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: [EMAIL PROTECTED] 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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