updating REBASE data

[trevor]

i'd like to update the included REBASE data. does anyone have an objection to this?

currently the source has this page stating the terms:
http://rebase.neb.com/rebase/rebcit.html

Those seeking to distribute REBASE files with their software packages are welcome to do so, providing it is clear to your users that they are not being charged for the REBASE data. It should be transparent that REBASE is a free and independent resource, with the following bibliographical reference:

Roberts, R.J., Vincze, T., Posfai, J., Macelis, D. (2010)
REBASE--a database for DNA restriction and modification: enzymes, genes and genomes.
Nucl. Acids Res. 38: D234-D236. 

could i add that to the LICENSE file?

[ngoto]

i'd like to update the included REBASE data. does anyone have an objection to this?

Objection. The license is regarded as "non-free".
See the discussions in debian-med and debian-science.
http://lists.debian.org/debian-med/2011/07/msg00146.html
http://lists.debian.org/debian-science/2011/07/msg00061.html

I plan to remove non-free files and add alternative codes to download them from websites.

could i add that to the LICENSE file?

No. For the purpose, "LEGAL".
But I don't like to add non free license.

[trevor]

@ngoto thanks for the pointers, i'll see if i can push the concerns upstream and have the requirements changed

[trevor]

@ngoto just to clarify to better help me craft the request, what exactly is the objection? i don't think "It should be transparent that REBASE is a free and independent resource, with the following bibliographical reference" qualifies as a non-free license?

the links you provided are specific to the EMBOSS project, i'm having trouble extending the analogy.

[ngoto]

providing it is clear to your users that they are not being charged for the REBASE data.

Charging or not is depending on distributors. Forcing not being charged is not a free software license.

It should be transparent that REBASE is a free and independent resource, with the following bibliographical reference:

It seems no problem, as far as my understanding that the sentence does not force to advertise the reference.

[tomoakin]

They just say "not being charged for the REBASE data"; i.e. charging on REBASE containing software as a whole, integration, modification, and packaging, etc. is allowed, but must make it clear that it is not for the REBASE data itself.
Thus, having a statement that the charge if any is not for REBASE data in addition to the reference to REBASE should be sufficient. I don't think this would hurt the freedom of the software that include it.

More problematic, as in the debian discussion, is whether modification as derivative work is allowed to be distributed.
This point is unclear from their statement.

[ngoto]

The statement "providing it is clear to your users that they are not being charged for the REBASE data" itself never be a part of a free software / open source license, because this prohibits user's right to distribute the data with charge.
This means the statement must be treated as an "exception".

But such exception sometimes damages whole software, for example, when providing BioRuby with pay-as-you-go plan.
If someone set up charged download service for bioruby-x.x.x.tar.gz with 1 cent per 1kB (except users' network access cost), the REBASE data could be regarded as "charged" from the users. The bundle of such exception may also discourage unique future services especially with cloud computing.

So, I don't like to add more exceptions.

More problematic, as in the debian discussion, is whether modification as derivative work is allowed to be distributed.
This point is unclear from their statement.

I think this point is also unclear.

[tomoakin]

While I don't think the clause prohibit distribution (or download service) of the data with charge as far as the charge is stated for distribution or transfer but not for the data, I agree that situation would be complicated due to ambiguity and uncertainty, and may discourage development by headache of license interpretation.

Thus, it is surely better to have written permission to distribute under GPL v.2 or other well-known formal terms.

I hope they will give such permission. Otherwise, I prefer adding codes to fetch them from ftp sites.

[trevor]

i've discussed this with Dana, the page ( http://rebase.neb.com/rebase/rebcit.html ) now states:

No license is required for users to include REBASE in their projects, since we do not have any software available for sharing at this time. Thus those seeking to distribute REBASE files or utilize our data are welcome to do so, having cited us as a bibliographical resource:

the citation can be added as comments in the dataset. i believe this resolves the issue?

[ngoto]

I think so. The change will soon be included. Thanks trevor. Many thanks to Dr. Dana Macelis, Dr. Rich Roberts and REBASE staff.

[pjotrp]

Since Trevor is maintaining a biogem for this, I feel BioRuby should migrate to using the plugin, rather than having everything duplicated.

[ngoto]

Pjotr, you are right, but for short-term benefit of existing users, the change will be included.