Re: scientific publishing task force update

Absolutely - I completely agree with Yong.

Defining formal representations of experimental assays and data  
provenance is being addressed in several major projects.   
Bioinformaticists from all domains are coming to recognize how  
critical this is to hosting shared data repositories capable of doing  
re-analyzing existing data sets - pooling data across studies - and  
using such federated access to existing data to correlate each new  
data collection with the existing info base.

The group working on FuGO is expecting to extend the foundational  
work they've done on this front to create an "investigation" ontology.

Several of the major data format projects in neuroscience - and  
neuroimaging in general - are or have addressed various aspects of  
this domain, such as NifTI (http://nifti.nimh.nih.gov/), DICOM  
(http://medical.nema.org/), Analyze (http://www.mayo.edu/bir/Software/ 
Analyze/AnalyzeTechInfo.html), the BIRN XCEDE XSD (http:// 
www.nbirn.net/Resources/Downloads/XCEDE/index.htm), data management  
models produced by the fMRI Data Center (http://www.fmridc.org/f/ 
fmridc), etc..

There is also the Open Microscopy Environment (OME - http:// 
www.openmicroscopy.org/) for light microscopy which, despite its  
"warts" addresses many of these issues as relates to acquiring light  
microscopy images.

The BrainML/BrainMetaL neuroscience data exchange format (http:// 
brainml.org/goto.do?page=.home) also addresses some of these issues  
across a broader domain of neuroscientific experimentation.

Of course, it's very important to recognize the distinction between  
data models, data formats, and semantic approaches (including use of  
ontologies) to classifying experimental data provenance, but it's  
useful to recognize the overlap across these efforts.

FuGO & EXPO are considerably more broad in scope than the other  
projects mentioned.

On a related note, Larissa Soldatova who is the first author on the  
EXPO paper will be one of the lead-in speakers at the  upcoming FuGO  
meeting in late July (http://fugo.sourceforge.net/news/index.php).

Cheers,
Bill


On Jun 14, 2006, at 12:58 PM, Gao, Yong wrote:

>
> As I was curious about the claims made in the article that Mark M  
> pointed out, I
> had a look at the EXPO ontology and also found a couple of  
> references to EXPO
> and two discussion threads. (My apology if someone has already  
> posted these).
>
> http://www.jsbi.org/journal/GIW04/GIW04P180.pdf
> http://bbu.uwcm.ac.uk/awbw2006/talks/LarisaSoldatova.pdf
> http://www.nodalpoint.org/2006/06/07/ontology_for_experiments
> http://community.newscientist.com/thread.jspa?threadID=303&tstart=0
>
> Although it doesn't look like there exisits such a "translator" or  
> any software
> code beyond the OWL ontology, the EXPO model does seem to be well- 
> thought-of. In
> many aspects, it overlaps with what the SWAN (Semantic Web  
> Applications in
> Neuromedicine) project is trying to model, although the latter  
> focuses more on
> "application".
>
> It might be very ambitious to come up a "translator" that turns  
> experimental
> write-ups into EXPO representations.  However, it's  definitely  
> useful and
> doable to use things like EXPO to help scientists manage their  
> experimental
> data.
>
> Yong
>
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org on behalf of Mark Musen
> Sent: Fri 6/9/2006 1:29 PM
> To: AJ Chen
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: scientific publishing task force update
>
>
> On Jun 8, 2006, at 10:09 PM, AJ Chen wrote:
>> The first task is to develop an ontology for self-publishing of
>> experiment. I have proposed a list of objects and properties
>> related to self-publishing experiment. Please download the attached
>> file under Task Status and review the proposal. Your feedback and
>> comments will be greatly appreciated.  You may also edit the file
>> directly and email me the edited file.
>>
>
> A colleague just pointed me to this (rather vacuous) article.  Does
> anyone know more about this work?
>
> http://www.newscientisttech.com/article/dn9288-translator-lets-
> computers-understand-experiments-.html
>
> Mark
>
>
>

Bill Bug
Senior 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)


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Received on Wednesday, 14 June 2006 17:25:04 UTC