Hi Lena et al,
When you said data structure, did you mean the RDF structure. If so, is
a pointer to the structure that we can look at?
As discussed during yesterday's call, Jun and Satya will help create a
wiki page for listing some of the requirements for provenance/workflow
in the context of gene lists, perhaps we should also use it to help
coordinate some of the future activities (people also brought up Taverna
during the call yesterday). Please coordinate with Satya and Jun.
Cheers,
-Kei
Helena Deus wrote:
Hi all,
I apologize for missing the call yesterday! It seems you had a pretty
interesting discussion! :-)
If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into
RDF would result in obtaining only the raw and processed data files
but not the mechanism used to process it nor the resulting gene list.
That's also what I concluded after looking at the data structure
created by Tony Burdett's Limpopo parser.
However, having the raw data as linked data is already a great start!
Kei, should I be looking into Taverna in order to reprocessed the raw
files with a traceable analysis workflow?
Thanks!
Lena
On Tue, Nov 24, 2009 at 9:59 AM, mdmiller <mdmille...@comcast.net
<mailto:mdmille...@comcast.net>> wrote:
hi all,
(from the minutes)
"Yolanda/Kei/Scott: semantic annotation/description of workflow
would enable the retrieval of data relevant to that workflow (i.e.
data that could be used to populate that workflow for a different
experimental scenario)"
what is typically in a MAGE-TAB/MAGE-ML document are the protocols
for how the source was processed into the extract then how the
hybridization, feature extraction, error and normalization were
performed. these are interesting and different protocols can
cause differences at this level but it is pretty much a known art
and usually not of too much interest or variability.
what is usually missing from those documents, along with the final
gene list, is how that gene list was obtained, what higher level
analysis was used, that is generally only in the paper unfortunately.
cheers,
michael
.
----- Original Message ----- From: "Kei Cheung"
<kei.che...@yale.edu <mailto:kei.che...@yale.edu>>
To: "HCLS" <public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>>
Sent: Monday, November 23, 2009 1:27 PM
Subject: Re: BioRDF Telcon
Today's BioRDF minutes are available at the following:
http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
Thanks to Rob for scribing.
Cheers,
-Kei
Kei Cheung wrote:
This is a reminder that the next BioRDF telcon call will
be held at 11 am EDT (5 pm CET) on Monday, November 23
(see details below).
Cheers,
-Kei
== Conference Details ==
* Date of Call: Monday November 23, 2009
* Time of Call: 11:00 am Eastern Time
* Dial-In #: +1.617.761.6200 (Cambridge, MA)
* Dial-In #: +33.4.89.06.34.99 (Nice, France)
* Dial-In #: +44.117.370.6152 (Bristol, UK)
* Participant Access Code: 4257 ("HCLS")
* IRC Channel: irc.w3.org <http://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
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>
for IRC access.
* Duration: ~1 hour
* Frequency: bi-weekly
* Convener: Kei Cheung
* Scribe: to-be-determined
== Agenda ==
* Roll call & introduction (Kei)
* RDF representation of microarray experiment and data (All)
* Provenance and workflow (All)
