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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 22:41:14 -0400
Message-Id: <D35617B5-E69D-4494-A8F0-D78BE72282B2@DrexelMed.edu>
Cc: Kei Cheung <kei.cheung@yale.edu>, Barry Smith <phismith@buffalo.edu>, Vipul Kashyap <VKASHYAP1@PARTNERS.ORG>, Matthias Samwald <samwald@gmx.at>, Allyson Lister <a.l.lister@newcastle.ac.uk>
To: public-semweb-lifesci hcls <public-semweb-lifesci@w3.org>, obo-relations@lists.sourceforge.net, OBI Developers <obi-devel@lists.sourceforge.net>
P.S.: Allyson Lister who participates on the Newcastle U. project I  
cited below is also a very active participant on the OBI project.
	http://www.cisban.ac.uk/staff.html

P.P.S.: Sorry for the cross-posting, but I believe there are others  
on the OBI developer list who might be interested in this specific  
discussion.

On May 31, 2007, at 10:36 PM, William Bug wrote:

> 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
>
>
>
>



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 02:38:57 GMT

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