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gmod-schema-cmts
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From: <sco...@us...> - 2010-08-25 20:26:26
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Revision: 23699
http://gmod.svn.sourceforge.net/gmod/?rev=23699&view=rev
Author: scottcain
Date: 2010-08-25 20:26:10 +0000 (Wed, 25 Aug 2010)
Log Message:
-----------
updating default schemas for changes in natdiv module
Modified Paths:
--------------
schema/trunk/chado/modules/default_nofuncs.sql
schema/trunk/chado/modules/default_schema.sql
Modified: schema/trunk/chado/modules/default_nofuncs.sql
===================================================================
--- schema/trunk/chado/modules/default_nofuncs.sql 2010-08-20 19:02:14 UTC (rev 23698)
+++ schema/trunk/chado/modules/default_nofuncs.sql 2010-08-25 20:26:10 UTC (rev 23699)
@@ -3811,7 +3811,7 @@
-- represent geo information.
CREATE TABLE nd_geolocation (
- geolocation_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id serial PRIMARY KEY NOT NULL,
description character varying(255),
latitude real,
longitude real,
@@ -3834,55 +3834,55 @@
-CREATE TABLE nd_assay (
- assay_id serial PRIMARY KEY NOT NULL,
- geolocation_id integer NOT NULL references nd_geolocation (geolocation_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment (
+ nd_experiment_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
--
---used to be nd_diversityexperiemnt_project
-CREATE TABLE nd_assay_project (
- assay_project_id serial PRIMARY KEY NOT NULL,
+--used to be nd_diversityexperiment_project
+--then was nd_assay_project
+CREATE TABLE nd_experiment_project (
+ nd_experiment_project_id serial PRIMARY KEY NOT NULL,
project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED
);
-CREATE TABLE nd_assayprop (
- assayprop_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experimentprop (
+ nd_experimentprop_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
value character varying(255) NOT NULL,
rank integer NOT NULL default 0,
- constraint nd_assayprop_c1 unique (assay_id,cvterm_id,rank)
+ constraint nd_experimentprop_c1 unique (nd_experiment_id,cvterm_id,rank)
);
-create table nd_assay_pub (
- assay_pub_id serial not null,
- primary key (assay_pub_id),
- assay_id int not null,
- foreign key (assay_id) references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+create table nd_experiment_pub (
+ nd_experiment_pub_id serial PRIMARY KEY not null,
+ nd_experiment_id int not null,
+ foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- constraint assay_pub_c1 unique (assay_id,pub_id)
+ constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id)
);
-create index assay_pub_idx1 on nd_assay_pub (assay_id);
-create index assay_pub_idx2 on nd_assay_pub (pub_id);
+create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id);
+create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id);
-COMMENT ON TABLE nd_assay_pub IS 'Linking nd_assay(s) to publication(s)';
+COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)';
CREATE TABLE nd_geolocationprop (
- geolocationprop_id serial PRIMARY KEY NOT NULL,
- geolocation_id integer NOT NULL references nd_geolocation (geolocation_id) on delete cascade INITIALLY DEFERRED,
+ nd_geolocationprop_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(250),
- rank integer NOT NULL,
- constraint nd_geolocationprop_c1 unique (geolocation_id,cvterm_id,rank)
+ rank integer NOT NULL DEFAULT 0,
+ constraint nd_geolocationprop_c1 unique (nd_geolocation_id,cvterm_id,rank)
);
COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment';
@@ -3895,22 +3895,22 @@
CREATE TABLE nd_protocol (
- protocol_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id serial PRIMARY KEY NOT NULL,
name character varying(255) NOT NULL unique
);
-COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the assay.';
+COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.';
COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.';
CREATE TABLE nd_reagent (
- reagent_id serial PRIMARY KEY NOT NULL,
+ nd_reagent_id serial PRIMARY KEY NOT NULL,
name character varying(80) NOT NULL,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
feature_id integer
);
-COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping assays, or in any other kind of assay.';
+COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.';
COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.';
@@ -3921,25 +3921,25 @@
CREATE TABLE nd_protocol_reagent (
- protocol_reagent_id serial PRIMARY KEY NOT NULL,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED,
- reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocol_reagent_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
+ reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
CREATE TABLE nd_protocolprop (
- protocolprop_id serial PRIMARY KEY NOT NULL,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocolprop_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_protocolprop_c1 unique (protocol_id,cvterm_id,rank)
+ constraint nd_protocolprop_c1 unique (nd_protocol_id,cvterm_id,rank)
);
COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.';
-COMMENT ON COLUMN nd_protocolprop.protocol_id IS 'The protocol to which the property applies.';
+COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.';
COMMENT ON COLUMN nd_protocolprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
@@ -3949,53 +3949,53 @@
-CREATE TABLE nd_assay_stock (
- assay_stock_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stock (
+ nd_experiment_stock_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_stock IS 'Part of a stock or a clone of a stock that is used in an assay';
+COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment';
-COMMENT ON COLUMN nd_assay_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';
+COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';
-CREATE TABLE nd_assay_protocol (
- assay_protocol_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED
+CREATE TABLE nd_experiment_protocol (
+ nd_experiment_protocol_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_protocol IS 'Linking table: assays to the protocols they involve.';
+COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.';
-CREATE TABLE nd_assay_phenotype (
- assay_phenotype_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL UNIQUE REFERENCES nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_phenotype (
+ nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL UNIQUE REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_phenotype IS 'Linking table: assays to the phenotypes they produce. There is a one-to-one relationship between an assay and a phenotype since each phenotype record should point to one assay. Add a new assay_id for each phenotype record.';
+COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.';
-CREATE TABLE nd_assay_genotype (
- assay_genotype_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL UNIQUE references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_genotype (
+ nd_experiment_genotype_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL UNIQUE references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_genotype IS 'Linking table: assays to the genotypes they produce. There is a one-to-one relationship between an assay and a genotype since each genotype record should point to one assay. Add a new assay_id for each genotype record.';
+COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.';
CREATE TABLE nd_reagent_relationship (
- reagent_relationship_id serial PRIMARY KEY NOT NULL,
- subject_reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
- object_reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_reagent_relationship_id serial PRIMARY KEY NOT NULL,
+ subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
+ object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme assay reagents.';
+COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.';
COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';
@@ -4005,55 +4005,55 @@
CREATE TABLE nd_reagentprop (
- reagentprop_id serial PRIMARY KEY NOT NULL,
- reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_reagentprop_id serial PRIMARY KEY NOT NULL,
+ nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_reagentprop_c1 unique (reagent_id,cvterm_id,rank)
+ constraint nd_reagentprop_c1 unique (nd_reagent_id,cvterm_id,rank)
);
-CREATE TABLE nd_assay_stockprop (
- assay_stockprop_id serial PRIMARY KEY NOT NULL,
- assay_stock_id integer NOT NULL references nd_assay_stock (assay_stock_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stockprop (
+ nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_assay_stockprop_c1 unique (assay_stock_id,cvterm_id,rank)
+ constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,cvterm_id,rank)
);
-COMMENT ON TABLE nd_assay_stockprop IS 'Property/value associations for assay_stocks. This table can store the properties such as treatment';
+COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment';
-COMMENT ON COLUMN nd_assay_stockprop.assay_stock_id IS 'The assay_stock to which the property applies.';
+COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.';
-COMMENT ON COLUMN nd_assay_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_experiment_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
-COMMENT ON COLUMN nd_assay_stockprop.value IS 'The value of the property.';
+COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.';
-COMMENT ON COLUMN nd_assay_stockprop.rank IS 'The rank of the property value, if the property has an array of values.';
+COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.';
-CREATE TABLE nd_assay_stock_dbxref (
- assay_stock_dbxref_id serial PRIMARY KEY NOT NULL,
- assay_stock_id integer NOT NULL references nd_assay_stock (assay_stock_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stock_dbxref (
+ nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_stock_dbxref IS 'Cross-reference assay_stock to accessions, images, etc';
+COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc';
-CREATE TABLE nd_assay_dbxref (
- assay_dbxref_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_dbxref (
+ nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_dbxref IS 'Cross-reference assay to accessions, images, etc';
+COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc';
-CREATE TABLE nd_assay_contact (
- assay_contact_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_contact (
+ nd_experiment_contact_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED
);
Modified: schema/trunk/chado/modules/default_schema.sql
===================================================================
--- schema/trunk/chado/modules/default_schema.sql 2010-08-20 19:02:14 UTC (rev 23698)
+++ schema/trunk/chado/modules/default_schema.sql 2010-08-25 20:26:10 UTC (rev 23699)
@@ -36634,6 +36634,18 @@
--
-- y
--
+-- OR, you could execute this command (the materialized view tool has been
+-- updated to allow this all to be supplied on the command line):
+--
+-- (yes, it's all one really long line, to make copy and pasting easier)
+-- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer" --sql_query "SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name,organism_id FROM feature UNION SELECT feature_id, name, organism_id FROM feature where name is not null UNION SELECT fs.feature_id,s.name,f.organism_id FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value from 0 for 255) as varchar(255)) as name,f.organism_id FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "create index all_feature_names_lower_name on all_feature_names (lower(name))" --yes
+--
+--
+-- OR, even more complicated, you could use this command to create a materialized view
+-- for use with full text searching on PostgreSQL 8.4 or better:
+--
+-- gmod_materialized_view_tool.pl --create_view --view_name all_feature_names --table_name public.all_feature_names --refresh_time daily --column_def "feature_id integer,name varchar(255),organism_id integer,searchable_name tsvector" --sql_query "SELECT feature_id, CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255)) AS name, organism_id, to_tsvector('english', CAST(substring(uniquename FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM feature UNION SELECT feature_id, name, organism_id, to_tsvector('english', name) AS searchable_name FROM feature WHERE name IS NOT NULL UNION SELECT fs.feature_id, s.name, f.organism_id, to_tsvector('english', s.name) AS searchable_name FROM feature_synonym fs, synonym s, feature f WHERE fs.synonym_id = s.synonym_id AND fs.feature_id = f.feature_id UNION SELECT fp.feature_id, CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255)) AS name, f.organism_id, to_tsvector('english',CAST(substring(fp.value FROM 0 FOR 255) AS varchar(255))) AS searchable_name FROM featureprop fp, feature f WHERE f.feature_id = fp.feature_id UNION SELECT fd.feature_id, d.accession, f.organism_id,to_tsvector('english',d.accession) AS searchable_name FROM feature_dbxref fd, dbxref d,feature f WHERE fd.dbxref_id = d.dbxref_id AND fd.feature_id = f.feature_id" --index_fields "feature_id,name" --special_index "CREATE INDEX searchable_all_feature_names_idx ON all_feature_names USING gin(searchable_name)" --yes
+--
CREATE OR REPLACE VIEW all_feature_names (
feature_id,
name,
@@ -36993,7 +37005,7 @@
-- represent geo information.
