non-OBO PURLs in Foundry ontologies

[wdduncan]

Making an issue for question asked on the google group.

I am working with a group that wants to use the Behavior Change and Intervention Ontology (BCIO) in conjunction with OBO ontologies (e.g., mental functioning ontology).

If they want to submit their ontology to the OBO Foundry, do we allow these ontologies to use non-OBO PURLs? For example, BCIO has the relation 'has study sample':
http://humanbehaviourchange.org/ontology/BCIOR_000001

Although BCIO is the specific use case, there are ontologies to consider (e.g., the Common Core Ontologies or Industrial Ontologies Foundry).

Possible principles for using non-OBO purls:

• The IRI must resolve in a web browser
• PURLs not to use their own domain name
• Some kind of good-faith but strong evidence that a bespoke URL base will continue to be maintained after funding ends

I'm on the fence about this. On one hand, I like it b/c it avoids OBO ontologies duplicating work done elsewhere. But, on the other hand, it may introduce a lot of crap into the OBO Foundry space.

Perhaps we classify ontologies using non-OBO PURLs as so-called "application ontologies". I'm also in favor of permitting application ontologies to inject axioms (see discussion here).

cc @cmungall @matentzn @addiehl

[cmungall]

I don't think use of non-OBO PURLs is a deal-breaker, but with my non-OBO hat I would strongly recommend that groups do not use their own domain name in PURLs or bespoke URLs. Use an existing system like purl.org, w3id.org, or purl.obolibrary.org. For OBO, if we do allow non-OBO namespaces (see discussion on FMA), I recommend some kind of good-faith but strong evidence that a bespoke URL base will continue to be maintained after funding ends (and that good practice will be followed while you have funding). I think this is just good broad semweb practice, nothing to do with OBO per se. I would be curious to see what the reasons are for needing a bespoke URL

On Sat, Dec 21, 2024 at 11:46 AM Bill Duncan ***@***.***> wrote: Making an issue for question asked on the google group

<https://groups.google.com/g/obo-operations-committee/c/iCqfKvO6TeI/m/J3n3CLL5AAAJ?utm_medium=email&utm_source=footer&pli=1> . I am working with a group that wants to use the Behavior Change and Intervention Ontology (BCIO) <https://www.bciontology.org/> in conjunction with OBO ontologies (e.g., mental functioning ontology). If they want to submit their ontology to the OBO Foundry, do we allow these ontologies to use non-OBO PURLs? For example, BCIO has the relation 'has study sample': http://humanbehaviourchange.org/ontology/BCIOR_000001 Although BCIO is the specific use case, there are ontologies to consider (e.g., the Common Core Ontologies or Industrial Ontologies Foundry). Possible principles for using non-OBO purls: - The IRI must resolve in a web browser - PURLs not to use their own domain name - Some kind of good-faith but strong evidence that a bespoke URL base will continue to be maintained after funding ends I'm on the fence about this. On one hand, I like it b/c it avoids OBO ontologies duplicating work done elsewhere. But, on the other hand, it may introduce a lot of crap into the OBO Foundry space. Perhaps we classify ontologies using non-OBO PURLs as so-called "application ontologies". I'm also in favor of permitting application ontologies to inject axioms (see discussion here <#1443 (comment)> ). cc @cmungall <https://github.com/cmungall> @matentzn <https://github.com/matentzn> @addiehl <https://github.com/addiehl> —

…

Reply to this email directly, view it on GitHub <#2667>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMONBWR74TIBYYLOHE732GXASBAVCNFSM6AAAAABUA4XAG6VHI2DSMVQWIX3LMV43ASLTON2WKOZSG42TIMZTGQYTENI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[wdduncan]

I would strongly recommend that groups do not use their own domain name
in PURLs
Interestingly, the BCIO is part of a larger effort: The Behavioural and Social Sciences Ontology (BSSO) Foundry

The BSSOF includes many namespaces.

I recommend some kind of good-faith but strong evidence that a bespoke URL
base will continue to be maintained after funding ends

I agree. I suppose we need to assess what counts as "good-faith but strong evidence".

[ddooley]

I'll say that a mini-project in an upcoming FoodOn hackathon is to create an RDF graph of geographical names and some geographical relations extracted from Wikidata/Wikipedia for use within FoodOn and GenEpiO, taking over from past use of GAZ. So this is a case where non-OBO purls will be offered to all on a script-driven github site I think. Hope that goes down well! The Wikidata "slim" will be offered to all. If this seems problematic let me know!

[cmungall]

That sounds eminently sensible @ddooley. I don't know if there is a way for OBO to be meaningfully involved, this is more like what many of us do for conversion of biological knowledge bases

See:

• How should we standardise the use of database identifiers in OWL Axioms? #1981
• https://github.com/biopragmatics/obo-db-ingest
• https://docs.google.com/presentation/d/1aySEHTgkags7UPJYHyvQ9frYvAIqr1G5A3u7dGF26Y4/edit#slide=id.p

[matentzn]

Here is an importat warning story why never to use simple URLs for domain without a long term maintenance plan for IRIs:

#2425