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Re: magetab2magerdf

From: mdmiller <mdmiller53@comcast.net>
Date: Sat, 19 Dec 2009 09:08:39 -0800
Message-ID: <B29158BE5B974E8DAB18EE48D7235433@mmPC>
To: "Kei Cheung" <kei.cheung@yale.edu>
Cc: "Jim McCusker" <james.mccusker@yale.edu>, "w3c semweb HCLS" <public-semweb-lifesci@w3.org>
hi kei,

mage-tab and its extension isa-tab is designed from the principal of a DAG, 
in essence it is a flattening of the dag into a spreadsheet which is 
describe in the MAGE-TAB 1.0 spec [1] in great detail.  i believe the 
MAGE-TAB parser stores the nodes as a DAG [2].  EBI has also developed a 
suite of tools around the MAGE standard [3] including a DAG visualization. 
ArrayExpress for each experiment also has a visualized view of the 
experiment as a DAG that can be downloaded.  in MAGE-ML the '_ref' elements 
are used to describe the DAG in a MAGE document.

is the one mentioned below editable?  that's the one thing about the EBI 
visualization, it is not editable.

by the by, MAGE-TAB is also being used to report next-gen sequencing 
experiments in ArrayExpress.


[1] www.mged.org
[2] https://sourceforge.net/projects/limpopo/
[3] http://bioinformatics.oxfordjournals.org/cgi/content/full/25/2/279

----- Original Message ----- 
From: "Kei Cheung" <kei.cheung@yale.edu>
To: "mdmiller" <mdmiller53@comcast.net>
Cc: "Jim McCusker" <james.mccusker@yale.edu>; "w3c semweb HCLS" 
Sent: Sunday, December 13, 2009 6:34 PM
Subject: Re: magetab2magerdf

> 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.mccusker@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.mccusker@yale.edu | (203) 785-6330
>>> http://krauthammerlab.med.yale.edu
>>> PhD Student
>>> Tetherless World Constellation
>>> Rensselaer Polytechnic Institute
>>> mccusj@cs.rpi.edu
>>> http://tw.rpi.edu
Received on Saturday, 19 December 2009 17:09:08 UTC

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