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[bioontology-support] Gap in term services?

Trish Whetzel whetzel at stanford.edu
Tue Apr 2 13:38:18 PDT 2013


> 1) The wiki seems to be a bit out of date in this respect. It gives examples for the alt virtual signature like:
> 
> http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=BRO:Software&apikey=YourAPIKey
> 
> Which I think should be:
> 
> http://rest.bioontology.org/bioportal/virtual/ontology/1104?conceptid=http%3A//bioontology.org/ontologies/BiomedicalResourceOntology.owl%23Software&apikey=YourAPIKey
> 
> (I would edit it myself, but I was denied a user account for the wiki, so I hope you guys don't mind me bugging you about these things)

Yes, thanks for pointing out that the signature was not entirely correct given the title of Alt virtual signature. I've updated the two examples now. I'm not sure why your wiki account request was denied. Ray, are user account requests for the wiki no longer approved?


> 2) The new urls are working some of the time, but I'm still getting some funny 404's. For example, given the following results:
> 
> 8	47638/Field	Data Field	http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Field	Field [...]
> 
> I construct a URL like 
> 
> http://rest.bioontology.org/bioportal/virtual/ontology/1032?conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23Field&apikey=<apikey>
> 
> Which gives a 'concept not found' error. When I searched for the term through the web interface, I found it living at:
> 
> http://bioportal.bioontology.org/ontologies/1032?p=terms&conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23C25507
> 
> I'm not sure what the 23C70773 is, but it doesn't seem to be anywhere in the tab-delimited results I get back for that concept.

A new version of the NCIt was loaded yesterday and in this version the ontology term IDs are changed from human readable strings, e.g. Data Field, to codes, e.g. C25507. The resulting issue with the "Get Term" call in this case is that the concept id "Data Field" in the latest version of NCIt does not exist and by using the ontology id the latest version is being accessed. The concept id for the latest version is now: C25507.

Options to generate a correctly formatted Term web service call are: 
1) we re-process NCIt for use with the Annotator and therefore the updated localConceptId and fullIds would be returned from the Annotator
 --> I've submitted this request, but this may take some time before it is available in production use for the Annotator

2) change from using the ontology id to the version id when navigating from the Annotator results to the "Get Term" web service. Therefore the call would be:
http://rest.bioontology.org/bioportal/concepts/47638?conceptid=http%3A%2F%2Fncicb.nci.nih.gov%2Fxml%2Fowl%2FEVS%2FThesaurus.owl%23Field&apikey=YourAPIKey
- the ontology version id is found in the <localOntologyId> attribute of the Annotator results
- the concept id is found in the <fullId> attribute and should be uri-encoded when used with the Term web service. 
Sorry, I guess in this case it is better to use the ontology version id in the "Get Term" call when navigating from Annotator results to the details of a term. 

Trish 


> On Mon, Apr 1, 2013 at 3:08 PM, Trish Whetzel <whetzel at stanford.edu> wrote:
> In this case, the ontology abbreviation is included as part of the "conceptid", therefore either the abbreviation also needs to be included as part of the conceptid:
> http://rest.bioontology.org/bioportal/virtual/ontology/1086?conceptid=ODGI%3ACharacterized&apikey=<apikey>
> OR 
> the preferred method is to use the full Id of the term (URL encoded) in the call formatted as:
> http://rest.bioontology.org/bioportal/virtual/ontology/1086?conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FODGI.owl%23Characterized&apikey=<apikey>
> 
> Trish 
> 
> 
> On Mar 27, 2013, at 2:32 PM, Colin Morris wrote:
> 
>> Hi,
>> 
>> One of the concepts I got as output from the NCBO annotator was term 'Characterized' in ontology 39579 (ODGI - virtual ontology id 1086). 
>> 
>> But using the 'alt virtual signature' described in the documentation (http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Term_services) to build a url for this concept gives me a 404:
>> 
>> http://rest.bioontology.org/bioportal/virtual/ontology/1086?conceptid=Characterized&apikey=<apikey>
>> 
>> Can you think of any reason why this would be?
>> 
>> Thanks,
>> Colin
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
> 
> 

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