Hi Kei,
Furtunatelly arrayexpress provides both the IDF and SDRF for that
acession number,
at http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-4757
I have a small RDF document of that IDF
at http://magetab2rdf.googlecode.com/svn/trunk/E-GEOD-4757.idf.rdf
Thanks
Lena
On Tue, Dec 1, 2009 at 9:20 PM, Kei Cheung <kei.che...@yale.edu
<mailto:kei.che...@yale.edu>> wrote:
Hi Lena,
Helena Deus wrote:
@Kei,
When you said data structure, did you mean the RDF structure
For now, all I have is the java object returned by parser.
I've been using Limpopo, which creates an object that I can
then parse to RDF uing Jena. The challenge, though, has been
coming up with the predicates to formalize the relationships
between the various elements. I'm using the XML structures fir
IDF/SDRF etc. at http://magetab-om.sourceforge.net to
automatically generate the structure that will contain the
data. My plan is to then create the RDF triples that use the
attributes described in those documents and populate them with
the data from the MAGE-TAB java object created by Limpopo.
Thanks for the pointer and explaining your strategy. We might not
need to convert everything from mage-tab for our purposes.
Right now all I have is a very raw RDF/XML document describing
the relationships in the IDF structure:
http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf
The triples for that had to be encoded manually using Jena by
reading the model.
I think IDF is a good start. For a real example for our use case,
I wonder if any mage-tab file is available for experiment
E-GEOD-4757 (transcription profiling of human neurons with and
without neurofibriallary tangles from Alzheimer's patients). Helen
may know.
Cheers,
-Kei
@Satya and Jun
I would very much like to be involved in that effort, do you
already have a URL that I can look at?
Thanks
Lena
On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung
<kei.che...@yale.edu <mailto:kei.che...@yale.edu>
<mailto:kei.che...@yale.edu <mailto:kei.che...@yale.edu>>> wrote:
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>
<mailto:mdmille...@comcast.net <mailto:mdmille...@comcast.net>>
<mailto:mdmille...@comcast.net
<mailto:mdmille...@comcast.net>
<mailto: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>
<mailto:kei.che...@yale.edu <mailto:kei.che...@yale.edu>>
<mailto:kei.che...@yale.edu
<mailto:kei.che...@yale.edu> <mailto:kei.che...@yale.edu
<mailto:kei.che...@yale.edu>>>>
To: "HCLS" <public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>
<mailto:public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>>
<mailto:public-semweb-lifesci@w3.org
<mailto:public-semweb-lifesci@w3.org>
<mailto: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> <http://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>
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>>
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
<http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls>
<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)
