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[bioontology-support] Bioportal Release

Eamonn Maguire maguire at ebi.ac.uk
Mon Mar 29 23:52:02 PDT 2010


Ok, things seem to be fine anyway...i've only tested on OBI so far, I'll
have a look at the others today :) but things are looking good!

many thanks,

eamonn

On 29 March 2010 20:45, Trish Whetzel <whetzel at stanford.edu> wrote:

> To add on to this, the ontologies below do contain the XML elements for
> <fullId> and <definitions> regardless of whether these elements have a
> value. Therefore, in cases where the ontology does not provide a definition,
> the empty element <definitions/> will be present.
>
> However, for ontologies that have not yet been updated, these XML elements
> are not present. We will discuss providing these XML elements for all
> ontologies tomorrow, i.e. in the interim as these ontologies are updated for
> consistency of the XML output.
>
> Trish
>
>
>
> On Mar 28, 2010, at 11:13 AM, Natasha Noy wrote:
>
>  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
>>>>>>>>>
>>>>>>>>
>>>>>>
>>>>
>>


-- 
Eamonn Maguire

maguire at ebi.ac.uk
eamonnmag at gmail.com

http://www.ebi.ac.uk/~maguire
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