SE-155 YeastX mzXML datasets: data model

SVN: 13000

rtd_yeastx/source/sql/postgresql/004/schema-004.sql

+-----------------------------------
+-- Version 003
+-----------------------------------
+
+-- Create domain types section -------------------------------------------------
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN CODE AS VARCHAR(40);
+
+CREATE DOMAIN FILE_NAME as VARCHAR(255);
+
+CREATE DOMAIN FILE_PATH as VARCHAR(1000);
+
+CREATE DOMAIN SHORT_LABEL as VARCHAR(20); 
+
+CREATE DOMAIN LONG_LABEL as VARCHAR(100); 
+
+CREATE DOMAIN CHAR as VARCHAR(1);
+
+CREATE DOMAIN ms_quantification_software_kind AS character varying(40)
+	CONSTRAINT ms_quantification_software_kind_check CHECK (((VALUE)::text = 
+		ANY ((ARRAY['msSoft'::character varying, 'Xcalibur'::character varying, 
+								'Analyst'::character varying, 'MassHunter'::character varying])::text[])));
+
+
+-- Create tables section -------------------------------------------------
+
+-- Table EXPERIMENTS
+
+CREATE TABLE EXPERIMENTS (
+  ID BIGSERIAL NOT NULL,
+  PERM_ID CODE NOT NULL,
+  NAME LONG_LABEL NOT NULL,
+  PRIMARY KEY (ID),
+  UNIQUE (PERM_ID)
+);
+
+-- Table SAMPLES
+
+CREATE TABLE SAMPLES (
+  ID BIGSERIAL NOT NULL,
+  PERM_ID CODE NOT NULL,
+  NAME LONG_LABEL NOT NULL,
+  EXPE_ID TECH_ID NOT NULL,
+  PRIMARY KEY (ID),
+  UNIQUE (PERM_ID),
+  CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table DATA_SETS
+
+CREATE TABLE DATA_SETS (
+  ID BIGSERIAL NOT NULL,
+  PERM_ID CODE NOT NULL,  
+  EXPE_ID TECH_ID NOT NULL,
+  SAMP_ID TECH_ID,
+  PRIMARY KEY (ID),
+  UNIQUE (PERM_ID),
+  CONSTRAINT FK_DATA_SET_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FK_DATA_SET_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table EIC_MS_RUNS
+
+CREATE TABLE EIC_MS_RUNS (
+  ID BIGSERIAL NOT NULL,
+  EXPE_ID TECH_ID NOT NULL,
+  SAMP_ID TECH_ID,
+  DS_ID TECH_ID NOT NULL,
+  RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
+  RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
+  ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
+  INSTRUMENT_TYPE SHORT_LABEL DEFAULT NULL,
+  INSTRUMENT_MANUFACTURER LONG_LABEL DEFAULT NULL,
+  INSTRUMENT_MODEL LONG_LABEL DEFAULT NULL,
+  METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
+  METHOD_SEPARATION LONG_LABEL DEFAULT NULL,
+  OPERATOR SHORT_LABEL DEFAULT NULL,
+  MS_RUN_ID BIGINT DEFAULT NULL,
+  SET_ID TECH_ID DEFAULT NULL,
+  START_TIME REAL NOT NULL,
+  END_TIME REAL NOT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_EIC_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FK_EIC_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FK_EIC_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX EIC_MS_RUNS_FK_DS_ID_IDX ON EIC_MS_RUNS(DS_ID);
+CREATE INDEX EIC_MS_RUNS_FK_SAMP_ID_IDX ON EIC_MS_RUNS(SAMP_ID);
+CREATE INDEX EIC_MS_RUNS_FK_EXPE_ID_IDX ON EIC_MS_RUNS(EXPE_ID);
+
+-- Table EIC_CHROMATOGRAMS
+
+CREATE TABLE EIC_CHROMATOGRAMS (
+  ID BIGSERIAL NOT NULL,
+  EIC_MS_RUN_ID TECH_ID NOT NULL,
+  Q1_MZ REAL NOT NULL,
+  Q3_LOW_MZ REAL NOT NULL,
+  Q3_HIGH_MZ REAL NOT NULL,
+  LABEL LONG_LABEL DEFAULT NULL,
+  POLARITY CHAR DEFAULT NULL,
+  RUN_TIMES TEXT NOT NULL,
+  INTENSITIES TEXT NOT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_EIC_CHROMATOGRAM_1 FOREIGN KEY (EIC_MS_RUN_ID) REFERENCES EIC_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX EIC_CHROMATOGRAM_FK_IDX ON EIC_CHROMATOGRAMS(EIC_MS_RUN_ID);
