[Bioc-devel] License question for experimental data package
Lyle Burgoon
burgoon.lyle at gmail.com
Fri Mar 4 16:17:48 CET 2016
Also keep in mind US copyright rules for data are different from European.
We ran into this recently when wanting to publish european data from a web
database.
On Mar 4, 2016 10:05 AM, "Tim Triche, Jr." <tim.triche at gmail.com> wrote:
> Data (facts) are not copyright worthy, but databases (collections of
> facts) can be. See Feist v Rural for precedent; in short, there must be an
> inobvious and creative aspect to the database for it to be elevated to
> copyrightable status. I doubt that a collection of datasets would clear
> this bar, but it's still worth noting.
>
> --t
>
> > On Mar 4, 2016, at 6:22 AM, Robert M. Flight <rflight79 at gmail.com>
> wrote:
> >
> > I am pretty sure in general "data" is not copyrightable per se (
> > http://www.lib.umich.edu/copyright/facts-and-data), so while I might
> > contact the original authors as a courtesy, if the data has been released
> > into any public database, then you should be free to do with it as you
> > please. Providing the original accession numbers for the data and
> relevant
> > citations (if they exist) so that it is easy for you and others to be
> given
> > credit if the data is used would be a good thing to do.
> >
> > Also, I would personally go with the CC0 (waive of copyright, see
> > https://wiki.creativecommons.org/wiki/CC0) for a data package, as the
> data
> > is already publicly available, you have just packaged it together into a
> > useful set.
> >
> > My 2 cents.
> >
> > -Robert
> >
> > Robert M Flight, PhD
> > Bioinformatics Research Associate
> > Resource Center for Stable Isotope Resolved Metabolomics
> > Manager, Systems Biology and Omics Integration Journal Club
> > Markey Cancer Center
> > CC434 Roach Building
> > University of Kentucky
> > Lexington, KY
> >
> > Twitter: @rmflight
> > Web: rmflight.github.io
> > ORCID: http://orcid.org/0000-0001-8141-7788
> > EM rflight79 at gmail.com
> > PH 502-509-1827
> >
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> say
> > what the experiment died of. - Ronald Fisher
> >
> >
> >
> > On Fri, Mar 4, 2016 at 8:52 AM Kasper Daniel Hansen <
> > kasperdanielhansen at gmail.com> wrote:
> >
> >> For data packages, which does not contain any code, it seems weird to
> use a
> >> software license such as GPL or GPL-2. It seems better to use something
> >> like Artistic-2.0 or one of the CC licenses.
> >>
> >> On Thu, Mar 3, 2016 at 5:15 PM, davide risso <risso.davide at gmail.com>
> >> wrote:
> >>
> >>> 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.
> >>>
> >>> Best,
> >>> davide
> >>>
> >>>
> >>>
> >>>
> >>> 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
> >>>> datasets
> >>>>> 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
> >>>> thinking
> >>>>> 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
> >>>> wondering
> >>>>> what is the best practice in terms of license / data sharing. Since
> >>> there
> >>>>> are many experimental data packages in Bioconductor, I'm guessing
> >> that
> >>>> I'm
> >>>>> 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
> >>>> the
> >>>>> 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
> >>>> redistribute?
> >>>>> 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?
> >>>>
> >>>> H.
> >>>>
> >>>>>
> >>>>> 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
> >>>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
> >>> _______________________________________________
> >>> Bioc-devel at r-project.org mailing list
> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>>
> >>
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> >>
> >> _______________________________________________
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> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
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> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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>
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