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[bioontology-support] Web services: retrieving superclasses

Trish Whetzel whetzel at stanford.edu
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: 
http://rest.bioontology.org/bioportal/virtual/rootpath/1062/PR%3A000025533?apikey=YourAPIKey

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. 

Trish 


[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Term_services
[2] http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_paths_to_root.2Fleaves_from_a_concept_in_the_latest_version_of_a_given_ontology



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:
> 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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Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378
http://www.bioontology.org

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