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! scope="row" rowspan="3" | Date/Time
! scope="row" rowspan="3" | Date/Time
| [[has date::21 Mar 2023 15:00 GMT]]
| [[has date::22 Mar 2023 16:00 GMT]]
|-
|-
| 8:00am PDT/11:00am EDT
| 9:00am PDT/12:00pm EDT
|-
|-
| 3:00pm GMT/4:00pm CST
| 4:00pm GMT/5:00pm CST
|-
! scope="row" | Convener
| [[convener::GaryBergCross|Gary Berg-Cross]]
|}
|}


= OBO Academy with WikiData =
= [[OntologySummit2023|Ontology Summit 2023]] {{#show:{{PAGENAME}}|?session}} =
{{:OntologySummit2023/Description}}


== Agenda ==
== Agenda ==
* '''Andra Waagmeester''' and '''Tiago Lubiana''' will be presenting ''Introduction to WikiData''
* '''[[GaryBergCross|Gary Berg-Cross]]''' ''Followup of OBO Academy with Wikidata'' [https://bit.ly/42A0FNh Slides]
* Wikidata is the all-purpose knowledge graph of the Wikimedia Foundation, available for anyone to query and to edit. Over the past 10 years, Wikidata has grown as a Linked Open Data hub in the web, providing structured information for Wikipedia, for the Google Knowledge graph and beyond. In this webinar, two Wikidata editors specialized in the life sciences domain will present the inner working of Wikidata, how anyone can connect their research information (and metainformation) to the platform, and how it can further connect OBO ontologies with society.
* Discussion to follow the [[ConferenceCall_2023_03_21|Introduction to Wikidata]]
* '''Tiago Lubiana''' is a PhD Candidate in computational biology at the University of São Paulo, studying modelling of cell types in the context of the Human Cell Atlas and Wikidata. He is a member of the Brazilian NGO Wiki Movement Brazil, as well as an active member of the Cell Ontology and the International Society for Biocuration.
* [https://bit.ly/3U3uXUs Video Recording]
* '''Andra Waagmeester''' is a linked/FAIR data jack of all trades. His main focus of work is on linked data and curation pipelines in Biomedical and Biodiversity projects. Andra has also been involved in the Gene Wiki project. Between 2014 and 2022 Gene Wiki build and maintained a family of bots and pipelines to align wikidata with public data sources on genes, proteins, diseases and chemical compounds. Some of those resources were OBO ontologies.
* Sponsored by the Monarch Initiative OBO Academy: [https://oboacademy.github.io/obook/courses/monarch-obo-training/]


== Conference Call Information ==
== Conference Call Information ==
* Date: '''Wednesday, 21 Mar 2023'''  
* Date: '''Wednesday, 22 Mar 2023'''  
* Start Time: 8:00am PDT / 11:00am EDT / 4:00pm CET / 3:00pm GMT / 1500 UTC
* Start Time: 9:00am PDT / 12:00pm EDT / 5:00pm CET / 4:00pm GMT / 1600 UTC
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=03&day=21&year=2023&hour=11&min=00&sec=0&p1=179 World Clock]
** ref: [http://www.timeanddate.com/worldclock/fixedtime.html?month=03&day=22&year=2023&hour=12&min=00&sec=0&p1=179 World Clock]
** Note: The US and Canada are on Daylight Saving Time while Europe has not yet changed.
** Note: The US and Canada are on Daylight Saving Time while Europe has not yet changed.
* Expected Call Duration: 1 hour
* Expected Call Duration: 1 hour
* Conference Call Information
{{:OntologySummit2023/ConferenceCallInformation}}
** Zoom Meeting [https://lbnl.zoom.us/j/98450763854?pwd=N2lhajNMNER0ekZVaFlyWFM2TXUwZz09]
 
