This directory contains version 1.0 of the full set of schemas used in the
sqlite-based annotation data packages.

Version 1.0 is our target for the BioC 2.2 release.

Version 1.0 has been successfully tested (i.e. imported) with SQLite
(3.4.1), MySQL+InnoDB (5.0.26) and PostgreSQL (8.1.9) on a 64-bit openSUSE
10.2 system. It has not been tested on Oracle yet.

All the *.sqlite files using one of the 1.0 schemas must set DBSCHEMAVERSION
to 1.0 in their "metadata" table.

See the DataTypes.txt file for all the data types used across the 1.0 schemas.


SUMMARY OF CHANGES SINCE VERSION 0.9
------------------------------------

Note that those changes are disruptive (i.e. they potentially break the
SQL queries written for version 0.9).

New schemas:

  o replaced RODENT_DB schema by MOUSE_DB and RAT_DB schemas
  o replaced RODENTCHIP_DB schema by MOUSECHIP_DB and RATCHIP_DB schemas
  o added the Inparanoid schemas: INPARANOIDHOMSA_DB, INPARANOIDMUSMU_DB,
    INPARANOIDRATNO_DB, INPARANOIDDROME_DB and INPARANOIDSACCE_DB
  o added the PFAM_DB schema

All schemas:

  o renamed "qcdata" table -> "map_counts"

All probe-based and org-based schemas:

  o renamed internal id "id" -> "_id"
  o renamed chromosome_locations.chromosome -> chromosome_locations.seqname
  o renamed kegg.kegg_id col -> kegg.path_id
  o renamed chrlengths.chr col -> chrlengths.chromosome

All probe-based schemas:

  o moved "_id" col to last position in "probes" table
  o removed the "accessions" table

Schemas for Human, Mouse and Rat:

  o added "ensembl" table

HUMAN_DB and RAT_DB schemas:

  o added "ensembl_prot" table

MOUSE_DB and MOUSECHIP_DB schemas:

  o added "mgi" table

FLY_DB and FLYCHIP_DB schemas:

  o added "flybase_cg" table

FLY_DB schema:

  o added "flybase_prot" table

GO_DB schema:

  o renamed "term_id" cols -> "_id"
  o renamed "offspring_id" cols -> "_offspring_id"
  o renamed "parent_id" cols -> "_parent_id"
  o renamed "evidence" cols -> "relationship_type"
  o removed "gene2go_evidence" table
  o moved "ontology" col to 1st position in "go_ontology" table
  o removed go_obsolete.term_id column and made go_obsolete.go_id the
    new PRIMARY KEY

  Note that, ideally, we could add UNIQUE constraints on (_id, _parent_id) in
  the go_[bp|cc|mf]_parents tables and on (_id, _offspring_id) in the
  go_[bp|cc|mf]_offspring tables but the cost of doing this is high (+5M for
  the size of GO.sqlite: 37M instead of 32M).

KEGG_DB schema:

  o renamed "gene_id" col -> "gene_or_orf_id"