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Wikibase Community User Group/Meetings/2025-10-30

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Regular meeting of the Wikibase Community User Group.

Participants (Who is here?)

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  • Valerie WMDE
  • Laurence "GreenReaper" Parry (WBUG / WikiFur.com)
  • Ismael Olea (LaOficina/WBUG)
  • Kara

Agenda

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Notes

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From @Kbseah: Unfortunately I can't join the meeting because of time zone differences, but I'd like to introduce a database I built with Wikibase.cloud, called PPSDB: Protist-Prokaryote Symbiosis Database https://ppsdb.wikibase.cloud/. It documents symbiotic interactions between two major categories of microorganisms, protists (protozoans and algae) and prokaryotes (bacteria and archaea). My peer reviewed paper on it was published earlier this month: https://doi.org/10.1111/jeu.70049 This is not the first time someone has tried to make a database on biological interactions, but I came to this having dabbled in Wikidata and ontologies, and thought that the knowledge graph and LOD paradigms are actually very applicable here. Interactions may involve multiple partners, be context-dependent, or have other nuances that can be naturally represented in statement triples, but more cumbersome to implement in rectangular tables. Translating information from text and figures from scientific papers into formal statements in the data model made me aware of how often metadata and contextual information go unreported. When information was incomplete, it forced me be precise about where exactly the uncertainty lay, especially in statements about biological taxonomy. The native support for references and qualifiers to statements in Wikibase was vital to this project because it enables verifiability/sourcing. Federation with Wikidata was a bonus, because I could leverage the biological taxonomy tree and linked identifiers for biological taxon items in Wikidata; I also took the opportunity to create and curate relevant Wikidata items. In sharing about PPSDB here I hope others in the Wikibase community might find some of my design solutions useful (and cite my paper...), and to raise awareness of KBs and LOD in the biodiversity field. My dream is for there to be some kind of lightweight, client-side tool that allows federated searches of not just Wikibase/Wikidata but also other linked ontologies and knowledge bases, in particular the various specialist biological ontologies and taxonomy databases out there.

Chat log

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Valerie: https://etherpad.wikimedia.org/p/WBUG_2025_10_29 

15:58
kara: 👋 

16:11
Ismael Olea: o/ 
GreenReaper: Something like an https://en.wikipedia.org/wiki/Registered_association_(Germany) 

16:26
GreenReaper: https://ec.europa.eu/info/funding-tenders/opportunities/portal/screen/opportunities/calls-for-proposals?isExactMatch=true&status=31094501,31094502,31094503&order=DESC&pageNumber=1&pageSize=50&sortBy=startDate&frameworkProgramme=43251814 for example is CfPs from Creative Europe (CREA). 

16:29
GreenReaper: https://nlnet.nl/funding.html I imagine 

16:30
Ismael Olea: exactly 
Ismael Olea: NGI Zero Commons 
Ismael Olea: We sent a lovely proposal to Creative Europe and we are waiting for answer this November, but have no idea of our % success 😃 
❤️
16:34
kara: I need to drop off. Thanks for letting me listen in ! 

16:41
Ismael Olea: CIDOC-CRM 4 Wikibase instance demo: https://tmp-18769876427228.wikibase.cloud/wiki/Main_Page
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