** Meeting ID: 984 5076 3854
== Attendees ==
** Passcode: wikidata
* Aleix Puig
** For more information see [[ConferenceCall_2023_03_21/ConferenceCallInformation]]
* Alexander Diehl
* [[AlexShkotin|Alex Shkotin]]
* Arwa Ibrahim
* Asiyah Yu Lin - NIAID
* Chris Kindermann
* Emily Hatley
* [[FanLi|Fan Li]]
* [[GaryBergCross|Gary Berg-Cross]]
* [[JamesOverton|James Overton]]
* Jie Zhang
* [[KenBaclawski|Ken Baclawski]]
* Michelle McGee
* Nancy Wiegand
* [[RobertRovetto|Robert Rovetto]]
* Ronglin Wang
* Sierra Moxon
* Tiago Lubiana
* Vincent Vialard
 
== Discussion ==
=== Vaccine Ontology ===
 
[09:16] Tiago Lubiana: Now the scraper has run, here is the auto mappings and suggestions for the Vaccine Ontology: https://mix-n-match.toolforge.org/#/catalog/5849
 
[09:19] Asiyah Yu Lin - NIAID: Tiago, we could work with you on VO and Wikidata. I will connect you with Oliver He.
 
[09:20] Tiago Lubiana: Thanks Asiyah! I set up the mapping infrastructure, but I cannot actually work on that for the moment. Hopefully in the future!
 
[09:21] Asiyah Yu Lin - NIAID: I believe that's the same for Oliver. A lot on plate now. I will circle back to you.
 
=== Wikidata Disambiguation ===
 
[09:33] Vincent Vialard: having worked on entity disambiguation using addresses, i can testify that places are NOT well defined in wikidata. it checks most of the issues listed by gary...
 
[09:36] Tiago Lubiana: There is some discussion on schemas on subdomains here: https://www.wikidata.org/wiki/Wikidata:WikiProject_Schemas
 
=== Detecting Misinformation ===
 
[09:38] Tiago Lubiana: yep, that is a good point. It is relatively simple to go back and fix once bullshit is spotted, though
 
[09:39] James Overton: I accept Vincent's point that stuff like ChatGPT generates BS that can be harder to my BS detector to detect.
 
[09:40] Tiago Lubiana: one thing that Wikidata has that is kind of unique is the open "Discussion" forums on each entry on Wikidata, where people can agree and disagree on an entity-by-entity basis
 
[09:44] Tiago Lubiana: @Vincent this article discusses just that: classes, metaclasses and ontological disarray on Wikidata: https://nemo.inf.ufes.br/wp-content/papercite-data/pdf/type_or_individual_evidence_of_large_scale_conceptual_disarray_in_wikidata_2021.pdf
 
[09:45] Tiago Lubiana: Also, people are working on subsetting Wikidata to extract subdomains that might be more structured using ShEx: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation
 
[09:46] Tiago Lubiana: It is searchable in SPARQL, so it can be converted in RDF
 
=== Literals ===
 
[09:50] Tiago Lubiana: I don't know if I understood it completely the question, James, sorry!
 
Here are the Wikidata dumps: https://www.wikidata.org/wiki/Wikidata:Database_download
 
Wikibase has some different datatypes that might play the role of Literals: https://www.wikidata.org/wiki/Help:Data_type
 
[09:51] James Overton: No worries. Your answer was good! Thanks
 
=== Wikidata Channel ===
 
[09:51] Tiago Lubiana: (I do have to leave now, unfortunately, thank you for opening this space! We have a Wikidata channel in the OBO slack by the way, if anyone has other questions: https://obo-communitygroup.slack.com/archives/C0440CBHYA3)
 
=== KGSQL ===
 
[09:52] Vincent Vialard: https://ken.baclawski.com/pub/2021/47/public.pdf
 
=== DBPedia ===
 
[09:56] James Overton: This page discusss DBPedia and Wikidata, but I'm still a bit confused: https://meta.wikimedia.org/wiki/Wikidata/Notes/DBpedia_and_Wikidata
 
== Resources ==
* [https://bit.ly/3U3uXUs Video Recording]
* [https://youtu.be/QmoPpXV74nQ Video Recording on YouTube]


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

Latest revision as of 16:36, 1 June 2023

Session Wikidata
Duration 1 hour
Date/Time 22 Mar 2023 16:00 GMT
9:00am PDT/12:00pm EDT
4:00pm GMT/5:00pm CST
Convener Gary Berg-Cross

