	* [https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]		* [https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]
			* [https://youtu.be/HAprZl0pldk Video Recording on YouTube]

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

Forum: /* Discussion */

2023-03-08T16:40:35Z

Discussion

← Older revision		Revision as of 16:40, 8 March 2023
Line 71:		Line 71:

	== Discussion ==		== Discussion ==
			[11:56] RaviSharma: welcome everyone

			[12:07] RaviSharma: Nico, So we find common word in two or more ontologies but do not we have to also see that content meaning of blood constituents are also the same?

			[12:10] RaviSharma: Nico, we like the common infrastructure with tools that gives stability like the Operating systems did in early computing

			[12:11] James Overton: Ravi: The import system is built on identifiers (CURIEs/IRIs) not labels. So we would ask for UBERON:0000178 'blood'

			[12:17] RaviSharma: Damien, does github provide or your team has a regular compatibility check or do you execute scripts for Make to test integrability?

			[12:20] James Overton: Ravi: ODK uses GitHub Actions for continuous integration testing, which calls Make tests: https://github.com/INCATools/ontology-development-kit/tree/master/.github/workflows

			[12:27] RaviSharma: Damien - are the output files run by a user tagged so that there is versioning by users running similar commands?

			[12:28] RaviSharma: how different commands are available and is there a ? option!

			[12:30] Allen Baron: Great question and very clear explanation. Thanks Damien.

			[12:32] From Nico Matentzoglu: Damien, maybe we could run “./run.sh ls /tools/“ to get a good set of most apps, and also “./run.sh pip list” for the python stuff, and we could perhaps curate a `/tools/help` script prints these..

			[12:32] James Overton: Ravi: ODK does not tag files. We rely on git for version control, and branch-and-merge workflows, usually supported by GitHub or GitLab.

			[12:33] James Overton: Damien's answer for Ravi: The ODK paper includes a list of all the included tools, but it would be good to add a documentation page with a list of common ODK tools/commands.

			[12:35] Damien Goutte-Gattat (FlyBase): `help` would conflict with the shell builtin of the same name. But overall, yeah, some kind of inline help would be good.

			[12:44] David Osumi-Sutherland: Damien, maybe we could


			[12:40] RaviSharma: Philip - what are the minimum metadata beside ID of ontology so the rest are taken as defaults, as many users may not have knowledge of ODKfull?

			[12:45] RaviSharma: Philip great comment about refresh version, but how do you handle compatibility between older versions of out integration namely provenance compatibility?

			[12:51] RaviSharma: For Anita or any presenters - do you have places where you store error files?

			[12:55] Sydney Cohen: is there anywhere to find a more detailed report for the violations of the SPARQL checks?

			[12:55] Sydney Cohen: would that go into the reports folder?

			[12:56] James Overton: The built-in ROBOT report commands each have a page with "problem-solution" documentation: http://robot.obolibrary.org/report_queries/'

			[12:56] James Overton: And ROBOT reports can output in text, TSV, and HTML formats.

			[12:57] James Overton: Small HTML example: http://dashboard.obofoundry.org/dashboard/obi/robot_report.html

			[12:57] Sydney Cohen: okay thank you

			[13:01] Ugur Bayindir: Side question; the editor Anita was using looks neat, what was that? And do you suggest using it in daily ontology editing tasks?

			[13:03] Anita Caron: I agree.

			[13:01] Allen Baron: Looked like Microsoft VS code to me.

			[13:03] Anita Caron: I agree.

			[13:01] Allen Baron: …. and Protege for editing the ontology file itself.

			[13:08] Anita Caron: I agree.

			[13:02] Anita Caron: Hi Ugur, yes, I recommend using VS code in your daily ontology editing.

			[13:03] Ugur Bayindir: I agree.

			[13:02] Mike Bennett: My concern is that in such a deep dev environment, devs may write tests that only apply to application-focused ontologies (e.g. we saw redundant sub-class relations) which may not always be applicable to a concept ontology. Process needs to account for tests v stated style / aim of the ontology itself.

			[13:04] Nico Matentzoglu: Very good point Mike, I totally agree

			[13:05] Nico Matentzoglu: Customisability is key±

			[13:08] Allen Baron: What’s included the documentation ODK can automatically generate about an ontology?

