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BioSQL stable version: 1.0.1

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Releases

BioSQL release v1.0.2 plans

This could be a small release adding an SQLite3 version of the schema, which is already in the repository and supported by Biopython. What remains to be done is updating the BioSQL Perl scripts (e.g. the taxonomy loader) to support SQLite.

BioSQL release v1.0.1

This is an update release of the v1.0 core BioSQL schema (code-named Tokyo), not including recent extensions.

Note: open questions are in italics. If you have thoughts or feedback on any of the below, please email them to biosql-l@lists.open-bio.org.

  1. Update INSTALL file Done. –Hilmar 05:02, 1 August 2008 (UTC)
    • Fix inconsistencies in naming of the BioSQL database instance (here and with Bioperl-db). Will name it simply biosql from now on.
    • Add note about current incompatibility with PostgreSQL v8.3+.
  2. Implement scheduled changes Done. –Hilmar 02:24, 2 August 2008 (UTC)
    • Widen column width constraint of dbxref.accession and correspondingly bioentry.accession. Will use 128 chars for now.
    • Add migration scripts at least for Pg, MySQL, and Oracle.
  3. Fix load_ncbi_taxonomy.pl to not rely on primary key and NCBI taxon ID to be identical. Done. –Hilmar 02:24, 2 August 2008 (UTC)
  4. Update Changes file. Done. –Hilmar 05:02, 1 August 2008 (UTC)
  5. Merge changes to biosql-release-1-0 branch. Done. –Hilmar 12:21, 2 August 2008 (UTC)
  6. Write release announcement. Done. –Hilmar 12:21, 2 August 2008 (UTC)
  7. Tag release with biosql-rel-1.0.1 Done. –Hilmar 13:42, 2 August 2008 (UTC)
  8. Package BioSQL for release, upload to download site (http://biosql.org/DIST) Done. –Hilmar 13:42, 2 August 2008 (UTC)
  9. Release: Done on Aug 2, except for the news post which was done by Peter Cock a few days later.
    • Add download and release link to wiki on front page.
    • Post announcement to biosql-l and news.open-bio.org.

BioSQL release v1.0.0

This is a release of the core BioSQL schema, not including recent extensions.

Note: open questions are in italics. If you have thoughts or feedback on any of the below, please email them to biosql-l@lists.open-bio.org.

  1. Update license for BioSQL and all its DDL and software scripts. Done. This is now the LGPL license for all schema files. –Hilmar 20:23, 21 February 2008 (EST)
    • The current license refers to the ‘same terms as Perl’ and the Perl Artistic Licence. Not only does Perl now dual-license under Artistic License v2.0 or GPL (because the original Perl Artistic License v1.0 has problems), but also there isn’t a good reason to tie the BioSQL license to that of Perl.
  2. Update, fix, or remove various ancillary files that don’t seem to have been touched in a long time.
    • biosql-accelerators-pg.sql Updated/fixed, and now also retired. –Hilmar 23:40, 22 February 2008 (EST)
    • biosqldb-views-pg.sql Done. –Hilmar 20:31, 21 February 2008 (EST)
  3. Rename biosql-ora to biosqldb-ora for consistency with the other schema versions Done. –Hilmar 20:31, 21 February 2008 (EST)
  4. Regenerate HTML documentation from schema DDL (using sqlt) Doesn’t work, sqlt seems to be broken at present. –Hilmar 21:11, 21 February 2008 (EST)
  5. Update Changes file. Done. –Hilmar 23:41, 22 February 2008 (EST)
  6. Update documentation in the repository. Done, for Biopython (see PDF) and BioJava/Oracle. Unfortunately, realized this not before, but only after branching off, so need to merge all changes to the branch. –Hilmar 12:06, 24 February 2008 (EST)
  7. Create biosql-release-1-0 branch. Done. –Hilmar 23:43, 22 February 2008 (EST)
  8. Remove from biosql-release-1-0 branch all schema modules or versions and all scripts that aren’t release-ready yet, or are not yet or no longer supported. Done. –Hilmar 23:43, 22 February 2008 (EST)
    • This includes the following:
      • phylodb module DDLs
      • phylodb ERD
      • phy* scripts (depend on phylodb, and not up-to-date)
      • load_itis_taxonomy.pl, tree-precompute.pl scripts (depend on phylodb, and not up-to-date)
      • phylodb-topo-queries.sql (depends on phylodb)
    • Can the HSQLDB version be tested by anyone for syntactic correctness and compatibility with a current revision of HSQLDB?
  9. Write release announcement. Done. –Hilmar 10:52, 5 March 2008 (EST)
  10. Tag release with biosql-rel-1.0.0 Done. –Hilmar 10:53, 5 March 2008 (EST)
  11. Package BioSQL for release, upload to download site (http://biosql.org/DIST) Done, with MD5 signatures. –Hilmar 17:07, 6 March 2008 (EST)
  12. Release: Done. –Hilmar 22:02, 6 March 2008 (EST)
    • Add download and release link to wiki on front page (also add Downloads page ot sidebar).
    • Post announcement to biosql-l and news.open-bio.org.