Re: [Obi-devel] Modularity tool and OBI

[Yongqun He <yon...@me...>]

Hi Jie,
That sounds good plan. Thanks.
Oliver

>>> jie zheng <jie...@pc...> 4/5/2011 7:02 PM >>>
I had a brief discussion about it with Allen. After this OBI release 
out, I am going to add an extra annotation property for the terms
needed 
by the Functional Genomics Data (FGED) community. And then we can try
to 
use ontoFox to generate FGED view of OBI. I will send email out when I

have the owl file ready to use for this task and would like to work 
together with all who are interested in this work.

Jie


On 4/5/2011 6:18 PM, Bill Hogan wrote:
> I'll second that motion and express our strong desire (here in
> Arkansas) to collaborate with the community on this effort.
>
> Bill
>
> On Tue, Apr 5, 2011 at 5:14 PM, Yongqun He<yon...@me...> 
wrote:
>> Hi Thomas, Melanie, Jie, and all,
>>
>> I think we can work together on this task. An OntoFox-based
community view
>> extraction is possible, and we can offer to do
>> coding. Through collaboration, we should be able to do a decent job
>> here. Maybe we need to set up some time to discuss this in more
detail?
>>
>> Oliver
>>
>> Yongqun "Oliver" He, DVM, PhD
>> Assistant Professor
>> Unit for Laboratory Animal Medicine
>> Department of Microbiology and Immunology
>> and Center for Computational Medicine and Bioinformatics
>> University of Michigan Medical School
>> Office: Room 105, Animal Research Facility (ARF)
>> Mailing: 018 ARF, 1150 W. Medical Center Dr.
>> Ann Arbor, MI 48109
>> Email: yon...@me... 
>> Tel: 734-615-8231 (O); 734-615-2455 (L)
>> Fax: 734-936-3235
>> http://www.hegroup.org/ 
>>
>>>>> Thomas Schneider<tsc...@in...>  4/5/2011
5:27 AM
>> Hi Melanie,
>>
>> sorry for the late reply. I'm happy to collaborate in the extraction
of
>> "community views", and I can offer to contribute to the logical
foundations
>> of the tool you have in mind. You specified several formal
guarantees you
>> require of the tool, and I think I can help in the process of
ensuring that
>> they are in place. Since my time is rather limited at the moment, I
cannot
>> offer to do any coding for the time being.
>>
>> Just let me know if this is acceptable.
>>
>> Cheers
>>
>> Thomas
>>
>> On 24.03.2011, at 21:52, Melanie Courtot wrote:
>>
>>> Hi Thomas,
>>>
>>> I am contacting you on behalf of the OBI developers as we are
interested
>>> in your modularity tool at
http://owl.cs.manchester.ac.uk/modularity/.
>>>
>>> We are trying to export what we call "community views", i.e.,
subset of
>>> terms particularly relevant to some users groups. For example,
people
>>> interested only in specific types of experiments, and/or people
using
>>> specific labels as synonyms. Another example would be only OBI main
classes,
>>> to make it more accessible to the general public.
>>>
>>> Bjoern gathered an initial list of requirements for such a tool:
>>>
>>> 0) Work using as an input only the OWL file containing OBI, and
output
>>> another OWL file containing the 'view'
>>> 1) Create alternative labels for OBI terms that are view specific
>>> 2) Indicate for a given OBI class if it should be included in a
view,
>>> 3) Create an ontology that contains only the view specific terms
AND one
>>> of the following
>>> - all parents
>>> - everything required for reasoning
>>> - just the terms specified
>>>
>>> and we think your modularity tool would be a good place to start.
We would
>>> however most probably need to extend it to address our specific
>>> requirements, and we were wondering if this is something you would
be
>>> interested in collaborating on?
>>>
>>> Cheers,
>>> Melanie
>>>
>>> ---
>>> Mélanie Courtot
>>> MSFHR trainee, TFL- BCCRC
>>> 675 West 10th Avenue
>>> Vancouver, BC
>>> V5Z 1L3, Canada
>>>
>>>
>>>
>>>
>>>
>>>
>>
----------------------------------------------------------------------
>> Dr. Thomas Schneider
>> Universität Bremen, FB 03
>> MZH, Raum 3100
>> Postfach 330440
>> 28334 Bremen
>> Germany
>> +49 421 218-64432
>> http://www.informatik.uni ( http://www.informatik.uni/
)-bremen.de/~ts/
>>
----------------------------------------------------------------------
>>
>> Zigong (n.)
>> Screeching skid made by cartoon character prior to turning round and
running
>> back in the opposite direction.
>>
>> Douglas Adams, John Lloyd: The Deeper Meaning of Liff
>>
>>
>>
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