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This directory tree contains the Oracle version of the BioSQL schema.
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The Oracle version presently is further decoupled from the other
RDBMSs so far supported. While the relational model is identical to
the MySQL and PostgreSQL versions, notable differences are the naming
convention used and the richness of the complete schema instance.

This Oracle version of Biosql is also the database of the Symgene
platform developed at GNF, a gene-centric database of integrated gene
and genome annotation. Development of this platform has driven the
advancement of the Oracle version in the past and can be anticipated
to keep doing so.

Compatibility with the BioSQL naming convention as used in the MySQL
and PostgreSQL versions of the schema is achieved via a compatibility
layer that establishes synonyms and an API consisting of
views. Because of this being possible, it is not necessary to
sacrifice naming conventions just to achieve compatibility.

Compared to the MySQL and PostgreSQL versions the Oracle version has
the following extra functionality:

	- Customizable, very modular instantiation (see BS-create-all
	and BS-defs-local)

	- Complete API both for SELECTs as views and for programming
	as PL/SQL packages for all tables, see also general user
	programming API as exposed in the SGAPI package (which just
	delegates into the table APIs)

	- Load API using denormalized views with insert triggers (only on
	a few entities, and if you won't ever insert anything through
	sql*plus you're not going to hit this)

	- Ready-to-use scripts for allocating staged permission levels
	to different roles

	- Warehouse views with maintenance scripts, so far for genome
	mappings and accession/name/symbol searching

	- Ready-to-use scripts for generating context indexes (basically,
	Oracle's text search engine) on descriptions, references, and
	function-related annotation

	- coming: gene expression warehouse table, and whatever else GNF
	is going to develop for our Symgene platform.

For installation instructions read the INSTALL document. See LICENSE
for the license terms under which you may use biosql-ora.
