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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 22:44:02 -0400
Message-Id: <D1A66FFA-2983-4CC5-8749-6C62E6644D26@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.P.S.: Oops - forgot to mention this Newcastle U. project has also  
implemented use of LSID, which is obviously of great interest to this  
list.

On May 31, 2007, at 10:41 PM, William Bug wrote:

> 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
>
>
>
>



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 02:41:47 GMT

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