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(Created page with "{| class="wikitable" style="float:right; margin-left: 10px;" border="1" cellpadding="10" |- ! scope="row" | Session | session::ROBOT |- ! scope="row" | Duration | duration::1 hour |- ! scope="row" rowspan="3" | Date/Time | has date::01 Feb 2023 17:00 GMT |- | 9:00am PST/12:00pm EST |- | 5:00pm GMT/6:00pm CST |- ! scope="row" | Convener | Gary Berg-Cross |} = Ontology Summit 2023 {{#show:{{PAGENAME}}|?session...")
 
 
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== Agenda ==
== Agenda ==
* 12:00 - 12:30 '''[[JamesOverton|James Overton]]''' ''ROBOT: A command line tool to automate ontology workflows''
* 12:00 - 12:30 '''[[JamesOverton|James Overton]]''' ''ROBOT: A command line tool to automate ontology workflows'' [http://bit.ly/3jnEOH4 Slides]
* 12:30 - 13:00 Discussion
* 12:30 - 12:40 '''[[ChrisMungall|Chris Mungall]]''' ''Ontology Access Kit'' (OAK) [https://bit.ly/3joEBmM Slides]
* 12:40 - 13:00 Discussion
* [https://bit.ly/3HpDc7E Video Recording]


== Conference Call Information ==
== Conference Call Information ==
Line 33: Line 35:


== Attendees ==
== Attendees ==
* [[AlexanderDiehl|Alexander Diehl]]
* [[AlexShkotin|Alex Shkotin]]
* [[AliHasanzadeh|Ali Hasanzadeh]]
* [[AllenBaron|Allen Baron]]
* [[ArwaIbrahim|Arwa Ibrahim]]
* [[AzanziJiomekong|Azanzi JIOMEKONG]]
* [[BBowthorpe|B. Bowthorpe USBP]]
* [[BevCorwin|Bev Corwin]]
* [[ChrisKindermann|Chris Kindermann]]
* [[ChrisMungall|Chris Mungall]]
* [[ClarePilgrim|Clare Pilgrim]]
* [[ClaudiaSanchezBeatoJohnson|Claudia Sanchez-Beato Johnson]]
* [[ClausWeiland|Claus Weiland]]
* [[CMAlvarez|C.M. Alvarez]]
* [[DarrenNatale|Darren Natale]]
* [[DouglasMiles|Douglas Miles]]
* [[FanLi|Fan Li]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[JamesOverton|James Overton]]
* [[JenniferGiron|Jennifer C. Girón]]
* [[JieZheng|Jie Zheng]]
* [[JimBalhoff|Jim Balhoff]]
* [[JohnJudkins|John Judkins]]
* [[JonasGrieb|Jonas Grieb]]
* Kai
* [[KatieMullen|Katie Mullen]]
* [[KenBaclawski|Ken Baclawski]]
* [[MarciaZeng|Marcia Zeng]]
* [[MarkUnderwood|Mark Underwood]]
* [[MichaelDeBellis|Michael DeBellis]]
* [[MikeBennett|Mike Bennett]]
* [[NancyWiegand|Nancy Wiegand]]
* Naoual
* [[NicoMatentzoglu|Nico Matentzoglu]]
* [[PhilipStromert|Philip Strömert]]
* [[RaviSharma|Ravi Sharma]]
* [[RayStefancsik|Ray Stefancsik]]
* [[RiannonCameron|Riannon Cameron]]
* [[RobertRovetto|Robert Rovetto]]
* [[SamsonTu|Samson Tu]]
* [[SusanBello|Susan Bello]]
* [[SydneyCohen|Sydney Cohen]]
* [[ThomasExner|Thomas Exner]]
* [[UgurBayindir|Ugur Bayindir]]
* [[VincentVialard|Vincent Vialard]]
* [[ViniciusDeSouza|Vinicius de Souza]]
* [[YaseminBridges|Yasemin Bridges]]
* Yousif
* [[ZoeMayPendlington|Zoë May Pendlington]]


