[Gmod-schema-cmts] schema/chado/modules default_schema.sql,1.1,1.2

[Scott C. <sco...@us...>]

Update of /cvsroot/gmod/schema/chado/modules
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2062/modules

Modified Files:
	default_schema.sql 
Log Message:
updated AutoDBI.PL, also added new gbrowse release to the manifest


Index: default_schema.sql
===================================================================
RCS file: /cvsroot/gmod/schema/chado/modules/default_schema.sql,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** default_schema.sql	12 Mar 2004 02:13:54 -0000	1.1
--- default_schema.sql	25 Mar 2004 21:10:06 -0000	1.2
***************
*** 90,94 ****
  COMMENT ON TABLE project IS NULL;
  
! -- The cvterm module design is based on the ontology 
  
  -- ================================================
--- 90,94 ----
  COMMENT ON TABLE project IS NULL;
  
! -- See cv-intro.txt
  
  -- ================================================
***************
*** 223,227 ****
  create index dbxrefprop_idx1 on dbxrefprop (dbxref_id);
  create index dbxrefprop_idx2 on dbxrefprop (type_id);
- 
  -- ================================================
  -- TABLE: organism
--- 223,226 ----
***************
*** 782,786 ****
  -- [id:FBgn001, type:gene] <-- [id:FBal001, type:gene]
  --
! -- with the genetic module, features can either be attached
  -- to features of type sequence_variation, or to features of
  -- type 'gene' (in the case of mutant alleles).
--- 781,785 ----
  -- [id:FBgn001, type:gene] <-- [id:FBal001, type:gene]
  --
! -- with the genetic module, phenotypes can either be attached
  -- to features of type sequence_variation, or to features of
  -- type 'gene' (in the case of mutant alleles).
***************
*** 1495,1501 ****
  COMMENT ON TABLE channel IS 'different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but affy uses only one)';
  
! create table array (
!     array_id serial not null,
! 	primary key (array_id),
      manufacturer_id int not null,
  	foreign key (manufacturer_id) references contact (contact_id) on delete cascade,
--- 1494,1500 ----
  COMMENT ON TABLE channel IS 'different array platforms can record signals from one or more channels (cDNA arrays typically use two CCD, but affy uses only one)';
  
! create table arraydesign (
!     arraydesign_id serial not null,
! 	primary key (arraydesign_id),
      manufacturer_id int not null,
  	foreign key (manufacturer_id) references contact (contact_id) on delete cascade,
***************
*** 1522,1543 ****
      unique(name)
  );
! create index array_idx1 on array (manufacturer_id);
! create index array_idx2 on array (platformtype_id);
! create index array_idx3 on array (substratetype_id);
! create index array_idx4 on array (protocol_id);
! create index array_idx5 on array (dbxref_id);
  
! COMMENT ON TABLE array IS 'general properties about an array.  and array is a template used to generate physical slides, etc.  it contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions(in rows/columns).';
  
  create table arrayprop (
      arrayprop_id serial not null,
  	primary key (arrayprop_id),
!     array_id int not null,
! 	foreign key (array_id) references array (array_id) on delete cascade,
      type_id int not null,
  	foreign key (type_id) references cvterm (cvterm_id) on delete cascade,
      value varchar(100) not null
  );
! create index arrayprop_idx1 on arrayprop (array_id);
  create index arrayprop_idx2 on arrayprop (type_id);
  
--- 1521,1542 ----
      unique(name)
  );
! create index arraydesign_idx1 on arraydesign (manufacturer_id);
! create index arraydesign_idx2 on arraydesign (platformtype_id);
! create index arraydesign_idx3 on arraydesign (substratetype_id);
! create index arraydesign_idx4 on arraydesign (protocol_id);
! create index arraydesign_idx5 on arraydesign (dbxref_id);
  
! COMMENT ON TABLE arraydesign IS 'general properties about an array.  and array is a template used to generate physical slides, etc.  it contains layout information, as well as global array properties, such as material (glass, nylon) and spot dimensions(in rows/columns).';
  
  create table arrayprop (
      arrayprop_id serial not null,
  	primary key (arrayprop_id),
!     arraydesign_id int not null,
! 	foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade,
      type_id int not null,
  	foreign key (type_id) references cvterm (cvterm_id) on delete cascade,
      value varchar(100) not null
  );
! create index arrayprop_idx1 on arrayprop (arraydesign_id);
  create index arrayprop_idx2 on arrayprop (type_id);
  
***************
*** 1547,1552 ****
      assay_id serial not null,
  	primary key (assay_id),
!     array_id int not null,
! 	foreign key (array_id) references array (array_id) on delete cascade,
      protocol_id int null,
  	foreign key (protocol_id) references protocol (protocol_id) on delete set null,
--- 1546,1551 ----
      assay_id serial not null,
  	primary key (assay_id),
!     arraydesign_id int not null,
! 	foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade,
      protocol_id int null,
  	foreign key (protocol_id) references protocol (protocol_id) on delete set null,
***************
*** 1562,1566 ****
      unique(name)
  );
! create index assay_idx1 on assay (array_id);
  create index assay_idx2 on assay (protocol_id);
  create index assay_idx3 on assay (operator_id);
--- 1561,1565 ----
      unique(name)
  );
! create index assay_idx1 on assay (arraydesign_id);
  create index assay_idx2 on assay (protocol_id);
  create index assay_idx3 on assay (operator_id);
***************
*** 1831,1836 ****
      feature_id int null,
  	foreign key (feature_id) references feature (feature_id) on delete set null,
!     array_id int not null,
! 	foreign key (array_id) references array (array_id) on delete cascade,
      type_id int null,
  	foreign key (type_id) references cvterm (cvterm_id) on delete set null,
--- 1830,1835 ----
      feature_id int null,
  	foreign key (feature_id) references feature (feature_id) on delete set null,
!     arraydesign_id int not null,
! 	foreign key (arraydesign_id) references arraydesign (arraydesign_id) on delete cascade,
      type_id int null,
  	foreign key (type_id) references cvterm (cvterm_id) on delete set null,
***************
*** 1855,1859 ****
  );
  create index element_idx1 on element (feature_id);
! create index element_idx2 on element (array_id);
  create index element_idx3 on element (type_id);
  create index element_idx4 on element (dbxref_id);
--- 1854,1858 ----
  );
  create index element_idx1 on element (feature_id);
! create index element_idx2 on element (arraydesign_id);
  create index element_idx3 on element (type_id);
  create index element_idx4 on element (dbxref_id);