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= [[OntologySummit2023|Ontology Summit 2023]] {{#show:{{PAGENAME}}|?session}} =
= [[OntologySummit2023|Ontology Summit 2023]]  
{{:OntologySummit2023/Description}}
 
== Helping scientific researchers make better use of ontologies: Tools, Methods and Best Practices ==
 
 
{{border|{{border|<center>In memoriam</center><center>'''[[PeterYim|Peter Yim]]'''</center><center>1951-2022</center>Our friend and Ontolog Forum founder [[PeterYim|Peter P. Yim]] has passed away. It is very sad news to all of us who worked with him, and a great loss to the community he founded and nurtured for many years. He will be missed. This Ontology Summit is dedicated to the memory of Peter.|width=5px|color=white}}|width=5px|color=black|display=block}}


== Agenda ==
== Agenda ==
* 12:00 - 12:05 [[KenBaclawski|Ken Baclawski]] Summit Kickoff and Introduction of the Summit Co-Chairs
* 12:00 - 12:05 '''[[KenBaclawski|Ken Baclawski]]''' Tribute to [[PeterYim|Peter Yim]]
* 12:05 - 12:15 [[GaryBergCross|Gary Berg-Cross]] and [[JamesOverton|James Overton]] Summit Vision
* 12:05 - 12:10 '''[[KenBaclawski|Ken Baclawski]]''' Summit Kickoff and Introduction of the Summit Co-Chairs
* 12:15 - 12:25 [[AsiyahLin|Asiyah Lin]] US2TS Panel Summary
* 12:10 - 12:20 '''[[GaryBergCross|Gary Berg-Cross]]''' and '''[[JamesOverton|James Overton]]''' ''Summit Vision'' [https://bit.ly/3HeJ1WI Slides]
* 12:25 - 12:35 [[GaryBergCross|Gary Berg-Cross]] Summit Schedule
* 12:20 - 12:40 '''[[GaryBergCross|Gary Berg-Cross]]''' and '''[[JamesOverton|James Overton]] ''Summit Schedule''
* 12:35 - 12:45 [[PascalHitzler|Pascal Hitzler]] Methods and Tools
* 12:40 - 12:50 '''Cogan Matthew Shimizu/Pascal Hitzler''' ''Methods and Tools'' [https://bit.ly/3ZJpmW0 Slides]
* 12:45 - 13:00 [[GaryBergCross|Gary Berg-Cross]] Conclusion and Discussion
* 12:50 - 13:00 '''[[GaryBergCross|Gary Berg-Cross]]''' Conclusion and Discussion
* [https://bit.ly/3WkN2Nq Video Recording]


== Conference Call Information ==
== Conference Call Information ==
Line 37: Line 42:


== Attendees ==
== Attendees ==
* [[AdamShepherd|Adam Shepherd]]
* [[AlexShkotin|Alex Shkotin]]
* [[AlexanderDiehl|Alexander Diehl]]
* [[AllenBaron|Allen Baron]]
* [[AndreaWesterinen|Andrea Westerinen]]
* [[AnitaCaron|Anita Caron]]
* [[BartGajderowicz|Bart Gajderowicz]]
* [[CharlieHoyt|Charlie Hoyt]]
* [[ChristopherLozinski|Christopher Lozinski]]
* [[ClaudiaSanchezBeatoJohnson|Claudia Sanchez-Beato Johnson]]
* [[CoganShimizu|Cogan Shimizu]]
* [[DamienGoutteGattat|Damien Goutte-Gattat]]
* [[DamionDooley|Damion Dooley]]
* [[DougHolmes|Doug Holmes]]
* [[ElizabethFlorescu|Elizabeth Florescu]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[JamesOverton|James A. Overton]]
* [[JenniferGiron|Jennifer C. Gir&oacute;n]]
* [[JieZheng|Jie Zheng]]
* [[JimBalholt|Jim Balholt]]
* [[JoanneLuciano|Joanne Luciano]]
* Kai
* [[KenBaclawski|Ken Baclawski]]
* [[LynnSchriml|Lynn Schriml]]
* [[MarciaZeng|Marcia Zeng]]
* [[MarkFox|Mark Fox]]
* [[MarkUnderwood|Mark Underwood]]
* [[MikeBennett|Mike Bennett]]
* [[MikeRiben|Mike Riben]]
* [[NancyWiegand|Nancy Wiegand]]
* [[NicoMatentzoglu|Nico Matentzoglu]]
* [[PhilipStroemert|Philip Str&ouml;mert]]
* [[RandiVita|Randi Vita]]
* [[RaviSharma|Ravi Sharma]]
* [[RhiannonCameron|Rhiannon Cameron]]
* [[RobertRovetto|Robert Rovetto]]
* [[SabriaToro|Sabria Toro]]
* [[SamsonTu|Samson Tu]]
* [[SierraMoxon|Sierra Moxon]]
* [[SteveRay|Steve Ray]]
* [[SusanBello|Susan Bello]]
* [[ThomasExner|Thomas Exner]]
* [[ToddSchneider|Todd Schneider]]
* [[TomWalpole|Tom Walpole]]


