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[bioontology-support] searching concept ids via REST services

Natasha Noy noy at stanford.edu
Thu Aug 13 10:44:26 PDT 2009


Tomasz,

I think it would make sense to ask for these and we will look into  
updating our metadata form to require not just for properties that the  
ontology uses for preferred name and synonym, but also definition and  
maybe concept code (I am still a bit concerned about concept code  
since in OWL it is technically the id). We'll touch base with you when  
we work on that to make sure what we are doing makes sense.

Thanks a lot!

Natasha


On Aug 13, 2009, at 5:55 AM, Tomasz Adamusiak wrote:

> Thanks for clarifying that for me. At least in EFO we always map to  
> concept codes as most ontologies provide them (even if using human- 
> readable label as the main identifier). Main motivation being that  
> in theory concept codes should be more stable than labels.
>
> That is why it would be nice to have a dedicated BioPortal REST  
> query for concept codes, synonyms and text definitions. But as Trish  
> mentioned that would require extra work from submitters. We can  
> still map concept codes to labels with an extra properties search,  
> so it's not really a problem.
>
> Thanks
> Tomasz
>
> Natasha Noy wrote, On 2009-08-01 22:37:
>> 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
>>>
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