			[13:11] Anita Caron: Complete tutorial for adding custom SPARQL check https://oboacademy.github.io/obook/tutorial/custom-qc/

			[13:12] C.M. Alvarez (USBP): I agree.

			[13:02] RaviSharma: James and Team today - great integration development and output effort.

			[13:05] James Overton: Yes, the editor Anita was using is VS Code.

			[13:11] RaviSharma: Thanks for informing that 40-70 users use this toolset and apps regularly.

			[13:19] James Overton: 40-70 ontology projects use ODK, that we know of. It's an open source project, so who knows how many people use it.

	== Resources ==		== Resources ==

Forum: /* Attendees */

2023-02-15T17:47:42Z

Attendees

← Older revision		Revision as of 17:47, 15 February 2023
Line 36:		Line 36:

	== Attendees ==		== Attendees ==
			* [[AleixPuig\|Aleix Puig]]
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[AllenBaron\|Allen Baron]]
			* [[AndreaWesterinen\|Andrea Westerinen]]
			* [[AnitaCaron\|Anita Caron]]
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[BartGajderowicz\|Bart Gajderowicz]]
			* [[BobbinTeegarden\|Bobbin Teegarden]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato]]
			* [[CMAlvarez\|C.M. Alvarez]]
			* [[DamianGoutteGattat\|Damian Goutte-Gattat]]
			* [[FanLi\|Fan Li]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[JamesOverton\|James Overton]]
			* [[JenniferGiron\|Jennifer Girón]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JinjingGuo\|Jinjing Guo]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[MikeBennett\|Mike Bennett]]
			* [[NancyWiegand\|Nancy Wiegand]]
			* [[NicoMatentzoglu\|Nico Matentzoglu]]
			* [[PhilippeRoccaSerra\|Philippe Rocca-Serra]]
			* [[PhilipStroemert\|Philip Strömert]]
			* randi
			* [[RaviSharma\|Ravi Sharma]]
			* [[RayStefancsik\|Ray Stefancsik]]
			* [[RobertRovetto\|Robert Rovetto]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[StefanoDeGiorgis\|Stefano De Giorgis]]
			* [[SydneyCohen\|Sydney Cohen]]
			* [[UgurBayindir\|Ugur Bayindir]]

	== Discussion ==		== Discussion ==

Forum: /* Resources */

2023-02-09T19:51:31Z

Resources

← Older revision		Revision as of 19:51, 9 February 2023
Line 40:		Line 40:

	== Resources ==		== Resources ==
	[https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]		* [https://bit.ly/3YDzVIJ Video Recording]
			* [https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]

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

Forum: /* Agenda */

2023-02-09T19:51:18Z

Agenda

← Older revision		Revision as of 19:51, 9 February 2023
Line 26:		Line 26:
	* [https://bit.ly/40MyKsj Slides]		* [https://bit.ly/40MyKsj Slides]
	* [https://bit.ly/3Xo8ku6 Setting up your own repository]		* [https://bit.ly/3Xo8ku6 Setting up your own repository]
			* [https://bit.ly/3YDzVIJ Video Recording]

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

Forum: /* Resources */

2023-02-09T16:06:22Z

Resources

← Older revision		Revision as of 16:06, 9 February 2023
Line 39:		Line 39:

	== Resources ==		== Resources ==
			[https://oboacademy.github.io/obook/tutorial/custom-qc/ Tutorial: How to add custom quality checks with ODK]

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

Forum: /* Agenda */

2023-02-09T15:30:53Z

Agenda

← Older revision		Revision as of 15:30, 9 February 2023
Line 24:		Line 24:
	* The Ontology Development Kit (ODK)		* The Ontology Development Kit (ODK)
	* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron		* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron
			* [https://bit.ly/40MyKsj Slides]
			* [https://bit.ly/3Xo8ku6 Setting up your own repository]