== Discussion ==
== Discussion ==
[12:11] RaviSharma: We start with condolences for Peter Yim who founded Ontolog Forum and ran it for several years. Welcome to the Summit 2023
[12:15] RaviSharma: we are excited to see 43 participants in the opening session and welcome everyone.
[12:24] Nico Matentzoglu: OBO Academy: https://oboacademy.github.io/obook
OBO Tools Workshop recording at ICBO 2022: youtube.com/watch?v=ayHsUkC4nZo
[12:24] UnCensoredNews.US I am new to ontologies.  I am interested in climate change ontologies.
[12:26] RaviSharma: welcome, we did cover some of it in last year summit, please review some of the sessions on environmental disasters and recordings and slides.
[12:29] Christopher Lozinski: Are OBO ontologies just trees?
[12:30] Christopher Lozinski: What language is OBO written in?  What database?
[12:30] Nico Matentzoglu: At OBO there are no climate change ontologies per se, but we have some very active people in COP27 and other such conferences. For example, the godfather of ENVO (https://github.com/EnvironmentOntology/envo), Pier Luigi Buttigieg, is very active on deep water related efforts related to climate.
[12:31] Nico Matentzoglu: Climate change is so complex - basically all ontologies are relevant to it I think
[12:31] Cogan Shimizu: You might also reach out to Ellie Young, who is focused on this space, from a community driven standpoint.
[12:32] Kai: The ESIP community as well Earth Science Information Partnership
[12:32] Alex Shkotin: soaphub is better as it will be on the session page later.
[12:33] Alex Shkotin: http://webconf.soaphub.org/conf/room/ontology_summit_2023
[12:36] Nico Matentzoglu: For those of you familiar with the OWL API, ROBOT can be seen in many ways as a CLI for OWL API. There is nothing really OBO-esque about it, it can be used for any OWL ontology parseable with the OWL API.
[12:37] Lynn Schriml: Check out ROBOT at http://robot.obolibrary.org
[12:37] RaviSharma: Q for James about Relationship Ontology, is there an agreed irreducible set of relationships or these have not been analyzed yet?
[12:38] RaviSharma: from other chat zoom
[12:38] Alex Shkotin: What about Jena?
[12:38] Nico Matentzoglu: Yes, in a very limited way as well. ODK includes riot, but in ROBOT we use Jena as a SPARQL endpoint
[12:39] Alex Shkotin: OK
[12:40] James Overton: Yes: ROBOT builds on both OWLAPI and Apache Jena.
[12:40] Susan Bello: OBO foundry home page https://obofoundry.org/
[12:40] Mark Underwood: Public Service Announcement: A former Ontolog participant James Schoening is chairing two IEEE Standards WGs "P3195 Requirements for a Mid-Level Ontology and Extensions" and P3195.1 Common Core Ontology (CCO) (Conforms to ISO/IEC-JTC1-21838-2 Basic Formal Ontology See https://sagroups.ieee.org/oswg/  This is open to the public; IEEE membership helpful but not required
[12:41] Nico Matentzoglu: Cogan, we can present DOS-DP which is the design pattern system we use in OBO if you are interested/there is time
[12:42] Nico Matentzoglu: Ahhhhh Haha I JUST organised a great Seminar on Wikidata with two excellent Wikidata experts… on the 21st March!
[12:42] James A. Overton: Replying to Christopher Lozinski: OBO projects use OWL (Web Ontology Language), and so they are more than just tree.
[12:43] Nico Matentzoglu: oops
[12:43] Cogan Shimizu: yes, dos-dp patterns have been on my radar for some time, but I haven't really had a chance to carve out bandwidth to discuss the interoperability of our paradigms. Perhaps this is a good kick -- we can possibly perhaps have a call this month?
[12:43] Nico Matentzoglu: I will follow up with you on slack
[12:43] Cogan Shimizu: possibly perhaps /facepalm
[12:44] James A. Overton: Replying to RaviSharma: RO may not be as formal as you are suggesting. The core RO relations owe a lot to older versions of BFO, but have not followed recent changes to relations in ISO BFO 2020.
[12:48] Mark Underwood: @Nico Can you post a link to the March Wikipdata meeting you alluded to?  Thx
[12:48] Nico Matentzoglu: (To whoever is organising the Wikidata session: I am happy to try and redirect our Wikidata seminar under the wings of ontosummit, but I need to talk to the speakers first)
[12:48] ToddSchneider: Where/when does ontological analysis come in?
Competency question by themselves are not sufficient. They are only a subset of requirements for development of an ontology.
[12:54] James A. Overton: Nico: I'll reach out to you and Gary about the Wikidata session.
[10:01] James Overton: Thanks for coming to our kickoff session everyone! Looking forward to seeing you next week!
[13:02] Joanne Luciano: It's so wonderful to see everyone and honor Peter. I have to leave for another meeting. Happy New Year -and all the best in good health! Take care, bye for now.
[13:04] RaviSharma: Q for Corbin have the geolocation accuracies or relevance improved with these design patterns
[13:06] RaviSharma: Robert Rovetto commented among others education and ISO and Cogan's work.


