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Re: magetab2magerdf

From: Jim McCusker <james.mccusker@yale.edu>
Date: Wed, 6 Jan 2010 01:43:03 -0500
Message-ID: <68084f3e1001052243x17542239m7a192d8eaef3ced0@mail.gmail.com>
To: w3c semweb HCLS <public-semweb-lifesci@w3.org>
I have checked in a first (complete) cut for magetab2magerdf 0.9a.
Everything should be there, both IDF and SDRF, but I haven't tested against
a wide range of files yet. This is alpha software.


   - Conversion of nearly all (see known issues) data from IDF and SDRF
   MAGE-TAB files into RDF.
   - RDF is compliant with the MGED Ontology, with minimal additional
   classes and properties.
   - RDF conforms to DAG structure with direct links between nodes
   (has_derivative and has_derivation_source) as well as through
   ProtocolApplication instances.
   - Terms and Term Sources are automatically mapped onto the OWL Classes
   and Individuals that are available, and will "guess" at URIs for terms that
   do not map onto an actual OWL ontology.
   - Validation of Terms and Term Sources through the above mapping process.
   If an ontology is loaded and there is no term available in it, the converter
   errors out.

*Known issues:*

   - Units for characteristics and factor values are ignored. I assume that
   if there is a unit type then these are non-terms, and should be handled
   differently. Ideas?
   - All protocols listed for a given SDRF node are used to produce all
   child nodes of that node. As I mentioned before, I'm not sure how I'm
   supposed to distinguish these in the Limpopo API.


   - Example RDF is at
   - Add-on MAGE-OM ontology is available at

*Availability:* http://code.google.com/p/magetab2rdf/

Jim McCusker
Received on Wednesday, 6 January 2010 06:43:58 UTC

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