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[bioontology-support] Bioportal Release

Natasha Noy noy at stanford.edu
Wed Mar 24 18:35:22 PDT 2010


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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