- From: Helena Deus <helenadeus@gmail.com>
- Date: Wed, 2 Dec 2009 17:27:58 -0600
- To: Kei Cheung <kei.cheung@yale.edu>
- Cc: mdmiller <mdmiller53@comcast.net>, HCLS <public-semweb-lifesci@w3.org>
- Message-ID: <6bd01db90912021527t33333858t551f41f31108c425@mail.gmail.com>
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)
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>
Received on Wednesday, 2 December 2009 23:28:39 UTC