- From: Kei Cheung <kei.cheung@yale.edu>
- Date: Mon, 07 Dec 2009 10:12:06 -0500
- To: Helena Deus <helenadeus@gmail.com>
- Cc: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>, Helen Parkinson <parkinson@ebi.ac.uk>
Hi Lena,
Thanks for finding the IDF and SDRF files corresponding to the
experiment (E-GEOD-4757). It looks like the SDRF file contains richer
metadata that can support richer semantic queries across experiments
(e.g., finding experiments that involve the same cell types for the
same/related brain regions for the same species).
I noticed in the SDRF file that there are 20 samples (10 normal and 10
AD with neurofibriallary tangle). According to the abstract of the paper
(http://www.ncbi.nlm.nih.gov/pubmed/16242812?dopt=Abstract), it says the
following:
" ... we compared gene expression profiles of NFT-bearing entorhinal
cortex neurons from 19 AD patients, adjacent non-NFT-bearing entorhinal
cortex neurons from the same patients, and non-NFT-bearing entorhinal
cortex neurons from 14 non-demented, histopathologically normal controls
(ND). "
If I understand it correctly, there should be a total of 33 samples (19
AD and 14 normal). This may be more of a curation question for the
ArrayExpress team. Maybe I missed something.
Cheers,
-Kei
Helena Deus wrote:
> 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.cheung@yale.edu
> <mailto:kei.cheung@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.cheung@yale.edu <mailto:kei.cheung@yale.edu>
> <mailto: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>>
> <mailto: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>>
> <mailto: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>>
> <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)
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
Received on Monday, 7 December 2009 15:20:54 UTC