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[bioontology-support] synonyms

Trish Whetzel whetzel at stanford.edu
Thu Jan 17 10:32:06 PST 2013


Hi Himanso, 

To get more information about a term, e.g. super- and subclasses, synonyms, and other properties the "Get Term" Web service [1] can be used. For example, for Pompe's disease the "Get Term" call would look like:
http://rest.bioontology.org/bioportal/virtual/ontology/1422?conceptid=10036143&apikey=YourAPIKey 
- Note the value of the conceptid field in this example call uses the ID (Web displayed field name) for the term, which corresponds to the value of the attribute <conceptIdShort> from the Search Web service
OR 
http://rest.bioontology.org/bioportal/virtual/ontology/1422?conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FMDR%2F10036143&apikey=YourAPIKey 
- Note this uses the url-encoded Full Id (Web displayed field name) of the term, which corresponds to the value of the attribute <conceptId> from the Search Web service.

Therefore, using either of these attributes from the Search Web service you can generate the "Get Term" call. Both of these forms of the call are documented [1].

I did notice that the RQ property does not appear to be recognized as a synonym property for the Search Web service and have reported this bug [2]. 

Trish 

[1] http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Get_term.2C_including_its_properties.2C_subclasses.2C_and_superclasses
[2] https://bmir-gforge.stanford.edu/gf/project/ncbo/tracker/?action=TrackerItemEdit&tracker_item_id=4393&start=0


On Jan 17, 2013, at 6:33 AM, Sahni, Himanso * (FDA) wrote:

> Hello Bioportal Team,
>  
> According to http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_BioPortal
> includeproperties=[1/0] – include attributes in the search (default: 0 and includes the preferred name, term identifier, and synonym properties)
>  
> unfortunately including or excluding this flag does not change the output for MEDdra searches
>  
> For example:
>  
> As  “Pompe's disease” and “Glycogen storage disease type II” are synonyms but the RESTful API does not provide any  synonyms or any  parent tree nodes for Pompe’s disease.
> The bioportal browser search  for Pompe’s diease does bring the “Glycogen storage disease type II” as an RQ, but there are no RQ or Synonym nodes in  the XML returned by the web services.
>  
> http://bioportal.bioontology.org/ontologies/42280?p=terms&conceptid=10036143
> http://bioportal.bioontology.org/ontologies/42280?p=terms&conceptid=10053185
> 
> Basically I am interested in finding a way to retrieve synonyms for the terms, is there a different vocabulary that I should be using for synonyms.
>  
> Himanso Sahni
> Himanso.Sahni at fda.hhs.gov
> Contractor-Recombinant Data Corp.
> HSahni at recomdata.com
>  
>  
>  
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support

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