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[bioontology-support] hierarchy web services

Tomasz Adamusiak tomasz at ebi.ac.uk
Thu Jul 8 04:04:01 PDT 2010


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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