added new schema file

tripal_core/chado_schema/default_schema-1.11-1.2-diff.sql

@@ -0,0 +1,570 @@
+ create table cvprop (
+     cvprop_id serial not null,
+     primary key (cvprop_id),
+     cv_id int not null,
+     foreign key (cv_id) references cv (cv_id) INITIALLY DEFERRED,
+     type_id int not null,
+     foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
+     value text,
+     rank int not null default 0,
+     constraint cvprop_c1 unique (cv_id,type_id,rank)
+ );
+ 
+ COMMENT ON TABLE cvprop IS 'Additional extensible properties can be attached to a cv using this table.  A notable example would be the cv version';
+ 
+ COMMENT ON COLUMN cvprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.';
+ COMMENT ON COLUMN cvprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.';
+ 
+ COMMENT ON COLUMN cvprop.rank IS 'Property-Value ordering. Any
+ cv 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.';
+ 
+ create table chadoprop (
+     chadoprop_id serial not null,
+     primary key (chadoprop_id),
+     type_id int not null,
+     foreign key (type_id) references cvterm (cvterm_id) INITIALLY DEFERRED,
+     value text,
+     rank int not null default 0,
+     constraint chadoprop_c1 unique (type_id,rank)
+ );
+ 
+ COMMENT ON TABLE chadoprop IS 'This table is different from other prop tables in the database, as it is for storing information about the database itself, like schema version';
+ 
+ COMMENT ON COLUMN chadoprop.type_id IS 'The name of the property or slot is a cvterm. The meaning of the property is defined in that cvterm.';
+ COMMENT ON COLUMN chadoprop.value IS 'The value of the property, represented as text. Numeric values are converted to their text representation.';
+ 
+ COMMENT ON COLUMN chadoprop.rank IS 'Property-Value ordering. Any
+ cv 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.';
+
+ALTER TABLE genetic_code.gencode_startcodon ADD  CONSTRAINT gencode_startcodon_unique UNIQUE( gencode_id, codon );
+
+ALTER TABLE phenotype ADD COLUMN name TEXT default null;
+
+ALTER TABLE genotype ADD COLUMN type_id INT NOT NULL;
+ALTER TABLE genotype ADD CONSTRAINT genotype_type_id_fkey FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE CASCADE;
+
+
+ create table genotypeprop (
+     genotypeprop_id serial not null,
+     primary key (genotypeprop_id),
+     genotype_id int not null,
+     foreign key (genotype_id) references genotype (genotype_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 genotypeprop_c1 unique (genotype_id,type_id,rank)
+ );
+ create index genotypeprop_idx1 on genotypeprop (genotype_id);
+ create index genotypeprop_idx2 on genotypeprop (type_id);
+ 
+ CREATE TABLE projectprop (
+ 	projectprop_id serial NOT NULL,
+ 	PRIMARY KEY (projectprop_id),
+ 	project_id integer NOT NULL,
+ 	FOREIGN KEY (project_id) REFERENCES project (project_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, type_id, rank)
+ );
+ 
+ -- ================================================
+ -- TABLE: project_relationship
+ -- ================================================
+ 
+ CREATE TABLE project_relationship (
+ 	project_relationship_id serial NOT NULL,
+ 	PRIMARY KEY (project_relationship_id),
+ 	subject_project_id integer NOT NULL,
+ 	FOREIGN KEY (subject_project_id) REFERENCES project (project_id) ON DELETE CASCADE,
+ 	object_project_id integer NOT NULL,
+ 	FOREIGN KEY (object_project_id) REFERENCES project (project_id) ON DELETE CASCADE,
+ 	type_id integer NOT NULL,
+ 	FOREIGN KEY (type_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT,
+ 	CONSTRAINT project_relationship_c1 UNIQUE (subject_project_id, object_project_id, type_id)
+ );
+ COMMENT ON TABLE project_relationship IS 'A project can be composed of several smaller scale projects';