CREATE TABLE nd_geolocation (
- geolocation_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id serial PRIMARY KEY NOT NULL,
description character varying(255),
latitude real,
longitude real,
@@ -37016,55 +37028,55 @@
-CREATE TABLE nd_assay (
- assay_id serial PRIMARY KEY NOT NULL,
- geolocation_id integer NOT NULL references nd_geolocation (geolocation_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment (
+ nd_experiment_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
--
---used to be nd_diversityexperiemnt_project
-CREATE TABLE nd_assay_project (
- assay_project_id serial PRIMARY KEY NOT NULL,
+--used to be nd_diversityexperiment_project
+--then was nd_assay_project
+CREATE TABLE nd_experiment_project (
+ nd_experiment_project_id serial PRIMARY KEY NOT NULL,
project_id integer not null references project (project_id) on delete cascade INITIALLY DEFERRED,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED
);
-CREATE TABLE nd_assayprop (
- assayprop_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experimentprop (
+ nd_experimentprop_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
value character varying(255) NOT NULL,
rank integer NOT NULL default 0,
- constraint nd_assayprop_c1 unique (assay_id,cvterm_id,rank)
+ constraint nd_experimentprop_c1 unique (nd_experiment_id,cvterm_id,rank)
);
-create table nd_assay_pub (
- assay_pub_id serial not null,
- primary key (assay_pub_id),
- assay_id int not null,
- foreign key (assay_id) references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+create table nd_experiment_pub (
+ nd_experiment_pub_id serial PRIMARY KEY not null,
+ nd_experiment_id int not null,
+ foreign key (nd_experiment_id) references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- constraint assay_pub_c1 unique (assay_id,pub_id)
+ constraint nd_experiment_pub_c1 unique (nd_experiment_id,pub_id)
);
-create index assay_pub_idx1 on nd_assay_pub (assay_id);
-create index assay_pub_idx2 on nd_assay_pub (pub_id);
+create index nd_experiment_pub_idx1 on nd_experiment_pub (nd_experiment_id);
+create index nd_experiment_pub_idx2 on nd_experiment_pub (pub_id);
-COMMENT ON TABLE nd_assay_pub IS 'Linking nd_assay(s) to publication(s)';
+COMMENT ON TABLE nd_experiment_pub IS 'Linking nd_experiment(s) to publication(s)';
CREATE TABLE nd_geolocationprop (
- geolocationprop_id serial PRIMARY KEY NOT NULL,
- geolocation_id integer NOT NULL references nd_geolocation (geolocation_id) on delete cascade INITIALLY DEFERRED,
+ nd_geolocationprop_id serial PRIMARY KEY NOT NULL,
+ nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(250),
- rank integer NOT NULL,
- constraint nd_geolocationprop_c1 unique (geolocation_id,cvterm_id,rank)
+ rank integer NOT NULL DEFAULT 0,
+ constraint nd_geolocationprop_c1 unique (nd_geolocation_id,cvterm_id,rank)
);
COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment';
@@ -37077,22 +37089,22 @@
CREATE TABLE nd_protocol (
- protocol_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id serial PRIMARY KEY NOT NULL,
name character varying(255) NOT NULL unique
);
-COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the assay.';
+COMMENT ON TABLE nd_protocol IS 'A protocol can be anything that is done as part of the experiment.';
COMMENT ON COLUMN nd_protocol.name IS 'The protocol name.';
CREATE TABLE nd_reagent (
- reagent_id serial PRIMARY KEY NOT NULL,
+ nd_reagent_id serial PRIMARY KEY NOT NULL,
name character varying(80) NOT NULL,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
feature_id integer
);
-COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping assays, or in any other kind of assay.';
+COMMENT ON TABLE nd_reagent IS 'A reagent such as a primer, an enzyme, an adapter oligo, a linker oligo. Reagents are used in genotyping experiments, or in any other kind of experiment.';
COMMENT ON COLUMN nd_reagent.name IS 'The name of the reagent. The name should be unique for a given type.';
@@ -37103,25 +37115,25 @@
CREATE TABLE nd_protocol_reagent (
- protocol_reagent_id serial PRIMARY KEY NOT NULL,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED,
- reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocol_reagent_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
+ reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
CREATE TABLE nd_protocolprop (
- protocolprop_id serial PRIMARY KEY NOT NULL,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocolprop_id serial PRIMARY KEY NOT NULL,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_protocolprop_c1 unique (protocol_id,cvterm_id,rank)
+ constraint nd_protocolprop_c1 unique (nd_protocol_id,cvterm_id,rank)
);
COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.';
-COMMENT ON COLUMN nd_protocolprop.protocol_id IS 'The protocol to which the property applies.';
+COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.';
COMMENT ON COLUMN nd_protocolprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
@@ -37131,53 +37143,53 @@
-CREATE TABLE nd_assay_stock (
- assay_stock_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stock (
+ nd_experiment_stock_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
stock_id integer NOT NULL references stock (stock_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_stock IS 'Part of a stock or a clone of a stock that is used in an assay';
+COMMENT ON TABLE nd_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment';
-COMMENT ON COLUMN nd_assay_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';
+COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';
-CREATE TABLE nd_assay_protocol (
- assay_protocol_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
- protocol_id integer NOT NULL references nd_protocol (protocol_id) on delete cascade INITIALLY DEFERRED
+CREATE TABLE nd_experiment_protocol (
+ nd_experiment_protocol_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
+ nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_protocol IS 'Linking table: assays to the protocols they involve.';
+COMMENT ON TABLE nd_experiment_protocol IS 'Linking table: experiments to the protocols they involve.';
-CREATE TABLE nd_assay_phenotype (
- assay_phenotype_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL UNIQUE REFERENCES nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_phenotype (
+ nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL UNIQUE REFERENCES nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
phenotype_id integer NOT NULL references phenotype (phenotype_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_phenotype IS 'Linking table: assays to the phenotypes they produce. There is a one-to-one relationship between an assay and a phenotype since each phenotype record should point to one assay. Add a new assay_id for each phenotype record.';
+COMMENT ON TABLE nd_experiment_phenotype IS 'Linking table: experiments to the phenotypes they produce. There is a one-to-one relationship between an experiment and a phenotype since each phenotype record should point to one experiment. Add a new experiment_id for each phenotype record.';
-CREATE TABLE nd_assay_genotype (
- assay_genotype_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL UNIQUE references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_genotype (
+ nd_experiment_genotype_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL UNIQUE references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
genotype_id integer NOT NULL references genotype (genotype_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_genotype IS 'Linking table: assays to the genotypes they produce. There is a one-to-one relationship between an assay and a genotype since each genotype record should point to one assay. Add a new assay_id for each genotype record.';
+COMMENT ON TABLE nd_experiment_genotype IS 'Linking table: experiments to the genotypes they produce. There is a one-to-one relationship between an experiment and a genotype since each genotype record should point to one experiment. Add a new experiment_id for each genotype record.';
CREATE TABLE nd_reagent_relationship (
- reagent_relationship_id serial PRIMARY KEY NOT NULL,
- subject_reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
- object_reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_reagent_relationship_id serial PRIMARY KEY NOT NULL,
+ subject_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
+ object_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme assay reagents.';
+COMMENT ON TABLE nd_reagent_relationship IS 'Relationships between reagents. Some reagents form a group. i.e., they are used all together or not at all. Examples are adapter/linker/enzyme experiment reagents.';
COMMENT ON COLUMN nd_reagent_relationship.subject_reagent_id IS 'The subject reagent in the relationship. In parent/child terminology, the subject is the child. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';
@@ -37187,55 +37199,55 @@
CREATE TABLE nd_reagentprop (
- reagentprop_id serial PRIMARY KEY NOT NULL,
- reagent_id integer NOT NULL references nd_reagent (reagent_id) on delete cascade INITIALLY DEFERRED,
+ nd_reagentprop_id serial PRIMARY KEY NOT NULL,
+ nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_reagentprop_c1 unique (reagent_id,cvterm_id,rank)
+ constraint nd_reagentprop_c1 unique (nd_reagent_id,cvterm_id,rank)
);
-CREATE TABLE nd_assay_stockprop (
- assay_stockprop_id serial PRIMARY KEY NOT NULL,
- assay_stock_id integer NOT NULL references nd_assay_stock (assay_stock_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stockprop (
+ nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_assay_stockprop_c1 unique (assay_stock_id,cvterm_id,rank)
+ constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,cvterm_id,rank)
);
-COMMENT ON TABLE nd_assay_stockprop IS 'Property/value associations for assay_stocks. This table can store the properties such as treatment';
+COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment';
-COMMENT ON COLUMN nd_assay_stockprop.assay_stock_id IS 'The assay_stock to which the property applies.';
+COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.';
-COMMENT ON COLUMN nd_assay_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_experiment_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
-COMMENT ON COLUMN nd_assay_stockprop.value IS 'The value of the property.';
+COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.';
-COMMENT ON COLUMN nd_assay_stockprop.rank IS 'The rank of the property value, if the property has an array of values.';
+COMMENT ON COLUMN nd_experiment_stockprop.rank IS 'The rank of the property value, if the property has an array of values.';
-CREATE TABLE nd_assay_stock_dbxref (
- assay_stock_dbxref_id serial PRIMARY KEY NOT NULL,
- assay_stock_id integer NOT NULL references nd_assay_stock (assay_stock_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_stock_dbxref (
+ nd_experiment_stock_dbxref_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_stock_dbxref IS 'Cross-reference assay_stock to accessions, images, etc';
+COMMENT ON TABLE nd_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc';
-CREATE TABLE nd_assay_dbxref (
- assay_dbxref_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_dbxref (
+ nd_experiment_dbxref_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
dbxref_id integer NOT NULL references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED
);
-COMMENT ON TABLE nd_assay_dbxref IS 'Cross-reference assay to accessions, images, etc';
+COMMENT ON TABLE nd_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc';
-CREATE TABLE nd_assay_contact (
- assay_contact_id serial PRIMARY KEY NOT NULL,
- assay_id integer NOT NULL references nd_assay (assay_id) on delete cascade INITIALLY DEFERRED,
+CREATE TABLE nd_experiment_contact (
+ nd_experiment_contact_id serial PRIMARY KEY NOT NULL,
+ nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
contact_id integer NOT NULL references contact (contact_id) on delete cascade INITIALLY DEFERRED
);
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2010-10-21 18:48:00
|
Revision: 24015
http://gmod.svn.sourceforge.net/gmod/?rev=24015&view=rev
Author: scottcain
Date: 2010-10-21 18:47:50 +0000 (Thu, 21 Oct 2010)
Log Message:
-----------
in the process of updating the default schema--need to finish on a different machine (no graphviz on this computer)
Modified Paths:
--------------
schema/trunk/chado/modules/default_nofuncs.sql
schema/trunk/chado/modules/default_schema.sql
schema/trunk/chado/modules/nofuncs.html
schema/trunk/chado/modules/project/project.html
Modified: schema/trunk/chado/modules/default_nofuncs.sql
===================================================================
--- schema/trunk/chado/modules/default_nofuncs.sql 2010-10-21 17:24:04 UTC (rev 24014)
+++ schema/trunk/chado/modules/default_nofuncs.sql 2010-10-21 18:47:50 UTC (rev 24015)
@@ -2211,11 +2211,11 @@
PRIMARY KEY (projectprop_id),
project_id integer NOT NULL,
FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE,
- cvterm_id integer NOT NULL,
- FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE,
+ type_id integer NOT NULL,
+ FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE,
value text,
rank integer not null default 0,
- CONSTRAINT projectprop_c1 UNIQUE (project_id, cvterm_id, rank)
+ CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank)
);
-- ================================================
@@ -3397,6 +3397,33 @@
COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links
a stock collection to the stocks which are contained in the collection.';
+
+
+
+-- ================================================
+-- TABLE: stock_dbxrefprop
+-- ================================================
+
+create table stock_dbxrefprop (
+ stock_dbxrefprop_id serial not null,
+ primary key (stock_dbxrefprop_id),
+ stock_dbxref_id int not null,
+ foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank)
+);
+create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id);
+create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id);
+
+COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of
+slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to
+hardcoding a list of columns in the relational schema, and is
+completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for
+the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';
+
-- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $
-- =================================================================
-- Dependencies:
@@ -3854,10 +3881,10 @@
CREATE TABLE nd_experimentprop (
nd_experimentprop_id serial PRIMARY KEY NOT NULL,
nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
value character varying(255) NOT NULL,
rank integer NOT NULL default 0,
- constraint nd_experimentprop_c1 unique (nd_experiment_id,cvterm_id,rank)
+ constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank)
);
create table nd_experiment_pub (
@@ -3879,15 +3906,15 @@
CREATE TABLE nd_geolocationprop (
nd_geolocationprop_id serial PRIMARY KEY NOT NULL,
nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(250),
rank integer NOT NULL DEFAULT 0,
- constraint nd_geolocationprop_c1 unique (nd_geolocation_id,cvterm_id,rank)
+ constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank)
);
COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment';
-COMMENT ON COLUMN nd_geolocationprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.';
@@ -3931,17 +3958,17 @@
CREATE TABLE nd_protocolprop (
nd_protocolprop_id serial PRIMARY KEY NOT NULL,
nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_protocolprop_c1 unique (nd_protocol_id,cvterm_id,rank)
+ constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank)
);
COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.';
COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.';
-COMMENT ON COLUMN nd_protocolprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.';
@@ -4007,26 +4034,26 @@
CREATE TABLE nd_reagentprop (
nd_reagentprop_id serial PRIMARY KEY NOT NULL,
nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_reagentprop_c1 unique (nd_reagent_id,cvterm_id,rank)
+ constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank)
);
CREATE TABLE nd_experiment_stockprop (
nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL,
nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,cvterm_id,rank)
+ constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank)
);
COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment';
COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.';
-COMMENT ON COLUMN nd_experiment_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.';
Modified: schema/trunk/chado/modules/default_schema.sql
===================================================================
--- schema/trunk/chado/modules/default_schema.sql 2010-10-21 17:24:04 UTC (rev 24014)
+++ schema/trunk/chado/modules/default_schema.sql 2010-10-21 18:47:50 UTC (rev 24015)
@@ -34790,11 +34790,11 @@
PRIMARY KEY (projectprop_id),
project_id integer NOT NULL,
FOREIGN KEY (project_id) REFERENCES project (project_id) ON DELETE CASCADE,
- cvterm_id integer NOT NULL,
- FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE,
+ type_id integer NOT NULL,
+ FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE,
value text,
rank integer not null default 0,
- CONSTRAINT projectprop_c1 UNIQUE (project_id, cvterm_id, rank)
+ CONSTRAINT projectprop_c1 UNIQUE (project_id, type_id, rank)
);
-- ================================================
@@ -35976,6 +35976,33 @@
COMMENT ON TABLE stockcollection_stock IS 'stockcollection_stock links
a stock collection to the stocks which are contained in the collection.';
+
+
+
+-- ================================================
+-- TABLE: stock_dbxrefprop
+-- ================================================
+
+create table stock_dbxrefprop (
+ stock_dbxrefprop_id serial not null,
+ primary key (stock_dbxrefprop_id),
+ stock_dbxref_id int not null,
+ foreign key (stock_dbxref_id) references stock_dbxref (stock_dbxref_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint stock_dbxrefprop_c1 unique (stock_dbxref_id,type_id,rank)
+);
+create index stock_dbxrefprop_idx1 on stock_dbxrefprop (stock_dbxref_id);
+create index stock_dbxrefprop_idx2 on stock_dbxrefprop (type_id);
+
+COMMENT ON TABLE stock_dbxrefprop IS 'A stock_dbxref can have any number of
+slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to
+hardcoding a list of columns in the relational schema, and is
+completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for
+the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';
+
-- $Id: library.sql,v 1.10 2008-03-25 16:00:43 emmert Exp $
-- =================================================================
-- Dependencies:
@@ -36452,13 +36479,15 @@
as attribute
FROM feature_relationship fr, feature parent
WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id
-FROM cvterm WHERE name='part_of')
+FROM cvterm WHERE name='part_of' and cv_id in (select cv_id
+ FROM cv WHERE name='relationship'))
UNION ALL
-SELECT fr.subject_id as feature_id, 'Derived_from' as type,
+SELECT fr.subject_id as feature_id, 'Derives_from' as type,
parent.uniquename as attribute
FROM feature_relationship fr, feature parent
WHERE fr.object_id=parent.feature_id AND fr.type_id = (SELECT cvterm_id
-FROM cvterm WHERE name='derives_from')
+FROM cvterm WHERE name='derives_from' and cv_id in (select cv_id
+ FROM cv WHERE name='relationship'))
UNION ALL
SELECT fl.feature_id, 'Target' as type, target.name || ' ' || fl.fmin+1
|| ' ' || fl.fmax || ' ' || fl.strand as attribute
@@ -36485,7 +36514,11 @@
) AS
SELECT
f.feature_id, sf.name, gffdbx.accession, cv.name,
-fl.fmin+1, fl.fmax, af.significance, fl.strand,
+fl.fmin+1, fl.fmax, af.significance,
+ CASE WHEN fl.strand=-1 THEN '-'
+ WHEN fl.strand=1 THEN '+'
+ ELSE '.'
