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[bioontology-support] hierarchy web services

Trish Whetzel whetzel at stanford.edu
Wed Jul 21 00:25:50 PDT 2010


Hi Tomasz,

Thanks for pointing that out. There were two versions of Uberon and  
the entry for ontology id=1111 needs to be removed from the Lucene  
Index.

Trish


On Jul 8, 2010, at 4:04 AM, Tomasz Adamusiak wrote:

> Hi Trish,
>
> Thanks for a prompt reply. On an unrelated note, when searching for  
> uberon terms:
>
> http://rest.bioontology.org/bioportal/search/UBERON:0000071
>
> I'm ending up with two different ontology ids: 1111, 1404.
>
> 1111 is not resolvable:
> http://rest.bioontology.org/bioportal/virtual/ontology/1111
>
> And 1404 is not listed under:
> http://rest.bioontology.org/obs/ontologies
>
> Possible bug?
>
> Thanks
> Tomasz
>
> On 07/07/2010 16:37, Trish Whetzel wrote:
>> Hi Tomasz,
>>
>> In updating the data used for the Hierarchy Web services, there was  
>> an
>> error in processing a few ontologies including the Gene Ontology. In
>> order to see which ontologies are available for use with the  
>> Hierarchy
>> Web services, please see the results of the Web service call:
>> http://rest.bioontology.org/obs/ontologies for ontologies with a  
>> value
>> of 28 for the status field.
>>
>> If use of the Gene Ontology is mission critical, there is a possible
>> workaround by accessing the extended version of the Gene Ontology
>> (virtual ontology id=1506) via the Hierarchy Web services. For  
>> example:
>> http://rest.bioontology.org/bioportal/virtual/parents/1506/GO:0043227?email=example@example.org
>>
>>
>> http://rest.bioontology.org/bioportal/virtual/children/1506/GO:0043227?email=example@example.org
>>
>>
>> http://rest.bioontology.org/bioportal/virtual/rootpath/1506/GO:0043227?email=example@example.org
>>
>>
>> However, the Web service call for search in subtree does not seem  
>> to be
>> working with this ontology id.
>>
>> Please note that in the near future it is likely that we will merge  
>> the
>> two entries for the Gene Ontology under the ontology id=1070 and
>> therefore deprecate the extended version of the Gene Ontology with
>> ontology id=1506. The result will be that the content of the ontology
>> found with ontology id=1070 will be for the extended version of the  
>> Gene
>> Ontology. We are currently discussing this with Jane and the  
>> developers
>> here on how best to represent the extended version of GO.
>>
>> Apologies for this inconvenience.
>>
>> Trish
>>
>>
>> On Jul 7, 2010, at 7:24 AM, Tomasz Adamusiak wrote:
>>
>>> Hi,
>>>
>>> I started getting internal server errors when querying GO through
>>> hierarchy web services:
>>>
>>> http://rest.bioontology.org/bioportal/virtual/parents/1070/GO:0043227?email=example@example.org
>>>
>>>
>>> http://rest.bioontology.org/bioportal/virtual/children/1070/GO:0043227?email=example@example.org
>>>
>>>
>>> http://rest.bioontology.org/bioportal/virtual/rootpath/1070/GO:0043227?email=example@example.org
>>>
>>>
>>> Also sub tree search seems to be affected (no error but no results
>>> either):
>>>
>>> http://rest.bioontology.org/bioportal/search/membrane/?ontologyids=1070&subtreerootconceptid=GO:0043227
>>>
>>>
>>> Please help.
>>>
>>> Thanks
>>> Tomasz
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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