[BioSQL-l] Announcement: BioSQL v1.0.1 Release (corrected)

Hilmar Lapp hlapp at gmx.net
Sat Aug 2 10:08:17 EDT 2008

(the previous announcement contained a small error)

BioSQL v1.0.1 Release

I am pleased to announce the release of version 1.0.1 of BioSQL, the
second release in the Tokyo release series. The release can be
downloaded from the following locations:

http://biosql.org/DIST/biosql-1.0.1.zip (has Windows-style EOL)

The core BioSQL schema is a generic, extensible relational model for
sequences, sequence features, their annotation, and ontology terms. It
is also designed as the interoperable persistence interface between
the Bio* projects.

This release contains
  - the core BioSQL schema as DDL (Data Definition Language) for the
    following RDBMSs: MySQL, PostgreSQL, Oracle, HSQLDB, and Apache
  - migration scripts from v1.0.0 for PostgreSQL, MySQL, and Oracle,
  - ancillary (but optional) schema files for PostgreSQL,
  - scripts providing experimental support for the Bioperl and
    possibly other language bindings to BioSQL with PostgreSQL v8.3+
    (v8.2 and earlier are supported fine),
  - documentation and an ERD (Entity-Relationship Diagram), and
  - a Perl script that can pre-load (and update) a BioSQL instance with
    the NCBI taxonomy.

This version of the schema should be fully backwards compatible with
the v1.0.0 schema for nearly all software and queries. The only change
is relaxing the column width constraint (previously 40 chars, now 128)
of bioentry.accession and dbxref.accession. Migration scripts are
included for PostgreSQL, MySQL, and Oracle for those who want to
simply upgrade their existing database.

In addition, the script load_ncbi_taxonomy.pl has been fixed to no
longer require the taxon primary key and the NCBI taxon ID to be
identical. If you previously relied on this (documented but not
guaranteed) behavior, you will need to adjust your respective
software. To my knowledge, none of the Bio* language bindings should
be affected by this change.

The complete change log is listed in the file Changes, and installation
instructions for MySQL and PostgreSQL are in the file INSTALL.

Additional information regarding BioSQL, including links to language
bindings, a roadmap to future releases and enhancements, and possible
local optimizations is available from the BioSQL website at

On behalf of the BioSQL developers,

       Hilmar Lapp


BioSQL in general and in particular this point release owes to the
community of users and developers who provide feedback, advice, and
ideas, and report issues on the BioSQL mailing list
(biosql-l{at}lists.open-bio.org). Credit also goes to those who have
helped testing, in particular Peter Cock. This project would not exist
without their contributions and the support of other developers and
users from the Bio* community.

The 1.0.x release series is code-named Tokyo in recognition of the
role the BioHackathon 2008 played in getting the first of the series
(v1.0.0) out the door, and in keeping with an informal tradition held
up since the first BioHackathon.

Thank you to everyone!


BioSQL is free software: you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License as published
by the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

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