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OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
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custom synonym/definition properties in YAML #162

Open simonjupp opened 8 years ago

simonjupp commented 8 years ago

I’ve noticed a few ontologies coming from OBO (MAMO and KISAO specifically) are using SKOS for prefLabel, synonym and definitions. If we are going to get the config for these from OBO then it would be good to have this info in that config.

OLS config supports the following

label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property:

If these were present in for example the mamo.md would they make it to the master YAML file?

cmungall commented 8 years ago

On 4 Nov 2015, at 5:28, simonjupp wrote:

I’ve noticed a few ontologies coming from OBO (MAMO and KISAO specifically) are using SKOS for prefLabel, synonym and definitions. If we are going to get the config for these from OBO then it would be good to have this info in that config.

+1

In an ideal world we would all use the same vocab, but that hasn't happened.

OLS config supports the following

label_property: http://www.w3.org/2004/02/skos/core#prefLabel definition_property:

would you list the 4 obo properties here? I assume OLS needs to collapse these from the POV of supporting autocomplete etc, but preserve the original property for display?

If these were present in for example the mamo.md would they make it to the master YAML file?

Yes. No special code is required, it's all mirrored faithfully

Reply to this email directly or view it on GitHub: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/162

cmungall commented 7 years ago

I see no other comments, I am in favor of implementing this. Just need the answer to one 1: For the oio vocab, would we add 4 props each time? Or could we have some shorthand for this?

simonjupp commented 7 years ago

Do you mean for the 4 different synonym predicates? I guess by default applications should assume oio predicates for everything so you shouldn't need to specify this for every ontology. Then use this field as flag for cases where a particular ontology wants to force a limited or different set of predicates to be used.

cmungall commented 7 years ago

OK, I'm good with that

nlharris commented 4 years ago

did this happen?

alanruttenberg commented 4 years ago

Sounds like a good idea to me (include the info in the config) The alternative is to normalize as part of the build process - some ROBOT task. Alan

On Tue, Jun 16, 2020 at 12:35 PM Nomi Harris notifications@github.com wrote:

did this happen?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/162#issuecomment-644876575, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAB3CDQWXDCFY5QRTO2HO2DRW6NNRANCNFSM4BTO6INQ .

nlharris commented 2 months ago

Can this be closed?

cmungall commented 2 months ago

It's useful, it has not been done. It's not clear all the metadata has to live on the OBO side vs OMO properties to indicate which OMO Profile is followed

nlharris commented 2 months ago

Ok, just trying to see if any of these very old tickets could be closed. I'll leave this one alone for another few years.