Actions

ConferenceCall 2023 03 01: Difference between revisions

Ontolog Forum
 
(13 intermediate revisions by 2 users not shown)
Line 22: Line 22:


== Agenda ==
== Agenda ==
* Panel Discussion
* '''[[GaryBergCross|Gary Berg-Cross]]'''
** [[KrzysztofJanowicz|Krzysztof Janowicz]]
** ''Some Context for the Panel''
** [[DeborahMcGuiness|Deborah McGuiness]]
** [https://bit.ly/3J4Kq35 Slides]
** [[ChrisMungall|Chris Mungall]]
* Panel Discussion moderated by '''[[JamesOverton|James Overton]]'''
** [[JamesOverton|James Overton]]
** '''[[KrzysztofJanowicz|Krzysztof Janowicz]]'''
** [[NicoMatentzoglu|Nico Matentzoglu]]
** '''[[ChrisMungall|Chris Mungall]]'''
** '''[[CoganMatthewShimizu|Cogan Matthew Shimizu]]'''
* [https://bit.ly/3KUXxFn Video Recording]


== Conference Call Information ==
== Conference Call Information ==
Line 37: Line 39:


== Attendees ==
== Attendees ==
* [[AlexanderDiehl|Alexander Diehl]]
* [[AllenBaron|Allen Baron]]
* [[AnitaCaron|Anita Caron]]
* [[AnupamaGururaj|Anupama Gururaj]]
* [[ArwaIbrahim|Arwa Ibrahim]]
* [[AsiyahLin|Asiyah Lin]]
* [[ChrisKindermann|Chris Kindermann]]
* [[ChrisMungall|Chris Mungall]]
* [[ClaudiaSanchezBeatoJohnson|Claudia Sanchez-Beato Johnson]]
* [[CoganShimizu|Cogan Shimizu]]
* [[DarrenNatale|Darren A. Natale]]
* [[DitchTownsend|Ditch Townsend]]
* [[FanLi|Fan Li]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[HendrickBorgelt|Hendrick Borgelt]]
* [[HilmarLapp|Hilmar Lapp]]
* [[JamesOverton|James Overton]]
* [[JanetSinger|Janet Singer]]
* [[JieZheng|Jie Zheng]]
* [[JimBalhoff|Jim Balhoff]]
* [[JohnJudkins|John Judkins]]
* [[KaiBlumberg|Kai Blumberg]]
* [[KatieMullen|Katie Mullen]]
* [[KenBaclawski|Ken Baclawski]]
* [[KrysztofJanowicz|Krysztof Janowicz]]
* [[Leigh Carmody|Leigh Carmody]]
* [[LindaBlevens|Linda Blevens]]
* [[MichelleKathrynMcGee|Michelle Kathryn McGee]]
* [[NicoMatentzoglu|Nico Matentzoglu]]
* [[PhilipStroemert|Philip Stroemert]]
* randi
* [[RaviSharma|Ravi Sharma]]
* [[RayStefancsik|Ray Stefancsik]]
* [[RobertRovetto|Robert Rovetto]]
* [[SabrinaToro|Sabrina Toro]]
* [[SierraMoxon|Sierra Moxon]]
* [[SusanBello|Susan Bello]]
* [[VincentVialard|Vincent Vialard]]
* [[YvonneBradford|Yvonne Bradford]]


