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RE: [BioRDF] W3C Note on expression RDF

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 7 Nov 2011 09:36:38 -0800
Message-ID: <e255048538cb565da26e0ed08f5e37aa@mail.gmail.com>
To: expressionrdf@googlegroups.com
Cc: HCLS <public-semweb-lifesci@w3.org>, Chris Mungall <cjmungall@lbl.gov>
hi lena,

if you could send me some sample files (or point me at them) at the
analyzed level, i could take a look.  i'm also going to see if i can find
out how TCGA records the information.



Michael Miller

Software Engineer

Institute for Systems Biology

*From:* expressionrdf@googlegroups.com [mailto:
expressionrdf@googlegroups.com] *On Behalf Of *Helena Deus
*Sent:* Monday, November 07, 2011 8:44 AM
*To:* Chris Mungall
*Cc:* M. Scott Marshall; expressionrdf@googlegroups.com; HCLS
*Subject:* Re: [BioRDF] W3C Note on expression RDF

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:


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.






<*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

*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

*James:* Some matching of terms isn't perfect.

This is the IPAW paper:



<*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*> slide 81

<*tomasz*> thanks, bye

<*sudeshna*> bye

Helena F. Deus

Post-Doctoral Researcher at DERI/NUIG

Received on Monday, 7 November 2011 17:37:07 UTC

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