- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Tue, 01 Dec 2009 22:20:35 -0500
- To: Helena Deus <helenadeus@gmail.com>
- CC: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>
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.cheung@yale.edu
> <mailto:kei.cheung@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
> <mdmiller53@comcast.net <mailto:mdmiller53@comcast.net>
> <mailto:mdmiller53@comcast.net
> <mailto:mdmiller53@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.cheung@yale.edu <mailto:kei.cheung@yale.edu>
> <mailto:kei.cheung@yale.edu <mailto:kei.cheung@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>>>
>
> 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> 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>>
> 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)
>
>
>
>
>
>
>
>
>
>
>
>
>
Received on Wednesday, 2 December 2009 03:21:07 UTC