View source for ConferenceCall 2023 02 08

{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10"
|-
! scope="row" | Session
| [[session::ODK]]
|-
! scope="row" | Duration
| [[duration::1.5 hour]]
|-
! scope="row" rowspan="3" | Date/Time
| [[has date::08 Feb 2023 17:00 GMT]]
|-
| 9:00am PST/12:00pm EST
|-
| 5:00pm GMT/6:00pm CST
|-
! scope="row" | Convener
| [[convener::JamesOverton|James Overton]]
|}

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

== Agenda ==
* The Ontology Development Kit (ODK)
* Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Str&ouml;mert, Ray Stefancsik and/or Anita Caron
* [https://bit.ly/40MyKsj Slides]
* [https://bit.ly/3Xo8ku6 Setting up your own repository]
* [https://bit.ly/3YDzVIJ Video Recording]

== Conference Call Information ==
* Date: '''Wednesday, 08 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=08&year=2023&hour=12&min=00&sec=0&p1=179 World Clock] 
* Expected Call Duration: 1.5 hour
{{:OntologySummit2023/ConferenceCallInformation}}

== 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 Gir&oacute;n]]
* [[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 Str&ouml;mert]]
* randi
* [[RaviSharma|Ravi Sharma]]
* [[RayStefancsik|Ray Stefancsik]]
* [[RobertRovetto|Robert Rovetto]]
* [[SabrinaToro|Sabrina Toro]]
* [[StefanoDeGiorgis|Stefano De Giorgis]]
* [[SydneyCohen|Sydney Cohen]]
* [[UgurBayindir|Ugur Bayindir]]

== 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 ==
* [https://bit.ly/3YDzVIJ Video Recording]
* [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 ==
{{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[<<ConferenceCall_2023_02_08]]
        |?|?Session|mainlabel=-|order=desc|limit=3}}
	
== Next Meetings ==
{{#ask: [[Category:OntologySummit2023]] [[Category:Icom_conf_Conference]] [[>>ConferenceCall_2023_02_08]]
        |?|?Session|mainlabel=-|order=asc|limit=3}}

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