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Re: BioRDF Telcon

From: Satya Sahoo <sahoo.2@wright.edu>
Date: Tue, 01 Dec 2009 15:36:41 -0500
To: mdmiller <mdmiller53@comcast.net>, Helena Deus <helenadeus@gmail.com>
Cc: Kei Cheung <kei.cheung@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
Message-id: <6420bcc911c634.4b153809@wright.edu>
Hi all,
michael wrote:
> 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.

Could you list some specific terms that describe "how gene list was obtained" and "higher level of analysis"? - we can include these in the list of provenance terms I am compiling to describe the experiment context. An initial list of provenance terms from a MAGE-ML file [1] is located at [2].
 
lena: I am trying to get edit rights for the wiki pages (I believe my username "SatyaSahoo" needs to be added to a list according to the new W3C wiki policy). I will send out an update and link once I get access.
 
Best,
satya
 
Kno.e.sis center, WSU
http://knoesis.wright.edu/researchers/satya
 
[1] http://np2.ctrl.ucla.edu/np2/mage/mageml.jsp
[2]  http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt
 
 

> On Tue, Nov 24, 2009 at 9:59 AM, mdmiller 
<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>>
> >     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 #
> >
Received on Tuesday, 1 December 2009 20:37:15 UTC

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