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RE: How to access RDF for NeuroFibrillaryTangle (NFT) microarray study?

From: Michael Miller <mmiller@systemsbiology.org>
Date: Thu, 12 May 2011 08:43:14 -0700
Message-ID: <a21654b56c3df3eb673b9bf5563676c5@mail.gmail.com>
To: anita bandrowski <bandrow@gmail.com>
Cc: Maryann Martone <maryann@ncmir.ucsd.edu>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>, jgrethe@ucsd.edu, Amarnath Gupta <gupta@sdsc.edu>
hi anita,



thanks for your reply.



"... so we would have a large mess on our hands if we did this "



yes, that's very true.  what other kind of RDF links are possible, or are
those two records i found isolated from the rest of the terms in NIF?  we'd
like to be able to send some sort of sparql query to see what we could find.



cheers,

michael





*From:* anita bandrowski [mailto:bandrow@gmail.com]
*Sent:* Wednesday, May 11, 2011 12:27 PM
*To:* Michael Miller
*Cc:* Maryann Martone; M. Scott Marshall; HCLS; jgrethe@ucsd.edu; Amarnath
Gupta
*Subject:* Re: How to access RDF for NeuroFibrillaryTangle (NFT) microarray
study?



Dear Scott and Michael,

Sorry about the late response.  We don't store the raw data from GEO (just
the metadata) as it often needs substantial cleaning and standardization so
we would have a large mess on our hands if we did this.

We do have data from Geo after one of the microarray projects such as Gemma
or GeneNetwork has cleaned it and standardized it, but this dataset is not
yet included in one of those databases.  Though I can ask Paul (from Gemma)
if he would be willing to put this one up in priority for addition to Gemma
(then you can use their tools to see how it fits with other data).

The raw data can be downloaded from the bottom of this page:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4757

Tar file location:
ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE4757/GSE4757%5FRAW%2Etar

Best,
anita
ps. I have not heard of the enigma project and don't have it in the
registry.  Wonder if it ever made it onto the web?

On Wed, May 11, 2011 at 9:30 AM, Michael Miller <mmiller@systemsbiology.org>
wrote:

hi all,

thanks for taking a look at this.

to clarify what i saw in NIF was the two studies we are interested in but
only with rudimentary meta data.  it wasn't clear how to query the rest of
NIF for more information, data, protocols used, etc. about those
experiments.

cheers,
michael

> -----Original Message-----
> From: Maryann Martone [mailto:maryann@ncmir.ucsd.edu]
> Sent: Tuesday, May 10, 2011 7:25 PM
> To: M. Scott Marshall
> Cc: Anita Bandrowski; Michael Miller; HCLS; jgrethe@ucsd.edu Jeffrey;
> Amarnath Gupta
> Subject: Re: How to access RDF for NeuroFibrillaryTangle (NFT)
> microarray study?

>
> Hi Scott:
>
> Not sure whether we've exported these in RDF yet, but added Jeff and
> Amarnath to this thread.
>
> Maryann
>
> On May 10, 2011, at 2:36 PM, M. Scott Marshall wrote:
>
> > Hi Anita,
> >
> > Following up on our previous conversation, Michael Miller (CC'd)
> > looked into getting a NIF version of RDF for one of the NFT
> microarray
> > data sets that we've represented in RDF so that we could compare but
> > wasn't sure how to proceed. Could you help us?
> >
> > We are looking into harmonizing representations and documenting what
> > we find as a relatively stable target for RDF representations in a
> W3C
> > note.
> >
> > <QUOTE>
> > http://neuinfo.org/nif/nifgwt.html?query="nifall"&category=Nervous
> > System Level:Microarray then add GSE4757 to search
> > <mscottm> Michael: I will look into the NIF version of our datasets.
> > <Zakim> +SatyaSahoo
> > <michael> and GSE5281 also returns a hit
> > <michael> but it isn't clear to me how to use this info within NIF
> > </QUOTE>
> >
> > Something completely different: Have you heard of the Enigma Project?
> > I thought that it was housed at UCSD but couldn't google it. It
> > involves radiomics (mapping omics to brain image data). I heard about
> > it at a BBMRI (biobanking) conference last year.
> >
> > Cheers,
> > Scott
> >
> > --
> > M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> > http://staff.science.uva.nl/~marshall
> >
>
> Maryann Martone, Ph. D.
> Professor-in-Residence
> Department of Neuroscience
> University of California, San Diego
> San Diego, CA 92093-0446
>
> 858-822-0745




-- 
Anita Bandrowski, Ph.D.
NIF Project Lead
UCSD 858-822-3629
http://neuinfo.org
9500 Gillman Dr.#0446
la Jolla, CA 92093-0446
Received on Thursday, 12 May 2011 15:51:19 GMT

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