== Discussion ==
== Discussion ==
[12:06] RaviSharma: James Welcome
[12:06] James Overton: ROBOT slides: http://james.overton.ca/slides/robot-tutorial-2023/index.html#/title-slide
OAK slides: https://docs.google.com/presentation/d/1XK2fOlfLVXc25DrVFfS3kpt5jBpX8fQ3OePsM5rlSNE/edit#slide=id.p
[12:08] RaviSharma: Philosophy is mother of Mathematics and Physics or for that matter logic and reasoning. We sometimes call it metaphysics also. We are proud of Philosophers, and welcome you. This also has basis of ontology.
[12:15] RaviSharma: James can you explain the power of Query a bit more?
[12:16] RaviSharma: James does ROBOT work with Franz Gruff?
[12:17] RaviSharma: James, what are the commands relevant to construct KG?
[12:19] RaviSharma: James, how do we use some commands for NLP?
[12:22] RaviSharma: James you have given users power of Query I see now.
[12:23] RaviSharma: James, if you were or if community were to add commands, which ones would you prioritize?
[12:29] Nico Matentzoglu: What is Franz Gruff?
Added by Ken Baclawski: Gruff is a free Knowledge Graph visualization product from Franz Inc. https://allegrograph.com/products/gruff/
[12:29] Nico Matentzoglu: No commands for NLP directly in ROBOT, no
[12:32] Nico Matentzoglu: Ravi, re prioritizing commands, we do that here: https://github.com/ontodev/robot/issues It depends on the major projects at the time
[12:32] Nico Matentzoglu: But its a good question to ask in the QA later
[12:32] RaviSharma: James great tutorial a bit rushed at end but great tool and lot of capabilities, thanks.
[12:33] C.M. Alvarez: Do you have the slack link?
[12:33] RaviSharma: Chris Welcome back
[12:34] James Overton: Thanks Ravi. Yes, these slides were written for a longer presentation slot. I encourage anyone to look at the documentation site, or go over my slides more slowly: http://james.overton.ca/slides/robot-tutorial-2023/index.html
[12:35] RaviSharma: Chris, does OAK work with other than english language, same Q for James?
[12:35] Michael DeBellis: Chrome gives me a privacy
[12:36] Nico Matentzoglu: Me too. it's because you are going into a non-https side.. I didn't have that last time.
[12:36] Gary Berg-Cross: Yes, MD, but you can proceed safely
[12:36] Michael DeBellis: How does Oak compare with OWLReady2?
[12:38] James Overton: Ravi: Yes, but we could do better. We support RDF and OWL, which use Unicode and language tags, but we could do better to support multiple labels in different languages. I would *love* to do better, but I haven't had a project to fund that work.
[12:39] RaviSharma: Ken, can you kindly comment on KGSQL if it is applicable or interoperable?
Added by Ken Baclawski: KGSQL is applicable.  It extends KGs with additional features that would be useful.  However, KGSQL is not yet generally supported so it is not interoperable.
[12:39] James Overton: While there's some overlap, I would say that OAK is higher-level and more focused on browsing and analysis than OwlReady2.
[12:40] RaviSharma: Mike Bennett - congrats on being a technical director at OMG. Very proud of your accomplishments.
[12:40] Mike Bennett: Thanks Ravi!
[12:41] Mike Bennett: Great to see an ontology viz that uses a line for a restriction instead of a Nameless Box. Critical for business SME validation!
[12:42] RaviSharma: Chris, as compared to older GO tools how are we using OAK or ROBOT
[12:46] Vincent Vialard: Did you try the Konclude reasoner for Robot? It is both fast and complete (but not in Java)...
[12:47] James Overton: No, we haven't tried Konclude.
[12:49] Mike Bennett: An idea: would it be possible to use Robot or OAK to derive operational ontologies from a purely conceptual ontology (i.e. inserting datatypes and data surrogates for real world things)?
[12:50] StroemPhi: https://owlready2.readthedocs.io/en/v0.37/
[12:51] Chris Mungall: https://github.com/INCATools/ontology-access-kit/issues/102 - add links to other tools here!
[12:52] RaviSharma: Chris and James - appreciate your answering many or most of my Qs.
[12:53] RaviSharma: What XML capabilities are built in these commands, mostly for transport?
[12:54] James Overton: LinkML data modelling tool: http://linkml.io/
[12:59] RaviSharma: Again many thanks for two great presentations.
[12:59] C.M. Alvarez: Thanks for a great presentation!
[13:02] Thomas Exner: Thanks for the presentations. What were the other things you mentioned similar to LinkML?
[13:03] James Overton: LinkML is similar to various validation/schema languages such as JSON Schema, ShEx, and SHACL.
[13:03] Thomas Exner: Thanks.
[13:13] James Overton: XML capabilities: We use RDF/XML as our default data format, but support other RDF and OWL formats.


== Resources ==
== Resources ==
* [https://bit.ly/3joEBmM Ontology Access Kit Slides]
* [https://bit.ly/3HpDc7E Session Video Recording]
* [https://youtu.be/Qvz_qwaNy4Y Video Recording on YouTube]


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

Latest revision as of 16:28, 1 June 2023

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

Ontology Summit 2023 ROBOT

Helping scientific researchers make better use of ontologies

Agenda

Conference Call Information

  • Date: Wednesday, 01 Feb 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

[12:06] RaviSharma: James Welcome

[12:06] James Overton: ROBOT slides: http://james.overton.ca/slides/robot-tutorial-2023/index.html#/title-slide

OAK slides: https://docs.google.com/presentation/d/1XK2fOlfLVXc25DrVFfS3kpt5jBpX8fQ3OePsM5rlSNE/edit#slide=id.p

[12:08] RaviSharma: Philosophy is mother of Mathematics and Physics or for that matter logic and reasoning. We sometimes call it metaphysics also. We are proud of Philosophers, and welcome you. This also has basis of ontology.