Ontology Summit 2023 Wikidata

Helping scientific researchers make better use of ontologies

Agenda

Conference Call Information

  • Date: Wednesday, 22 Mar 2023
  • Start Time: 9:00am PDT / 12:00pm EDT / 5:00pm CET / 4:00pm GMT / 1600 UTC
    • ref: World Clock
    • Note: The US and Canada are on Daylight Saving Time while Europe has not yet changed.
  • Expected Call Duration: 1 hour
  • Video Conference URL
    • Conference ID: 837 8041 8377
    • Passcode: 323309
  • Chat Room

The unabbreviated URLs are:

Attendees

Discussion

Vaccine Ontology

[09:16] Tiago Lubiana: Now the scraper has run, here is the auto mappings and suggestions for the Vaccine Ontology: https://mix-n-match.toolforge.org/#/catalog/5849

[09:19] Asiyah Yu Lin - NIAID: Tiago, we could work with you on VO and Wikidata. I will connect you with Oliver He.

[09:20] Tiago Lubiana: Thanks Asiyah! I set up the mapping infrastructure, but I cannot actually work on that for the moment. Hopefully in the future!

[09:21] Asiyah Yu Lin - NIAID: I believe that's the same for Oliver. A lot on plate now. I will circle back to you.

Wikidata Disambiguation

[09:33] Vincent Vialard: having worked on entity disambiguation using addresses, i can testify that places are NOT well defined in wikidata. it checks most of the issues listed by gary...

[09:36] Tiago Lubiana: There is some discussion on schemas on subdomains here: https://www.wikidata.org/wiki/Wikidata:WikiProject_Schemas

Detecting Misinformation

[09:38] Tiago Lubiana: yep, that is a good point. It is relatively simple to go back and fix once bullshit is spotted, though

[09:39] James Overton: I accept Vincent's point that stuff like ChatGPT generates BS that can be harder to my BS detector to detect.

[09:40] Tiago Lubiana: one thing that Wikidata has that is kind of unique is the open "Discussion" forums on each entry on Wikidata, where people can agree and disagree on an entity-by-entity basis

[09:44] Tiago Lubiana: @Vincent this article discusses just that: classes, metaclasses and ontological disarray on Wikidata: https://nemo.inf.ufes.br/wp-content/papercite-data/pdf/type_or_individual_evidence_of_large_scale_conceptual_disarray_in_wikidata_2021.pdf

[09:45] Tiago Lubiana: Also, people are working on subsetting Wikidata to extract subdomains that might be more structured using ShEx: https://www.semantic-web-journal.net/content/wikidata-subsetting-approaches-tools-and-evaluation

[09:46] Tiago Lubiana: It is searchable in SPARQL, so it can be converted in RDF

Literals

[09:50] Tiago Lubiana: I don't know if I understood it completely the question, James, sorry!

Here are the Wikidata dumps: https://www.wikidata.org/wiki/Wikidata:Database_download

Wikibase has some different datatypes that might play the role of Literals: https://www.wikidata.org/wiki/Help:Data_type

[09:51] James Overton: No worries. Your answer was good! Thanks

Wikidata Channel

[09:51] Tiago Lubiana: (I do have to leave now, unfortunately, thank you for opening this space! We have a Wikidata channel in the OBO slack by the way, if anyone has other questions: https://obo-communitygroup.slack.com/archives/C0440CBHYA3)

KGSQL

[09:52] Vincent Vialard: https://ken.baclawski.com/pub/2021/47/public.pdf

DBPedia

[09:56] James Overton: This page discusss DBPedia and Wikidata, but I'm still a bit confused: https://meta.wikimedia.org/wiki/Wikidata/Notes/DBpedia_and_Wikidata

Resources

Previous Meetings

 Session
ConferenceCall 2023 03 21Wikidata
ConferenceCall 2023 03 15Design Patterns
ConferenceCall 2023 03 08Modules and Patterns
... further results

Next Meetings

 Session
ConferenceCall 2023 03 29Synthesis
ConferenceCall 2023 04 05Science on Schema.org
ConferenceCall 2023 04 12Panel
... further results
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