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[bioontology-support] Bioportal Release

Eamonn Maguire eamonnmag at googlemail.com
Wed Mar 24 16:06:26 PDT 2010


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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