|Date/Time||08 Feb 2023 17:00 GMT|
|9:00am PST/12:00pm EST|
|5:00pm GMT/6:00pm CST|
Helping scientific researchers make better use of ontologies
- The Ontology Development Kit (ODK)
- Presenters: Nico Matentzoglu, Damien Goutte-Gattat, Philip Strömert, Ray Stefancsik and/or Anita Caron
- 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
- 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
- Ravi Sharma
- Ray Stefancsik
- Robert Rovetto
- Sabrina Toro
- Stefano De Giorgis
- Sydney Cohen
- Ugur Bayindir
[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.
|ConferenceCall 2023 02 01||ROBOT|
|ConferenceCall 2023 01 25||COB|
|ConferenceCall 2023 01 18||Launch|
|... further results|
|ConferenceCall 2023 02 15||OBO Dashboards|
|ConferenceCall 2023 02 22||Ubergraph|
|ConferenceCall 2023 03 01||Panel|
|... further results|