[Bioc-devel] experiment package submission

Grant Izmirlian 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
asked me

   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, 
you would 

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
  nucleotide sequence.

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
   Nucleotide Sequences
  Expression Analyses
  Variation Data --SNP studies

For help, either dial the help line, 

or get support through their email address:
info at ncbi.nlm.nih.gov

Best Regards,
Grant Izmirlian
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
>> http://wiki.fhcrc.org/bioc/HowTo/Package_Contribution
>> 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
> process.
> 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,
> Martin
>> thanks!
>> robert.
>Martin Morgan
>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

More information about the Bioc-devel mailing list