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

12:00 - 12:30 James Overton ROBOT: A command line tool to automate ontology workflows Slides
12:30 - 12:40 Chris Mungall Ontology Access Kit (OAK) Slides
12:40 - 13:00 Discussion
Video Recording

Conference Call Information

Date: Wednesday, 01 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 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

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

Next Meetings

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

ConferenceCall 2023 02 01: Difference between revisions

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