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

Forum at 17:04, 8 February 2023

2023-02-08T17:04:16Z

← Older revision		Revision as of 17:04, 8 February 2023
Line 5:		Line 5:
	\|-		\|-
	! scope="row" \| Duration		! scope="row" \| Duration
	\| [[duration::1 hour]]		\| [[duration::1.5 hour]]
	\|-		\|-
	! scope="row" rowspan="3" \| Date/Time		! scope="row" rowspan="3" \| Date/Time
Line 15:		Line 15:
	\|-		\|-
	! scope="row" \| Convener		! scope="row" \| Convener
	\| [[convener::~~GaryBergCross~~\|~~Gary Berg-Cross~~]]		\| [[convener::JamesOverton\|James Overton]]
	\|}		\|}

Line 29:		Line 29:
	* Start Time: 9:00am PST / 12:00pm EST / 6:00pm CST / 5:00pm GMT / 1700 UTC		* 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=08&year=2023&hour=12&min=00&sec=0&p1=179 World Clock]		** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=02&day=08&year=2023&hour=12&min=00&sec=0&p1=179 World Clock]
	* Expected Call Duration: 1 hour		* Expected Call Duration: 1.5 hour
	{{:OntologySummit2023/ConferenceCallInformation}}		{{:OntologySummit2023/ConferenceCallInformation}}

Forum: /* Agenda */

2023-02-08T16:57:54Z

Agenda

← Older revision		Revision as of 16:57, 8 February 2023
Line 23:		Line 23:
	== Agenda ==		== Agenda ==
	* The Ontology Development Kit (ODK)		* The Ontology Development Kit (ODK)
	* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik ~~andor~~ Anita Caron		* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron

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

Forum: /* Agenda */

2023-02-08T16:57:36Z

Agenda

← Older revision		Revision as of 16:57, 8 February 2023
Line 23:		Line 23:
	== Agenda ==		== Agenda ==
	* The Ontology Development Kit (ODK)		* The Ontology Development Kit (ODK)
	* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip ~~Stroemert~~, Ray Stefancsik andor Anita Caron		* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik andor Anita Caron

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

← Older revision		Revision as of 17:47, 15 February 2023
Line 36:		Line 36:

	== Attendees ==		== Attendees ==
			* [[AleixPuig\|Aleix Puig]]
			* [[AlexanderDiehl\|Alexander Diehl]]
			* [[AlexShkotin\|Alex Shkotin]]
			* [[AllenBaron\|Allen Baron]]
			* [[AndreaWesterinen\|Andrea Westerinen]]
			* [[AnitaCaron\|Anita Caron]]
			* [[ArwaIbrahim\|Arwa Ibrahim]]
			* [[BartGajderowicz\|Bart Gajderowicz]]
			* [[BobbinTeegarden\|Bobbin Teegarden]]
			* [[ClaudiaSanchezBeatoJohnson\|Claudia Sanchez-Beato]]
			* [[CMAlvarez\|C.M. Alvarez]]
			* [[DamianGoutteGattat\|Damian Goutte-Gattat]]
			* [[FanLi\|Fan Li]]
			* [[GaryBergCross\|Gary Berg-Cross]]
			* [[JamesOverton\|James Overton]]
			* [[JenniferGiron\|Jennifer Girón]]
			* [[JieZheng\|Jie Zheng]]
			* [[JimBalhoff\|Jim Balhoff]]
			* [[JinjingGuo\|Jinjing Guo]]
			* [[KenBaclawski\|Ken Baclawski]]
			* [[MikeBennett\|Mike Bennett]]
			* [[NancyWiegand\|Nancy Wiegand]]
			* [[NicoMatentzoglu\|Nico Matentzoglu]]
			* [[PhilippeRoccaSerra\|Philippe Rocca-Serra]]
			* [[PhilipStroemert\|Philip Strömert]]
			* randi
			* [[RaviSharma\|Ravi Sharma]]
			* [[RayStefancsik\|Ray Stefancsik]]
			* [[RobertRovetto\|Robert Rovetto]]
			* [[SabrinaToro\|Sabrina Toro]]
			* [[StefanoDeGiorgis\|Stefano De Giorgis]]
			* [[SydneyCohen\|Sydney Cohen]]
			* [[UgurBayindir\|Ugur Bayindir]]

	== Discussion ==		== Discussion ==