[EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs

Peter Rice pmr at ebi.ac.uk
Fri Jul 29 07:28:48 UTC 2011

On 28/07/2011 15:38, Charles Plessy wrote:
> Dear EMBOSS developers,
> (CC Debian Med mailing list)
> while working on upgrading Debian's emboss package to version 6.4.0
> (congratulations, by the way), I found some files in EMBOSS that are
> not considered ‘Free software’ by Debian.  They were actually present
> in past releases as well. Here is their list:
> test/data/amir.swiss
> test/data/uniprotft.sw
> test/swiss/seq.dat
> test/swnew/trembl.dat

Huh? Example entries from UniProt? We can of course remove them from the 
distribution but then the QA tests will not work if anyone tries them.

I suspect amir.swiss predates this UniProt licensing, but the others are 
more recently updated.

Anyway, EMBOSS will work perfectly well without them. You can just 
delete them.

> and emboss/data/dbxref.txt

That one can go. It was a source for the DRCAT.dat data resource 
catalogue and yes we do have permission from UniProt to use it.

> Their license is Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND
> 3.0), and it disallows modification of the files.  The presence of these files
> in EMBOSS makes it impossible for Debian to redistribute it in our operating
> system.  I have confirmed with the UniProt consortium's helpdesk that, even in
> isolation, these files are covered by the CC BY-ND license.  I see three
> possible solutions.
>   a) Remove the files in Debian's EMBOSS package.
>   b) Distribute EMBOSS with the files, but in the non-free section of the Debian archive.
>   c) Replace the files by Free equivalents, for instance by re-creating records from scratch.
> I am not very comfortable with any of the solutions, and was wondering if you
> would have suggestions ?

I will also have words with the UniProt folk at EBI and if it really is 
not possible to include a few example entries with EMBOSS then I'll 
check with the other Open Bio projects. This is really silly.


Peter Rice

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