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] searching concept ids via REST services

Natasha Noy noy at stanford.edu
Sat Aug 1 14:37:56 PDT 2009


In OWL, rdf:ID *is* the unique identifier and there is nothing that  
prevents you from using the human-readable name as this identifier. In  
fact, there are two different schools of though: you could argue that  
this approach is better or that your IDs should be meaningless and  
immutable. Ultimately, this is the decision that the ontology authors  
take.

Natasha


On Jul 31, 2009, at 7:27 PM, Trish Whetzel wrote:

> 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
>
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at lists.stanford.edu
> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




More information about the bioontology-support mailing list