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[bioontology-support] Web services: retrieving superclasses

Paolo Ciccarese paolo.ciccarese at gmail.com
Wed Apr 11 08:54:54 PDT 2012


I use BioPortal from my web-applications to perform terms search in your
catalog of ontologies.
In order for the applications to be user friendly I have the need of
'understanding' terms types.

For instance, given the PRO entry PR_000004168 (APP) I have to understand
it has superclass PR_000000001 (Protein).
If I query the webservice with:
http://rest.bioontology.org/bioportal/concepts/46956?conceptid=PR_000004168&apikey=
I get that info from the entries 'is_a' or 'SuperClass' because the entity
I am looking for is a degree away from the class PR_000000001

However if I query for the entry PR_000025533 (amyloid beta A4 protein
(mouse)):
http://rest.bioontology.org/bioportal/concepts/46956?conceptid=PR_000025533&apikey=
The 'SuperClass' or 'is_a' I get back is the previous entry PR_000004168.
This is correct as PR_000025533 is SubClass of PR_000004168. However,
PR_000025533 is also a PR_000000001 (Protein).

I was wondering if it would be possible to return in the results the
inferred superclasses up to the root within that ontology. I understand it
could be complicated in certain cases but it would be a very useful feature.

Also, why there are two entries 'is_a' and 'SuperClass'? Are they supposed
to mean different things?

Thank you for the useful services you provide,
Best regards,
Paolo

-- 
Dr. Paolo Ciccarese
http://www.paolociccarese.info/
Biomedical Informatics Research & Development
Instructor of Neurology at Harvard Medical School
Assistant in Neuroscience at Mass General Hospital
+1-857-366-1524 (mobile)   +1-617-768-8744 (office)

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