+ END,
fl.phase, f.seqlen, f.name, f.organism_id
FROM feature f
LEFT JOIN featureloc fl ON (f.feature_id = fl.feature_id)
@@ -37048,10 +37081,10 @@
CREATE TABLE nd_experimentprop (
nd_experimentprop_id serial PRIMARY KEY NOT NULL,
nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
value character varying(255) NOT NULL,
rank integer NOT NULL default 0,
- constraint nd_experimentprop_c1 unique (nd_experiment_id,cvterm_id,rank)
+ constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank)
);
create table nd_experiment_pub (
@@ -37073,15 +37106,15 @@
CREATE TABLE nd_geolocationprop (
nd_geolocationprop_id serial PRIMARY KEY NOT NULL,
nd_geolocation_id integer NOT NULL references nd_geolocation (nd_geolocation_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(250),
rank integer NOT NULL DEFAULT 0,
- constraint nd_geolocationprop_c1 unique (nd_geolocation_id,cvterm_id,rank)
+ constraint nd_geolocationprop_c1 unique (nd_geolocation_id,type_id,rank)
);
COMMENT ON TABLE nd_geolocationprop IS 'Property/value associations for geolocations. This table can store the properties such as location and environment';
-COMMENT ON COLUMN nd_geolocationprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_geolocationprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_geolocationprop.value IS 'The value of the property.';
@@ -37125,17 +37158,17 @@
CREATE TABLE nd_protocolprop (
nd_protocolprop_id serial PRIMARY KEY NOT NULL,
nd_protocol_id integer NOT NULL references nd_protocol (nd_protocol_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_protocolprop_c1 unique (nd_protocol_id,cvterm_id,rank)
+ constraint nd_protocolprop_c1 unique (nd_protocol_id,type_id,rank)
);
COMMENT ON TABLE nd_protocolprop IS 'Property/value associations for protocol.';
COMMENT ON COLUMN nd_protocolprop.nd_protocol_id IS 'The protocol to which the property applies.';
-COMMENT ON COLUMN nd_protocolprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_protocolprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_protocolprop.value IS 'The value of the property.';
@@ -37201,26 +37234,26 @@
CREATE TABLE nd_reagentprop (
nd_reagentprop_id serial PRIMARY KEY NOT NULL,
nd_reagent_id integer NOT NULL references nd_reagent (nd_reagent_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_reagentprop_c1 unique (nd_reagent_id,cvterm_id,rank)
+ constraint nd_reagentprop_c1 unique (nd_reagent_id,type_id,rank)
);
CREATE TABLE nd_experiment_stockprop (
nd_experiment_stockprop_id serial PRIMARY KEY NOT NULL,
nd_experiment_stock_id integer NOT NULL references nd_experiment_stock (nd_experiment_stock_id) on delete cascade INITIALLY DEFERRED,
- cvterm_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value character varying(255),
rank integer DEFAULT 0 NOT NULL,
- constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,cvterm_id,rank)
+ constraint nd_experiment_stockprop_c1 unique (nd_experiment_stock_id,type_id,rank)
);
COMMENT ON TABLE nd_experiment_stockprop IS 'Property/value associations for experiment_stocks. This table can store the properties such as treatment';
COMMENT ON COLUMN nd_experiment_stockprop.nd_experiment_stock_id IS 'The experiment_stock to which the property applies.';
-COMMENT ON COLUMN nd_experiment_stockprop.cvterm_id IS 'The name of the property as a reference to a controlled vocabulary term.';
+COMMENT ON COLUMN nd_experiment_stockprop.type_id IS 'The name of the property as a reference to a controlled vocabulary term.';
COMMENT ON COLUMN nd_experiment_stockprop.value IS 'The value of the property.';
Modified: schema/trunk/chado/modules/nofuncs.html
===================================================================
--- schema/trunk/chado/modules/nofuncs.html 2010-10-21 17:24:04 UTC (rev 24014)
+++ schema/trunk/chado/modules/nofuncs.html 2010-10-21 18:47:50 UTC (rev 24015)
@@ -17,7 +17,7 @@
<hr />
<!--
- Table listing (168 tables)
+ Table listing (169 tables)
-->
<a name="top" />
@@ -1579,6 +1579,18 @@
-->
<!--
+ Start link to table 'stock_dbxrefprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_dbxrefprop-link" href="#stock_dbxrefprop">stock_dbxrefprop</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_dbxrefprop'
+ -->
+
+<!--
Start link to table 'library'
-->
@@ -16029,7 +16041,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="projectprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="projectprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -16089,12 +16101,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -16104,7 +16116,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>project_id, cvterm_id, rank</td>
+ <td>project_id, type_id, rank</td>
</tr>
</table>
@@ -25635,6 +25647,190 @@
<hr />
<!--
+ Starting table 'stock_dbxrefprop'
+ -->
+
+<a name="stock_dbxrefprop" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stock_dbxrefprop
+</h3></td>
+ <a name="stock_dbxrefprop"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: stock_dbxrefprop <br />
+ ================================================ <br />
+ A stock_dbxref can have any number of
+ slot-value property tags attached to it. This is useful for storing properties related to dbxref annotations of stocks, such as evidence codes, and references, and metadata, such as create/modify dates. This is an alternative to
+ hardcoding a list of columns in the relational schema, and is
+ completely extensible. There is a unique constraint, stock_dbxrefprop_c1, for
+ the combination of stock_dbxref_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock_dbxrefprop-stock_dbxrefprop_id">stock_dbxrefprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock_dbxrefprop-stock_dbxref_id">stock_dbxref_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#stock_dbxref-stock_dbxref_id">stock_dbxref.stock_dbxref_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock_dbxrefprop-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock_dbxrefprop-value">value</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault">NULL</td>
+ <td class="FieldCellOther"></td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock_dbxrefprop-rank">rank</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault">0</td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Indices
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Name
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_dbxrefprop_idx1</td>
+ <td>stock_dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_dbxrefprop_idx2</td>
+ <td>type_id</td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_dbxrefprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>stock_dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>rank</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>stock_dbxref_id, type_id, rank</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
Starting table 'library'
-->
@@ -29203,7 +29399,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="nd_experimentprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="nd_experimentprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -29263,12 +29459,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -29283,7 +29479,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>nd_experiment_id, cvterm_id, rank</td>
+ <td>nd_experiment_id, type_id, rank</td>
</tr>
<tr class="IndexCell">
@@ -29293,7 +29489,7 @@
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
</table>
@@ -29522,7 +29718,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="nd_geolocationprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="nd_geolocationprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -29582,12 +29778,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -29597,7 +29793,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>nd_geolocation_id, cvterm_id, rank</td>
+ <td>nd_geolocation_id, type_id, rank</td>
</tr>
<tr class="IndexCell">
@@ -29607,7 +29803,7 @@
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
</table>
@@ -30061,7 +30257,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="nd_protocolprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="nd_protocolprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -30121,12 +30317,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -30136,7 +30332,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>nd_protocol_id, cvterm_id, rank</td>
+ <td>nd_protocol_id, type_id, rank</td>
</tr>
<tr class="IndexCell">
@@ -30146,7 +30342,7 @@
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
</table>
@@ -30928,7 +31124,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="nd_reagentprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="nd_reagentprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -30988,12 +31184,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -31003,7 +31199,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>nd_reagent_id, cvterm_id, rank</td>
+ <td>nd_reagent_id, type_id, rank</td>
</tr>
<tr class="IndexCell">
@@ -31013,7 +31209,7 @@
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
</table>
@@ -31088,7 +31284,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="nd_experiment_stockprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="nd_experiment_stockprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -31148,12 +31344,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -31163,7 +31359,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>nd_experiment_stock_id, cvterm_id, rank</td>
+ <td>nd_experiment_stock_id, type_id, rank</td>
</tr>
<tr class="IndexCell">
@@ -31173,7 +31369,7 @@
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
</table>
@@ -31566,7 +31762,7 @@
<hr />
Created by <a href="http://sqlfairy.sourceforge.net">
-SQL::Translator 0.11005</a>
+SQL::Translator 0.11003</a>
</body>
</html>
Modified: schema/trunk/chado/modules/project/project.html
===================================================================
--- schema/trunk/chado/modules/project/project.html 2010-10-21 17:24:04 UTC (rev 24014)
+++ schema/trunk/chado/modules/project/project.html 2010-10-21 18:47:50 UTC (rev 24015)
@@ -288,7 +288,7 @@
</tr>
<tr class="tr-odd">
- <td class="FieldCellName"><a name="projectprop-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellName"><a name="projectprop-type_id">type_id</a></td>
<td class="FieldCellType">integer</td>
<td class="FieldCellSize">10</td>
<td class="FieldCellDefault"></td>
@@ -348,12 +348,12 @@
<tr class="IndexCell">
<td>NOT NULL</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
<td>FOREIGN KEY</td>
- <td>cvterm_id</td>
+ <td>type_id</td>
</tr>
<tr class="IndexCell">
@@ -363,7 +363,7 @@
<tr class="IndexCell">
<td>UNIQUE</td>
- <td>project_id, cvterm_id, rank</td>
+ <td>project_id, type_id, rank</td>
</tr>
</table>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2011-09-19 18:45:51
|
Revision: 25187
http://gmod.svn.sourceforge.net/gmod/?rev=25187&view=rev
Author: scottcain
Date: 2011-09-19 18:45:46 +0000 (Mon, 19 Sep 2011)
Log Message:
-----------
fixing a bug caught by Rob Syme.
