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Bug#382994: marked as done (ITP: rebase -- The restriction enzyme database, from New England Biolabs [med-bio])

Your message dated Wed, 5 Mar 2008 20:31:52 +0900
with message-id <20080305113152.GA28041@kunpuu.plessy.org>
and subject line Closing ITPs: we will manage data differently.
has caused the Debian Bug report #382994,
regarding ITP: rebase -- The restriction enzyme database, from New England Biolabs [med-bio]
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact owner@bugs.debian.org
immediately.)


-- 
382994: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=382994
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: wnpp
Severity: wishlist
Owner: Charles Plessy <charles-debian-nospam@plessy.org>

  Package name    : rebase
  Version         : NA
  Upstream Author : Dr. Richard J. Roberts and Dana Macelis (http://rebase.neb.com/rebase/rebase.staff.html)
  URL             : http://rebase.neb.com
  License         : Permission obtained by email (see below)
  Description     : The restriction enzyme database, from New England Biolabs


  The Restriction Enzyme data BASE is a collection of information about
  restriction enzymes and related proteins. It contains published and
  unpublished references, recognition and cleavage sites, isoschizomers,
  commercial availability, methylation sensitivity, crystal and sequence
  data. DNA methyltransferases, homing endonucleases, nicking enzymes,
  specificity subunits and control proteins are also included. Most
  recently, putative DNA methyltransferases and restriction enzymes, as
  predicted from analysis of genomic sequences, are also listed. REBASE
  is continuously updated and the web pages not dynamically generated
  are refreshed on a nightly basis.


The data in REBASE consists in 39 files which are used by external
software such as PerlPrimer (distributed in Debian), EMBOSS (unofficial
Debian package), or Staden (unfficial Debian package). Packaging REBASE
will make it available to these progams and allow to update the data
without to update the debian package of these programs themeselves. The
packaging of REBASE is a first step towards a high-quality packaging of
EMBOSS, which is very important in the field of molecular biology and
bioinformatics.


I explained the upstream authors the difference between main and
non-free, and asked if they think that we can redistribute their data in
a dfsg-free manner, and here is their answer:

"REBASE is free to its users and they may use the data however
they'd like, but when this use involves repackaging the data
and redistribututing it, the common courtesy we always provide
one another is to credit the source of this data.

Users expect bibliographical content showing the sources of
your material.  This could be contained in a README file, or
a menu item, whatever.

So if you include a note such as -

 References:

  REBASE, the Restriction Enzyme Database
  Dr. R.J. Roberts and D. Macelis
  rebase.neb.com

somewhere in your distribution, that's fine."

--- End Message ---
--- Begin Message --- 
REbase, miRbase, and many other databases will be managed by Debian-Med
using a different approach than source/binary Debian packages.

Please refer to the following links to know more about it:

http://wiki.debian.org/SummerOfCode2008/biodata
http://wiki.debian.org/DebianBiologyDatabases

-- 
Charles Plessy
Debian-Med packaging team
Wakō, Saitama, Japan

--- End Message ---
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