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Re: BioRDF Telcon

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 24 Nov 2009 15:26:09 -0500
To: mdmiller <mdmiller53@comcast.net>
Cc: Helena Deus <helenadeus@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
Message-id: <4B0C4161.3040605@yale.edu>
mdmiller wrote:
> 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.
I think it's also important for EFO to be harmonized with existing 
ontologies like the one in NCBO.

Cheers,

-Kei
>  
> 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 <mailto:helenadeus@gmail.com>
>     *To:* mdmiller <mailto:mdmiller53@comcast.net>
>     *Cc:* Kei Cheung <mailto:kei.cheung@yale.edu> ; HCLS
>     <mailto:public-semweb-lifesci@w3.org>
>     *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
>     <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)
>
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Received on Tuesday, 24 November 2009 20:26:43 GMT

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