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EBISPOT / OLS

Ontology Lookup Service from SPOT at EBI
http://www.ebi.ac.uk/ols
Apache License 2.0
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"Ontology history" ... tweak needed? #148

Open joncison opened 7 years ago

joncison commented 7 years ago

Hi Jupp

The ontology history in http://www.ebi.ac.uk/ols/ontologies/edam is potentially extremely useful, but I'm not sure it's capturing the changes made to EDAM, e.g.

Cheers!

simonjupp commented 7 years ago

Hi Jon, We looked into this. OLS detects obsoletes in one of two ways

1 - terms that are subclasses of http://www.geneontology.org/formats/oboInOwl#ObsoleteClass 2 - Terms that have an annotation property http://www.w3.org/2002/07/owl#deprecated "true"

In EDAM we don't recognise your deprecated class, where did you get that from? I also note that in the past you had been using method 2, but you seemed to have stopped doing this for the past few releases. So you need to do either 1 or 2 and it will start detecting them again. I spoke to @hmenager about this briefly the other night.

For term tracking we bundle all the synonyms into one synonym field.

joncison commented 7 years ago

Strange, we haven't stopped using method 2 (take a peak in EDAM.owl and you'll see, e.g. search for <obsolete_since>1.17</obsolete_since>.

For 1., see https://www.w3.org/TR/owl-ref/#Deprecation : I think OLS maybe should support this?

We do use some oboInOwl stuff though. Is there something I should be doing different ? Thanks!

simonjupp commented 7 years ago

Strange, this isn't in the OWL 2 syntax spec https://www.w3.org/TR/owl2-syntax/. I don't think it is supported properly by OWL API or Protege either. owl:DeprecatedClass is a metaclass, so you shouldn't be subclassing it. Basically doing option 2 is the recommended way and the way most other ontologies are doing it now.

Need to investigate further why this class is detected as obsolete but not being picked up by our term tracker. https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Foperation_0311

joncison commented 7 years ago

Cool, thanks. I can easily strip out the subclassing of owl:DeprecatedClass, and just rely on 2 above (once I'm satisfied things look nice in OLS, BioPortal etc.)