[EMBOSS] Files included in EMBOSS but licensed ...

Peter Rice pmr at ebi.ac.uk
Fri Jul 29 08:39:46 UTC 2011

On 07/29/2011 08:46 AM, Peter Rice wrote:
> 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. 

While we're on the topic of licensing, some other data files in EMBOSS
6.4.0 have licences.

emboss/data/OBO contains copies of several Open Bio-Ontologies for which
EMBOSS includes index files - so you need the data file version that
matches the index files.

For example, the Gene Ontology terms
http://www.geneontology.org/GO.cite.shtml are:

GO Usage Policy

The GO Consortium gives permission for any of its products to be used
without license for any purpose under three conditions:

    That the Gene Ontology Consortium is clearly acknowledged as the
source of the product;
    That any GO Consortium file(s) displayed publicly include the
date(s) and/or version number(s) of the relevant GO file(s) (the GO is
evolving and changes will occur with time);
    That neither the content of the GO file(s) nor the logical
relationships embedded within the GO file(s) be altered in any way.

which looks rather like the problem you had with Creative Commons.

Licenses that protect the official database release from derives
versions are entirely reasonable and standard in bioinformatics.
Basically, making sure that when you refer to a UniProt entry, or a, OBO
ontology term, everyone agrees you are referring to one agreed entry or

EMBOSS does depend on these files. The database names are hard-coded
into some of the new (and more to come) applications.

You could download the databases and indexes from our rsync copies we
use to keep developers in sync. These are at

It might make things clearer if someone from Debian could explain:

(a) why a Creative Commons licence is an issue for you

(b) why you appear to consider a copy of a whole or part of a public
biological database as part of an "operating system"


Peter Rice

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