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Wikidata integration #1905

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dosumis opened this issue Mar 21, 2023 · 10 comments
Open
3 tasks

Wikidata integration #1905

dosumis opened this issue Mar 21, 2023 · 10 comments
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@dosumis
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dosumis commented Mar 21, 2023

EPIC ticket with some suggestions for better wikidata integration. This should be discussed on a future CL call where we agree which items in this epic should be turned into separate tickets. This issue can be closed once all items have been discussed and we've decided which to implement.

Currently mapped terms with Wikipedia links, as known to wikidata: https://w.wiki/6WGX
Currently mapped terms regardless of Wikipedia links: https://w.wiki/7x$K

@dosumis dosumis self-assigned this Mar 21, 2023
@dosumis dosumis added the Epic label Mar 21, 2023
@lubianat lubianat self-assigned this May 1, 2023
@lubianat
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lubianat commented May 1, 2023

Some Wikidata constraint checks in CL mappings:

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This issue has not seen any activity in the past 6 months; it will be closed automatically in one year from now if no action is taken.

@gouttegd
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I’ll investigate the possibility of using SSSOM for that. If we can somehow get a SSSOM mapping set (either directly from Wikidata or possibly through mapping-commons), we could easily derive a component ready to be imported into CL.

@lubianat
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@gouttegd that sounds very doable; I'll work on deriving this SSSOM mapping set,

@lubianat
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@gouttegd here is the SPARQL query for the minimal SSSOM set: https://w.wiki/7x$C

something like:

subject_id predicate_id object_id match_type
wd:Q116343126 skos:closeMatch http://purl.obolibrary.org/obo/CL_0000735 Complex
wd:Q116446765 skos:closeMatch http://purl.obolibrary.org/obo/CL_0000744 Complex

(...)

And here is a Wikipedia-only version of the set: https://w.wiki/7x$S

@lubianat
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I've just found this by @dosumis from ~8 years ago: https://github.com/OBOFoundry/obo_wikidata_mapping

Might be relevant.

@matentzn
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cc @andrawaag FYI

@lubianat
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Comming back here, did we have any updates on this? The (basic) SSSOM mapping to add to CL was done, but I am not sure if we have a pipeline in place to generate ontology changes from that. @gouttegd do you have any thoughts?

@gouttegd
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I had no time to work on that until now, but I should be able to find it now that the whole overhaul of Uberon’s composite-metazoan is done. And the upcoming ODK 1.5 will come with the SSSOM plugin built-in, so deriving a component from the SSSSOM set should be easy.

@lubianat
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Nice! Thank you for the reply, @gouttegd. I'll likely talk about that in Biocuration 2024 in India, good to know we have a plan :)

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