Modified Paths:
--------------
schema/trunk/chado/modules/default_schema.sql
schema/trunk/chado/modules/general/functions/general-loading.plpgsql
Modified: schema/trunk/chado/modules/default_schema.sql
===================================================================
--- schema/trunk/chado/modules/default_schema.sql 2011-09-16 20:54:47 UTC (rev 25186)
+++ schema/trunk/chado/modules/default_schema.sql 2011-09-19 18:45:46 UTC (rev 25187)
@@ -96,7 +96,7 @@
RETURNS INT AS
'DECLARE
v_dbname ALIAS FOR $1;
- v_accession ALIAS FOR $1;
+ v_accession ALIAS FOR $2;
v_db_id INTEGER;
v_dbxref_id INTEGER;
Modified: schema/trunk/chado/modules/general/functions/general-loading.plpgsql
===================================================================
--- schema/trunk/chado/modules/general/functions/general-loading.plpgsql 2011-09-16 20:54:47 UTC (rev 25186)
+++ schema/trunk/chado/modules/general/functions/general-loading.plpgsql 2011-09-19 18:45:46 UTC (rev 25187)
@@ -24,7 +24,7 @@
RETURNS INT AS
'DECLARE
v_dbname ALIAS FOR $1;
- v_accession ALIAS FOR $1;
+ v_accession ALIAS FOR $2;
v_db_id INTEGER;
v_dbxref_id INTEGER;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <sco...@us...> - 2011-09-20 19:04:52
|
Revision: 25193
http://gmod.svn.sourceforge.net/gmod/?rev=25193&view=rev
Author: scottcain
Date: 2011-09-20 19:04:39 +0000 (Tue, 20 Sep 2011)
Log Message:
-----------
adding some left out doc
Added Paths:
-----------
schema/trunk/chado/modules/cell_line/cell_line.html
schema/trunk/chado/modules/stock/stock.html
Added: schema/trunk/chado/modules/cell_line/cell_line.html
===================================================================
--- schema/trunk/chado/modules/cell_line/cell_line.html (rev 0)
+++ schema/trunk/chado/modules/cell_line/cell_line.html 2011-09-20 19:04:39 UTC (rev 25193)
@@ -0,0 +1,1832 @@
+<!DOCTYPE html
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
+<head>
+<title>Description of Schema</title>
+<meta name="generator" content="SQL::Translator::Producer::HTML" />
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+</head>
+<body>
+
+
+<h1 class="SchemaDescription">
+ Description of Schema
+</h1>
+
+<hr />
+
+<!--
+ Table listing (11 tables)
+ -->
+
+<a name="top" />
+
+<table class="LinkTable" width="100%">
+
+<tr>
+ <td class="LinkTableCell"><h2 class="LinkTableTitle">
+ Tables
+</h2></td>
+</tr>
+
+<!--
+ Start link to table 'cell_line'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line-link" href="#cell_line">cell_line</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line'
+ -->
+
+<!--
+ Start link to table 'cell_line_relationship'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_relationship-link" href="#cell_line_relationship">cell_line_relationship</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_relationship'
+ -->
+
+<!--
+ Start link to table 'cell_line_synonym'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_synonym-link" href="#cell_line_synonym">cell_line_synonym</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_synonym'
+ -->
+
+<!--
+ Start link to table 'cell_line_cvterm'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_cvterm-link" href="#cell_line_cvterm">cell_line_cvterm</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_cvterm'
+ -->
+
+<!--
+ Start link to table 'cell_line_dbxref'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_dbxref-link" href="#cell_line_dbxref">cell_line_dbxref</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_dbxref'
+ -->
+
+<!--
+ Start link to table 'cell_lineprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_lineprop-link" href="#cell_lineprop">cell_lineprop</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_lineprop'
+ -->
+
+<!--
+ Start link to table 'cell_lineprop_pub'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_lineprop_pub-link" href="#cell_lineprop_pub">cell_lineprop_pub</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_lineprop_pub'
+ -->
+
+<!--
+ Start link to table 'cell_line_feature'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_feature-link" href="#cell_line_feature">cell_line_feature</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_feature'
+ -->
+
+<!--
+ Start link to table 'cell_line_cvtermprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_cvtermprop-link" href="#cell_line_cvtermprop">cell_line_cvtermprop</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_cvtermprop'
+ -->
+
+<!--
+ Start link to table 'cell_line_pub'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_pub-link" href="#cell_line_pub">cell_line_pub</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_pub'
+ -->
+
+<!--
+ Start link to table 'cell_line_library'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="cell_line_library-link" href="#cell_line_library">cell_line_library</a></td>
+</tr>
+
+<!--
+ End link to table 'cell_line_library'
+ -->
+
+</table>
+
+<!--
+ Starting table 'cell_line'
+ -->
+
+<a name="cell_line" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line
+</h3></td>
+ <a name="cell_line"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ========================================== <br />
+ Chado cell line module <br />
+ ============ <br />
+ DEPENDENCIES <br />
+ ============ <br />
+ :import feature from sequence <br />
+ :import synonym from sequence <br />
+ :import library from library <br />
+ :import cvterm from cv <br />
+ :import dbxref from general <br />
+ :import pub from pub <br />
+ :import organism from organism <br />
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <br />
+ ================================================ <br />
+ TABLE: cell_line <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line-name">name</a></td>
+ <td class="FieldCellType">varchar</td>
+ <td class="FieldCellSize">255</td>
+ <td class="FieldCellDefault">NULL</td>
+ <td class="FieldCellOther"></td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line-uniquename">uniquename</a></td>
+ <td class="FieldCellType">varchar</td>
+ <td class="FieldCellSize">255</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line-organism_id">organism_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#organism-organism_id">organism.organism_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line-timeaccessioned">timeaccessioned</a></td>
+ <td class="FieldCellType">timestamp</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">current_timestamp</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line-timelastmodified">timelastmodified</a></td>
+ <td class="FieldCellType">timestamp</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">current_timestamp</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>uniquename</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>organism_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>organism_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>timeaccessioned</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>timelastmodified</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>uniquename, organism_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_relationship'
+ -->
+
+<a name="cell_line_relationship" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_relationship
+</h3></td>
+ <a name="cell_line_relationship"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_relationship <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_relationship-cell_line_relationship_id">cell_line_relationship_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_relationship-subject_id">subject_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_relationship-object_id">object_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_relationship-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_relationship_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>subject_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>subject_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>object_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>object_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>subject_id, object_id, type_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_synonym'
+ -->
+
+<a name="cell_line_synonym" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_synonym
+</h3></td>
+ <a name="cell_line_synonym"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_synonym <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_synonym-cell_line_synonym_id">cell_line_synonym_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_synonym-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_synonym-synonym_id">synonym_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#synonym-synonym_id">synonym.synonym_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_synonym-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_synonym-is_current">is_current</a></td>
+ <td class="FieldCellType">boolean</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">false</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_synonym-is_internal">is_internal</a></td>
+ <td class="FieldCellType">boolean</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">false</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_synonym_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>synonym_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>synonym_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>is_current</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>is_internal</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>synonym_id, cell_line_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_cvterm'
+ -->
+
+<a name="cell_line_cvterm" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_cvterm
+</h3></td>
+ <a name="cell_line_cvterm"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_cvterm <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvterm-cell_line_cvterm_id">cell_line_cvterm_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_cvterm-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvterm-cvterm_id">cvterm_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_cvterm-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvterm-rank">rank</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault">0</td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_cvterm_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cvterm_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cvterm_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>rank</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, cvterm_id, pub_id, rank</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_dbxref'
+ -->
+
+<a name="cell_line_dbxref" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_dbxref
+</h3></td>
+ <a name="cell_line_dbxref"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_dbxref <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_dbxref-cell_line_dbxref_id">cell_line_dbxref_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_dbxref-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_dbxref-dbxref_id">dbxref_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#dbxref-dbxref_id">dbxref.dbxref_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_dbxref-is_current">is_current</a></td>
+ <td class="FieldCellType">boolean</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">true</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>is_current</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, dbxref_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_lineprop'
+ -->
+
+<a name="cell_lineprop" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_lineprop
+</h3></td>
+ <a name="cell_lineprop"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_lineprop <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_lineprop-cell_lineprop_id">cell_lineprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_lineprop-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_lineprop-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_lineprop-value">value</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault">NULL</td>
+ <td class="FieldCellOther"></td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_lineprop-rank">rank</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault">0</td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_lineprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>rank</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, type_id, rank</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_lineprop_pub'
+ -->
+
+<a name="cell_lineprop_pub" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_lineprop_pub
+</h3></td>
+ <a name="cell_lineprop_pub"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_lineprop_pub <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_lineprop_pub-cell_lineprop_pub_id">cell_lineprop_pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_lineprop_pub-cell_lineprop_id">cell_lineprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_lineprop-cell_lineprop_id">cell_lineprop.cell_lineprop_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_lineprop_pub-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_lineprop_pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_lineprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_lineprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_lineprop_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_feature'
+ -->
+
+<a name="cell_line_feature" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_feature
+</h3></td>
+ <a name="cell_line_feature"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_feature <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_feature-cell_line_feature_id">cell_line_feature_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_feature-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_feature-feature_id">feature_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#feature-feature_id">feature.feature_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_feature-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_feature_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>feature_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>feature_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, feature_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_cvtermprop'
+ -->
+
+<a name="cell_line_cvtermprop" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_cvtermprop
+</h3></td>
+ <a name="cell_line_cvtermprop"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_cvtermprop <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvtermprop-cell_line_cvtermprop_id">cell_line_cvtermprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_cvtermprop-cell_line_cvterm_id">cell_line_cvterm_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line_cvterm-cell_line_cvterm_id">cell_line_cvterm.cell_line_cvterm_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvtermprop-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_cvtermprop-value">value</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault">NULL</td>
+ <td class="FieldCellOther"></td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_cvtermprop-rank">rank</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault">0</td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_cvtermprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_cvterm_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_cvterm_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>rank</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_cvterm_id, type_id, rank</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_pub'
+ -->
+
+<a name="cell_line_pub" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_pub
+</h3></td>
+ <a name="cell_line_pub"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_pub <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_pub-cell_line_pub_id">cell_line_pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_pub-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_pub-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'cell_line_library'
+ -->
+
+<a name="cell_line_library" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ cell_line_library
+</h3></td>
+ <a name="cell_line_library"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: cell_line_library <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_library-cell_line_library_id">cell_line_library_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_library-cell_line_id">cell_line_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cell_line-cell_line_id">cell_line.cell_line_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="cell_line_library-library_id">library_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#library-library_id">library.library_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="cell_line_library-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_library_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>cell_line_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>library_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>library_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>cell_line_id, library_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+Created by <a href="http://sqlfairy.sourceforge.net">
+SQL::Translator 0.11003</a>
+
+</body>
+</html>
Added: schema/trunk/chado/modules/stock/stock.html
===================================================================
--- schema/trunk/chado/modules/stock/stock.html (rev 0)
+++ schema/trunk/chado/modules/stock/stock.html 2011-09-20 19:04:39 UTC (rev 25193)
@@ -0,0 +1,2895 @@
+<!DOCTYPE html
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
+<head>
+<title>Description of Schema</title>
+<meta name="generator" content="SQL::Translator::Producer::HTML" />
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+</head>
+<body>
+
+
+<h1 class="SchemaDescription">
+ Description of Schema
+</h1>
+
+<hr />
+
+<!--
+ Table listing (15 tables)
+ -->
+
+<a name="top" />
+
+<table class="LinkTable" width="100%">
+
+<tr>
+ <td class="LinkTableCell"><h2 class="LinkTableTitle">
+ Tables
+</h2></td>
+</tr>
+
+<!--
+ Start link to table 'stock'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock-link" href="#stock">stock</a></td>
+</tr>
+
+<!--
+ End link to table 'stock'
+ -->
+
+<!--
+ Start link to table 'stock_pub'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_pub-link" href="#stock_pub">stock_pub</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_pub'
+ -->
+
+<!--
+ Start link to table 'stockprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stockprop-link" href="#stockprop">stockprop</a></td>
+</tr>
+
+<!--
+ End link to table 'stockprop'
+ -->
+
+<!--
+ Start link to table 'stockprop_pub'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stockprop_pub-link" href="#stockprop_pub">stockprop_pub</a></td>
+</tr>
+
+<!--
+ End link to table 'stockprop_pub'
+ -->
+
+<!--
+ Start link to table 'stock_relationship'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_relationship-link" href="#stock_relationship">stock_relationship</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_relationship'
+ -->
+
+<!--
+ Start link to table 'stock_relationship_cvterm'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_relationship_cvterm-link" href="#stock_relationship_cvterm">stock_relationship_cvterm</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_relationship_cvterm'
+ -->
+
+<!--
+ Start link to table 'stock_relationship_pub'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_relationship_pub-link" href="#stock_relationship_pub">stock_relationship_pub</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_relationship_pub'
+ -->
+
+<!--
+ Start link to table 'stock_dbxref'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_dbxref-link" href="#stock_dbxref">stock_dbxref</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_dbxref'
+ -->
+
+<!--
+ Start link to table 'stock_cvterm'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_cvterm-link" href="#stock_cvterm">stock_cvterm</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_cvterm'
+ -->
+
+<!--
+ Start link to table 'stock_cvtermprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_cvtermprop-link" href="#stock_cvtermprop">stock_cvtermprop</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_cvtermprop'
+ -->
+
+<!--
+ Start link to table 'stock_genotype'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_genotype-link" href="#stock_genotype">stock_genotype</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_genotype'
+ -->
+
+<!--
+ Start link to table 'stockcollection'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stockcollection-link" href="#stockcollection">stockcollection</a></td>
+</tr>
+
+<!--
+ End link to table 'stockcollection'
+ -->
+
+<!--
+ Start link to table 'stockcollectionprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stockcollectionprop-link" href="#stockcollectionprop">stockcollectionprop</a></td>
+</tr>
+
+<!--
+ End link to table 'stockcollectionprop'
+ -->
+
+<!--
+ Start link to table 'stockcollection_stock'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stockcollection_stock-link" href="#stockcollection_stock">stockcollection_stock</a></td>
+</tr>
+
+<!--
+ End link to table 'stockcollection_stock'
+ -->
+
+<!--
+ Start link to table 'stock_dbxrefprop'
+ -->
+
+<tr class="LinkTableRow">
+ <td class="LinkTableCell"><a id="stock_dbxrefprop-link" href="#stock_dbxrefprop">stock_dbxrefprop</a></td>
+</tr>
+
+<!--
+ End link to table 'stock_dbxrefprop'
+ -->
+
+</table>
+
+<!--
+ Starting table 'stock'
+ -->
+
+<a name="stock" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stock
+</h3></td>
+ <a name="stock"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ $Id: stock.sql,v 1.7 2007-03-23 15:18:03 scottcain Exp $ <br />
+ ========================================== <br />
+ Chado stock module <br />
+ DEPENDENCIES <br />
+ ============ <br />
+ :import cvterm from cv <br />
+ :import pub from pub <br />
+ :import dbxref from general <br />
+ :import organism from organism <br />
+ :import genotype from genetic <br />
+ :import contact from contact <br />
+ ================================================ <br />
+ TABLE: stock <br />
+ ================================================ <br />
+ Any stock can be globally identified by the
+ combination of organism, uniquename and stock type. A stock is the physical entities, either living or preserved, held by collections. Stocks belong to a collection; they have IDs, type, organism, description and may have a genotype.
