Question about Oral Health and Disease Ontology

[Michael DeBellis]

I want to reuse classes from the OHD ontology in an ontology I'm helping someone develop in Protege. I started with the Dental Procedure class. Normally, what I do is first add the IRI to the ontology prefixes tab in the active ontology tab. E.g., to use rdfs:label (this is already preconfigured in Protege but just to use a common example) the tab in Protege has the pairing: 

Prefix       Value

rdfs           http://www.w3.org/2000/01/rdf-schema#

And then when I enter rdfs:label in Protege it knows to create the IRI: http://www.w3.org/2000/01/rdf-schema#label   

But I'm confused as to how to do this for the OHD ontology. The IRI for the Dental_Procedure class is:  http://purl.obolibrary.org/obo/OHD_0000005

However, the IRI for the ontology is: http://purl.obolibrary.org/obo/ohd.owl This is from the top of the home page for the ontology: https://ontobee.org/ontology/OHD If I use that IRI with the last part of the Dental_Procedure IRI I would end up with:

http://purl.obolibrary.org/obo/ohd.owlOHD_0000005 

I'm guessing that what I want to do is:

Prefix       Value

ohd           http://purl.obolibrary.org/obo/OHD_

and then use 0000005 for the Dental_Procedure class, is that correct?

Thanks,

Michael

https://www.michaeldebellis.com/blog 

[James A. Overton]

Hi Michael,

Yes, it's common practise in the OBO community to do exactly what you said: define a prefix "OHD" which expands to "http://purl.obolibrary.org/obo/OHD_", and then use identifiers (called "CURIE"s) such as "OHD:0000005".

There's a good technical reason why the "#" is appropriate for small ontologies by not for large ones. When you put the URL "http://www.w3.org/2000/01/rdf-schema#label" into your browser, it will fetch the full resource at "http://www.w3.org/2000/01/rdf-schema" and then scroll to a section identified by the part after "#", e.g. "label". RDF Schema is small, so downloading all of "http://www.w3.org/2000/01/rdf-schema" every time is not a problem. But many OBO ontologies are much larger, dozens or hundreds of megabytes, so this approach becomes infeasible.

Instead we provide a URL to download the full resource, e.g. the OWL file at "http://purl.obolibrary.org/obo/ohd.owl", and also URLs for each term, such as "http://purl.obolibrary.org/obo/OHD_0000005". The term URL identifies the term and also links to an ontology term browser (such as Ontobee) that provides more information about that term.

There's lots of documentation on topics like this at <https://oboacademy.github.io/obook/>, but I didn't find an article to answer your specific question. This Ontobee-discuss mailing list might not be the best place for this sort of question. The OBO Community Slack is a good place, if you use Slack <https://obo-communitygroup.slack.com/archives/C01DP18L5GW>. 

Best,

James

On Jan 26, 2023, at 13:52, Michael DeBellis <mdebe...@gmail.com> wrote:

I want to reuse classes from the OHD ontology in an ontology I'm helping someone develop in Protege. I started with the Dental Procedure class. Normally, what I do is first add the IRI to the ontology prefixes tab in the active ontology tab. E.g., to use rdfs:label (this is already preconfigured in Protege but just to use a common example) the tab in Protege has the pairing: 

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[Michael DeBellis]

Excellent. Thanks James  I'll come back if I have more questions but that makes sense and I think I get it. 

Michael