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[bioontology-support] Bioportal Release

Eamonn Maguire maguire at ebi.ac.uk
Wed Mar 24 11:04:34 PDT 2010


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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