Wikidata integration?

[photocyte]

My introduction & practical knowledge about linked data & triplestores etc, is via Wikidata.org . Might it be possible to mirror / sync the labware-databank ontology and individuals into Wikidata? That would provide a independent git-free way to add to the databank.

See here for an example of a wikidata individual:
https://www.wikidata.org/wiki/Q622664

[rpgoldman]

The concern with integrating via Wikidata is that Wikidata is very casually curated, and has very weak semantics.

If you take an OWL database and inadvertently add into it data that is poorly formulated, the entire thing can become corrupted.

Also, AFAIK Wikidata uses only RDF Schema, which means that there are things we can say in the Labware ontology that we cannot say in Wikidata.

I think a more appropriate way to integrate with Wikidata would be to find interesting bits of the very large existing Wikidata corpus and link it to the labware ontology. Then we could say, effectively, "this Wikidata entity (or class) is the same as that entity (or class) in the labware ontology." We could also, I believe, make additional statements about Wikidata entities and our entities (e.g., "this piece of equipment mentioned in Wikidata can accept this kind of microplate or is compatible with microplates that meet this description.")

I'm very much in favor of letting people build whatever they want on the labware ontology, but I agree with Jake that it's important that there be a canonical part of the ontology that is carefully curated and that can be used with high confidence

[photocyte]

Thanks for the info Robert! Useful to know. My only other 2 cents is properties can be added to Wikidata, so if there are especially useful triples to have directly represented in Wikidata, they can be proposed. Here is one such property that I proposed some time back:
https://www.wikidata.org/wiki/Wikidata:Property_proposal/has_sequenced_genome

Regarding encoding instruments. I've been poking around with doing that in Wikidata, here is an example:
https://www.wikidata.org/wiki/Q117052293

[markdoerr]

Thanks Tim (@photocyte), for the proposal,
I agree with Robert (@rpgoldman ) that Wikidata is be too limited in "expressebility". Nonetheless we might consider in the future to sync some of our most widely used labware with Wikidata (as you illustrated with the WellJet esample).
Regarding adding references to wikidata/wikipedia, I already started, with wikipedia (there is a very convenient support, I am using). I will also consider adding references to wikidata, if I find an easy way to find the IDs ;)

[photocyte]

I've been thinking a lot about filter plates lately. This is as far as I can get on Wikidata for representing two individual pieces of labware:

AcroPrep 24-well Filter Plate 30-40um PP/PE Filter

Cytiva Whatman UNIFILTER 24-Well Microplate ‒ 10 mL with Whatman GF/C filter media1

For the AcroPrep, Pall won't share the technical drawings, so I can't put much real information there.
For the UNIFILTER, Cytiva did share the technical drawings, so was able to put in the width/depth/height triples.

It pretty quickly broke down. I.e. I'd like to put in the vendor catalog number for these plates, but there isn't a wikidata property for such a thing yet... Although there is a Wikidata item but not a property: https://www.wikidata.org/wiki/Q399757

[photocyte]

Okay, I've gone ahead and collated all the multi-well plate manufactures that I've been able to track down (I've been stuck at home with nothing to do). See link below for table of said manufacturers:

Wikidata microplate manufacturer SPARQL query

How would one use this in the labware-databank?

[photocyte]

I've proposed a Wikidata Property for a generic stock keeping unit as I've found that would be useful for describing labware individuals. Comments welcome:

https://www.wikidata.org/wiki/Wikidata:Property_proposal/stock_keeping_unit

I think it's relatively straightforward to propose and get a Wikidata Property approved. The real trick would be making the Wikidata representation of the company / other factors (using "qualifiers") compatible with the rest of the RDF/OWL/federated ecosystem & the LabOP databank ontology.

[photocyte]

Pg. 26 and onwards of this slide deck suggested https://shex.io as a way to have more use of schema's on Wikidata.

https://upload.wikimedia.org/wikipedia/commons/f/fb/Obo_Wikidata_at_Biocuration_2023.pdf

I have no idea if that makes Wikidata expressive enough to match what Labware ontology could do.