Repository List / biosql / biosql-schema / trunk / Changes @ HEAD

Revision history for BioSQL
===========================

Note: this revision history only starts at the BioHackathon 2008,
Tokyo, prior to the v1.0 release.

BioSQL core schema
------------------

version 1.0.1:

  o Enlarged column width for dbxref.accession and bioentry.accession
    to 128 characters to deal with some very long accession numbers of
    pathway database entries.

  o Added migrate/ directory and migration scripts from 1.0.0 for Pg,
    MySQL, and Oracle (the latter is in the sql/biosql-ora/1.0/migrate
    directory).

  o Fixed INSTALL documentation to consistently use biosql as the
    schema (database) name.

  o Added note to INSTALL file about incompatibility with PostgreSQL v8.3+.

  o Added script to add back explicit typecasts to v8.3. This is
    experimental and untested, use at your own risk. If it does make
    v8.3+ work for you with bioperl-db, please let us know at
    biosql-l{at}lists{dot}open-bio{dot}org.

  o Fixed bug #2470: load_ncbi_taxonomy.pl will no longer require to
    use the NCBI taxon ID as the primary key value. Hence, the primary
    key will now be different from the NCBI taxon ID.

version 1.0.0:

  o Brought sql/biosql-accelerators-pg.sql to the 1.0 schema, but
    still retired it since no-one can have been using it.

  o Updated and fixed views and functions in sql/biosqldb-views-pg.sql
    to work with 1.0 schema. Apparently this hadn't been used for a while ...

  o Retired scripts/create_mysql_db.pl. Not sure what this was ever
    useful for, and the DDL path was wrong anyway.

  o Oracle version is now under sql/biosqldb-ora for consistency.

  o Added version for Apache Derby (Java embedded RDBMS).

  o Changed license to LGPL v3.

PhyloDB module
--------------

alpha - no release yet

  o Added SQL script to drop phyloDB tables and sequences.
 
  o Changed license to LGPL v3.

  o Added tables tree_dbxref and node_dbxref tables to allow storing
    identifiers and cross-references for trees and nodes.

  o Renamed edge_attribute_value and node_attribute_value to use
    'qualifier' instead of 'attribute', for the sake of consistency
    with the core schema (though attribute sounds like the better
    name).

  o Added tree_qualifier_value table to capture metadata for trees.

  o Replaced 1-n relationships (foreign keys) between bioentry and
    node and taxon and node, respectively, with n-n relationships
    (association tables).

  o Added tree_root table to allow storing of multiple roots (e.g., as
    resulting from Bayesian analysis) (11/13/2007)