[Bioc-devel] License question for experimental data package
davide risso
risso.davide at gmail.com
Fri Mar 4 21:12:02 CET 2016
Thank you all for the useful suggestions and links.
I like the idea of using a CC0 license. That's likely what I will go for.
Best,
davide
On Fri, Mar 4, 2016 at 7:42 AM Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> I was going to mention droit d'auteur under EU common law, but somehow
> that seemed more in Hervé's wheelhouse ;-).
>
> --t
>
> > On Mar 4, 2016, at 7:17 AM, Lyle Burgoon <burgoon.lyle at gmail.com> wrote:
> >
> > 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
> >> >>>
> >> >>
> >> >> [[alternative HTML version deleted]]
> >> >>
> >> >> _______________________________________________
> >> >> Bioc-devel at r-project.org mailing list
> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >> >
> >> > [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioc-devel at r-project.org mailing list
> >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >> [[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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