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[bioontology-support] Bioportal Release

Natasha Noy noy at stanford.edu
Sun Mar 28 11:13:10 PDT 2010


Eamonn,

The ontologies in your short listed are updated now. See for example:
http://rest.bioontology.org/bioportal/concepts/children/42488/EFO_0000001?email=example@example.org

Let us know if that's what you need!

Best,

Natasha


On Mar 25, 2010, at 12:50 AM, Eamonn Maguire wrote:

> 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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