== Resources ==
== Resources ==
* [https://bit.ly/3HeJ1WI Gary Berg-Cross and James Overton Slides]
* [https://bit.ly/3ZJpmW0 Cogan Shimizu Slides]
* [https://bit.ly/3WkN2Nq Video Recording]
* [https://youtu.be/MxCmNT3JhmA Video Recording on YouTube]


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

Latest revision as of 16:27, 1 June 2023

Session Launch
Duration 1 hour
Date/Time 18 Jan 2023 17:00 GMT
9:00am PST/12:00pm EST
5:00pm GMT/6:00pm CST
Convener Ken Baclawski

= Ontology Summit 2023

Helping scientific researchers make better use of ontologies: Tools, Methods and Best Practices

In memoriam
Peter Yim
1951-2022
Our friend and Ontolog Forum founder Peter P. Yim has passed away. It is very sad news to all of us who worked with him, and a great loss to the community he founded and nurtured for many years. He will be missed. This Ontology Summit is dedicated to the memory of Peter.

Agenda

Conference Call Information

  • Date: Wednesday, 18 Jan 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

[12:11] RaviSharma: We start with condolences for Peter Yim who founded Ontolog Forum and ran it for several years. Welcome to the Summit 2023

[12:15] RaviSharma: we are excited to see 43 participants in the opening session and welcome everyone.

[12:24] Nico Matentzoglu: OBO Academy: https://oboacademy.github.io/obook

OBO Tools Workshop recording at ICBO 2022: youtube.com/watch?v=ayHsUkC4nZo

[12:24] UnCensoredNews.US I am new to ontologies. I am interested in climate change ontologies.

[12:26] RaviSharma: welcome, we did cover some of it in last year summit, please review some of the sessions on environmental disasters and recordings and slides.

[12:29] Christopher Lozinski: Are OBO ontologies just trees?

[12:30] Christopher Lozinski: What language is OBO written in? What database?

[12:30] Nico Matentzoglu: At OBO there are no climate change ontologies per se, but we have some very active people in COP27 and other such conferences. For example, the godfather of ENVO (https://github.com/EnvironmentOntology/envo), Pier Luigi Buttigieg, is very active on deep water related efforts related to climate.

[12:31] Nico Matentzoglu: Climate change is so complex - basically all ontologies are relevant to it I think

[12:31] Cogan Shimizu: You might also reach out to Ellie Young, who is focused on this space, from a community driven standpoint.

