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Re: BioRDF Telcon

From: Helena Deus <helenadeus@gmail.com>
Date: Mon, 30 Nov 2009 09:47:03 -0600
Message-ID: <6bd01db90911300747i193a85c1x1dda316ac890dfa3@mail.gmail.com>
To: Kei Cheung <kei.cheung@yale.edu>
Cc: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>
@Kei,

When you said data structure, did you mean the RDF structure


For now, all I have is the java object returned by parser. I've been using
Limpopo, which creates an object that I can then parse to RDF uing Jena. The
challenge, though, has been coming up with the predicates to formalize the
relationships between the various elements. I'm using the XML structures fir
IDF/SDRF etc. at http://magetab-om.sourceforge.net to automatically generate
the structure that will contain the data. My plan is to then create the RDF
triples that use the attributes described in those documents and populate
them with the data from the MAGE-TAB java object created by Limpopo.

Right now all I have is a very raw RDF/XML document describing the
relationships in the IDF structure:
http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf
The triples for that had to be encoded manually using Jena by reading the
model.

@Satya and Jun

I would very much like to be involved in that effort, do you already have a
URL that I can look at?

Thanks
Lena

On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung <kei.cheung@yale.edu> wrote:

> 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)
>>
>>
>>
>>
>>
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>
>
Received on Monday, 30 November 2009 15:47:39 GMT

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