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[Gmod-schema-cmts] SF.net SVN: gmod:[25291] schema/trunk/chado/modules
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From: <em...@us...> - 2013-09-09 13:18:13
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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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