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Re: magetab2magerdf

From: Jim McCusker <james.mccusker@yale.edu>
Date: Tue, 5 Jan 2010 19:22:50 -0500
Message-ID: <68084f3e1001051622i6eb960c1s66c6c59fb6d32cf4@mail.gmail.com>
To: Michael Miller <mmiller@teranode.com>
Cc: mdmiller <mdmiller53@comcast.net>, w3c semweb HCLS <public-semweb-lifesci@w3.org>
I understand how the file format works, but I'm unclear how to resolve it in
the limpopo data structure.

Thanks,
Jim

On Tue, Jan 5, 2010 at 6:53 PM, Michael Miller <mmiller@teranode.com> wrote:

>  hi jim,
>
>
>
> from section 2.2.3, figure 6 (i hope the figure comes out, otherwise
> reference the MAGE-TAB specification [1] directly):
>
>
>
> *2.2.3 Example: Iterated Design dual channel*
>
> This is shown in Figure 6.
>
> (a) Investigation design graph
>
>
>
> (b) SDRF representation
>
> Figure 6: Iterated design, dual channel. LabeledExtract-Dye associations
> can be added as a separate “Label”
>
>
>
> Note that each source is repeated twice on a separate line so there is no
> ambiguity as to the different processing.  i highly recommend reading the
> spec, tim rayner did a great job of describing how different DAGs are
> represented by a spreadsheet.  also, you'll need to take into account that
> there can be multiple Protocol REF columns between each set of Name nodes.
>
>
>
> cheers,
>
> michael
>
>
>
> [1] http://www.mged.org/mage-tab/MAGE-TABv1.0.pdf
>
>
>
>
>
>
>
> *From:* public-semweb-lifesci-request@w3.org [mailto:
> public-semweb-lifesci-request@w3.org] *On Behalf Of *Jim McCusker
> *Sent:* Tuesday, January 05, 2010 3:10 PM
> *To:* mdmiller; w3c semweb HCLS
> *Subject:* Re: magetab2magerdf
>
>
>
> For what it's worth, I'm generating a DAG using ProtocolApplications as
> edges.
>
> Related to that, I have a limpopo question:
>
> In a case where there are 2 channel microarrays, different protocols are
> used to create labeled extracts. If there is a technical dye swap replicate
> (where the same extract is split and labeled differently), how does the list
> of ProtocolNodes (where one is a Cy5 labeling and the other is a Cy3
> labeling) relate each LabeledExtract to the source Extract? From what I can
> tell, this information is currently lost, as the Extract (say ext1) would
> have 2 protocol nodes (Cy5 and Cy3), and then two child nodes (labext1 and
> labext2). I need to be able to relate which is which.
>
> Thanks,
> Jim
>
> On Sat, Jan 2, 2010 at 10:50 PM, Kei Cheung <kei.cheung@yale.edu> wrote:
>
> Hi Michael et al,
>
> The question is what is the appropriate structure of the DAG for answering
> the semantic queries for our microarray use case.
>
>
>
> mdmiller wrote:
>
> 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.
>
>
>
> I don't think the one mentioned in the paper below is editable.
>
> Cheers,
>
> -Kei
>
>
>
>
> by the by, MAGE-TAB is also being used to report next-gen sequencing
> experiments in ArrayExpress.
>
> cheers,
> michael
>
> [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" <
> public-semweb-lifesci@w3.org>
> 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
>
>
>
>
>
>
>
>
>
>
>
>
> --
> 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
>



-- 
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 Wednesday, 6 January 2010 00:23:46 UTC

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