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[BioRDF] W3C Note on expression RDF

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 7 Nov 2011 15:03:37 +0100
Message-ID: <CACHzV2MkkDRvhA=k_4Did_b9LbNbKZiAqn0MYC+85bzk=qqtkg@mail.gmail.com>
To: expressionrdf@googlegroups.com, HCLS <public-semweb-lifesci@w3.org>
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.

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
Received on Monday, 7 November 2011 14:04:15 GMT

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