[Bioc-devel] experiment package submission
izmirlig at mail.nih.gov
Thu Jul 22 22:12:11 CEST 2010
It occurred to me that you could submit your data to NCBI.
The National Center for Biotechnology Information is the home
the GEO database and many, many other resources.
I went to their homepage and tried to determine how one
goes about submitting data there. I wasn't able to figure
that out quickly. I called their helpline and the librarian
what type of data is it?
The answer to that question determines the route
to submitting the data, as there are different tools
for submitting different types of data. I asked
is there a review process?
She told me that
the submitter remains the sole owner of the dataset and is
solely responsible for its content and quality.
For example, if you're wishing to send in a nucleotide sequence,
1. go to the NCBI homepage
2. click "All Resources (A to Z)" in the green pane on the upper left
side of the screen
3. next click "Bankit" under "B"
4. on that page there are detailed instructions for submitting your
Of course if the data is of another type, you would go about submitting
it in a different way. Some examples of datasets now being
accepted for publication at NCBI are
Variation Data --SNP studies
For help, either dial the help line,
or get support through their email address:
info at ncbi.nlm.nih.gov
Division of Cancer Prevention
National Cancer Institute
> Date: Thu, 22 Jul 2010 05:16:58 -0700
> From: Martin Morgan <mtmorgan at fhcrc.org>
> To: Robert Castelo <robert.castelo at upf.edu>
> Cc: "bioc-devel at stat.math.ethz.ch" <bioc-devel at stat.math.ethz.ch>
> Subject: Re: [Bioc-devel] experiment package submission
> Message-ID: <4C4836BA.40609 at fhcrc.org>
> Content-Type: text/plain; charset=ISO-8859-1
> Hi Robert --
> On 07/21/2010 11:57 PM, Robert Castelo wrote:
>> Martin, a question regarding this issue just when through my mind,
>> On Wed, 2010-07-21 at 19:20 -0700, Martin Morgan wrote:
>>> An experiment data package is additional work, but in exchange you get
>>> reproducible, reliable, and documented research.
>> i haven't found any especific reference to experiment data package
>> submission in
>> and links thereafter.
>> should an experiment data package be submitted following the same
>> procedure as a software package? does it go also through a peer-review
>> process? are there requirements or guidelines specific for experiment
>> data packages?
> Often experiment data packages are produced much like in Peter's case --
> to support analysis in a particular package or group of packages. They
> (the analysis and data packages) are then subject jointly to the preview
> Sometimes experiment data packages emerge after the fact, when it
> becomes apparent that work flows or packages would benefit from a common
> data set. These generally get introduced ad hoc, without formal preview,
> but of course the packages are being built and passing R CMD check.
> We don't usually start with a 'pure' experiment data package as a
> submission -- Bioconductor is not a data repository in that sense -- but
> if one were to come in we'd treat it as a new package and submit it to
> the same formal acceptance procedure.
> Hope that helps,
>Computational Biology / Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N.
>PO Box 19024 Seattle, WA 98109
>Location: Arnold Building M1 B861
>Phone: (206) 667-2793
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