+ COMMENT ON COLUMN project_relationship.type_id IS 'The type of relationship being stated, such as "is part of".';
+ 
+ 
+ create table project_pub (
+        project_pub_id serial not null,
+        primary key (project_pub_id),
+        project_id int not null,
+        foreign key (project_id) references project (project_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 project_pub_c1 unique (project_id,pub_id)
+ );
+ create index project_pub_idx1 on project_pub (project_id);
+ create index project_pub_idx2 on project_pub (pub_id);
+ 
+ COMMENT ON TABLE project_pub IS 'Linking project(s) to publication(s)';
+ 
+ 
+ create table project_contact (
+        project_contact_id serial not null,
+        primary key (project_contact_id),
+        project_id int not null,
+        foreign key (project_id) references project (project_id) on delete cascade INITIALLY DEFERRED,
+        contact_id int not null,
+        foreign key (contact_id) references contact (contact_id) on delete cascade INITIALLY DEFERRED,
+        constraint project_contact_c1 unique (project_id,contact_id)
+ );
+ create index project_contact_idx1 on project_contact (project_id);
+ create index project_contact_idx2 on project_contact (contact_id);
+ 
+ COMMENT ON TABLE project_contact IS 'Linking project(s) to contact(s)';
+
+ALTER TABLE stock alter organism_id drop not null;
+
+ COMMENT ON COLUMN stock.organism_id IS 'The organism_id is the organism to which the stock belongs. This column is mandatory.';
+ 
+ CREATE TABLE stock_relationship_cvterm (
+ 	stock_relationship_cvterm_id SERIAL NOT NULL,
+ 	PRIMARY KEY (stock_relationship_cvterm_id),
+ 	stock_relationship_id integer NOT NULL,
+ 	FOREIGN KEY (stock_relationship_id) references stock_relationship (stock_relationship_id) ON DELETE CASCADE INITIALLY DEFERRED,
+ 	cvterm_id integer NOT NULL,
+ 	FOREIGN KEY (cvterm_id) REFERENCES cvterm (cvterm_id) ON DELETE RESTRICT,
+ 	pub_id integer,
+ 	FOREIGN KEY (pub_id) REFERENCES pub (pub_id) ON DELETE RESTRICT
+ );
+COMMENT ON TABLE stock_relationship_cvterm is 'For germplasm maintenance and pedigree data, stock_relationship. type_id will record cvterms such as "is a female parent of", "a parent for mutation", "is a group_id of", "is a source_id of", etc The cvterms for higher categories such as "generative", "derivative" or "maintenance" can be stored in table stock_relationship_cvterm';
+
+
+alter table stock_cvterm add column is_not boolean not null default false;
+alter table stock_cvterm add column rank integer not null default 0;
+alter table stock_cvterm drop constraint stock_cvterm_c1;
+alter table stock_cvterm add constraint stock_cvterm_c1 unique (stock_id,cvterm_id,pub_id,rank)
+;
+
+
+ create table stock_cvtermprop (
+     stock_cvtermprop_id serial not null,
+     primary key (stock_cvtermprop_id),
+     stock_cvterm_id int not null,
+     foreign key (stock_cvterm_id) references stock_cvterm (stock_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 stock_cvtermprop_c1 unique (stock_cvterm_id,type_id,rank)
+ );
+ create index stock_cvtermprop_idx1 on stock_cvtermprop (stock_cvterm_id);
+ create index stock_cvtermprop_idx2 on stock_cvtermprop (type_id);
+ 
+ COMMENT ON TABLE stock_cvtermprop IS 'Extensible properties for
+ stock to cvterm associations. Examples: GO evidence codes;
+ qualifiers; metadata such as the date on which the entry was curated
+ and the source of the association. See the stockprop table for
+ meanings of type_id, value and rank.';
+ 
+ COMMENT ON COLUMN stock_cvtermprop.type_id IS 'The name of the
+ property/slot is a cvterm. The meaning of the property is defined in
+ that cvterm. cvterms may come from the OBO evidence code cv.';
+ 
+ COMMENT ON COLUMN stock_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 stock_cvtermprop.rank IS 'Property-Value
