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[bioontology-support] Bioportal Release

Natasha Noy noy at stanford.edu
Wed Mar 24 13:25:57 PDT 2010


Hi Eamonn,

Yes, that's exactly the way we understood your request. We just  
haven't pushed the change out yet. Should be pushed out shortly.

Natasha


On Mar 24, 2010, at 11:04 AM, Eamonn Maguire wrote:

> Hi all,
>
> So, I'm back again and finalising the ontology stuff. However, I  
> need to clarify one thing. When I said I would like more metadata, I  
> specified that I would like more metadata for the hierarchy services.
>
> e.g. http://rest.bioontology.org/bioportal/concepts/parents/42331/Melanoma?email=example@example.org
>
> At the minute you return this:
>
> <classBean>
> 	<ontologyVersionId>MSH</ontologyVersionId>
> 	<id>C0206769</id>
> 	<relations>
> 		<entry>
> 			<string>Level</string>
> 			<int>1</int>
> 		</entry>
> 	</relations>
> </classBean>
> but what we want is something like this:
>
> <classBean>
> 	<ontologyVersionId>MSH</ontologyVersionId>
> 	<id>C0206769</id>
> 	<fullId>purl for term</fullId>
> 	<label>whatever the label might be</label> etc....
> </classBean>
> The reason we want this is because at present I have to do 2 queries  
> to get this extra metadata (slow)...
>
> thanks,
>
> Eamonn
>
> On 12 Mar 2010, at 23:07, Trish Whetzel wrote:
>
>> Hi Philippe,
>>
>> Can you send an example? I tried the call: http://stagerest.bioontology.org/bioportal/concepts/40832/all?pagesize=50&pagenum=1 
>>  (currently only on the Stage server) and do see results such as:
>> <classBean>
>> <id>obo:OBI_0000310</id>
>> <fullId>http://purl.obolibrary.org/obo/OBI_0000310</fullId>
>> <label>adverse event trigger</label>
>>
>> Thanks,
>> Trish
>>
>>
>> On Mar 12, 2010, at 12:17 PM, Philippe Rocca-Serra wrote:
>>
>>> Hi Trish,
>>>
>>> Eamonn will be back in office in the middle of next week.
>>> OBI seems to return only id but not rdfs:label  so the current  
>>> display in our tool isn't that helpful.
>>> But I can not tell if it is down to do fixing on our side or not.
>>>
>>> Thanks for the notification and good week end
>>>
>>> P
>>>
>>>
>>> Trish Whetzel wrote:
>>>> Hi Eamonn,
>>>>
>>>> Just wanted to check back to confirm that the new getAllTerms Web  
>>>> service is working for you. Last I heard we are on target to  
>>>> release on Monday.
>>>>
>>>> Thanks,
>>>> Trish
>>>
>>>
>>> -- 
>>> /-----------------------------------------------\
>>> Philippe Rocca-Serra (PhD)
>>> EMBL-EBI
>>> NET-Project Technical Coordinator
>>> Tel: +44 (0)1223 492553
>>> Fax: +44 (0)1223 494
>>> URL:
>>> http://www.ebi.ac.uk/net-project/
>>> http://isatab.sourceforge.net/index.html
>>> \-----------------------------------------------/
>>>
>>
>> Trish Whetzel, PhD
>> Outreach Coordinator
>> The National Center for Biomedical Ontology
>> Ph: 650-721-2378
>> whetzel at stanford.edu
>> http://www.bioontology.org
>>
>>
>>
>
> Eamonn Maguire
> Software Engineer - NET Project
> http://www.ebi.ac.uk/~maguire
> http://ebiinterfaces.wordpress.com/
>
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> https://mailman.stanford.edu/mailman/listinfo/bioontology-support




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