[Bioc-devel] License question for experimental data package
risso.davide at gmail.com
Thu Mar 3 23:15:29 CET 2016
Hi Hervé and Sean,
thanks for your help. It will indeed be interesting to hear how other
people chose the license, especially for those package that redistribute a
dataset not from their lab.
I do have an experimental data package in Bioc, zebrafishRNASeq, but it's
an experiment from a collaborator and at the time I didn't pay much
attention on which license to use.
In this case, I'd like to redistribute data from different labs. I guess I
will contact the original authors at least as a courtesy.
But I'm still keen to hear opinions on which license(s) is appropriate for
experimental data sharing.
On Thu, Mar 3, 2016 at 12:50 PM Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Davide,
> On 03/01/2016 02:25 PM, davide risso wrote:
> > Dear Bioc developers,
> > I recently downloaded three publicly available single-cell RNA-seq
> > from the NCBI GEO/SRA repository and created an R package with some
> > gene-level summaries (read counts and FPKMs).
> > I'm currently using the package locally for my own tests, but I'm
> > that this may be a useful resource for the community and thinking of
> > sharing it on github and eventually submit it to Bioconductor.
> > I was not involved in any way with the original studies, and I'm
> > what is the best practice in terms of license / data sharing. Since there
> > are many experimental data packages in Bioconductor, I'm guessing that
> > not the first person wondering about this.
> >>From the NCBI website, I read (quote from
> > https://www.ncbi.nlm.nih.gov/home/about/policies.shtml):
> > Databases of molecular data on the NCBI Web site include such examples as
> > nucleotide sequences (GenBank), protein sequences, macromolecular
> > structures, molecular variation, gene expression, and mapping data. They
> > are designed to provide and encourage access within the scientific
> > community to sources of current and comprehensive information. Therefore,
> > NCBI itself places no restrictions on the use or distribution of the data
> > contained therein. Nor do we accept data when the submitter has requested
> > restrictions on reuse or redistribution. However, some submitters of the
> > original data (or the country of origin of such data) may claim patent,
> > copyright, or other intellectual property rights in all or a portion of
> > data (that has been submitted). NCBI is not in a position to assess the
> > validity of such claims and since there is no transfer of rights from
> > submitters to NCBI, NCBI has no rights to transfer to a third party.
> > Therefore, NCBI cannot provide comment or unrestricted permission
> > concerning the use, copying, or distribution of the information contained
> > in the molecular databases.
> > Should I contact the original authors for permission? Or is the fact that
> > the data were publicly shared enough to grant me permission to
> > In that case, is there a standard license that I should use?
> > Thanks for any feedback / thought!
> I don't have much to offer. AFAIK we don't really have guidelines or
> recommendations for what license to use for experimental data packages,
> except for the usual "make sure you use an appropriate license" advice.
> So far it has really been up to each author/maintainer to make sure
> they pick up a license that is compatible with the original
> license/copyright/patent of the original data they are packaging
> and with its redistribution thru the Bioconductor channel.
> FWIW here is a summary of the licenses used by the 276 experimental
> data packages currently in BioC devel:
> License Nb of packages
> ------------ --------------
> GPL 135
> Artistic-2.0 96
> LGPL 41
> other 4
> Would be interesting to hear from other developers about this. For
> example, how people choose between GPL vs Artistic-2.0? Is one
> license typically more appropriate for packaging and redistributing
> data that is already publicly available?
> > Best,
> > davide
> > [[alternative HTML version deleted]]
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
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