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[bioontology-support] Bioportal Release

Natasha Noy noy at stanford.edu
Wed Mar 24 15:52:31 PDT 2010


Eamonn,

In order for us to get you the ontologies you need as soon as possible  
(we have basically everything in place and now just need to re-index  
all ontologies to store that additional information that you asked  
for), can you give me a list of ontologies that are critical for you  
so that we can index them first? Or do you need all of them?

Thanks!

Natasha


On Mar 24, 2010, at 3:45 PM, Eamonn Maguire wrote:

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




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