v0.2 discussion tracking

[sherwoodf]

Branch with working example, and metadata: https://github.com/BioImage-Archive/gide-search/tree/input_rocrate_02/resources/rocrate/example-target-detached-rocrate-v0.2

Suggested discussion points for Thursday 2026/01/29:

• How we should reference non-published bio schemas types
• Context hosting? (for now use local)
• Should we use schema:name or dwc:scientificName for Taxons: scientificName
• Whether LabProtocol is the correct type for capturing Image Acquisition procedures
• Agreements on some of the more flaky string keywords if we want to use those at all (e.g. if we are keen on file size, or if we want to use http://www.w3.org/ns/dx/prof/hasRole )
• Do we want to include CRediT role for the author? [ optional]
• Run through Cardinality and Requirement level for fields to flag an immediately obvious changes (i'll keep working on the brach above tomorrow, so probably best to wait until the meeting for us to do this).
• Should identifier be required on the base dataset? [yes - required]

[lubianat]

really liked the profile on the branch! super complete

the SHOULDs, MUSTs and recommendeds all seem very reasonable.

I have just one comment, but that is again a bit nit picky:

where X can be a number of different relations (e.g. hasCellLine). If the connetion obj - X -> DefinedTerm is present, and Dataset - about/measurementMethod -> obj, then Dataset - about/measurementMethod -> DefinedTerm MUST also be included explicitly.

I got confused for a split second because in SPARQL property paths, "/" is syntax for chaning like Dataset --> about --> Y --> measurementMethod --> DefinedTerm. In SPARQL, we would have "|" indicate the alternate paths: Dataset - about | measurementMethod -> DefinedTerm.

I don't think it needs changing though, because the meaning is clear from context

[lubianat]

also little typo thumnailUrl --> thumbnailUrl

[kkyoda]

I created one example for SSBD:database. When I checked it with rocrate-validator, an error was reported for labEquipment, so I modified it as shown below.

"bioschemas": "https://bioschemas.org/terms/",
"labEquipment": {
  "@id": "bioschemas:labEquipment"
}

In addition, for measurementTechnique in #imaging-protocol, it was necessary to specify multiple FBbi terms, so I used square brackets [] as shown below.

            "measurementTechnique": [
                {
                        "@id": "http://purl.obolibrary.org/obo/FBbi_00000251"
                },
                {
                        "@id": "http://purl.obolibrary.org/obo/FBbi_00000249"
                }
            ],

ro-crate-metadata.json

[kkyoda]

Please try updating the @context URL in the above JSON file from
https://w3id.org/ro/crate/1.1/context
to
https://w3id.org/ro/crate/1.2/context.

[kkyoda]

@sherwoodf, I checked with rocrate-validator, and it seems that the following description may be required. However, since the validation is based on version 1.1, I am not entirely confident about this.

    "@context": [
        "https://w3id.org/ro/crate/1.2/context",
        {
            ...
            "taxonomicRange": {
                "@id": "http://schema.org/taxonomicRange"
            },
            ...
        }
    ],

[sherwoodf]

ah, good catch. I think taxonomicRange is included in the 1.2 context but not the 1.1. However, it still shouldn't error from what i know of the validator. I will double check i've not made a typo or something else...

[lubianat]

@sherwoodf I noticed the IDR "thumbnailUrls" do not serve thumbnails (https://idr.openmicroscopy.org/webclient/img_detail/1239777/)

instead https://idr.openmicroscopy.org/webgateway/render_thumbnail/1239777/ seems to be the service URL

should we use that instead?

[sherwoodf]

Ah yes, that looks like it would be better. I can update it in my next PR

[lubianat]

Another thought:

https://schema.org/copyrightNotice could be useful too. It is a plain text field for copyright notices.

IDR always provides the informaiton:

Copyright: Ledesma-Fernandez et al for https://idr.openmicroscopy.org/study/idr0011/

We can combine it for, say, "Ledesma-Fernandex et al, 2017, CC BY 4.0" or similar.

I am finding it difficult when porting the images around to know who owns the copyright there (is it all authors? one specific? all of them but one should be mentioned prominently?) If the resource has the answer for that (as IDR does) it may be helpful for reuse