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Re: BioRDF Telcon

From: Helena Deus <helenadeus@gmail.com>
Date: Wed, 2 Dec 2009 17:27:58 -0600
Message-ID: <6bd01db90912021527t33333858t551f41f31108c425@mail.gmail.com>
To: Kei Cheung <kei.cheung@yale.edu>
Cc: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>
Hi Kei,

Furtunatelly arrayexpress provides both the IDF and SDRF for that acession
number, at
http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=E-GEOD-4757

I have a small RDF document of that IDF at
http://magetab2rdf.googlecode.com/svn/trunk/E-GEOD-4757.idf.rdf

Thanks
Lena



On Tue, Dec 1, 2009 at 9:20 PM, Kei Cheung <kei.cheung@yale.edu> wrote:

> Hi Lena,
>
>
> Helena Deus wrote:
>
>  @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.
>>
>
>
> Thanks for the pointer and explaining your strategy. We might not need to
> convert everything from mage-tab for our purposes.
>
>
>
>> 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.
>>
>
> I think IDF is a good start. For a real example for our use case, I wonder
> if any mage-tab file is available for experiment E-GEOD-4757 (transcription
> profiling of human neurons with and without neurofibriallary tangles from
> Alzheimer's patients). Helen may know.
>
> Cheers,
>
> -Kei
>
>
>> @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 <mailto:
>> 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>
>>        <mailto: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>
>>        <mailto:kei.cheung@yale.edu <mailto:kei.cheung@yale.edu>>>
>>
>>
>>           To: "HCLS" <public-semweb-lifesci@w3.org
>>        <mailto:public-semweb-lifesci@w3.org>
>>           <mailto: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>
>>        <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>
>>                         <
>> 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 Wednesday, 2 December 2009 23:28:39 UTC

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