Scripps Team Demonstrates Feasibility of Unearthing Gene-Disease Links via Bio-Wiki Mashups

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Dave Clements

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Aug 8, 2011, 8:03:09 PM8/8/11
to BioWiki Group

Henning Stehr

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Aug 9, 2011, 4:37:31 AM8/9/11
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Full-text access for premium subscribers only :( But Google cache to
the rescue...

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Mike Cariaso

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Aug 9, 2011, 5:16:57 AM8/9/11
to Henning Stehr, BioWiki Group, Greg Lennon
didn't know about that trick for genomeweb, thanks Henning.

to save the rest of us the effort

http://webcache.googleusercontent.com/search?q=cache:4q2xP-p9GqwJ:www.genomeweb.com/informatics/scripps-team-demonstrates-feasibility-unearthing-gene-disease-links-bio-wiki-mas


Aside, I'm leaving the Netherlands, going to Berlin for the SMW conf, ...
and then wandering the globe for a few months. If anyone is interested
in playing host for a few days, I might wander your direction.
http://cariaso.livejournal.com/42440.html

--
--
Mike Cariaso
http://www.cariaso.com

Benjamin Good

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Aug 9, 2011, 10:55:33 AM8/9/11
to Henning Stehr, BioWiki Group
If anyone wants to read the original work, see the mashup paper she is primarily talking about here:

See also Andrew Su's keynote from the same meeting

-Ben

Mike Cariaso

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Aug 9, 2011, 11:26:04 AM8/9/11
to Benjamin Good, Henning Stehr, BioWiki Group
paper looks good, but I'm equally curious to see any raw data, code
etc that doesn't meet the definition of publishable. Surely there is
info there I can use to further curate SNPedia with my own bots. In
particular there was another image from the same conference, a
circulos I believe. I'd love to crank one of those out on SNPedia just
to see the purty colors.

--

Benjamin Good

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Aug 9, 2011, 11:37:50 AM8/9/11
to Mike Cariaso, BioWiki Group
Hi Mike,

 You can access the data via the mediawiki api at this URL (which we do not guarantee to be stable or reliable just yet...)

 You can also access data dumps used for the paper here:

 We had some help on that Circos image so i don't have code for you there.  All of the Circos code is open source and there is a Web-based access point for smallish datasets.  See 

 Say hi to our co-author Salvatore Loguercio at the SMWcon ;).  I'm sure he can fill you in on any more details you'd like.

-Ben

Dave Clements

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Aug 10, 2011, 12:26:20 AM8/10/11
to Mike Cariaso, Henning Stehr, BioWiki Group, Greg Lennon
Hi Mike, Henning,

I forgot about the "premium subscription" part. Thanks for finding the article through other means.  :-)

As an FYI, GenomeWeb does not require you to pay to access content if you create a login using an email address that ends in .edu.  My .org or gmail.com address would not do the trick.  I don't know how they work with educational domains outside the States.

Dave C.

Henning Stehr

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Aug 10, 2011, 8:15:00 AM8/10/11
to Dave Clements, BioWiki Group
Hi Dave,

I didn't know about the premium access for .edu emails. Thanks for
that information. I just sent an email to GenomeWeb to ask about their
policy for researchers at non-US institutes.

Henning

On Wed, Aug 10, 2011 at 6:26 AM, Dave Clements

Sujai

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Aug 10, 2011, 10:43:02 AM8/10/11
to BioWiki
Hi Henning

I can confirm that genomeweb access works for @ed.ac.uk logins

Of course - asking them for an official policy is better :-)

- Sujai

On Aug 10, 8:15 am, Henning Stehr <st...@molgen.mpg.de> wrote:
> Hi Dave,
>
> I didn't know about the premium access for .edu emails. Thanks for
> that information. I just sent an email to GenomeWeb to ask about their
> policy for researchers at non-US institutes.
>
> Henning
>
> On Wed, Aug 10, 2011 at 6:26 AM, Dave Clements
>
>
>
>
>
>
>
> <cleme...@galaxyproject.org> wrote:
> > Hi Mike, Henning,
>
> > I forgot about the "premium subscription" part. Thanks for finding the
> > article through other means.  :-)
>
> > As an FYI, GenomeWeb does not require you to pay to access content if you
> > create a login using an email address that ends in .edu.  My .org or
> > gmail.com address would not do the trick.  I don't know how they work with
> > educational domains outside the States.
>
> > Dave C.
>
> > On Tue, Aug 9, 2011 at 2:16 AM, Mike Cariaso <cari...@gmail.com> wrote:
>
> >> didn't know about that trick for genomeweb, thanks Henning.
>
> >> to save the rest of us the effort
>
> >>http://webcache.googleusercontent.com/search?q=cache:4q2xP-p9GqwJ:www...
>
> >> Aside, I'm leaving the Netherlands, going to Berlin for the SMW conf, ...
> >> and then wandering the globe for a few months. If anyone is interested
> >> in playing host for a few days, I might wander your direction.
> >>http://cariaso.livejournal.com/42440.html
>
> >> On Tue, Aug 9, 2011 at 10:37 AM, Henning Stehr <st...@molgen.mpg.de>
> >> wrote:
> >> > Full-text access for premium subscribers only :( But Google cache to
> >> > the rescue...
>
> >> > On Tue, Aug 9, 2011 at 2:03 AM, Dave Clements
> >> > <cleme...@galaxyproject.org> wrote:
> >> >> An article on GenomeWeb:
>
> >> >>http://www.genomeweb.com/informatics/scripps-team-demonstrates-feasib...

Henning Stehr

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Aug 10, 2011, 10:54:21 AM8/10/11
to Sujai, BioWiki
Here is the result of my inquiry:

They upgraded my account to premium but they didn't answer my question
about their general policy. So, at the moment, if you want premium
access (and don't have a .edu or .ac.uk email), you'll have to ask.
Maybe if enough people ask, they will bother to make this more
systematic...

Dave Clements

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Aug 10, 2011, 2:01:37 PM8/10/11
to Henning Stehr, Sujai, BioWiki
Hi All,

I just got this from Bernadette Toner at GenomeWeb.  They seem to really want academics/non-profits to have free access.

Dave C.

Subject: RE: [BioWiki] Scripps Team Demonstrates Feasibility of Unearthing Gene-Disease Links via Bio-Wiki Mashups
------------------------

From: Bernadette Toner <bto...@genomeweb.com>
Date: Wed, Aug 10, 2011 at 10:46 AM
To: clem...@galaxyproject.org


Hi Dave -

 

Saw this thread on the BioWiki list and don't want to butt in, but for the record any academic or non-profit researcher has free access to all content on GenomeWeb as long as they register and log in with their work e-mail address.

 

It would be great if you could pass the word along.

 

Thanks!

 

- Bernadette

................................
Bernadette Toner
Editorial Director
GenomeWeb Newsletters
www.genomeweb.com
+1 212-651-5636 voice
+1 212-269-3686 fax
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