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock-stock_id">stock_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock-dbxref_id">dbxref_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">The dbxref_id is an optional primary stable identifier for this stock. Secondary indentifiers and external dbxrefs go in table: stock_dbxref. </td>
+ <td class="FieldCellFK"><a href="#dbxref-dbxref_id">dbxref.dbxref_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock-organism_id">organism_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, The organism_id is the organism to which the stock belongs. This column should only be left blank if the organism cannot be determined. </td>
+ <td class="FieldCellFK"><a href="#organism-organism_id">organism.organism_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock-name">name</a></td>
+ <td class="FieldCellType">varchar</td>
+ <td class="FieldCellSize">255</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">The name is a human-readable local name for a stock. </td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock-uniquename">uniquename</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock-description">description</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">The description is the genetic description provided in the stock list. </td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL, The type_id foreign key links to a controlled vocabulary of stock types. The would include living stock, genomic DNA, preserved specimen. Secondary cvterms for stocks would go in stock_cvterm. </td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock-is_obsolete">is_obsolete</a></td>
+ <td class="FieldCellType">boolean</td>
+ <td class="FieldCellSize">0</td>
+ <td class="FieldCellDefault">false</td>
+ <td class="FieldCellOther">NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Indices
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Name
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_name_ind1</td>
+ <td>name</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_idx1</td>
+ <td>dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_idx2</td>
+ <td>organism_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_idx3</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_idx4</td>
+ <td>uniquename</td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>dbxref_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>organism_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>uniquename</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>is_obsolete</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>organism_id, uniquename, type_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'stock_pub'
+ -->
+
+<a name="stock_pub" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stock_pub
+</h3></td>
+ <a name="stock_pub"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: stock_pub <br />
+ ================================================ <br />
+ Provenance. Linking table between stocks and, for example, a stocklist computer file.
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock_pub-stock_pub_id">stock_pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stock_pub-stock_id">stock_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#stock-stock_id">stock.stock_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stock_pub-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Indices
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Name
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_pub_idx1</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stock_pub_idx2</td>
+ <td>pub_id</td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>stock_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'stockprop'
+ -->
+
+<a name="stockprop" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stockprop
+</h3></td>
+ <a name="stockprop"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: stockprop <br />
+ ================================================ <br />
+ A stock can have any number of
+ slot-value property tags attached to it. This is an alternative to
+ hardcoding a list of columns in the relational schema, and is
+ completely extensible. There is a unique constraint, stockprop_c1, for
+ the combination of stock_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stockprop-stockprop_id">stockprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stockprop-stock_id">stock_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#stock-stock_id">stock.stock_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stockprop-type_id">type_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#cvterm-cvterm_id">cvterm.cvterm_id</a></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stockprop-value">value</a></td>
+ <td class="FieldCellType">text</td>
+ <td class="FieldCellSize">64000</td>
+ <td class="FieldCellDefault">NULL</td>
+ <td class="FieldCellOther"></td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stockprop-rank">rank</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault">0</td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+</table>
+
+<h3>
+ Indices
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Name
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>stockprop_idx1</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stockprop_idx2</td>
+ <td>type_id</td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stockprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>stock_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>type_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>rank</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>stock_id, type_id, rank</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'stockprop_pub'
+ -->
+
+<a name="stockprop_pub" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stockprop_pub
+</h3></td>
+ <a name="stockprop_pub"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: stockprop_pub <br />
+ ================================================ <br />
+ Provenance. Any stockprop assignment can optionally be supported by a publication.
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stockprop_pub-stockprop_pub_id">stockprop_pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">11</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">PRIMARY KEY, NOT NULL</td>
+ <td class="FieldCellFK"></td>
+</tr>
+
+<tr class="tr-even">
+ <td class="FieldCellName"><a name="stockprop_pub-stockprop_id">stockprop_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#stockprop-stockprop_id">stockprop.stockprop_id</a></td>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldCellName"><a name="stockprop_pub-pub_id">pub_id</a></td>
+ <td class="FieldCellType">integer</td>
+ <td class="FieldCellSize">10</td>
+ <td class="FieldCellDefault"></td>
+ <td class="FieldCellOther">UNIQUE, NOT NULL</td>
+ <td class="FieldCellFK"><a href="#pub-pub_id">pub.pub_id</a></td>
+</tr>
+
+</table>
+
+<h3>
+ Indices
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Name
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>stockprop_pub_idx1</td>
+ <td>stockprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>stockprop_pub_idx2</td>
+ <td>pub_id</td>
+</tr>
+
+</table>
+
+<h3>
+ Constraints
+</h3>
+
+<table border="1">
+
+<tr class="IndexRow">
+ <th>
+ Type
+ </th>
+ <th>
+ Fields
+ </th>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stockprop_pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>stockprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>stockprop_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>NOT NULL</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>FOREIGN KEY</td>
+ <td>pub_id</td>
+</tr>
+
+<tr class="IndexCell">
+ <td>UNIQUE</td>
+ <td>stockprop_id, pub_id</td>
+</tr>
+
+</table>
+
+<hr />
+
+<!--
+ Starting table 'stock_relationship'
+ -->
+
+<a name="stock_relationship" />
+
+<table class="TableHeader" width="100%">
+ <tr class="TableHeaderRow">
+ <td class="TableHeaderCell"><h3>
+ stock_relationship
+</h3></td>
+ <a name="stock_relationship"> <td class="TableHeaderCell" align="right"><a href="#top">Top</a></td>
+ </tr>
+</table>
+
+<b>
+ Comments:
+</b>
+
+<br />
+
+<em>
+ <br />
+ ================================================ <br />
+ TABLE: stock_relationship <br />
+ ================================================
+</em>
+
+<table border="1">
+
+<tr>
+ <th class="FieldHeader">
+ Field Name
+ </th>
+ <th class="FieldHeader">
+ Data Type
+ </th>
+ <th class="FieldHeader">
+ Size
+ </th>
+ <th class="FieldHeader">
+ Default Value
+ </th>
+ <th class="FieldHeader">
+ Other
+ </th>
+ <th class="FieldHeader">
+ Foreign Key
+ </th>
+</tr>
+
+<tr class="tr-odd">
+ <td class="FieldC...
[truncated message content] |
|
From: <sco...@us...> - 2012-03-29 16:23:25
|
Revision: 25262
http://gmod.svn.sourceforge.net/gmod/?rev=25262&view=rev
Author: scottcain
Date: 2012-03-29 16:23:06 +0000 (Thu, 29 Mar 2012)
Log Message:
-----------
commiting Dave's/FlyBase's interaction module
Added Paths:
-----------
schema/trunk/chado/modules/interaction/
schema/trunk/chado/modules/interaction/interaction.sql
Added: schema/trunk/chado/modules/interaction/interaction.sql
===================================================================
--- schema/trunk/chado/modules/interaction/interaction.sql (rev 0)
+++ schema/trunk/chado/modules/interaction/interaction.sql 2012-03-29 16:23:06 UTC (rev 25262)
@@ -0,0 +1,316 @@
+
+
+-- ==========================================
+-- Chado interaction module
+--
+-- ==========================================
+-- NOTES:
+--
+-- Designed to represent various types of interactions
+-- initially to be deployed for physical interactions (protein-protein)
+-- between n number of chado features
+--
+-- prop and pub tables follow usual chado conventions
+--
+-- table:interaction serves as a coalescing table for all aspects of the interaction
+-- a uniquename and link to a cvterm for the type of interaction are stored here
+--
+-- table:feature_interaction links features to the interaction
+-- a cvterm_id for the role that the feature is playing in the interaction
+-- must be specified (eg. prey, bait, evidence_for)
+-- rank may be used to order interacting features in an interaction
+--
+
+-- ================================================
+-- TABLE: interaction
+-- ================================================
+drop table interaction cascade;
+create table interaction (
+ interaction_id serial NOT NULL,
+ primary key (interaction_id),
+ uniquename text NOT NULL,
+ type_id int NOT NULL,
+ foreign key (type_id) references cvterm (cvterm_id)
+ on delete cascade INITIALLY DEFERRED,
+ description text,
+ is_obsolete boolean not null default false,
+ constraint interaction_c1 unique(uniquename,type_id)
+);
+create index interaction_idx1 on interaction (uniquename);
+create index interaction_idx2 on interaction (type_id);
+
+grant all on interaction to public;
+grant all on interaction_interaction_id_seq to public;
+
+-- ================================================
+-- TABLE: interactionprop
+-- ================================================
+
+drop table interactionprop cascade;
+create table interactionprop (
+ interactionprop_id serial not null,
+ primary key (interactionprop_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint interactionprop_c1 unique (interaction_id,type_id,rank)
+);
+create index interactionprop_idx1 on interactionprop (interaction_id);
+create index interactionprop_idx2 on interactionprop (type_id);
+
+grant all on interactionprop to public;
+grant all on interactionprop_interactionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: interactionprop_pub
+-- ================================================
+create table interactionprop_pub (
+ interactionprop_pub_id serial not null,
+ primary key (interactionprop_pub_id),
+ interactionprop_id int not null,
+ foreign key (interactionprop_id) references interactionprop (interactionprop_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint interactionprop_pub_c1 unique (interactionprop_id,pub_id)
+);
+create index interactionprop_pub_idx1 on interactionprop_pub (interactionprop_id);
+create index interactionprop_pub_idx2 on interactionprop_pub (pub_id);
+
+
+grant all on interactionprop_pub to public;
+grant all on interactionprop_pub_interactionprop_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_pub
+-- ================================================
+
+drop table interaction_pub cascade;
+create table interaction_pub (
+ interaction_pub_id serial not null,
+ primary key (interaction_pub_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint interaction_pub_c1 unique(interaction_id,pub_id)
+);
+create index interaction_pub_idx1 on interaction_pub (interaction_id);
+create index interaction_pub_idx2 on interaction_pub (pub_id);
+
+grant all on interaction_pub to public;
+grant all on interaction_pub_interaction_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_expression
+-- ================================================
+
+drop table interaction_expression cascade;
+
+create table interaction_expression (
+ interaction_expression_id serial not null,
+ primary key (interaction_expression_id),
+ expression_id int not null,
+ foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(expression_id,interaction_id,pub_id)
+);
+create index interaction_expression_idx1 on interaction_expression (expression_id);
+create index interaction_expression_idx2 on interaction_expression (interaction_id);
+create index interaction_expression_idx3 on interaction_expression (pub_id);
+
+grant all on interaction_expression to public;
+grant all on interaction_expression_interaction_expression_id_seq to public;
+
+--================================================
+-- TABLE: interaction_expressionprop
+-- ================================================
+
+drop table interaction_expressionprop;
+create table interaction_expressionprop (
+ interaction_expressionprop_id serial not null,
+ primary key (interaction_expressionprop_id),
+ interaction_expression_id int not null,
+ foreign key (interaction_expression_id) references interaction_expression (interaction_expression_id) on delete cascade,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ unique (interaction_expression_id,type_id,rank)
+);
+
+
+create index interaction_expressionprop_idx1 on interaction_expressionprop (interaction_expression_id);
+create index interaction_expressionprop_idx2 on interaction_expressionprop (type_id);
+
+grant all on interaction_expressionprop to public;
+grant all on interaction_expressionprop_interaction_expressionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_cvterm
+-- ================================================
+
+drop table interaction_cvterm cascade;
+
+create table interaction_cvterm (
+ interaction_cvterm_id serial not null,
+ primary key (interaction_cvterm_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ cvterm_id int not null,
+ foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ unique(interaction_id,cvterm_id)
+);
+create index interaction_cvterm_idx1 on interaction_cvterm (interaction_id);
+create index interaction_cvterm_idx2 on interaction_cvterm (cvterm_id);
+create index interaction_cvterm_idx3 on interaction_cvterm (pub_id);
+
+grant all on interaction_cvterm to public;
+grant all on interaction_cvterm_interaction_cvterm_id_seq to public;
+
+--================================================
+-- TABLE: interaction_cvtermprop
+-- ================================================
+
+drop table interaction_cvtermprop;
+create table interaction_cvtermprop (
+ interaction_cvtermprop_id serial not null,
+ primary key (interaction_cvtermprop_id),
+ interaction_cvterm_id int not null,
+ foreign key (interaction_cvterm_id) references interaction_cvterm (interaction_cvterm_id) on delete cascade,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ unique (interaction_cvterm_id,type_id,rank)
+);
+
+
+create index interaction_cvtermprop_idx1 on interaction_cvtermprop (interaction_cvterm_id);
+create index interaction_cvtermprop_idx2 on interaction_cvtermprop (type_id);
+
+grant all on interaction_cvtermprop to public;
+grant all on interaction_cvtermprop_interaction_cvtermprop_id_seq to public;
+
+
+-- ================================================
+-- TABLE: library_interaction
+-- ================================================
+
+drop table library_interaction cascade;
+
+create table library_interaction (
+ library_interaction_id serial not null,
+ primary key (library_interaction_id),
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(interaction_id,library_id,pub_id)
+);
+create index library_interaction_idx1 on library_interaction (interaction_id);
+create index library_interaction_idx2 on library_interaction (library_id);
+create index library_interaction_idx3 on library_interaction (pub_id);
+
+grant all on library_interaction to public;
+grant all on library_interaction_library_interaction_id_seq to public;
+
+-- ================================================
+-- TABLE: feature_interaction
+-- ================================================
+
+drop table feature_interaction cascade;
+create table feature_interaction (
+ feature_interaction_id serial not null,
+ primary key (feature_interaction_id),
+ feature_id int not null,
+ foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ role_id int not null,
+ foreign key (role_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ unique(feature_id,interaction_id, role_id)
+);
+create index feature_interaction_idx1 on feature_interaction (feature_id);
+create index feature_interaction_idx2 on feature_interaction (interaction_id);
+create index feature_interaction_idx3 on feature_interaction (role_id);
+
+grant all on feature_interaction to public;
+grant all on feature_interaction_feature_interaction_id_seq to public;
+
+-- ? do we want to add rank to the unique key ? thinking stochiometry issues
+-- and might we have one form modified and not another ? may be too much
+
+-- ================================================
+-- TABLE: feature_interactionprop
+-- ================================================
+
+drop table feature_interactionprop cascade;
+create table feature_interactionprop (
+ feature_interactionprop_id serial not null,
+ primary key (feature_interactionprop_id),
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint feature_interactionprop_c1 unique (feature_interaction_id,type_id,rank)
+);
+create index feature_interactionprop_idx1 on feature_interactionprop (feature_interaction_id);
+create index feature_interactionprop_idx2 on feature_interactionprop (type_id);
+
+grant all on feature_interactionprop to public;
+grant all on feature_interactionprop_feature_interactionprop_id_seq to public;
+
+-- ================================================
+-- TABLE: feature_interaction_pub
+-- ================================================
+
+drop table feature_interaction_pub cascade;
+create table feature_interaction_pub (
+ feature_interaction_pub_id serial not null,
+ primary key (feature_interaction_pub_id),
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint feature_interaction_pub_c1 unique(feature_interaction_id,pub_id)
+);
+create index feature_interaction_pub_idx1 on feature_interaction_pub (feature_interaction_id);
+create index feature_interaction_pub_idx2 on feature_interaction_pub (pub_id);
+
+grant all on feature_interaction_pub to public;
+grant all on feature_interaction_pub_feature_interaction_pub_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_cell_line
+-- ================================================
+
+drop table interaction_cell_line cascade;
+
+create table interaction_cell_line (
+ interaction_cell_line_id serial not null,
+ primary key (interaction_cell_line_id),
+ cell_line_id int not null,
+ foreign key (cell_line_id) references cell_line (cell_line_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ unique(cell_line_id,interaction_id,pub_id)
+);
+create index interaction_cell_line_idx1 on interaction_cell_line (cell_line_id);
+create index interaction_cell_line_idx2 on interaction_cell_line (interaction_id);
+create index interaction_cell_line_idx3 on interaction_cell_line (pub_id);
+
+grant all on interaction_cell_line to public;
+grant all on interaction_cell_line_interaction_cell_line_id_seq to public;
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <em...@us...> - 2013-01-15 15:11:03
|
Revision: 25279
http://gmod.svn.sourceforge.net/gmod/?rev=25279&view=rev
Author: emmert
Date: 2013-01-15 15:10:50 +0000 (Tue, 15 Jan 2013)
Log Message:
-----------
Extensions to interaction, expression, and organism modules; extension to library module to link to these. All changes are back-compatible.
