Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Bioportal Release

Trish Whetzel whetzel at stanford.edu
Mon Mar 29 12:45:40 PDT 2010


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
>>>>>
>>>
>




More information about the bioontology-support mailing list