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Re: [BioRDF] W3C Note on expression RDF

From: Helena Deus <helenadeus@gmail.com>
Date: Mon, 7 Nov 2011 16:44:27 +0000
Message-ID: <CAPkJ_9ktU5LPPcuwLG0pv77y0r6AV5AZfhru3E5We6LBsAd2Fg@mail.gmail.com>
To: Chris Mungall <cjmungall@lbl.gov>
Cc: "M. Scott Marshall" <mscottmarshall@gmail.com>, expressionrdf@googlegroups.com, HCLS <public-semweb-lifesci@w3.org>
Hi guys,

Sorry I missed the telco (again)... I have contacted JBI regarding the
paper... Once it's out, it'll make writting the note a much easier task.
Also, any news on ArrayExpress SPARQL endpoint?

Regarding NGS data, it may be a good use case for HCLS globally... I've
been looking at some sample RNA-seq data but haven't had time to wrap my
head around it yet...


On Mon, Nov 7, 2011 at 3:35 PM, Chris Mungall <cjmungall@lbl.gov> wrote:

> On Nov 7, 2011, at 2:03 PM, M. Scott Marshall wrote:
> Dear BioRDF,
> I've pasted the minutes from our last meeting below. You can find them
> here: http://www.w3.org/2011/10/24-HCLS-minutes.html
>  Part of the discussion that isn't available in the minutes below was
> agreement that NGS expression could be minimally supported by, for example,
> providing a placeholder for information such as quantified expression. Phil
> gave us some slides (see link to PDF below) and pointed us to slide 81.
> Analogous to representing the *results* of differential expression analysis
> in microarrays (rather than all details of images analysis, etc.), we would
> like to be able to represent the results of analyzing RNA-seq data. A few
> of you expressed interest in looking into the minimal features needed to
> represent NGS RNA-seq analysis results (Michael, Phil, others?). Please
> also feel free to continue this discussion on the mailing list.
> What sort of thing do you have in mind for the RNA-seq data? Would this be
> subsumed by a generic RDF representation for interval based formats like
> GFF3 and formats like wiggle?
> What about downstream analyses, e.g. GOseq? I'd be interested in working
> on a standard format for the results of enrichment analyses. See:
> http://biostar.stackexchange.com/questions/11269/is-there-a-standard-format-for-go-term-enrichment-results
> Our current thinking is to define an abstract model independent of
> serialization, and concrete forms such as json, tab-delimited and rdf.
>  I haven't had time to trim down and restructure the google doc yet. I
> cannot make a teleconference in today's BioRDF timeslot but encourage you
> to call in if you want to continue the discussion with others that show up.
>  Cheers,
> Scott
> https://docs.google.com/document/d/1A5-3tOsifPWPpETBKU-ZA9d7O7wK_nBzTFUBEe-0Bzo/edit?authkey=CK-y8Y8C
>  http://purl.org/net/biordfmicroarray/demo
> http://ui.genexpressfusion.googlecode.com/hg/index.html
>  <Phil> it seems currently restriction to microarray based gene expression
> Scott (retroactively scribing): Repeated goal of W3C note - i.e. to give
> people confidence in *an* RDF representation and approach. Decide when we
> go to HTML and version control. What's missing?
> Scott: See if we can minimize differences between current representations?
>  Sudeshna: Make a new one as the standard?
>  Michael: But we already have enough to work with in the current set of
> representations.
>  James: I thought we were simply going to talk about some of the current
> work and how it can be used and 'cut it loose'.
>  Tomasz: Ours was meant to be a 'reference point'.
>  Michael: Yes, 'reference point' sounds better than 'cannonical RDF'.
>  James: Some news: A student project at EBI is just coming toward the
> end. Bulk of ArrayExpress in RDF. Not public data yet.
>  Jim: After using MGED in my IPAW paper, I converted to OBI. It's the
> MAGETAB2RDF work. Some issues with Limpopo.
>  James: I could send you (Jim) some stuff for you to take a look at.
>  Michael: Could you explain what you mean by "there are some limits to
> the translations"?
>  James: Some matching of terms isn't perfect.
>  This is the IPAW paper:
> http://www.springerlink.com/index/W10740804446172U.pdf
>  http://krauthammerlab.med.yale.edu/~jpm78/ArrayExpress/E-AFMX-1.rdf.ttl
>  http://swbig.googlecode.com
> <james> JM to post info on magetab 2 rdf at arrayexpress once beta is out
> - credit to Drashtti Vasant and Tony Burdett
>  <james> http://code.google.com/p/open-biomed/wiki/GeneExpressionAtlas
>  <james> example queries for gxa rdf
> <ericP> i can hear everything, but can't speak up to volunteer
> <james> congrats eric
> <JimMcCusker> BTW, congrats, eric!
> <tomasz> congrats, Eric!
> maggots have indeed been revalidated in recent years for keep wounds
> healing faster (they clean it up)
> Scott: Somebody brought up the need to deal with NGS and I agree. But
> that means more work..
>  <JimMcCusker> I have to drop off for a prov WG call. If you need
> anything from me towards the paper, let me know.
>  ok, thanks Jim
> <sudeshna> http://cufflinks.cbcb.umd.edu/
>  <tomasz> James: get it out for feedback for community as soon as possible
> <tomasz> I second that!
> <Phil>
> http://www.bioinformatics.auckland.ac.nz/workshops/NGS-workshop-update.pdf
>  <Phil> slide 81
> <tomasz> thanks, bye
> <sudeshna> bye

Helena F. Deus
Post-Doctoral Researcher at DERI/NUIG
Received on Monday, 7 November 2011 16:45:19 UTC

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