Modified Paths:
--------------
schema/trunk/chado/modules/expression/expression.sql
schema/trunk/chado/modules/interaction/interaction.sql
schema/trunk/chado/modules/library/library.sql
schema/trunk/chado/modules/organism/organism.sql
Modified: schema/trunk/chado/modules/expression/expression.sql
===================================================================
--- schema/trunk/chado/modules/expression/expression.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/expression/expression.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -21,11 +21,12 @@
uniquename text not null,
md5checksum character(32),
description text,
- constraint expression_c1 unique(uniquename)
+ constraint expression_c1 unique (uniquename)
);
COMMENT ON TABLE expression IS 'The expression table is essentially a bridge table.';
+
-- ================================================
-- TABLE: expression_cvterm
-- ================================================
@@ -40,12 +41,13 @@
rank int not null default 0,
cvterm_type_id int not null,
foreign key (cvterm_type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
- constraint expression_cvterm_c1 unique(expression_id,cvterm_id,cvterm_type_id)
+ constraint expression_cvterm_c1 unique (expression_id,cvterm_id,rank,cvterm_type_id)
);
create index expression_cvterm_idx1 on expression_cvterm (expression_id);
create index expression_cvterm_idx2 on expression_cvterm (cvterm_id);
create index expression_cvterm_idx3 on expression_cvterm (cvterm_type_id);
+
--================================================
-- TABLE: expression_cvtermprop
-- ================================================
@@ -112,7 +114,7 @@
foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- constraint expression_pub_c1 unique(expression_id,pub_id)
+ constraint expression_pub_c1 unique (expression_id,pub_id)
);
create index expression_pub_idx1 on expression_pub (expression_id);
create index expression_pub_idx2 on expression_pub (pub_id);
@@ -131,7 +133,7 @@
foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- constraint feature_expression_c1 unique(expression_id,feature_id,pub_id)
+ constraint feature_expression_c1 unique (expression_id,feature_id,pub_id)
);
create index feature_expression_idx1 on feature_expression (expression_id);
create index feature_expression_idx2 on feature_expression (feature_id);
Modified: schema/trunk/chado/modules/interaction/interaction.sql
===================================================================
--- schema/trunk/chado/modules/interaction/interaction.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/interaction/interaction.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -24,6 +24,7 @@
-- ================================================
-- TABLE: interaction
-- ================================================
+
drop table interaction cascade;
create table interaction (
interaction_id serial NOT NULL,
@@ -34,13 +35,11 @@
on delete cascade INITIALLY DEFERRED,
description text,
is_obsolete boolean not null default false,
- constraint interaction_c1 unique(uniquename,type_id)
+ constraint interaction_c1 unique (uniquename,type_id)
);
create index interaction_idx1 on interaction (uniquename);
create index interaction_idx2 on interaction (type_id);
-grant all on interaction to public;
-grant all on interaction_interaction_id_seq to public;
-- ================================================
-- TABLE: interactionprop
@@ -61,12 +60,12 @@
create index interactionprop_idx1 on interactionprop (interaction_id);
create index interactionprop_idx2 on interactionprop (type_id);
-grant all on interactionprop to public;
-grant all on interactionprop_interactionprop_id_seq to public;
-- ================================================
-- TABLE: interactionprop_pub
-- ================================================
+
+drop table interactionprop_pub cascade;
create table interactionprop_pub (
interactionprop_pub_id serial not null,
primary key (interactionprop_pub_id),
@@ -80,9 +79,6 @@
create index interactionprop_pub_idx2 on interactionprop_pub (pub_id);
-grant all on interactionprop_pub to public;
-grant all on interactionprop_pub_interactionprop_pub_id_seq to public;
-
-- ================================================
-- TABLE: interaction_pub
-- ================================================
@@ -100,15 +96,12 @@
create index interaction_pub_idx1 on interaction_pub (interaction_id);
create index interaction_pub_idx2 on interaction_pub (pub_id);
-grant all on interaction_pub to public;
-grant all on interaction_pub_interaction_pub_id_seq to public;
-- ================================================
-- TABLE: interaction_expression
-- ================================================
drop table interaction_expression cascade;
-
create table interaction_expression (
interaction_expression_id serial not null,
primary key (interaction_expression_id),
@@ -118,14 +111,12 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- unique(expression_id,interaction_id,pub_id)
+ constraint interaction_expression_c1 unique (expression_id,interaction_id,pub_id)
);
create index interaction_expression_idx1 on interaction_expression (expression_id);
create index interaction_expression_idx2 on interaction_expression (interaction_id);
create index interaction_expression_idx3 on interaction_expression (pub_id);
-grant all on interaction_expression to public;
-grant all on interaction_expression_interaction_expression_id_seq to public;
--================================================
-- TABLE: interaction_expressionprop
@@ -141,22 +132,17 @@
foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value text null,
rank int not null default 0,
- unique (interaction_expression_id,type_id,rank)
+ constraint interaction_expressionprop_c1 unique (interaction_expression_id,type_id,rank)
);
-
-
create index interaction_expressionprop_idx1 on interaction_expressionprop (interaction_expression_id);
create index interaction_expressionprop_idx2 on interaction_expressionprop (type_id);
-grant all on interaction_expressionprop to public;
-grant all on interaction_expressionprop_interaction_expressionprop_id_seq to public;
-- ================================================
-- TABLE: interaction_cvterm
-- ================================================
drop table interaction_cvterm cascade;
-
create table interaction_cvterm (
interaction_cvterm_id serial not null,
primary key (interaction_cvterm_id),
@@ -164,20 +150,17 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
cvterm_id int not null,
foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
- unique(interaction_id,cvterm_id)
+ constraint interaction_cvterm_c1 unique (interaction_id,cvterm_id)
);
create index interaction_cvterm_idx1 on interaction_cvterm (interaction_id);
create index interaction_cvterm_idx2 on interaction_cvterm (cvterm_id);
-create index interaction_cvterm_idx3 on interaction_cvterm (pub_id);
-grant all on interaction_cvterm to public;
-grant all on interaction_cvterm_interaction_cvterm_id_seq to public;
--================================================
-- TABLE: interaction_cvtermprop
-- ================================================
-drop table interaction_cvtermprop;
+drop table interaction_cvtermprop cascade;
create table interaction_cvtermprop (
interaction_cvtermprop_id serial not null,
primary key (interaction_cvtermprop_id),
@@ -187,42 +170,13 @@
foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
value text null,
rank int not null default 0,
- unique (interaction_cvterm_id,type_id,rank)
+ constraint interaction_cvtermprop_c1 unique (interaction_cvterm_id,type_id,rank)
);
-
-
create index interaction_cvtermprop_idx1 on interaction_cvtermprop (interaction_cvterm_id);
create index interaction_cvtermprop_idx2 on interaction_cvtermprop (type_id);
-grant all on interaction_cvtermprop to public;
-grant all on interaction_cvtermprop_interaction_cvtermprop_id_seq to public;
-
-- ================================================
--- TABLE: library_interaction
--- ================================================
-
-drop table library_interaction cascade;
-
-create table library_interaction (
- library_interaction_id serial not null,
- primary key (library_interaction_id),
- interaction_id int not null,
- foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
- library_id int not null,
- foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
- pub_id int not null,
- foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- unique(interaction_id,library_id,pub_id)
-);
-create index library_interaction_idx1 on library_interaction (interaction_id);
-create index library_interaction_idx2 on library_interaction (library_id);
-create index library_interaction_idx3 on library_interaction (pub_id);
-
-grant all on library_interaction to public;
-grant all on library_interaction_library_interaction_id_seq to public;
-
--- ================================================
-- TABLE: feature_interaction
-- ================================================
@@ -237,18 +191,16 @@
role_id int not null,
foreign key (role_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
rank int not null default 0,
- unique(feature_id,interaction_id, role_id)
+ constraint feature_interaction_c1 unique (feature_id,interaction_id, role_id)
);
create index feature_interaction_idx1 on feature_interaction (feature_id);
create index feature_interaction_idx2 on feature_interaction (interaction_id);
create index feature_interaction_idx3 on feature_interaction (role_id);
-grant all on feature_interaction to public;
-grant all on feature_interaction_feature_interaction_id_seq to public;
-
-- ? do we want to add rank to the unique key ? thinking stochiometry issues
-- and might we have one form modified and not another ? may be too much
+
-- ================================================
-- TABLE: feature_interactionprop
-- ================================================
@@ -268,8 +220,6 @@
create index feature_interactionprop_idx1 on feature_interactionprop (feature_interaction_id);
create index feature_interactionprop_idx2 on feature_interactionprop (type_id);
-grant all on feature_interactionprop to public;
-grant all on feature_interactionprop_feature_interactionprop_id_seq to public;
-- ================================================
-- TABLE: feature_interaction_pub
@@ -288,15 +238,12 @@
create index feature_interaction_pub_idx1 on feature_interaction_pub (feature_interaction_id);
create index feature_interaction_pub_idx2 on feature_interaction_pub (pub_id);
-grant all on feature_interaction_pub to public;
-grant all on feature_interaction_pub_feature_interaction_pub_id_seq to public;
-- ================================================
-- TABLE: interaction_cell_line
-- ================================================
drop table interaction_cell_line cascade;
-
create table interaction_cell_line (
interaction_cell_line_id serial not null,
primary key (interaction_cell_line_id),
@@ -306,11 +253,43 @@
foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
pub_id int not null,
foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
- unique(cell_line_id,interaction_id,pub_id)
+ constraint interaction_cell_line_c1 unique (cell_line_id,interaction_id,pub_id)
);
create index interaction_cell_line_idx1 on interaction_cell_line (cell_line_id);
create index interaction_cell_line_idx2 on interaction_cell_line (interaction_id);
create index interaction_cell_line_idx3 on interaction_cell_line (pub_id);
-grant all on interaction_cell_line to public;
-grant all on interaction_cell_line_interaction_cell_line_id_seq to public;
+
+-- ================================================
+-- TABLE: interaction_group
+-- ================================================
+
+drop table interaction_group cascade;
+create table interaction_group (
+ interaction_group_id serial not null,
+ primary key (interaction_group_id),
+ uniquename text NOT NULL,
+ is_obsolete boolean not null default false,
+ description text,
+ constraint interaction_group_c1 unique (uniquename)
+);
+create index interaction_group_idx1 on interaction_group (uniquename);
+
+
+-- ================================================
+-- TABLE: interaction_group_feature_interaction
+-- ================================================
+
+drop table interaction_group_feature_interaction cascade;
+create table interaction_group_feature_interaction (
+ interaction_group_feature_interaction_id serial not null,
+ primary key (interaction_group_feature_interaction_id),
+ interaction_group_id int not null,
+ foreign key (interaction_group_id) references interaction_group (interaction_group_id) on delete cascade INITIALLY DEFERRED,
+ feature_interaction_id int not null,
+ foreign key (feature_interaction_id) references feature_interaction (feature_interaction_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ constraint interaction_group_feature_interaction_c1 unique (interaction_group_id,feature_interaction_id,rank)
+);
+create index interaction_group_feature_interaction_idx1 on interaction_group_feature_interaction (interaction_group_id);
+create index interaction_group_feature_interaction_idx2 on interaction_group_feature_interaction (feature_interaction_id);
Modified: schema/trunk/chado/modules/library/library.sql
===================================================================
--- schema/trunk/chado/modules/library/library.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/library/library.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -7,6 +7,9 @@
-- :import cvterm from cv
-- :import pub from pub
-- :import organism from organism
+-- :import expression from expression
+-- :import interaction from interaction
+-- :import strain from strain
-- =================================================================
-- ================================================
@@ -178,6 +181,133 @@
create index library_dbxref_idx2 on library_dbxref (dbxref_id);
+-- ================================================
+-- TABLE: library_expression
+-- ================================================
+create table library_expression (
+ library_expression_id serial not null,
+ primary key (library_expression_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ expression_id int not null,
+ foreign key (expression_id) references expression (expression_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_expression_c1 unique (library_id,expression_id)
+);
+create index library_expression_idx1 on library_expression (library_id);
+create index library_expression_idx2 on library_expression (expression_id);
+create index library_expression_idx3 on library_expression (pub_id);
+-- ================================================
+-- TABLE: library_expressionprop
+-- ================================================
