README

## BIOSOURCE DEFINITION ##

Biosource is an Ambikon component designed to manage sample and protocol data. 
Both could be used to define sequences datasets, genomes, mRNA samples, tissue 
samples... Also it can be used to trace the changes of a sample, for example
a 454 sequence dataset for tomato mix of young and mature leaves could be 
defined by:
 
 Sample1 = S. lycopersicum young leaves
 Sample2 = S. lycopersicum mature leaves
 Sample3 = S. lycopersicum leaves mRNA
 Sample4 = S. lycopersicum 454 sequences dataset

 with the following relations:

 Sample1 (object) and Sample3 (subject), rank 1 relationship.
 Sample2 (object) and Sample3 (subject), rank 1 relationship.
 Sample3 (object) and Sample4 (subject), rank 2 relationship.


## DATABASE COMPONENTS ##

Biosource is composed by the following database tables:

biosource.bs_protocol, table to store protocol data like sequence processing
biosource.bs_protocol_pub, linking table for publications
biosource.bs_protocol_step, table to define protocol steps
biosource.bs_protocol_step_dbxref, linking table for external references
biosource.bs_tool, table to store tool data like a program
biosource.bs_tool_pub, linking table for tool publications
biosource.bs_sample, table to store sample data
biosource.bs_sample_pub, linking table for sample publications
biosource.bs_sample_dbxref, linking table for sample dbxrefs            
biosource.bs_sample_cvterm, linking table for sample cvterms
biosource.bs_sample_file, linking table for sample files
biosource.bs_sample_relationship, table to relate samples
         
[deprecated] biosource.bs_sample_element                                       
[deprecated] biosource.bs_sample_element_cvterm
[deprecated] biosource.bs_sample_element_dbxref
[deprecated] biosource.bs_sample_element_file
[deprecated] biosource.bs_sample_element_relation
                                          

## CODE COMPONENTS ##

db/ database patches to update the changes in the schema

lib/ perl modules divided into second level objects, 
     (wrappers of DBIx::Class sources that coordinates other data dependencies
      like metadbdata) and first level objects (DBIx::Class sources for 
      biosource tables).

script/ lo load data into the database

t/ test for the perl components