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Re: [BioRDF] W3C Note on expression RDF

From: Chris Mungall <cjmungall@lbl.gov>
Date: Mon, 7 Nov 2011 15:35:06 +0000
Cc: expressionrdf@googlegroups.com, HCLS <public-semweb-lifesci@w3.org>
Message-Id: <71925058-98E3-4559-BBD0-CF1C1FC7B273@lbl.gov>
To: "M. Scott Marshall" <mscottmarshall@gmail.com>

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
> 
> 
Received on Monday, 7 November 2011 15:35:49 GMT

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