+ ordering. Any stock_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.';
+ 
+ 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.';
+
+-- VIEW gffatts: a view to get feature attributes in a format that
+-- will make it easy to convert them to GFF attributes
+
+CREATE OR REPLACE VIEW gffatts (
+    feature_id,
+    type,
+    attribute
+) AS
+SELECT feature_id, 'Ontology_term' AS type,  s.name AS attribute
+FROM cvterm s, feature_cvterm fs
+WHERE fs.cvterm_id = s.cvterm_id
+UNION ALL
+SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS attribute
+FROM dbxref s, feature_dbxref fs, db d
+WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id
+UNION ALL
+SELECT feature_id, 'Alias' AS type, s.name AS attribute
+FROM synonym s, feature_synonym fs
+WHERE fs.synonym_id = s.synonym_id
+UNION ALL
+SELECT fp.feature_id,cv.name,fp.value
+FROM featureprop fp, cvterm cv
+WHERE fp.type_id = cv.cvterm_id
+UNION ALL
+SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS attribute
+FROM pub s, feature_pub fs
+WHERE fs.pub_id = s.pub_id;
+
+CREATE OR REPLACE VIEW gff3atts (
+    feature_id,
+    type,
+    attribute
+) AS
+SELECT feature_id,
+      'Ontology_term' AS type,
+      CASE WHEN db.name like '%Gene Ontology%'    THEN 'GO:'|| dbx.accession
+           WHEN db.name like 'Sequence Ontology%' THEN 'SO:'|| dbx.accession
+           ELSE                            CAST(db.name||':'|| dbx.accession AS varchar)
+      END
+FROM cvterm s, dbxref dbx, feature_cvterm fs, db
+WHERE fs.cvterm_id = s.cvterm_id and s.dbxref_id=dbx.dbxref_id and
+      db.db_id = dbx.db_id
+UNION ALL
+SELECT feature_id, 'Dbxref' AS type, d.name || ':' || s.accession AS
+attribute
+FROM dbxref s, feature_dbxref fs, db d
+WHERE fs.dbxref_id = s.dbxref_id and s.db_id = d.db_id and
+      d.name != 'GFF_source'
+UNION ALL
+SELECT f.feature_id, 'Alias' AS type, s.name AS attribute
+FROM synonym s, feature_synonym fs, feature f
+WHERE fs.synonym_id = s.synonym_id and f.feature_id = fs.feature_id and
+      f.name != s.name and f.uniquename != s.name
+UNION ALL
+SELECT fp.feature_id,cv.name,fp.value
+FROM featureprop fp, cvterm cv
+WHERE fp.type_id = cv.cvterm_id
+UNION ALL
+SELECT feature_id, 'pub' AS type, s.series_name || ':' || s.title AS
+attribute
+FROM pub s, feature_pub fs
+WHERE fs.pub_id = s.pub_id
+UNION ALL
+SELECT fr.subject_id as feature_id, 'Parent' 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='part_of' and cv_id in (select cv_id
+  FROM cv WHERE name='relationship'))
+UNION ALL
+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' 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
+FROM featureloc fl, feature target
+WHERE fl.srcfeature_id=target.feature_id
+        AND fl.rank != 0
+UNION ALL
+SELECT feature_id, 'ID' as type, uniquename as attribute
+FROM feature
+WHERE type_id NOT IN (SELECT cvterm_id FROM cvterm WHERE name='CDS')
+UNION ALL
+SELECT feature_id, 'chado_feature_id' as type, CAST(feature_id AS
+varchar) as attribute
+FROM feature
+UNION ALL
+SELECT feature_id, 'Name' as type, name as attribute
+FROM feature;
+
+
+-- =================================================================
+-- Dependencies:
+--
+-- :import feature from sequence
+-- :import cvterm from cv
+-- :import pub from pub
+-- :import phenotype from phenotype
+-- :import organism from organism
+-- :import genotype from genetic
+-- :import contact from contact
+-- :import project from project
+-- :import stock from stock
+-- :import synonym
+-- =================================================================
+
+
+-- this probably needs some work, depending on how cross-database we
+-- want to be.  In Postgres, at least, there are much better ways to 
+-- represent geo information.
