Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Web services: retrieving superclasses

Trish Whetzel whetzel at
Fri Apr 20 11:37:08 PDT 2012

Hi Paolo, 

In your first example below, using the "Get Term" web service call [1], it is intended to only provide information on direct super and subclasses. 

However, if you would like to get ancestors of a term you can use the "Get paths to root/leaves" [2] web service call. For example to get parents of PR_000025533 (amyloid beta A4 protein (mouse)) use:

If you want to get inferred parent terms, then the inferred version of PRO needs to be loaded.

As far as the duplicate entries for 'is_a' and 'SuperClass', I believe that is an artifact of the underlying data representation and they do not have different meanings. 



On Apr 11, 2012, at 8:54 AM, Paolo Ciccarese wrote:

> 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:
> 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)):
> 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
> 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)
> CONFIDENTIALITY NOTICE: This message is intended only for the addressee(s), may contain information that is considered
> to be sensitive or confidential and may not be forwarded or disclosed to any other party without the permission of the sender. 
> If you have received this message in error, please notify the sender immediately.
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

"Like" NCBO on Facebook:

Follow NCBO on Twitter:!/bioontology

Join in Discussions on LinkedIn:

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>

More information about the bioontology-support mailing list