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[bioontology-support] hierarchy web services

Trish Whetzel whetzel at stanford.edu
Wed Jul 7 08:37:54 PDT 2010


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




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