Hi Kei,
> isa-tab (how does this differ from mage-tab?)
ISA-Tab is a superset of MAGE-Tab and serves to report multi-omics (and
in general, multi-assays) studies. Please, see: http://isatab.sf.net and
details in the ISA-Tab specification.
Regards,
Susanna
--
Susanna-Assunta Sansone, PhD
Project Coordinator
http://isatab.sf.net
http://biosharing.org
http://www.ebi.ac.uk/net-project
Kei Cheung wrote:
Hi Jim, Michael,
The following paper describes how to convert mage-tab and isa-tab (how
does this differ from mage-tab?) into DAG for visualization purposes.
http://www.biomedcentral.com/1471-2105/10/133
Why not DAG for machine readability as well?
Cheers,
-Kei
mdmiller wrote:
hi jim,
looks like you're making great progress. i have a few comments
in-line below.
cheers,
michael
----- Original Message ----- From: "Jim McCusker"
<james.mccus...@yale.edu>
To: "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
Sent: Tuesday, December 08, 2009 6:05 AM
Subject: magetab2magerdf
I'm distinguishing between magetab2rdf (raw conversion of magetab into
an RDF structure) and magetab2magerdf (conversion of magetab into an
RDF-based MAGE-OM structure) here. My purposes and goals require a
magetab2magerdf approach, so that's what I've been working on.
I have checked in code for magetab2magerdf at the googlecode project
http://magetab2rdf.googlecode.com. The code can be checked out from:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/
and example RDF is in:
http://magetab2rdf.googlecode.com/svn/trunk/magetab2magerdf/examples/E-MEXP-986/
I currently load the IDF-related entities into the RDF. I'm beginning
work on SDRF next.
http://magetab2rdf.googlecode.com/svn/trunk/ontologies/mage-om.owl
contains the additional properties and classes needed to support an
RDF-based MAGE-OM on top of the MGED Ontology.
A few notes on E-MEXP-986:
The URI for the MGED Ontology is
http://mged.sourceforge.net/ontologies/MGEDontology.owl, but has been
set to http://mged.sourceforge.net/ontologies/MGEDontology.php in the
IDF. The actual Term Source name is "The MGED Ontology".
A common practice seems to be to refer to "MGED Ontology" without
reference to its URI.
as you probably noticed,
http://mged.sourceforge.net/ontologies/MGEDontology.php allows
appending "#{class name}" to go directly to the definition of the
term, so in a sense it is indeed a valid URI, that is a URL. it also
came before the owl format. can th epowl format be reached into over
he net to extract simply the class definition or does it need to be
downloaded and processed locally? my understanding is that a site
would have to have some sort of query, hopefully sparql, mechanism on
top to enable this.
Since I have to import the MGED ontology already for it's classes and
properties, I have already imported it under the correct URI. I have
added a kludge where if the term source name contains the string "MGED
Ontology", the code assumes you mean the MGED Ontology, and sets the
URI appropriately. However, this is a one-off solution.
think of it as same as
I went back and forth about importing the Term Source ontologies.
However, this particular experiment has used the "ArrayExpress" term
source using the URI "http://www.ebi.ac.uk/arrayexpress/"; which
doesn't correspond to an available ontology, but is technically a term
source.
yes, and it does support a query mechinism, albeit a one off for that
site. i believe they plan on adding support for a sparql endpoint but
aren't sure if or when.
I'm considering attempting to import the ontology if it's available
and validate if it is, but if it fails to resolve to a document the
validation will not happen against that term source.
A note on Limpopo:
The IDF Comment didn't seem to import on this experiment. I'm not sure
if it's a format problem or something else.
i ran into this also, the implementation assumes
"Comment[type]\ttext\ttext..." to coresspond to the format of the
other fields in the IDF. the MAGE-TAB 1.0 spec doesn't address, my
assumption was that it was simply "Comment[type]text" but that's not
what the parser expects. we'll be discussing this for the MAGE-TAB
1.1 spec to clarify it one way or another, possibly updating the
parser before that.
Thoughts and feedback are greatly appreciated.
Jim
--
Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccus...@yale.edu | (203) 785-6330
http://krauthammerlab.med.yale.edu
PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
mcc...@cs.rpi.edu
http://tw.rpi.edu
--
