Re: BioRDF Telcon

hi all,

the MAGE-TAB also can have (and often does) good phenotypic information on the sources (patients, mice, etc) of the samples used plus the experimental factors.

it does typically have the method to process from the raw to the processed data but what i meant was the information on how the normalized processed data was reduced to the gene list.

cheers,
michael
  ----- Original Message ----- 
  From: Helena Deus 
  To: mdmiller 
  Cc: Kei Cheung ; HCLS 
  Sent: Tuesday, November 24, 2009 10:06 AM
  Subject: Re: BioRDF Telcon


  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> 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>
    To: "HCLS" <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 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
        * 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)