== Discussion ==
== Discussion ==
[12:05] RaviSharma: Hello Jano Welcome again
[12:07] RaviSharma: Gary - kindly elaborate on what is measure implied for scientifically accurate, do you mean model conformant as there can be varied opinions?
[12:08] RaviSharma: Gary I liked the roles slide so what is also important is how useful are these tools for use by scientists and other professionals in biomed or health?
[12:11] James Overton: @Ravi: Gary is quoting the OBO mission statement. When we say "scientifically accurate" we don't have a formal notion in mind, but rather about keeping up with scientific state-of-the-art.
[12:16] Krzysztof Janowicz: Just for clarification, I am a Prof. at University of Vienna and at UC Santa Barbara,  I have no affiliation with University of Virginia.
[12:22] RaviSharma: Chris I agree this is valuable to trace subatomic to molecule and also to relevant genes (could be more than one) the transition of relevant info bout effects of chemicals or elements to target ed genes. Valuable.
[12:25] RaviSharma: Jano - how do you relate your work in last talk to us in 2022 relating to KnowWhere Graph?
[12:26] Alexander Diehl: It is clear that many in our community play or have played more than one of the roles listed, and this is one of our community strengths.
[12:26] Robert Rovetto: Regarding tools, Here is a list https://github.com/rrovetto/Ontology-Development-Guidelines/tree/master/Tools
[12:29] Nico Matentzoglu: As a follow up to Gary’s infrastructure focused question, I would be very interested to hear from the non-OBO panelists how OBO as a community is perceived in your domains. Are we a mystic cabal? Or does all we do make sense and is transparent to you?
[12:31] Philip Strömert: So can one say that shapes are more important for ABoxes than reasoners?  But for developing TBoxes reasoners are great to check for consistency?
[12:32} Cogan: I generally find this to be true, yes.
[12:39] James Overton: The next general topic I would like to emphasize is workflows and collaboration. OBO has put a lot of effort into open collaboration workflows, often centered on GitHub, including editing and quality control and releases and infrastructure. I would like to know if these topics have resonated with the non-OBO people in the audience.
[12:40] Gary Berg-Cross: Chris's point about what reasoning lines up with Biologists thinking reminds me of what Alan Rector has written about this.  How does the Manchester school's work align with the OBO Foundry?
[12:44] Philip Strömert: The KnowWhere Graph Schema https://stko-kwg.geog.ucsb.edu/lod/ontology
[12:46] Chris Mungall: SPOKE incorporates multiple OBO ontologies https://spoke.ucsf.edu/
[12:47] Cogan: https://spoke.ucsf.edu/ and https://spoke.ucsf.edu/data-tools
[12:48] Chris Mungall: There are a lot of these projects in biomedicine, Ubergraph is an example of this, same patterns, simple triples connecting classes and entities
[12:50] Asiyah Yu Lin - NIAID: @Ditch, can you explain NBO that you are working on?
Reply by Ditch: It's an ontology focused on behaviour. It may have tried to do too much by trying to be all things to everyone. It became essentially leaderless and unsupported, so I have volunteered to do what I can to revivify it. I came at it as a hopeful user that couldn't really use what was there, and have had to learn some basic curation around things like Protege.
[12:50] Nico Matentzoglu: Great question Ditch
[12:50] Nico Matentzoglu: https://github.com/obo-behavior/behavior-ontology
[12:53] Nico Matentzoglu: You will:
1. Need to know the communities that use your ontology
2. Need an access like a knowledge graph the the resources in that community to understand the use of a specific term
[12:54] Nico Matentzoglu: Ditch, if James would manage NBO he would probably not be as happy to obsolete 62 terms at once.
[12:56] Chris Mungall: An example of this is “disorder” in OGMS
[12:57] Asiyah Yu Lin - NIAID: Other examples are condition, health...
[12:58] Nico Matentzoglu: There are many communities emerging now like ontocommons, industry ontology foundry, NFDI4Chem etc building ontology communities. This is not as much a question (time is up on this) but it would be great if we could get a better understanding how we can help these new communities implement workflows and toolboxes to get up to a smoother start.
[13:00] Robert Rovetto: To panel: the replies didn't quite answer my question. would you kindly reach out offline?


== Resources ==
== Resources ==
* [https://bit.ly/3KUXxFn Video Recording]
* [https://youtu.be/8h_VuodDgbE Video Recording on YouTube]


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

Latest revision as of 16:29, 1 June 2023

Session Panel
Duration 1 hour
Date/Time 01 Mar 2023 17:00 GMT
9:00am PST/12:00pm EST
5:00pm GMT/6:00pm CST
Convener Gary Berg-Cross

Ontology Summit 2023 Panel

Helping scientific researchers make better use of ontologies

Agenda

Conference Call Information

  • Date: Wednesday, 01 Mar 2023
  • Start Time: 9:00am PST / 12:00pm EST / 6:00pm CST / 5:00pm GMT / 1700 UTC
  • Expected Call Duration: 1 hour
  • Video Conference URL
    • Conference ID: 837 8041 8377
    • Passcode: 323309
  • Chat Room

The unabbreviated URLs are:

Attendees

Discussion

[12:05] RaviSharma: Hello Jano Welcome again

[12:07] RaviSharma: Gary - kindly elaborate on what is measure implied for scientifically accurate, do you mean model conformant as there can be varied opinions?

[12:08] RaviSharma: Gary I liked the roles slide so what is also important is how useful are these tools for use by scientists and other professionals in biomed or health?

