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[bioontology-support] Web services: retrieving superclasses

Paolo Ciccarese paolo.ciccarese at gmail.com
Fri Apr 20 12:12:26 PDT 2012


Hi Trish,
thank you! I'll try that out!

Best,
Paolo

On Fri, Apr 20, 2012 at 2:37 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> 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)
>
> CONFIDENTIALITY NOTICE: This message is intended only for the
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> to be sensitive or confidential and may not be forwarded or disclosed to
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> If you have received this message in error, please notify the sender
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>
> _______________________________________________
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> http://www.bioontology.org
>
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>


-- 
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)

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.
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