#1164 #1165 Fixing the schema for gene regulatory network and protein…

… protein interactions to have timestamp and for gene and protein tables and annotation type for physical interactions table
dondi · Feb 9, 2025 · 8f856be · 8f856be
1 parent 82bf79f
commit 8f856be
Show file tree

Hide file tree

Showing 2 changed files with 29 additions and 15 deletions.
diff --git a/database2/schema/gene_regulatory_network_schema.sql b/database2/schema/gene_regulatory_network_schema.sql
@@ -11,8 +11,12 @@ CREATE TABLE gene_regulatory_network.gene (
   species VARCHAR,
   taxon_id VARCHAR,
   regulator BOOLEAN,
-  PRIMARY KEY(gene_id, taxon_id)
-); 
+  time_stamp TIMESTAMP WITH TIME ZONE,
+  source VARCHAR,
+  PRIMARY KEY(gene_id, taxon_id),
+  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source)
+);
+
 CREATE TABLE gene_regulatory_network.network (
   regulator_gene_id VARCHAR,
   target_gene_id VARCHAR,
@@ -21,5 +25,6 @@ CREATE TABLE gene_regulatory_network.network (
   source VARCHAR,
   FOREIGN KEY (regulator_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
   FOREIGN KEY (target_gene_id, taxon_id) REFERENCES gene_regulatory_network.gene(gene_id, taxon_id),
-  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source)
+  FOREIGN KEY (time_stamp, source) REFERENCES gene_regulatory_network.source(time_stamp, source),
+  CONSTRAINT unique_network UNIQUE (regulator_gene_id, target_gene_id, taxon_id, time_stamp, source)
 ); 
diff --git a/database2/schema/protein_protein_interactions_schema.sql b/database2/schema/protein_protein_interactions_schema.sql
@@ -10,7 +10,10 @@ CREATE TABLE protein_protein_interactions.gene (
   display_gene_id VARCHAR, -- standard like name
   species VARCHAR,
   taxon_id VARCHAR,
+  time_stamp TIMESTAMP WITH TIME ZONE,
+  source VARCHAR,
   PRIMARY KEY(gene_id, taxon_id)
+  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source)
 ); 
 
 CREATE TABLE protein_protein_interactions.protein (
@@ -20,18 +23,24 @@ CREATE TABLE protein_protein_interactions.protein (
   molecular_weight FLOAT,
   PI FLOAT,
   taxon_id VARCHAR,
-  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id)
-);
-
-CREATE TABLE protein_protein_interactions.physical_interactions (
-  protein1 VARCHAR,
-  protein2 VARCHAR,
-  interaction_detection_methods_identifier VARCHAR,
-  experiment_name VARCHAR,
   time_stamp TIMESTAMP WITH TIME ZONE,
   source VARCHAR,
-  FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name),
-  FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name),
-  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source),
-  CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, experiment_name, time_stamp, source)
+  FOREIGN KEY (gene_systematic_name, taxon_id) REFERENCES protein_protein_interactions.gene(gene_id, taxon_id)
+  FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source)
 );
+
+  CREATE TABLE protein_protein_interactions.physical_interactions (
+    protein1 VARCHAR,
+    protein2 VARCHAR,
+    gene_systematic_name1 VARCHAR,
+    gene_systematic_name2 VARCHAR,
+    interaction_detection_methods_identifier VARCHAR,
+    annotation_type VARCHAR,
+    experiment_name VARCHAR,
+    time_stamp TIMESTAMP WITH TIME ZONE,
+    source VARCHAR,
+    FOREIGN KEY (protein1) REFERENCES protein_protein_interactions.protein(standard_name),
+    FOREIGN KEY (protein2) REFERENCES protein_protein_interactions.protein(standard_name),
+    FOREIGN KEY (time_stamp, source) REFERENCES protein_protein_interactions.source(time_stamp, source),
+    CONSTRAINT unique_physical_interaction UNIQUE (protein1, protein2, interaction_detection_methods_identifier, annotation_type, experiment_name, time_stamp, source)
+  );