W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > May 2011

RE: BioRDF telcon on Monday at 11AM EDT / 5PM CET

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 2 May 2011 11:36:46 -0700
Message-ID: <c472ecd95d082cf15d2ed01df2eadbf2@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>
Cc: HCLS <public-semweb-lifesci@w3.org>
hi all,

lena, thanks for the excellent summary.

a few more comments vis-a-vis microarrays and next gen: we should make it
clear we are talking about next gen sequencing that is carrying out an
experiment where varying  experimental factors are being studied, as opposed
to purely establishing an individual genome; and in that context, the
difference between microarrays and next gen is pretty much how obtained and
the type of the raw data, which is why MAGE-TAB is suitable for both.  there
are some additional analysis possible for next gen, but this and the
previous difference come down to different protocols which our RDFizing
already can capture generically.



*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *Helena Deus
*Sent:* Monday, May 02, 2011 10:21 AM
*To:* M. Scott Marshall
*Cc:* HCLS
*Subject:* Re: BioRDF telcon on Monday at 11AM EDT / 5PM CET

Dear all,

This is the summary of what was discussed in the bioRDF telcon today:

1. Possible overlaps with Scientific Discouse: Anita and Paolo will look
into our the bioRDF provenance of microarray experiments example and try to
identify, with help from the bioRDF group, where the pieces of information
necessary to create the experimental context (e.g. region of the brain where
the samples came from; disease; progression of the disease) are located in
the article. The goal of this is to 1) create a standard that scientists can
use when reporting experimental results (not just from microarrays, possibly
also applicable to next-gen sequencing); and 2) help bioRDF automate the
process of extracting the experimental context from the papers automatically

2. SAGE bionetworks (http://sage.fhcrc.org/downloads/downloads.php) is an
open access integrative framework for scientists working on human disease.
Since SAGE already includes many microarray experiment results (including
TCGA), EricP suggests we start there and provide an RDF framework in which
SAGE members can represent the data.

Eric also suggests we use Bell to describe the experimental results (

Lena suggest that, in addition to "increases" and "decreases" expression, we
support "increase by how much" as the results from next-gen sequencing will
be able to provide that information.

3. To truly represent a microarray experiment (and the knowledge derived
from there), we need to be looking into three levels of provenance:

a) the experimental context of the experiment (for microarrays, it may be
easier to extract these from mage-tab; Jim McCusker has a tools to convert
these into RDF); this includes data that is only available on the "methods"
section of the paper

b) the statistical package and set of instructions to create the list of
genes (apparently part of Sage packages); also available on the methods
section of a paper.

c) the actual list of genes that are differentially expressed (part of the
Sage packages; James Malone is also creating an RDF representation of
these); usually available as supplementary material.

4) Plans for the future and an open question: should bioRDF start looking
into next-gen sequencing results and how to represent them using OBI?

(Note: mage-tab now includes a place for reporting next-gen sequencing


On Sun, May 1, 2011 at 9:57 PM, M. Scott Marshall <mscottmarshall@gmail.com>

Here is a reminder for Monday's BioRDF teleconference.



Conference Details

Date of Call: Monday, April 18, 2011
Time of Call: 11:00 am Eastern Time, 4 pm UK, 5 pm CET
Dial-In #: +1.617.761.6200 (Cambridge, MA)
[Note: limited access to European dial in numbers below]

Dial-In #: + (Nice, France)
Dial-In #: +44.203.318.0479 (Bristol, UK)
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for
details, or see Web IRC), Quick Start: Use
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for
IRC access.
Duration: ~1 hour
Convener: M. Scott Marshall
Scribe: TBD


Expression RDF, Progress on the W3C note - All



New participants please see http://esw.w3.org/topic/HCLSIG and
http://esw.w3.org/topic/HTML/Teleconferences and info about mibbit in
this message. Note: there is a clickable link for mibbit below
that will bring you directly to the right conference channel.



Mibbit IRC QuickStart (fill in your name at the prompt):

If you do not have an IRC client installed on your computer, you can
get one of the many free one (search "irc client" and your platform), or
you can use a web-based client.

Recent W3C Team info on new IRC facilities from W3C:
Thanks to Matt Womer for introducing us to qwebirc [1], we are now
running it [2] in place of cgi-irc.

Those who use to connect their irc clients to irc.w3.org on http port 80
due to corporate firewalls will need to switch to ftp port 21. These
changes are documented on our IRC page [3].

[1] http://qwebirc.org
[2] http://irc.w3.org
[3] http://www.w3.org/Project/IRC

M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls

Helena F. Deus

Post-Doctoral Researcher at DERI/NUIG

Received on Wednesday, 4 May 2011 15:48:09 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:46 UTC