+
+create table library_expressionprop (
+ library_expressionprop_id serial not null,
+ primary key (library_expressionprop_id),
+ library_expression_id int not null,
+ foreign key (library_expression_id) references library_expression (library_expression_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ value text null,
+ rank int not null default 0,
+ constraint library_expressionprop_c1 unique (library_expression_id,type_id,rank)
+);
+create index library_expressionprop_idx1 on library_expressionprop (library_expression_id);
+create index library_expressionprop_idx2 on library_expressionprop (type_id);
+
+
+-- ================================================
+-- TABLE: library_featureprop
+-- ================================================
+
+create table library_featureprop (
+ library_featureprop_id serial not null,
+ primary key (library_featureprop_id),
+ library_feature_id int not null,
+ foreign key (library_feature_id) references library_feature (library_feature_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ value text null,
+ rank int not null default 0,
+ constraint library_featureprop_c1 unique (library_feature_id,type_id,rank)
+);
+create index library_featureprop_idx1 on library_featureprop (library_feature_id);
+create index library_featureprop_idx2 on library_featureprop (type_id);
+
+
+-- ================================================
+-- TABLE: library_interaction
+-- ================================================
+
+create table library_interaction (
+ library_interaction_id serial not null,
+ primary key (library_interaction_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ interaction_id int not null,
+ foreign key (interaction_id) references interaction (interaction_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_interaction_c1 unique (interaction_id,library_id,pub_id)
+);
+create index library_interaction_idx1 on library_interaction (interaction_id);
+create index library_interaction_idx2 on library_interaction (library_id);
+create index library_interaction_idx3 on library_interaction (pub_id);
+
+
+-- ================================================
+-- TABLE: library_relationship
+-- ================================================
+
+create table library_relationship (
+ library_relationship_id serial not null,
+ primary key (library_relationship_id),
+ subject_id int not null,
+ foreign key (subject_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ object_id int not null,
+ foreign key (object_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id),
+ constraint library_relationship_c1 unique (subject_id,object_id,type_id)
+);
+create index library_relationship_idx1 on library_relationship (subject_id);
+create index library_relationship_idx2 on library_relationship (object_id);
+create index library_relationship_idx3 on library_relationship (type_id);
+
+
+-- ================================================
+-- TABLE: library_relationship_pub
+-- ================================================
+
+create table library_relationship_pub (
+ library_relationship_pub_id serial not null,
+ primary key (library_relationship_pub_id),
+ library_relationship_id int not null,
+ foreign key (library_relationship_id) references library_relationship (library_relationship_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id),
+ constraint library_relationship_pub_c1 unique (library_relationship_id,pub_id)
+);
+create index library_relationship_pub_idx1 on library_relationship_pub (library_relationship_id);
+create index library_relationship_pub_idx2 on library_relationship_pub (pub_id);
+
+
+-- ================================================
+-- TABLE: library_strain
+-- ================================================
+
+create table library_strain (
+ library_strain_id serial not null,
+ primary key (library_strain_id),
+ library_id int not null,
+ foreign key (library_id) references library (library_id) on delete cascade INITIALLY DEFERRED,
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ constraint library_strain_c1 unique (library_id,strain_id)
+);
+create index library_strain_idx1 on library_strain (library_id);
+create index library_strain_idx2 on library_strain (strain_id);
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2012-12-13 19:59:18 UTC (rev 25278)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-01-15 15:10:50 UTC (rev 25279)
@@ -1,4 +1,4 @@
--- $Id: organism.sql,v 1.19 2007-04-01 18:45:41 briano Exp $
+-- $Id: organism.sql,v 1.19 2007/04/01 18:45:41 briano Exp $
-- ==========================================
-- Chado organism module
--
@@ -13,6 +13,7 @@
-- TABLE: organism
-- ================================================
+drop table organism cascade;
create table organism (
organism_id serial not null,
primary key (organism_id),
@@ -37,10 +38,12 @@
this is appended onto the species name. Follows standard NCBI taxonomy
pattern.';
+
-- ================================================
-- TABLE: organism_dbxref
-- ================================================
+drop table organism_dbxref cascade;
create table organism_dbxref (
organism_dbxref_id serial not null,
primary key (organism_dbxref_id),
@@ -53,10 +56,12 @@
create index organism_dbxref_idx1 on organism_dbxref (organism_id);
create index organism_dbxref_idx2 on organism_dbxref (dbxref_id);
+
-- ================================================
-- TABLE: organismprop
-- ================================================
+drop table organismprop cascade;
create table organismprop (
organismprop_id serial not null,
primary key (organismprop_id),
@@ -73,3 +78,370 @@
COMMENT ON TABLE organismprop IS 'Tag-value properties - follows standard chado model.';
+
+-- ================================================
+-- TABLE: organismprop_pub
+-- ================================================
+
+drop table organismprop_pub cascade;
+create table organismprop_pub (
+ organismprop_pub_id serial not null,
+ primary key (organismprop_pub_id),
+ organismprop_id int not null,
+ foreign key (organismprop_id) references organismprop (organismprop_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint organismprop_pub_c1 unique (organismprop_id,pub_id)
+);
+create index organismprop_pub_idx1 on organismprop_pub (organismprop_id);
+create index organismprop_pub_idx2 on organismprop_pub (pub_id);
+
+COMMENT ON TABLE organismprop_pub IS 'Attribution for organismprop.';
+
+
+-- ================================================
+-- TABLE: organism_pub
+-- ================================================
+
+drop table organism_pub cascade;
+create table organism_pub (
+ organism_pub_id serial not null,
+ primary key (organism_pub_id),
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint organism_pub_c1 unique (organism_id,pub_id)
+);
+create index organism_pub_idx1 on organism_pub (organism_id);
+create index organism_pub_idx2 on organism_pub (pub_id);
+
+
+-- ================================================
+-- TABLE: organism_cvterm
+-- ================================================
+
+drop table organism_cvterm cascade;
+create table organism_cvterm (
+ organism_cvterm_id serial not null,
+ primary key (organism_cvterm_id),
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY
+DEFERRED,
+ cvterm_id int not null,
+ foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ rank int not null default 0,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint organism_cvterm_c1 unique(organism_id,cvterm_id,pub_id)
+);
+create index organism_cvterm_idx1 on organism_cvterm (organism_id);
+create index organism_cvterm_idx2 on organism_cvterm (cvterm_id);
+
+COMMENT ON TABLE organism_cvterm IS 'organism to cvterm associations. Examples: taxonomic name';
+
+COMMENT ON COLUMN organism_cvterm.rank IS 'Property-Value
+ordering. Any organism_cvterm can have multiple values for any particular
+property type - these are ordered in a list using rank, counting from
+zero. For properties that are single-valued rather than multi-valued,
+the default 0 value should be used';
+
+
+--================================================
+-- TABLE: organism_cvtermprop
+-- ================================================
+
+drop table organism_cvtermprop cascade;
+create table organism_cvtermprop (
+ organism_cvtermprop_id serial not null,
+ primary key (organism_cvtermprop_id),
+ organism_cvterm_id int not null,
+ foreign key (organism_cvterm_id) references organism_cvterm (organism_cvterm_id) on delete cascade,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint organism_cvtermprop_c1 unique (organism_cvterm_id,type_id,rank)
+);
+create index organism_cvtermprop_idx1 on organism_cvtermprop (organism_cvterm_id);
+create index organism_cvtermprop_idx2 on organism_cvtermprop (type_id);
+
+COMMENT ON TABLE organism_cvtermprop IS 'Extensible properties for
+organism to cvterm associations. Examples: qualifiers';
+
+COMMENT ON COLUMN organism_cvtermprop.type_id IS 'The name of the
+property/slot is a cvterm. The meaning of the property is defined in
+that cvterm. ';
+
+COMMENT ON COLUMN organism_cvtermprop.value IS 'The value of the
+property, represented as text. Numeric values are converted to their
+text representation. This is less efficient than using native database
+types, but is easier to query.';
+
+COMMENT ON COLUMN organism_cvtermprop.rank IS 'Property-Value
+ordering. Any organism_cvterm can have multiple values for any particular
+property type - these are ordered in a list using rank, counting from
+zero. For properties that are single-valued rather than multi-valued,
+the default 0 value should be used';
+
+
+-- ================================================
+-- TABLE: strain
+-- ================================================
+
+drop table strain cascade;
+create table strain (
+ strain_id serial not null,
+ primary key (strain_id),
+ name varchar(255) null,
+ uniquename text not null,
+ organism_id int not null,
+ foreign key (organism_id) references organism (organism_id) on delete cascade INITIALLY DEFERRED,
+ dbxref_id int null,
+ foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED,
+ is_obsolete boolean not null default 'false',
+ constraint strain_c1 unique (organism_id, uniquename)
+);
+
+create index strain_idx1 on strain (uniquename);
+create index strain_idx2 on strain (name);
+
+COMMENT ON TABLE strain IS 'A characterized strain of a given organism.';
+
+
+-- ================================================
+-- TABLE: strain_cvterm
+-- ================================================
+
+drop table strain_cvterm cascade;
+create table strain_cvterm (
+ strain_cvterm_id serial not null,
+ primary key (strain_cvterm_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ cvterm_id int not null,
+ foreign key (cvterm_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint strain_cvterm_c1 unique(strain_id,cvterm_id,pub_id)
+);
+create index strain_cvterm_idx1 on strain_cvterm (strain_id);
+create index strain_cvterm_idx2 on strain_cvterm (cvterm_id);
+
+COMMENT ON TABLE strain_cvterm IS 'strain to cvterm associations. Examples: GOid';
+
+--================================================
+-- TABLE: strain_cvtermprop
+-- ================================================
+
+drop table strain_cvtermprop cascade;
+create table strain_cvtermprop (
+ strain_cvtermprop_id serial not null,
+ primary key (strain_cvtermprop_id),
+ strain_cvterm_id int not null,
+ foreign key (strain_cvterm_id) references strain_cvterm (strain_cvterm_id) on delete cascade,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint strain_cvtermprop_c1 unique (strain_cvterm_id,type_id,rank)
+);
+create index strain_cvtermprop_idx1 on strain_cvtermprop (strain_cvterm_id);
+create index strain_cvtermprop_idx2 on strain_cvtermprop (type_id);
+
+COMMENT ON TABLE strain_cvtermprop IS 'Extensible properties for
+strain to cvterm associations. Examples: qualifiers';
+
+COMMENT ON COLUMN strain_cvtermprop.type_id IS 'The name of the
+property/slot is a cvterm. The meaning of the property is defined in
+that cvterm. ';
+
+COMMENT ON COLUMN strain_cvtermprop.value IS 'The value of the
+property, represented as text. Numeric values are converted to their
+text representation. This is less efficient than using native database
+types, but is easier to query.';
+
+COMMENT ON COLUMN strain_cvtermprop.rank IS 'Property-Value
+ordering. Any strain_cvterm can have multiple values for any particular
+property type - these are ordered in a list using rank, counting from
+zero. For properties that are single-valued rather than multi-valued,
+the default 0 value should be used';
+
+
+-- ================================================
+-- TABLE: strain_relationship
+-- ================================================
+
+drop table strain_relationship cascade;
+create table strain_relationship (
+ strain_relationship_id serial not null,
+ primary key (strain_relationship_id),
+ subject_id int not null,
+ foreign key (subject_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ object_id int not null,
+ foreign key (object_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint strain_relationship_c1 unique (subject_id, object_id, type_id, rank)
+);
+create index strain_relationship_idx1 on strain_relationship (subject_id);
+create index strain_relationship_idx2 on strain_relationship (object_id);
+
+COMMENT ON TABLE strain_relationship IS 'Relationships between strains, eg, progenitor.';
+
+
+-- ================================================
+-- TABLE: strainprop
+-- ================================================
+
+drop table strainprop cascade;
+create table strainprop (
+ strainprop_id serial not null,
+ primary key (strainprop_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint strainprop_c1 unique (strain_id, type_id, rank)
+);
+create index strainprop_idx1 on strainprop (strain_id);
+create index strainprop_idx2 on strainprop (type_id);
+
+COMMENT ON TABLE strainprop IS 'Attributes of a given strain';
+
+
+-- ================================================
+-- TABLE: strainprop_pub
+-- ================================================
+
+drop table strainprop_pub cascade;
+create table strainprop_pub (
+ strainprop_pub_id serial not null,
+ primary key (strainprop_pub_id),
+ strainprop_id int not null,
+ foreign key (strainprop_id) references strainprop (strainprop_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint strainprop_pub_c1 unique (strainprop_id,pub_id)
+);
+create index strainprop_pub_idx1 on strainprop_pub (strainprop_id);
+create index strainprop_pub_idx2 on strainprop_pub (pub_id);
+
+COMMENT ON TABLE strainprop_pub IS 'Provenance. Any strainprop assignment can optionally be supported by a publication.';
+
+