[12:11] James Overton: @Ravi: Gary is quoting the OBO mission statement. When we say "scientifically accurate" we don't have a formal notion in mind, but rather about keeping up with scientific state-of-the-art.

[12:16] Krzysztof Janowicz: Just for clarification, I am a Prof. at University of Vienna and at UC Santa Barbara, I have no affiliation with University of Virginia.

[12:22] RaviSharma: Chris I agree this is valuable to trace subatomic to molecule and also to relevant genes (could be more than one) the transition of relevant info bout effects of chemicals or elements to target ed genes. Valuable.

[12:25] RaviSharma: Jano - how do you relate your work in last talk to us in 2022 relating to KnowWhere Graph?

[12:26] Alexander Diehl: It is clear that many in our community play or have played more than one of the roles listed, and this is one of our community strengths.

[12:26] Robert Rovetto: Regarding tools, Here is a list https://github.com/rrovetto/Ontology-Development-Guidelines/tree/master/Tools

[12:29] Nico Matentzoglu: As a follow up to Gary’s infrastructure focused question, I would be very interested to hear from the non-OBO panelists how OBO as a community is perceived in your domains. Are we a mystic cabal? Or does all we do make sense and is transparent to you?

[12:31] Philip Strömert: So can one say that shapes are more important for ABoxes than reasoners? But for developing TBoxes reasoners are great to check for consistency?

[12:32} Cogan: I generally find this to be true, yes.

[12:39] James Overton: The next general topic I would like to emphasize is workflows and collaboration. OBO has put a lot of effort into open collaboration workflows, often centered on GitHub, including editing and quality control and releases and infrastructure. I would like to know if these topics have resonated with the non-OBO people in the audience.

[12:40] Gary Berg-Cross: Chris's point about what reasoning lines up with Biologists thinking reminds me of what Alan Rector has written about this. How does the Manchester school's work align with the OBO Foundry?

[12:44] Philip Strömert: The KnowWhere Graph Schema https://stko-kwg.geog.ucsb.edu/lod/ontology

[12:46] Chris Mungall: SPOKE incorporates multiple OBO ontologies https://spoke.ucsf.edu/

[12:47] Cogan: https://spoke.ucsf.edu/ and https://spoke.ucsf.edu/data-tools

[12:48] Chris Mungall: There are a lot of these projects in biomedicine, Ubergraph is an example of this, same patterns, simple triples connecting classes and entities

[12:50] Asiyah Yu Lin - NIAID: @Ditch, can you explain NBO that you are working on?

Reply by Ditch: It's an ontology focused on behaviour. It may have tried to do too much by trying to be all things to everyone. It became essentially leaderless and unsupported, so I have volunteered to do what I can to revivify it. I came at it as a hopeful user that couldn't really use what was there, and have had to learn some basic curation around things like Protege.

[12:50] Nico Matentzoglu: Great question Ditch

[12:50] Nico Matentzoglu: https://github.com/obo-behavior/behavior-ontology

[12:53] Nico Matentzoglu: You will:

1. Need to know the communities that use your ontology

2. Need an access like a knowledge graph the the resources in that community to understand the use of a specific term

[12:54] Nico Matentzoglu: Ditch, if James would manage NBO he would probably not be as happy to obsolete 62 terms at once.

[12:56] Chris Mungall: An example of this is “disorder” in OGMS

[12:57] Asiyah Yu Lin - NIAID: Other examples are condition, health...

[12:58] Nico Matentzoglu: There are many communities emerging now like ontocommons, industry ontology foundry, NFDI4Chem etc building ontology communities. This is not as much a question (time is up on this) but it would be great if we could get a better understanding how we can help these new communities implement workflows and toolboxes to get up to a smoother start.

[13:00] Robert Rovetto: To panel: the replies didn't quite answer my question. would you kindly reach out offline?

Resources

Previous Meetings

 Session
ConferenceCall 2023 02 22Ubergraph
ConferenceCall 2023 02 15OBO Dashboards
ConferenceCall 2023 02 08ODK
... further results

Next Meetings

 Session
ConferenceCall 2023 03 08Modules and Patterns
ConferenceCall 2023 03 15Design Patterns
ConferenceCall 2023 03 21Wikidata
... further results
Retrieved from "https://ontologforum.com/index.php?title=ConferenceCall_2023_03_01&oldid=4604"