ConferenceCall 2023 02 08

Session	ODK
Duration	1.5 hour
Date/Time	08 Feb 2023 17:00 GMT
	9:00am PST/12:00pm EST
	5:00pm GMT/6:00pm CST
Convener	James Overton

Ontology Summit 2023 ODK

Helping scientific researchers make better use of ontologies

Agenda

• The Ontology Development Kit (ODK)
• Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron
• Slides
• Setting up your own repository
• 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: World Clock
• Expected Call Duration: 1.5 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

Attendees

• Aleix Puig
• Alexander Diehl
• Alex Shkotin
• Allen Baron
• Andrea Westerinen
• Anita Caron
• Arwa Ibrahim
• Bart Gajderowicz
• Bobbin Teegarden
• Claudia Sanchez-Beato
• C.M. Alvarez
• Damian Goutte-Gattat
• Fan Li
• Gary Berg-Cross
• James Overton
• Jennifer Girón
• Jie Zheng
• Jim Balhoff
• Jinjing Guo
• Ken Baclawski
• Mike Bennett
• Nancy Wiegand
• Nico Matentzoglu
• Philippe Rocca-Serra
• Philip Strömert
• randi
• Ravi Sharma
• Ray Stefancsik
• Robert Rovetto
• Sabrina Toro
• Stefano De Giorgis
• Sydney Cohen
• 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

• Video Recording
• Tutorial: How to add custom quality checks with ODK
• Video Recording on YouTube

Previous Meetings

	Session
ConferenceCall 2023 02 01	ROBOT
ConferenceCall 2023 01 25	COB
ConferenceCall 2023 01 18	Launch
... further results

Next Meetings

	Session
ConferenceCall 2023 02 15	OBO Dashboards
ConferenceCall 2023 02 22	Ubergraph
ConferenceCall 2023 03 01	Panel
... further results