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

Adam Sjøgren asjo at koldfront.dk
Sat Jul 30 11:36:54 UTC 2011

On Sat, 30 Jul 2011 09:58:07 +0100, Peter wrote:

> A specific example might help. About 5 years ago a release of the
> UniProt database (as plain text files) broke the Wisconsin (GCG)
> sequence analysis package.


This is the opposite problem of what I tried to sketch.

Your example has closed source software that can't be fixed, leading to
either preprocessing or changing the database rather than fixing the
real problem.

If the software had been free, you could just have fixed the software.

Switch around "software" and "database", and you have the example I was
trying to paint.

> I expect there are many problems that arise if data ... and
> documentation ... are considered to be software.

Sure. The whole GFDL debate took quite a while, I think.

But that doesn't change that one of the solutions outlined by Charles
Plessy is necessary for Debian to distribute EMBOSS (and any other piece
of free/redistributable software).

>> (I personally think it would make sense to change to a Creative Commons
>> license that allows derivative works - Uniprot and others are going to
>> be the canonical source for the data anyway, so nothing will be lost by
>> them by doing that, as far as I can see.)

> Unlikely. The no-derivatives version is specifically there to prevent
> derivatives - for example Debian distributing a modified UniProt
> without permission.

What I was trying to say is that I don't think that that clause gives
any value to the owners of Uniprot and other databases.

Why would Uniprot want to prevent derivative works? They'll always be
the canonical source for the correct information.

You are free to distribute a modified version of the man-page for ls(1)
- but if you introduce errors in it or make it worse, nobody will choose
your derived version.

> The ontologies are similar, but do allow for the use case of importing
> terms from one ontology into another if the ontology name is changed
> (and preferably if cross-references to the original are provided).

> Again, the need is to protect the integrity of the original ontology
> content so references to a GO term or a UniProt entry are clearly
> defined.

I think the problem that is being protected against is non-existing.

People don't want to break stuff that works, they want to be able to fix
stuff that doesn't.

> This is essential for many of the public bioinformatics databases.

Why? Only a hypothetical derivative would be changed, not the original.

If someome distributed a derivative that was broken, I think people
would quickly abandon it.

Again, just my point of view - not representing or speaking for anyone :-)

  Best regards,


 "Good car to drive after a war"                              Adam Sjøgren
                                                         asjo at koldfront.dk

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