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Re: BioRDF Telcon

From: Helena Deus <helenadeus@gmail.com>
Date: Tue, 24 Nov 2009 12:06:29 -0600
Message-ID: <6bd01db90911241006l320ead08j86e99ab97e74204b@mail.gmail.com>
To: mdmiller <mdmiller53@comcast.net>
Cc: Kei Cheung <kei.cheung@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
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)
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>
Received on Tuesday, 24 November 2009 18:06:56 GMT

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