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Pedro: Free OpenSource Data Entry Tool for Genomics and Proteomics Domains

Kevin Garwood garwood at cs.man.ac.uk
Mon Apr 26 01:54:35 EST 2004


Hello,

I'm Kevin Garwood a software developer  for Pedro 
(http://pedrodownload.man.ac.uk).  The tool basically takes a variety of 
XML Schemas and renders data entry forms for them.  Users use the forms 
to create files that will validate against the original schema.  

The application was originally developed to support the PEDRo proteomics 
model and played a significant role in promoting the standard to other 
people.  You can read more about it in the 2003 Nature Biotech Paper:
"A systematic approach to modeling, capturing, and disseminating 
proteomics experimental data"
http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n3/abs/nbt0303-247.html

The tool doesn't have a single line of domain-specific code - we had to 
make it this way in order to cope with changes we were experiencing in 
the proteomics model.  With that in mind, we knew we could apply Pedro 
to other domains.  Since its initial release a little over a year ago, 
it has been applied to genomics and distributed computing areas of 
research.  We've recently had interest from groups in health informatics 
and quantum chemistry to use it as a tool to help rapidly develop models 
that can be validated with an end-user focus group.

If you go to the "Download Models" page, you'll see that Pedro can load 
the MAGE genomics model.  The download includes a couple of test files 
of microarray data that were taken from the EBI's Array Express site.  
I'd just like to say thanks to the EBI's Helen Parkinson, Kai Runte and 
Chris Taylor for helping out on this.

Pedro doesn't just make record field forms - it also allows data 
modellers to associate controlled vocabulary services with text fields. 
If you download the MAGE-ML model from the site, you'll discover that an 
MGED ontology service has been associated with the OntologyEntry 
record's "category" and "value" fields.  If you'd like to see how 
sophisticated Pedro's controlled vocabulary services can get, try 
downloading the "ontology.zip" model from the site.

The release is hosted on source forge under the Academic Free License.  
The tool will be supported for the proteomics community and we do care 
that it works.

Cheers,
Kev







-- 
========================================================
Kevin Garwood
Software Developer
Computer Science Department
Work: http://www.cs.man.ac.uk/~garwood
Play: http://uk.geocities.com/zaredbaron


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