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[bioontology-support] searching concept ids via REST services

Trish Whetzel whetzel at stanford.edu
Fri Jul 31 19:27:02 PDT 2009


In this case, the search by id is designed to search the rdf:ID field.
However, the contents of this property value vary depending on the metadata
scheme used by the developers of the ontology. 

FMA adds a value in the rdf:ID field that is a human readable string that
contains semantic meaning, e.g. Thymus and uses an annotation property to
store a unique identifier.

Other OWL ontologies use the rdf:ID field as the unique identifier for the
node and use any one of a variety of properties for the human readable label
for the node.

Perhaps with this added feature, ontology developers should indicate which
property contains a unique node identifier (for OWL ontologies if it is not
the rdf:ID field) as well as the values used for preferred name and
synonym???

Trish


>-----Original Message-----
>From: Tomasz Adamusiak [mailto:tomasz at ebi.ac.uk]
>Sent: Friday, July 31, 2009 6:51 AM
>To: Trish Whetzel
>Cc: tomasz.adamusiak at ebi.ac.uk; support at bioontology.org; Helen Parkinson
>Subject: Re: [bioontology-support] searching concept ids via REST
>services
>
>Hi Trish,
>
>Excellent. Thanks a lot.
>
>Just a minor comment. I noticed that some of the ontologies use labels
>as a concept IDs, e.g. NCIThesaurus or FMA, e.g.:
>http://rest.bioontology.org/bioportal/virtual/1053/Thymus?email=tomasz@e
>bi.ac.uk
>
>so
>http://rest.bioontology.org/bioportal/virtual/1053/FMAID:9607?email=toma
>sz at ebi.ac.uk
>
>returns an error.
>
>Is that a design decison or the way they were loaded by the original
>submitters?
>
>Thanks
>Tomasz
>
>
>Trish Whetzel wrote, On 2009-07-30 17:43:
>> Hi Tomasz,
>>
>> A new feature has been added to BioPortal to allow search by concept
>> ids. Let us know if you have any comments or questions on this
>feature.
>>
>> Trish
>>
>>
>> On May 28, 2009, at 4:36 AM, Tomasz Adamusiak wrote:
>>
>>> Hi,
>>>
>>> I'd like to use BioPortal WS to search for concept ids. So the
>following
>>> query will find a reference to DOID:9778 in the Experimental Factor
>>> Ontology, but will not bring up the actual record in Disesase
>Ontology:
>>>
>>>
>http://rest.bioontology.org/bioportal/search/DOID%239778/?includepropert
>ies=1&email=tomasz at ebi.ac.uk
>>>
>>>
>>> I guess to get to the actual concept I need a separate query like
>this:
>>>
>http://rest.bioontology.org/bioportal/virtual/1009/DOID:9778/?email=toma
>sz at ebi.ac.uk
>>>
>>>
>>> The disadvantage of the latter approach is that I need to know the
>>> ontology id, the concept is coming from, beforehand. Is there a way
>>> around this?
>>>
>>> Cheers
>>> Tomasz
>>>
>>> --
>>> Tomasz Adamusiak, MD, PhD
>>> European Bioinformatics Institute
>>> +44 (0) 1223 492 562
>>> tomasz.adamusiak at ebi.ac.uk
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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