+-- ================================================
+-- TABLE: strain_dbxref
+-- ================================================
+
+drop table strain_dbxref cascade;
+create table strain_dbxref (
+ strain_dbxref_id serial not null,
+ primary key (strain_dbxref_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ dbxref_id int not null,
+ foreign key (dbxref_id) references dbxref (dbxref_id) on delete cascade INITIALLY DEFERRED,
+ is_current boolean not null default 'true',
+ constraint strain_dbxref_c1 unique (strain_id,dbxref_id)
+);
+create index strain_dbxref_idx1 on strain_dbxref (strain_id);
+create index strain_dbxref_idx2 on strain_dbxref (dbxref_id);
+
+
+-- ================================================
+-- TABLE: strain_synonym
+-- ================================================
+
+drop table strain_synonym cascade;
+create table strain_synonym (
+ strain_synonym_id serial not null,
+ primary key (strain_synonym_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ synonym_id int not null,
+ foreign key (synonym_id) references synonym (synonym_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ is_current boolean not null default 'false',
+ is_internal boolean not null default 'false',
+ constraint strain_synonym_c1 unique (synonym_id,strain_id,pub_id)
+);
+create index strain_synonym_idx1 on strain_synonym (synonym_id);
+create index strain_synonym_idx2 on strain_synonym (strain_id);
+create index strain_synonym_idx3 on strain_synonym (pub_id);
+
+COMMENT ON TABLE strain_synonym IS 'Linking table between strain and synonym.';
+
+
+-- ================================================
+-- TABLE: strain_feature
+-- ================================================
+
+drop table strain_feature cascade;
+create table strain_feature (
+ strain_feature_id serial not null,
+ primary key (strain_feature_id),
+ strain_id int not null,
+ foreign key (strain_id) references strain (strain_id) on delete cascade INITIALLY DEFERRED,
+ feature_id int not null,
+ foreign key (feature_id) references feature (feature_id) on delete cascade INITIALLY DEFERRED,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint strain_feature_c1 unique (strain_id,feature_id,pub_id)
+);
+create index strain_feature_idx1 on strain_feature (strain_id);
+create index strain_feature_idx2 on strain_feature (feature_id);
+
+COMMENT ON TABLE strain_feature IS 'strain_feature links a strain to features associated with the strain. Type may
+be, eg, "homozygous" or "heterozygous".';
+
+
+-- ================================================
+-- TABLE: strain_featureprop
+-- ================================================
+
+drop table strain_featureprop cascade;
+create table strain_featureprop (
+ strain_featureprop_id serial not null,
+ primary key (strain_featureprop_id),
+ strain_feature_id int not null,
+ foreign key (strain_feature_id) references strain_feature (strain_feature_id) on delete cascade INITIALLY DEFERRED,
+ type_id int not null,
+ foreign key (type_id) references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+ value text null,
+ rank int not null default 0,
+ constraint strain_featureprop_c1 unique (strain_feature_id,type_id,rank)
+);
+create index strain_featureprop_idx1 on strain_featureprop (strain_feature_id);
+create index strain_featureprop_idx2 on strain_featureprop (type_id);
+
+COMMENT ON TABLE strain_featureprop IS 'Attributes of a strain_feature relationship. Eg, a comment';
+
+
+-- ================================================
+-- TABLE: strain_phenotype
+-- ================================================
+
+drop table strain_phenotype cascade;
+create table strain_phenotype (
+ strain_phenotype_id SERIAL NOT NULL,
+ primary key (strain_phenotype_id),
+ strain_id INT NOT NULL,
+ foreign key (strain_id) references strain (strain_id) on delete cascade,
+ phenotype_id INT NOT NULL,
+ foreign key (phenotype_id) references phenotype (phenotype_id) on delete cascade,
+ pub_id int not null,
+ foreign key (pub_id) references pub (pub_id) on delete cascade INITIALLY DEFERRED,
+ constraint strain_phenotype_c1 unique (strain_id,phenotype_id,pub_id)
+);
+create index strain_phenotype_idx1 ON strain_phenotype (strain_id);
+create index strain_phenotype_idx2 ON strain_phenotype (phenotype_id);
+
+COMMENT on table strain_phenotype IS 'Links phenotype(s) associated with a given strain. Types may be, eg, "selected" or "unassigned".';
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From: <em...@us...> - 2013-09-09 13:18:13
|
Revision: 25291
http://sourceforge.net/p/gmod/svn/25291
Author: emmert
Date: 2013-09-09 13:17:56 +0000 (Mon, 09 Sep 2013)
Log Message:
-----------
Added documentation to new tables and made some minor formatting changes where neccesary for consistency.
Modified Paths:
--------------
schema/trunk/chado/modules/library/library.sql
schema/trunk/chado/modules/organism/organism.sql
schema/trunk/chado/modules/phenotype/phenotype.sql
Modified: schema/trunk/chado/modules/library/library.sql
===================================================================
--- schema/trunk/chado/modules/library/library.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/library/library.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -35,8 +35,7 @@
create index library_idx2 on library (type_id);
create index library_idx3 on library (uniquename);
-COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links
-to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"';
+COMMENT ON COLUMN library.type_id IS 'The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library"';
-- ================================================
@@ -60,9 +59,13 @@
create index library_synonym_idx2 on library_synonym (library_id);
create index library_synonym_idx3 on library_synonym (pub_id);
+COMMENT ON TABLE library_synonym IS 'Linking table between library and synonym.';
+
COMMENT ON COLUMN library_synonym.is_current IS 'The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library.';
+
COMMENT ON COLUMN library_synonym.pub_id IS 'The pub_id link is for
relating the usage of a given synonym to the publication in which it was used.';
+
COMMENT ON COLUMN library_synonym.is_internal IS 'Typically a synonym
exists so that somebody querying the database with an obsolete name
can find the object they are looking for under its current name. If
@@ -85,7 +88,9 @@
create index library_pub_idx1 on library_pub (library_id);
create index library_pub_idx2 on library_pub (pub_id);
+COMMENT ON TABLE library_pub IS 'Attribution for a library.';
+
-- ================================================
-- TABLE: libraryprop
-- ================================================
@@ -104,7 +109,9 @@
create index libraryprop_idx1 on libraryprop (library_id);
create index libraryprop_idx2 on libraryprop (type_id);
+COMMENT ON TABLE libraryprop IS 'Tag-value properties - follows standard chado model.';
+
-- ================================================
-- TABLE: libraryprop_pub
-- ================================================
@@ -121,7 +128,9 @@
create index libraryprop_pub_idx1 on libraryprop_pub (libraryprop_id);
create index libraryprop_pub_idx2 on libraryprop_pub (pub_id);
+COMMENT ON TABLE libraryprop_pub IS 'Attribution for libraryprop.';
+
-- ================================================
-- TABLE: library_cvterm
-- ================================================
@@ -180,7 +189,9 @@
create index library_dbxref_idx1 on library_dbxref (library_id);
create index library_dbxref_idx2 on library_dbxref (dbxref_id);
+COMMENT ON TABLE library_dbxref IS 'Links a library to dbxrefs.';
+
-- ================================================
-- TABLE: library_expression
-- ================================================
@@ -200,7 +211,9 @@
create index library_expression_idx2 on library_expression (expression_id);
create index library_expression_idx3 on library_expression (pub_id);
+COMMENT ON TABLE library_expression IS 'Links a library to expression statements.';
+
-- ================================================
-- TABLE: library_expressionprop
-- ================================================
@@ -219,7 +232,9 @@
create index library_expressionprop_idx1 on library_expressionprop (library_expression_id);
create index library_expressionprop_idx2 on library_expressionprop (type_id);
+COMMENT ON TABLE library_expressionprop IS 'Attributes of a library_expression relationship.';
+
-- ================================================
-- TABLE: library_featureprop
-- ================================================
@@ -238,7 +253,9 @@
create index library_featureprop_idx1 on library_featureprop (library_feature_id);
create index library_featureprop_idx2 on library_featureprop (type_id);
+COMMENT ON TABLE library_featureprop IS 'Attributes of a library_feature relationship.';
+
-- ================================================
-- TABLE: library_interaction
-- ================================================
@@ -258,7 +275,9 @@
create index library_interaction_idx2 on library_interaction (library_id);
create index library_interaction_idx3 on library_interaction (pub_id);
+COMMENT ON TABLE library_interaction IS 'Links a library to an interaction.';
+
-- ================================================
-- TABLE: library_relationship
-- ================================================
@@ -278,7 +297,9 @@
create index library_relationship_idx2 on library_relationship (object_id);
create index library_relationship_idx3 on library_relationship (type_id);
+COMMENT ON TABLE library_relationship IS 'Relationships between libraries.';
+
-- ================================================
-- TABLE: library_relationship_pub
-- ================================================
@@ -295,7 +316,9 @@
create index library_relationship_pub_idx1 on library_relationship_pub (library_relationship_id);
create index library_relationship_pub_idx2 on library_relationship_pub (pub_id);
+COMMENT ON TABLE library_relationship_pub IS 'Provenance of library_relationship.';
+
-- ================================================
-- TABLE: library_strain
-- ================================================
@@ -311,3 +334,5 @@
);
create index library_strain_idx1 on library_strain (library_id);
create index library_strain_idx2 on library_strain (strain_id);
+
+COMMENT ON TABLE library_strain IS 'Links a library to a strain.';
Modified: schema/trunk/chado/modules/organism/organism.sql
===================================================================
--- schema/trunk/chado/modules/organism/organism.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/organism/organism.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -56,7 +56,9 @@
create index organism_dbxref_idx1 on organism_dbxref (organism_id);
create index organism_dbxref_idx2 on organism_dbxref (dbxref_id);
+COMMENT ON TABLE library_dbxref IS 'Links a library to dbxrefs.';
+
-- ================================================
-- TABLE: organismprop
-- ================================================
@@ -118,7 +120,9 @@
create index organism_pub_idx1 on organism_pub (organism_id);
create index organism_pub_idx2 on organism_pub (pub_id);
+COMMENT ON TABLE organism_pub IS 'Attribution for organism.';
+
-- ================================================
-- TABLE: organism_cvterm
-- ================================================
@@ -374,11 +378,13 @@
create index strain_dbxref_idx1 on strain_dbxref (strain_id);
create index strain_dbxref_idx2 on strain_dbxref (dbxref_id);
+COMMENT ON TABLE strain_dbxref IS 'Links a strain to dbxrefs. This is for secondary identifiers; primary identifiers should use strain.dbxref_id.';
--- ================================================
--- TABLE: strain_pub
--- ================================================
+-- ================================================
+-- TABLE: strain_pub
+-- ================================================
+
drop table strain_pub cascade;
create table strain_pub (
strain_pub_id serial not null,
@@ -392,7 +398,9 @@
create index strain_pub_idx1 on strain_pub (strain_id);
create index strain_pub_idx2 on strain_pub (pub_id);
+COMMENT ON TABLE strain_pub IS 'Provenance. Linking table between strains and publications that mention them.';
+
-- ================================================
-- TABLE: strain_synonym
-- ================================================
Modified: schema/trunk/chado/modules/phenotype/phenotype.sql
===================================================================
--- schema/trunk/chado/modules/phenotype/phenotype.sql 2013-07-26 17:23:56 UTC (rev 25290)
+++ schema/trunk/chado/modules/phenotype/phenotype.sql 2013-09-09 13:17:56 UTC (rev 25291)
@@ -45,6 +45,7 @@
COMMENT ON COLUMN phenotype.cvalue_id IS 'Phenotype attribute value (state).';
COMMENT ON COLUMN phenotype.assay_id IS 'Evidence type.';
+
-- ================================================
-- TABLE: phenotype_cvterm
-- ================================================
@@ -62,8 +63,9 @@
CREATE INDEX phenotype_cvterm_idx1 ON phenotype_cvterm (phenotype_id);
CREATE INDEX phenotype_cvterm_idx2 ON phenotype_cvterm (cvterm_id);
-COMMENT ON TABLE phenotype_cvterm IS NULL;
+COMMENT ON TABLE phenotype_cvterm IS 'phenotype to cvterm associations.';
+
-- ================================================
-- TABLE: feature_phenotype
-- ================================================
@@ -80,9 +82,12 @@
CREATE INDEX feature_phenotype_idx1 ON feature_phenotype (feature_id);
CREATE INDEX feature_phenotype_idx2 ON feature_phenotype (phenotype_id);
-COMMENT ON TABLE feature_phenotype IS NULL;
+COMMENT ON TABLE feature_phenotype IS 'Linking table between features and phenotypes.';
+-- ================================================
+-- TABLE: phenotypeprop
+-- ================================================
create table phenotypeprop (
phenotypeprop_id serial not null,
@@ -98,8 +103,4 @@
create index phenotypeprop_idx1 on phenotypeprop (phenotype_id);
create index phenotypeprop_idx2 on phenotypeprop (type_id);
-COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of
-slot-value property tags attached to it. This is an alternative to
-hardcoding a list of columns in the relational schema, and is
-completely extensible. There is a unique constraint, phenotypeprop_c1, for
-the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';
+COMMENT ON TABLE phenotypeprop IS 'A phenotype can have any number of slot-value property tags attached to it. This is an alternative to hardcoding a list of columns in the relational schema, and is completely extensible. There is a unique constraint, phenotypeprop_c1, for the combination of phenotype_id, rank, and type_id. Multivalued property-value pairs must be differentiated by rank.';
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