[12:15] RaviSharma: James can you explain the power of Query a bit more?

[12:16] RaviSharma: James does ROBOT work with Franz Gruff?

[12:17] RaviSharma: James, what are the commands relevant to construct KG?

[12:19] RaviSharma: James, how do we use some commands for NLP?

[12:22] RaviSharma: James you have given users power of Query I see now.

[12:23] RaviSharma: James, if you were or if community were to add commands, which ones would you prioritize?

[12:29] Nico Matentzoglu: What is Franz Gruff?

Added by Ken Baclawski: Gruff is a free Knowledge Graph visualization product from Franz Inc. https://allegrograph.com/products/gruff/

[12:29] Nico Matentzoglu: No commands for NLP directly in ROBOT, no

[12:32] Nico Matentzoglu: Ravi, re prioritizing commands, we do that here: https://github.com/ontodev/robot/issues It depends on the major projects at the time

[12:32] Nico Matentzoglu: But its a good question to ask in the QA later

[12:32] RaviSharma: James great tutorial a bit rushed at end but great tool and lot of capabilities, thanks.

[12:33] C.M. Alvarez: Do you have the slack link?

[12:33] RaviSharma: Chris Welcome back

[12:34] James Overton: Thanks Ravi. Yes, these slides were written for a longer presentation slot. I encourage anyone to look at the documentation site, or go over my slides more slowly: http://james.overton.ca/slides/robot-tutorial-2023/index.html

[12:35] RaviSharma: Chris, does OAK work with other than english language, same Q for James?

[12:35] Michael DeBellis: Chrome gives me a privacy

[12:36] Nico Matentzoglu: Me too. it's because you are going into a non-https side.. I didn't have that last time.

[12:36] Gary Berg-Cross: Yes, MD, but you can proceed safely

[12:36] Michael DeBellis: How does Oak compare with OWLReady2?

[12:38] James Overton: Ravi: Yes, but we could do better. We support RDF and OWL, which use Unicode and language tags, but we could do better to support multiple labels in different languages. I would *love* to do better, but I haven't had a project to fund that work.

[12:39] RaviSharma: Ken, can you kindly comment on KGSQL if it is applicable or interoperable?

Added by Ken Baclawski: KGSQL is applicable. It extends KGs with additional features that would be useful. However, KGSQL is not yet generally supported so it is not interoperable.

[12:39] James Overton: While there's some overlap, I would say that OAK is higher-level and more focused on browsing and analysis than OwlReady2.

[12:40] RaviSharma: Mike Bennett - congrats on being a technical director at OMG. Very proud of your accomplishments.

[12:40] Mike Bennett: Thanks Ravi!

[12:41] Mike Bennett: Great to see an ontology viz that uses a line for a restriction instead of a Nameless Box. Critical for business SME validation!

[12:42] RaviSharma: Chris, as compared to older GO tools how are we using OAK or ROBOT

[12:46] Vincent Vialard: Did you try the Konclude reasoner for Robot? It is both fast and complete (but not in Java)...

[12:47] James Overton: No, we haven't tried Konclude.

[12:49] Mike Bennett: An idea: would it be possible to use Robot or OAK to derive operational ontologies from a purely conceptual ontology (i.e. inserting datatypes and data surrogates for real world things)?

[12:50] StroemPhi: https://owlready2.readthedocs.io/en/v0.37/

[12:51] Chris Mungall: https://github.com/INCATools/ontology-access-kit/issues/102 - add links to other tools here!

[12:52] RaviSharma: Chris and James - appreciate your answering many or most of my Qs.

[12:53] RaviSharma: What XML capabilities are built in these commands, mostly for transport?

[12:54] James Overton: LinkML data modelling tool: http://linkml.io/

[12:59] RaviSharma: Again many thanks for two great presentations.

[12:59] C.M. Alvarez: Thanks for a great presentation!

[13:02] Thomas Exner: Thanks for the presentations. What were the other things you mentioned similar to LinkML?

[13:03] James Overton: LinkML is similar to various validation/schema languages such as JSON Schema, ShEx, and SHACL.

[13:03] Thomas Exner: Thanks.

[13:13] James Overton: XML capabilities: We use RDF/XML as our default data format, but support other RDF and OWL formats.

Resources

Previous Meetings

 Session
ConferenceCall 2023 01 25COB
ConferenceCall 2023 01 18Launch
ConferenceCall 2022 12 14Planning
... further results

Next Meetings

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