On Jul 29, 2011, at 3:39 AM, Peter Rice wrote: > 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 > term. > > 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 > rsync://emboss.open-bio.org/EMBOSS/ > > 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" > > regards, > > Peter Rice > EMBOSS Team
Charles, >From the BioPerl perspective, this will very likely be a problem for us as >well as all other Bio* language (Biopython, BioJava, BioRuby); we typically >include data derived from these sources. We may have a bit more flexibility >in that the vast majority are mainly only for tests, but I believe some data >is hard-coded in. Fallback data like REBase for restriction analysis and GO >(as Peter mentioned above) come to mind. chris Christopher Fields Senior Research Scientist National Center for Supercomputing Applications Institute for Genomic Biology University of Illinois Urbana-Champaign 1206 W. Gregory Dr. , MC-195 Urbana, IL 61801 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
