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[bioontology-support] disease ontology on bioportal ...

Lynn Schriml lynn.schriml at gmail.com
Fri Dec 3 09:41:21 PST 2010


Hello Trish,
     Please do allow searching and display of the obsolete terms.

Lynn

On Tue, Nov 16, 2010 at 9:58 PM, Trish Whetzel <whetzel at stanford.edu> wrote:

> Hi Lynn,
>
> Since DOID:9998 is an obsolete term and since OBO format ontologies do not
> include a parent node for obsolete terms, the obsolete terms are not
> displayed in the tree hierarchy view for OBO format ontologies. However
> obsolete terms can be accessed from the BioPortal Web services, including
> the Search web service and therefore details about the term can still be
> accessed. We plan to modify how obsolete terms are handled. What is your
> preference as to whether obsolete terms should be displayed in the search
> results and/or displayed in the tree hierarchy for terms from the Human
> disease ontology?
>
> BioPortal loads new ontology versions daily. However, there appears to be a
> bug in pulling the most recent versions of the Human disease ontology the
> last few days.  I have reported this bug and loaded the Nov. 16 release of
> the Human disease ontology into BioPortal in the meantime.
>
> Best regards,
> Trish
>
>
> On Nov 16, 2010, at 11:40 AM, Lynn Schriml wrote:
>
> Hello Trish,
>    Warren had noticed that an obsoleted term was the parent of the tree
> DOID 9998.
>
> Are you also seeing this problem ?
>
> Also: what is your cycle for updates, for the file ?
>
> Would it be possible to update the file to the most recent DO file ?
>
> Thank you Trish,
> Lynn
>
>
>
> On Tue, Nov 16, 2010 at 2:16 PM, Trish Whetzel <whetzel at stanford.edu>wrote:
>
>> Hi Lynn,
>>
>> The last two versions of the Human Disease ontology with release dates
>> listed for 11/04 and 11/05 are able to be browsed. Is there a specific
>> problem that you have encountered?
>>
>> Trish
>>
>>
>>
>> Hello Trish,
>>     We just noticed that the file is having a problem,
>>    with everything is under ID 9998
>>
>> The date on the file is November 2nd.
>>
>> Have you had any problems loading more recent files ?
>>
>> Thank you,
>> Lynn
>>
>> On Thu, Nov 4, 2010 at 5:34 PM, Trish Whetzel <plwhetzel at gmail.com>wrote:
>>
>>> Hi Lynn,
>>>
>>> Are you moving to developing the Disease Ontology in OWL? Either format
>>> will be fine for BioPortal, however we'll need to update the format metadata
>>> if changing to OWL.
>>>
>>> Trish
>>>
>>>
>>>
>>>
>>> On Thu, Nov 4, 2010 at 1:26 PM, Lynn Schriml <lynn.schriml at gmail.com>wrote:
>>>
>>>> Hello Bjoern,
>>>>      we did have a problem with the file yesterday, it has been updated
>>>> in SF, the OBO foundry file no longer has the parsing problem,
>>>> *http://www.berkeleybop.org/ontologies/owl/DOID***<http://www.google.com/url?sa=t&source=web&cd=7&sqi=2&ved=0CDsQFjAG&url=http%3A%2F%2Fieeexplore.ieee.org%2Fiel5%2F5312461%2F5332407%2F05333961.pdf%3Farnumber%3D5333961&rct=j&q=cytoscape%20social%20network&ei=Pw_TTIGGJsqr8Aad_PU_&usg=AFQjCNFHwfJWrMec7P0lmUsM0Cq1aYdbRg&sig2=9TycRz55Dp3krEMUrXSRJQ&cad=rja>The new file should be available at bioportal tomorrow, I would think.
>>>>
>>>> Please also note, in our SF directory, we now have a logical definition
>>>> file and a file with no xrefs.
>>>>
>>>> Best,
>>>> Lynn
>>>>
>>>>
>>>> On Thu, Nov 4, 2010 at 2:41 PM, Bjoern Peters <bpeters at liai.org> wrote:
>>>>
>>>>> ... seems broken (shows parsing error for the last two releases). Using
>>>>> one of the older releases unfortunately means the 'jump to' navigation
>>>>> doesn't work, so right now we are stuck. Can you please help?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Bjoern
>>>>>
>>>>> --
>>>>> Bjoern Peters
>>>>> Assistant Member
>>>>> La Jolla Institute for Allergy and Immunology
>>>>> 9420 Athena Circle
>>>>> La Jolla, CA 92037, USA
>>>>> Tel: 858/752-6914
>>>>> Fax: 858/752-6987
>>>>> http://www.liai.org/pages/faculty-peters
>>>>>
>>>>
>>>>
>>>
>>
>>
>>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> whetzel at stanford.edu
> http://www.bioontology.org
>
>
>
>
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