[12:32] Kai: The ESIP community as well Earth Science Information Partnership

[12:32] Alex Shkotin: soaphub is better as it will be on the session page later.

[12:33] Alex Shkotin: http://webconf.soaphub.org/conf/room/ontology_summit_2023

[12:36] Nico Matentzoglu: For those of you familiar with the OWL API, ROBOT can be seen in many ways as a CLI for OWL API. There is nothing really OBO-esque about it, it can be used for any OWL ontology parseable with the OWL API.

[12:37] Lynn Schriml: Check out ROBOT at http://robot.obolibrary.org

[12:37] RaviSharma: Q for James about Relationship Ontology, is there an agreed irreducible set of relationships or these have not been analyzed yet?

[12:38] RaviSharma: from other chat zoom

[12:38] Alex Shkotin: What about Jena?

[12:38] Nico Matentzoglu: Yes, in a very limited way as well. ODK includes riot, but in ROBOT we use Jena as a SPARQL endpoint

[12:39] Alex Shkotin: OK

[12:40] James Overton: Yes: ROBOT builds on both OWLAPI and Apache Jena.

[12:40] Susan Bello: OBO foundry home page https://obofoundry.org/

[12:40] Mark Underwood: Public Service Announcement: A former Ontolog participant James Schoening is chairing two IEEE Standards WGs "P3195 Requirements for a Mid-Level Ontology and Extensions" and P3195.1 Common Core Ontology (CCO) (Conforms to ISO/IEC-JTC1-21838-2 Basic Formal Ontology See https://sagroups.ieee.org/oswg/ This is open to the public; IEEE membership helpful but not required

[12:41] Nico Matentzoglu: Cogan, we can present DOS-DP which is the design pattern system we use in OBO if you are interested/there is time

[12:42] Nico Matentzoglu: Ahhhhh Haha I JUST organised a great Seminar on Wikidata with two excellent Wikidata experts… on the 21st March!

[12:42] James A. Overton: Replying to Christopher Lozinski: OBO projects use OWL (Web Ontology Language), and so they are more than just tree.

[12:43] Nico Matentzoglu: oops

[12:43] Cogan Shimizu: yes, dos-dp patterns have been on my radar for some time, but I haven't really had a chance to carve out bandwidth to discuss the interoperability of our paradigms. Perhaps this is a good kick -- we can possibly perhaps have a call this month?

[12:43] Nico Matentzoglu: I will follow up with you on slack

[12:43] Cogan Shimizu: possibly perhaps /facepalm

[12:44] James A. Overton: Replying to RaviSharma: RO may not be as formal as you are suggesting. The core RO relations owe a lot to older versions of BFO, but have not followed recent changes to relations in ISO BFO 2020.

[12:48] Mark Underwood: @Nico Can you post a link to the March Wikipdata meeting you alluded to? Thx

[12:48] Nico Matentzoglu: (To whoever is organising the Wikidata session: I am happy to try and redirect our Wikidata seminar under the wings of ontosummit, but I need to talk to the speakers first)

[12:48] ToddSchneider: Where/when does ontological analysis come in?

Competency question by themselves are not sufficient. They are only a subset of requirements for development of an ontology.

[12:54] James A. Overton: Nico: I'll reach out to you and Gary about the Wikidata session.

[10:01] James Overton: Thanks for coming to our kickoff session everyone! Looking forward to seeing you next week!

[13:02] Joanne Luciano: It's so wonderful to see everyone and honor Peter. I have to leave for another meeting. Happy New Year -and all the best in good health! Take care, bye for now.

[13:04] RaviSharma: Q for Corbin have the geolocation accuracies or relevance improved with these design patterns

[13:06] RaviSharma: Robert Rovetto commented among others education and ISO and Cogan's work.

Resources

Previous Meetings

 Session
ConferenceCall 2022 12 14Planning
ConferenceCall 2022 12 07Data Principles
ConferenceCall 2022 11 30Planning
... further results

Next Meetings

 Session
ConferenceCall 2023 01 25COB
ConferenceCall 2023 02 01ROBOT
ConferenceCall 2023 02 08ODK
... further results
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