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Re: BioRDF Telcon

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 24 Nov 2009 15:19:21 -0500
To: Helena Deus <helenadeus@gmail.com>
Cc: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>
Message-id: <4B0C3FC9.5030704@yale.edu>
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>> 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 #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>
>             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 Tuesday, 24 November 2009 20:20:03 GMT

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