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[bioontology-support] Bioportal Release

Eamonn Maguire eamonnmag at googlemail.com
Wed Mar 24 15:45:54 PDT 2010


Hi natasha,

Thanks! I was just a bit confused by trish's Last email and I was  
worried I didn't explain myself properly when I asked for the extra  
metadata!

Eamonn

--
Eamonn Maguire
eamonnmag at gmail.com
maguire at ebi.ac.uk

On 24 Mar 2010, at 20:25, Natasha Noy <noy at stanford.edu> wrote:

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



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