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Re: [Obo-relations] Advancing translational research with the Semantic Web (Not clear about definition of <is_location_of_process>)

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 31 May 2007 22:36:23 -0400
Message-Id: <66D8F2FF-F116-43C7-ABDC-EF5658703927@DrexelMed.edu>
Cc: "Smith, Barry" <phismith@buffalo.edu>, "Kashyap, Vipul" <VKASHYAP1@PARTNERS.ORG>, samwald@gmx.at, public-semweb-lifesci@w3.org, obo-relations@lists.sourceforge.net
To: Kei Cheung <kei.cheung@yale.edu>
Hi Kei,

Yes - you are right, of course - right now the TGEN infrastructure  
for the consortium is committed to providing MAGE-ML instances [1].

My understanding from speaking with FuGE folks is that the the FuGE- 
stk [2] will provide a means to "convert" MAGE-ML to FuGE-ML (may  
require a MAGE-ML import into a FuGE DDL database - then export from  
the database - I'm not clear on this yet).  Since many of the FuGE  
model developers were a part of the MGED MAGE model development  
project, there is both an eye toward - and a need for - automatic  
conversion. As FuGE is intended to cover ALL of functional genomics  
beyond microarray alone, there's a bit more abstraction in the data  
model and some more specific parts of the model will likely not be  
needed for microarray data.

I'm not completely clear on how automatic it will be, but folks such  
as Michael Miller who have contributed to the HCLS IG list before  
would certainly be able to give us the most comprehensive answer to  
that question that is available at this time.

One example I found recently is out of the bioinformatics unit at  
Newcastle U. - the Centre for Integrated System Biology of Aging and  
Nutrition [3] [4].  In addition to being one of the first public  
systems based on the Milestone 3 release of FuGE & the FuGE-stk, it  
has a means of transferring data from the ArrayExpress backend -  
maxdLoad2 [5].  Since the latter system is capable of importing MAGE- 
ML instances, this provides a route via which one can get from MAGE- 
ML to FuGE-ML.

Of course, we could skip the FuGE step and just look at how to use  
OBI and other OBO Foundry ontologies to create a SemWebTech  
repository for NIH Neuroscience Microarray Consortium data as is - in  
MAGE-ML or in the backend model - akin to the ones Alan et al. have  
set up for the HCLS demo at the NeuroCommons.  We are working with  
annotating MAGE-based microarray data within MouseBIRN as well, so it  
would be wonderful, if there were some way for this to be included.   
One of the goals of what we are doing for microarray data in BIRN is  
to stay in sync with the consortium in such a way so as to make it  
possible for us to query consortium data - and visa versa.  There are  
some folks on BIRN whose are also associated with the consortium (I  
believe the Autism groups recently added to BIRN are participants of  
the consortium).

Do you know whether others on the consortium - or TGEN itself - are  
working on this task?  We might want to have a call that includes  
some of the core informatics folks in the consortium, in addition to  
yourself.

Cheers,
Bill


[1] http://arrayconsortium.tgen.org/np2/public/ 
dataAndAnalysisPolicies.jsp
[2] http://fuge.sourceforge.net/dev/index.php
[3] http://www.cisban.ac.uk/cisbanDPI.html
[4] http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016
[5] http://www.cisban.ac.uk/resources.html

On May 31, 2007, at 10:05 PM, Kei Cheung wrote:

> Hi Bill,
>
> Thanks for describing the evolution of MGED into FuGO. As I  
> understand it, the consortium's microarray data can be exported in  
> MAGE-ML (XML) format. Would it be possible to convert it to the  
> FuGE format?
>
> Cheers,
>
> -Kei
>
> William Bug wrote:
>
>> Barry beat me to the punch here -
>> BUT -
>> I would not want to miss out on the specific value of the proposal  
>> Kei has made.
>>
>> I believe looking closely at how the OBI representation of  
>> microarray-associated instruments, protocols, reagents, data  
>> artifacts, algorithms, etc. - could be put to use in describing  
>> some of the data being produced for the NIH Neuroscience  
>> Microarray Consortium that you are contributing to, Kei.  As you  
>> may already know, many of the experts working on FuGE (grown out  
>> of MAGE which used the MGED Ontology as its shared semantic  
>> framework) are looking for assistance in how to make use of  
>> ontologies when representing microarray data in a FuGE instance.   
>> As you also probably know, the original FuGE-associated ontology,  
>> FuGO, has expanded its domain to cover all forms of biomedical  
>> investigation (Ontology of Biomedical Investigation - aka the OBI  
>> that Barry cited).  This was a part of the evolution of FuGO as it  
>> began to participate in the OBO Foundry AND make a commitment to  
>> use BOTH the OBO Relations ontology and BFO.
>>
>> With that in mind - and considering the NIH Neuroscience  
>> Microarray Consortium is committed to providing array data in FuGE  
>> format - it could be very helpful both to understand how OBI can  
>> be used to provide a formal semantic representation of important  
>> experimental provenance information AND how SemWebTech in general  
>> could be used to provide a more flexible - and query-able -  
>> framework in which to access this semantic information.
>>
>> Cheers,
>> Bill
>>
>> On May 31, 2007, at 9:21 PM, Kei Cheung wrote:
>>
>>>
>>> Smith, Barry wrote:
>>>
>>>> At 08:52 PM 5/31/2007, Kei Cheung wrote:
>>>>
>>>>> Hi Barry,
>>>>>
>>>>> Welcome to the SWHCLS list. Such a discussion reminds me of the  
>>>>> Nature paper: "Are the current ontologies in biology good  
>>>>> ontologies?" (http://www.nature.com/nbt/journal/v23/n9/full/ 
>>>>> nbt0905-1095.html). The paper uses the MGED (microarray)  
>>>>> ontology to illustrate some of the ontological issues. I'm just  
>>>>> curious how the BFO principles and practice can help make such  
>>>>> a microarray ontology more ontologically sound and therefore  
>>>>> more machine readable.
>>>>
>>>>
>>>>
>>>> We are already working on it:
>>>>
>>>> http://obi.sf.net
>>>>
>>>> BS
>>>>
>>> That's great! I hope we can develop some real use case of it.
>>>
>>> -Kei
>>>
>>>
>>
>>
>>
>> Bill Bug
>> Senior Research Analyst/Ontological Engineer
>>
>> Laboratory for Bioimaging  & Anatomical Informatics
>> www.neuroterrain.org
>> Department of Neurobiology & Anatomy
>> Drexel University College of Medicine
>> 2900 Queen Lane
>> Philadelphia, PA    19129
>> 215 991 8430 (ph)
>> 610 457 0443 (mobile)
>> 215 843 9367 (fax)
>>
>>
>> Please Note: I now have a new email - William.Bug@DrexelMed.edu  
>> <mailto:William.Bug@DrexelMed.edu>
>>
>>
>>
>>
>
>

Bill Bug
Senior Research Analyst/Ontological Engineer

Laboratory for Bioimaging  & Anatomical Informatics
www.neuroterrain.org
Department of Neurobiology & Anatomy
Drexel University College of Medicine
2900 Queen Lane
Philadelphia, PA    19129
215 991 8430 (ph)
610 457 0443 (mobile)
215 843 9367 (fax)


Please Note: I now have a new email - William.Bug@DrexelMed.edu
Received on Friday, 1 June 2007 02:34:10 GMT

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