+
+CREATE TABLE nd_geolocation (
+    nd_geolocation_id serial PRIMARY KEY NOT NULL,
+    description character varying(255),
+    latitude real,
+    longitude real,
+    geodetic_datum character varying(32),
+    altitude real
+);
+
+COMMENT ON TABLE nd_geolocation IS 'The geo-referencable location of the stock. NOTE: This entity is subject to change as a more general and possibly more OpenGIS-compliant geolocation module may be introduced into Chado.';
+
+COMMENT ON COLUMN nd_geolocation.description IS 'A textual representation of the location, if this is the original georeference. Optional if the original georeference is available in lat/long coordinates.';
+
+
+COMMENT ON COLUMN nd_geolocation.latitude IS 'The decimal latitude coordinate of the georeference, using positive and negative sign to indicate N and S, respectively.';
+
+COMMENT ON COLUMN nd_geolocation.longitude IS 'The decimal longitude coordinate of the georeference, using positive and negative sign to indicate E and W, respectively.';
+
+COMMENT ON COLUMN nd_geolocation.geodetic_datum IS 'The geodetic system on which the geo-reference coordinates are based. For geo-references measured between 1984 and 2010, this will typically be WGS84.';
+
+COMMENT ON COLUMN nd_geolocation.altitude IS 'The altitude (elevation) of the location in meters. If the altitude is only known as a range, this is the average, and altitude_dev will hold half of the width of the range.';
+
+
+
+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_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,
+    nd_experiment_id integer NOT NULL references nd_experiment (nd_experiment_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,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED ,
+    value text null,
+    rank integer NOT NULL default 0,
+    constraint nd_experimentprop_c1 unique (nd_experiment_id,type_id,rank)
+);
+
+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 nd_experiment_pub_c1 unique (nd_experiment_id,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_experiment_pub IS 'Linking nd_experiment(s) to publication(s)';
+
+
+
+
+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,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+    value text null,
+    rank integer NOT NULL DEFAULT 0,
+    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.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.';
+
+COMMENT ON COLUMN nd_geolocationprop.rank IS 'The rank of the property value, if the property has an array of values.';
+
+
+CREATE TABLE nd_protocol (
+    nd_protocol_id serial PRIMARY KEY  NOT NULL,
+    name character varying(255) NOT NULL unique,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED
+);
+
+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 (
+    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 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.';
+
+COMMENT ON COLUMN nd_reagent.type_id IS 'The type of the reagent, for example linker oligomer, or forward primer.';
+
+COMMENT ON COLUMN nd_reagent.feature_id IS 'If the reagent is a primer, the feature that it corresponds to. More generally, the corresponding feature for any reagent that has a sequence that maps to another sequence.';
+
+
+
+CREATE TABLE nd_protocol_reagent (
+    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 (
+    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,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+    value text null,
+    rank integer DEFAULT 0 NOT NULL,
+    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.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.';
+
+COMMENT ON COLUMN nd_protocolprop.rank IS 'The rank of the property value, if the property has an array of values.';
+
+
+
+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_experiment_stock IS 'Part of a stock or a clone of a stock that is used in an experiment';
+
+
+COMMENT ON COLUMN nd_experiment_stock.stock_id IS 'stock used in the extraction or the corresponding stock for the clone';
+
+
+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_experiment_protocol IS 'Linking table: experiments to the protocols they involve.';
+
+
+CREATE TABLE nd_experiment_phenotype (
+    nd_experiment_phenotype_id serial PRIMARY KEY NOT NULL,
+    nd_experiment_id integer NOT NULL 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,
+   constraint nd_experiment_phenotype_c1 unique (nd_experiment_id,phenotype_id)
+); 
+
+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_experiment_genotype (
+    nd_experiment_genotype_id serial PRIMARY KEY NOT NULL,
+    nd_experiment_id integer NOT NULL 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 ,
+    constraint nd_experiment_genotype_c1 unique (nd_experiment_id,genotype_id)
+);
+
+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 (
+    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 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.';
+
+COMMENT ON COLUMN nd_reagent_relationship.object_reagent_id IS 'The object reagent in the relationship. In parent/child terminology, the object is the parent. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';
+
+COMMENT ON COLUMN nd_reagent_relationship.type_id IS 'The type (or predicate) of the relationship. For example, in "linkerA 3prime-overhang-linker enzymeA" linkerA is the subject, 3prime-overhand-linker is the type, and enzymeA is the object.';
+
+
+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,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+    value text null,
+    rank integer DEFAULT 0 NOT NULL,
+    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,
+    type_id integer NOT NULL references cvterm (cvterm_id) on delete cascade INITIALLY DEFERRED,
+    value text null,
+    rank integer DEFAULT 0 NOT NULL,
+    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.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.';
+
+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_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_experiment_stock_dbxref IS 'Cross-reference experiment_stock to accessions, images, etc';
+
+
+
+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_experiment_dbxref IS 'Cross-reference experiment to accessions, images, etc';
+
+
+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
+);