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[bioontology-support] Bioportal Release

Eamonn Maguire eamonnmag at googlemail.com
Thu Mar 25 00:50:41 PDT 2010


Thank you! :)

Eamonn

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

On 25 Mar 2010, at 01:35, Natasha Noy <noy at stanford.edu> wrote:

> Thanks, Eamonn! The ontologies from this list should be available in  
> a day or two and the remaining ones shortly thereafter. Apologies  
> for the delay.
>
> Natasha
>
>
> On Mar 24, 2010, at 4:06 PM, Eamonn Maguire wrote:
>
>> So in particular we'd like:
>>
>> OBI;
>> EFO;
>> NCI THESAURUS; and
>> CHEBI.
>>
>> If these can be up an running asap that'd be great. In the not so  
>> distant future, If all OBO foudry ontologies were available that'd  
>> be even better!
>>
>> This leads me on to the next Request which would be to make the  
>> isFoundry Boolean value correspond to whether or not an ontology is  
>> an OBO foundry ontology. The current meaning of this is a bit  
>> ambiguous since I believe it means that the ontology in question  
>> imports terms from an OBO foundry ontology. This change would make  
>> it easier to filter out the ontologies we don't want to search on!
>>
>> I need to look at the search branch feature again too, I believe I  
>> was having problems with it though and what was getting returned.  
>> I'll test again on Friday (i'm away at a meeting tomorrow) and let  
>> you guys know what's happening!
>>
>> Many thanks as always,
>>
>> Eamonn
>>
>> -- 
>> Eamonn Maguire
>> eamonnmag at gmail.com
>> maguire at ebi.ac.uk
>>
>> On 24 Mar 2010, at 22:52, Natasha Noy <noy at stanford.edu> wrote:
>>
>>> 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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