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Property vs class vs range and VPConnection #2

Open mroos opened 3 weeks ago

mroos commented 3 weeks ago

In the onboarding documentation of Guideline (and maybe other elements too), everything is called a 'Property' (see https://vp-onboarding-doc.readthedocs.io/en/latest/level_1/properties/guideline.html#guideline).

Am I right that in the metadata schema, VPDiscoverable is defined as an owl:Class and subclass of VPConnection, subclass of DUO's 'data use modifier' < 'data entity' < 'information content entity' << 'continuant' << 'entity' in IAO/BFO?

In the onboarding documentation it is stated that the Range of the VPConnection Property (?) is VPDiscoverable, but does that make sense if VPDiscoverable is defined as a subclass of VPConnection?

I copied the section form the metadata model below, and below that the section from the onboarding documentation.

FWIW

-- snippet from https://w3id.org/ejp-rd/vocabulary --

<owl:Class rdf:about="https://w3id.org/ejp-rd/vocabulary#VPConnection">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000017"/>
    <rdfs:label>VPConnection</rdfs:label>
    <owl:deprecated>true</owl:deprecated>
</owl:Class>

<!-- https://w3id.org/ejp-rd/vocabulary#VPDiscoverable -->

<owl:Class rdf:about="https://w3id.org/ejp-rd/vocabulary#VPDiscoverable">
    <rdfs:subClassOf rdf:resource="https://w3id.org/ejp-rd/vocabulary#VPConnection"/>
    <rdfs:label>VPDiscoverable</rdfs:label>
    <owl:deprecated>true</owl:deprecated>
</owl:Class>

-- snippet from https://vp-onboarding-doc.readthedocs.io/en/latest/level_1/properties/guideline.html#guideline --

VP Connection |  This property is attached to every portion of your Metadata record that you wish the VP to explore (e.g. Dataset X, Data Service Y, but NOT Dataset Z). If you do not add this tag to at least the description of your resource, you will not be onboarded. The range is https://w3id.org/ejp-rd/vocabulary#VPDiscoverable

markwilkinson commented 3 weeks ago

Hi! No, that's not correct.  Dcterms: type should be, in the best case,  child of edam:operation (from my recollection).For Beacon services, we have ejp: Beacon2_individuals/catalog/biosample as the range for dcterms:type, which (unless I made an error) are children of edam: operation in the EJP ontology.Hope that helps! MOn Aug 18, 2024 12:13, Marco @.***> wrote: Is the property 'dcterms:type', with dcat:DataService as Domain and VPConnection as Range? I found that somewhere in an example FDP. Henceforth, is this correct in the draft of the Deliverable 12.04? • Beacon-2 Discovery services: resources in the VP network are programmatically discoverable by minimally offering search operations conforming to the GA4GH Beacon-2 framework [6] and denoting this by instantiating a dcat:DataService with the dcterms:type property set to ‘VPBeacons2’. In the final release of the VP by the EJP RD ‘’ can be ‘catalog’ (searches on the description of a resource) and ‘individuals’ (searches on the types of data records that a resource gives access to under defined conditions, and some values). The set of targets is extended in the VP labs, starting with the resource types of section 5.1.1.1.1 NB should we add an issue for future, post-EJP RD, work to add example RDF snippets to the documentation? - unless this is already there I did not find it yet of course.

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markwilkinson commented 3 weeks ago

(by the way, this use of dcterms:type is what is recommended by DCAT for description of services... Including in the documented examples.  We didn't make it up ;-) )MOn Aug 18, 2024 12:13, Marco @.***> wrote: Is the property 'dcterms:type', with dcat:DataService as Domain and VPConnection as Range? I found that somewhere in an example FDP. Henceforth, is this correct in the draft of the Deliverable 12.04? • Beacon-2 Discovery services: resources in the VP network are programmatically discoverable by minimally offering search operations conforming to the GA4GH Beacon-2 framework [6] and denoting this by instantiating a dcat:DataService with the dcterms:type property set to ‘VPBeacons2’. In the final release of the VP by the EJP RD ‘’ can be ‘catalog’ (searches on the description of a resource) and ‘individuals’ (searches on the types of data records that a resource gives access to under defined conditions, and some values). The set of targets is extended in the VP labs, starting with the resource types of section 5.1.1.1.1 NB should we add an issue for future, post-EJP RD, work to add example RDF snippets to the documentation? - unless this is already there I did not find it yet of course.

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markwilkinson commented 3 weeks ago

(for the EURO-NMD ontology I did the same thing and created terms for every one of their KPI calculations that inherit from edam... I'm trying to be consistent 😀)MOn Aug 18, 2024 12:13, Marco @.***> wrote: Is the property 'dcterms:type', with dcat:DataService as Domain and VPConnection as Range? I found that somewhere in an example FDP. Henceforth, is this correct in the draft of the Deliverable 12.04? • Beacon-2 Discovery services: resources in the VP network are programmatically discoverable by minimally offering search operations conforming to the GA4GH Beacon-2 framework [6] and denoting this by instantiating a dcat:DataService with the dcterms:type property set to ‘VPBeacons2’. In the final release of the VP by the EJP RD ‘’ can be ‘catalog’ (searches on the description of a resource) and ‘individuals’ (searches on the types of data records that a resource gives access to under defined conditions, and some values). The set of targets is extended in the VP labs, starting with the resource types of section 5.1.1.1.1 NB should we add an issue for future, post-EJP RD, work to add example RDF snippets to the documentation? - unless this is already there I did not find it yet of course.

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mroos commented 3 weeks ago

@markwilkinson thank you for the clarification here and in the call today.

Would you be able to point me to the definition of ejprd:vpConnection? I find the VPConnection class, but not the vpConnection property. I do find the property used in the RDF of existing FDPs.