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Re: magetab2magerdf

From: mdmiller <mdmiller53@comcast.net>
Date: Wed, 6 Jan 2010 06:47:14 -0800
Message-ID: <82FB116A1FE144A18A243F83A8F449C4@mmPC>
To: "Jim McCusker" <james.mccusker@yale.edu>, "Tony Burdett" <tburdett@ebi.ac.uk>
Cc: "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
hi jim,

great progress!

and i believe you are right about how limpopo parser stores the protocols, i've included tony, who's been the lead developer of the parser on the email and he might be able to shed some light.

if tony can outline a plan, i might have the time to correct this.

  ----- Original Message ----- 
  From: Jim McCusker 
  To: w3c semweb HCLS 
  Sent: Tuesday, January 05, 2010 10:43 PM
  Subject: Re: magetab2magerdf

  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.


    a.. Conversion of nearly all (see known issues) data from IDF and SDRF MAGE-TAB files into RDF.
    b.. RDF is compliant with the MGED Ontology, with minimal additional classes and properties.
    c.. RDF conforms to DAG structure with direct links between nodes (has_derivative and has_derivation_source) as well as through ProtocolApplication instances. 
    d.. 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.
    e.. 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:

    a.. 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?
    b.. 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. 

    a.. Example RDF is at http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986/E-MEXP-986.rdf 
    b.. Add-on MAGE-OM ontology is available at http://magetab2rdf.googlecode.com/svn/trunk/ontologies/mage-om.owl

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

  Jim McCusker
Received on Wednesday, 6 January 2010 14:47:48 UTC

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