ConferenceCall 2023 04 12

Session	Panel
Duration	1 hour
Date/Time	12 Apr 2023 16:00 GMT
	9:00am PDT/12:00pm EDT
	4:00pm GMT/5:00pm CST
Convener	Gary Berg-Cross

Ontology Summit 2023 Panel

Helping scientific researchers make better use of ontologies

Agenda

• 12:00 - 12:10 Sierra Moxon Introduction to LinkML Slides
• 12:10 - 12:20 Asiyah Lin FOHTI-22 US2TS Summary Slides
• 12:30 - 12:30 Torsten Hahmann Upper Level Domain Models Slides
• 12:30 - 13:00 Open Discussion
• Video Recording

Conference Call Information

• Date: Wednesday, 12 Apr 2023
• Start Time: 9:00am PDT / 12:00pm EDT / 6:00pm CEST / 5:00pm BST / 1600 UTC
  • ref: World Clock
• Expected Call Duration: 1 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

• Alexander Diehl
• Alex Shkotin
• Allen Baron
• Asiyah Lin
• Chris Kindermann
• Chris Mungall
• Damion Dooley
• Gary Berg-Cross
• James Overton
• Janet Singer
• Ken Baclawski
• Leigh Carmody
• Mark Ressler
• Mike Bennett
• Patrick Logan
• Ravi Sharma
• Rhiannon Cameron
• Russell Reinsch
• Sabrina Toro
• Susan Bello
• Torsten Hahmann

Discussion

[12:14] RaviSharma: Sierra - is LinkML a language translator or is more than that namely language API integrator or allows interoperation by meaningfully Querying using these different languages

[12:16] Kai Blumberg: Looks like my PhD thesis work

[12:17] Chris Mungall: It's not really either. It's a modeling framework

[12:18] RaviSharma: then how does it relate to various languages shown by

[12:18] RaviSharma: For those of you that have been around the ontolog group for a while, the closest analog is Frames. But a key difference is that is allows translation to other frameworks, whether semantic (e.g SHACL) or more traditional (e.g. JSON-Schema)

[12:25] RaviSharma: Asiyah -Ramona hopes to have single integrated very difficult. acceptable ontology which is

[12:26] RaviSharma: very difficult.

[12:27] Gary Berg-Cross: Our speaker next week, Martin, will be talking about using ontology templates to make Ont development easier.

[12:31] RaviSharma: It is so difficult to reach both consensus as well as data meanings

[12:33] RaviSharma: Internet does not have to make sense but ontology is meant for meaningful relations among entities?

[12:34] Damion Dooley: The unified ontology family effort is basically like the development of Esperanto, but for the science and data science community. Have to create/learn the syntax and grammar, and test it out over and over in expressing things. Like going to school in Groundhog Day movie!

[12:38] RaviSharma: Asiyah - the real problem is that OWL is not semantics inclusive? It related only to URLs etc.

[12:38] RaviSharma: RDF framework is what we mean

[12:39] RaviSharma: Data element is not a rich enough concept but data combinations at information level is amenable to semantics!

[12:43] Chris Mungall: I am not sure I agree OWL is only related to URLs. These are just identifiers as far as the OWL semantics is concerned (and in fact any IRI can be used)

[12:47] RaviSharma: Torsten - hence domain ref ont addresses what John sowa tells us namely logic. reasoning etc for ontology

[12:48] RaviSharma: How will you use DRO and domain ontology

[12:50] Nico Matentzoglu: Domain reference ontology is a good term I think and we could adopt it for OBO. The goal for OBO 2024 would be to separate domain reference ontologies from domain ontologies and promote increase dependency on domain reference ontologies and decrease dependency on domain ontologies.

[12:50] Asiyah: @Ravi, the CDE is more granular than ontology. But to harmonize the CDEs we need standard terms that is defined and with semantics. The best is that people will try to use ontology terms for their CDEs instead of creating their own variation. The famous example is age.

[12:52] RaviSharma: Torsten are you trying to model ontology and are you creating physics model backed by Logic and inference?

[12:53] RaviSharma: Torsten how would you connect HyFO and FEO

[12:54] janet singer: Damien, Are you speaking about unified ontology family efforts in general or about a particular project?

[12:54] Nico Matentzoglu: Oh I think I misunderstood something. Seems the domain reference ontology would be more like COB, not eg Uberon..

[12:54] Kai Blumberg: That's my interpretation but I could be wrong

[12:55] James Overton: I hadn't heard of macleod before. Is it simpler to set up and use than HETS?

[12:57] Damion Dooley: @janet It was a general comment - the challenge of creating an Esperanto style language, whichever ontology community one participates in.

[12:58] Damion Dooley: But of course this is what we face in OBO community.

[13:03] janet singer: @Damion, Yes that's a good point. Of course Esperanto fell far short of expectations, so a good topic to explore is why that's been the case. And what could be done differently

[13:03] RaviSharma: From Kai to Everyone 09:54 AM

[13:04] TorstenHahmann: @James: we are working on providing a pypi package for macleod

Resources

• Video Recording
• Video Recording on YouTube

Previous Meetings

	Session
ConferenceCall 2023 04 05	Science on Schema.org
ConferenceCall 2023 03 29	Synthesis
ConferenceCall 2023 03 22	Wikidata
... further results

Next Meetings

	Session
ConferenceCall 2023 04 19	Ontology Development
ConferenceCall 2023 04 26	Synthesis
ConferenceCall 2023 05 03	Communiqué
... further results