+
+-- Table FIA_MS_RUNS
+
+CREATE TABLE FIA_MS_RUNS (
+  ID BIGSERIAL NOT NULL,
+  EXPE_ID TECH_ID NOT NULL,
+  SAMP_ID TECH_ID,
+  DS_ID TECH_ID NOT NULL,
+  RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
+  RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
+  ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
+  INSTRUMENT_TYPE SHORT_LABEL DEFAULT NULL,
+  INSTRUMENT_MANUFACTURER LONG_LABEL DEFAULT NULL,
+  INSTRUMENT_MODEL LONG_LABEL DEFAULT NULL,
+  METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
+  METHOD_SEPARATION LONG_LABEL DEFAULT NULL,
+  POLARITY VARCHAR(1) DEFAULT NULL,
+  LOW_MZ REAL NOT NULL,
+  HIGH_MZ REAL NOT NULL,
+  INTERNAL_STANDARD REAL NOT NULL,
+  -- Is this a good name?
+  OD REAL NOT NULL,
+  OPERATOR SHORT_LABEL DEFAULT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_FIA_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FK_EIA_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT FK_EIA_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_MS_RUNS_FK_DS_ID_IDX ON FIA_MS_RUNS(DS_ID);
+CREATE INDEX FIA_MS_RUNS_FK_SAMP_ID_IDX ON FIA_MS_RUNS(SAMP_ID);
+CREATE INDEX FIA_MS_RUNS_FK_EXPE_ID_IDX ON FIA_MS_RUNS(EXPE_ID);
+
+-- Table FIA_PROFILES
+
+CREATE TABLE FIA_PROFILES (
+  ID BIGSERIAL NOT NULL,
+  FIA_MS_RUN_ID TECH_ID NOT NULL,
+  LOW_MZ REAL NOT NULL,
+  HIGH_MZ REAL NOT NULL,
+  MZ TEXT NOT NULL,
+  INTENSITIES TEXT NOT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_FIA_PROFILE_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_PROFILE_I_ID on FIA_PROFILES(FIA_MS_RUN_ID);
+CREATE INDEX FIA_PROFILE_I_ID_MZ on FIA_PROFILES(FIA_MS_RUN_ID, LOW_MZ, HIGH_MZ);
+
+-- Table FIA_CENTROIDS
+
+CREATE TABLE FIA_CENTROIDS (
+  ID BIGSERIAL NOT NULL,
+  FIA_MS_RUN_ID TECH_ID NOT NULL,
+  MZ REAL NOT NULL,
+  INTENSITY REAL NOT NULL,
+  CORRELATION REAL NOT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_FIA_CENTROID_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_CENTROID_I_ID ON FIA_CENTROIDS(FIA_MS_RUN_ID);
+CREATE INDEX FIA_CENTROID_I_ID_MZ ON FIA_CENTROIDS(FIA_MS_RUN_ID, MZ);
+ 
+-- Table MS_QUANTIFICATIONS
+
+CREATE TABLE MS_QUANTIFICATIONS (
+  ID BIGSERIAL NOT NULL,
+  DS_ID TECH_ID NOT NULL,
+  EXPE_ID TECH_ID NOT NULL,
+  SOURCE MS_QUANTIFICATION_SOFTWARE_KIND NOT NULL,
+  VALID BOOLEAN NOT NULL,
+  COMMENT TEXT,
+  REGISTRATOR SHORT_LABEL DEFAULT NULL,
+  REGISTRATION_DATE TIMESTAMP DEFAULT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT MS_QUANTIFICATION_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+  CONSTRAINT MS_QUANTIFICATION_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX MS_QUANTIFICATION_FK_DS_ID_IDX ON MS_QUANTIFICATIONS(DS_ID);
+CREATE INDEX MS_QUANTIFICATION_FK_EXPE_ID_IDX ON MS_QUANTIFICATIONS(EXPE_ID);
+
+-- Table MS_QUANT_CONCENTRATIONS
+
+CREATE TABLE MS_QUANT_CONCENTRATIONS (
+  ID BIGSERIAL NOT NULL,
+  MS_QUANTIFICATION_ID TECH_ID NOT NULL,
+  PARENT_DS_PERM_ID CODE NOT NULL,
+  AMOUNT REAL NOT NULL,
+  UNIT SHORT_LABEL NOT NULL,
+  VALID BOOLEAN NOT NULL,
+  COMMENT TEXT,
+  RETENTION_TIME REAL NOT NULL,
+  Q1 REAL NOT NULL,
+  Q3 REAL NOT NULL,
+  INTERNAL_STANDARD VARCHAR(30) NOT NULL,
+  PRIMARY KEY (ID),
+  CONSTRAINT FK_QUANT_CONCENTRATIONS_1 FOREIGN KEY (MS_QUANTIFICATION_ID) REFERENCES MS_QUANTIFICATIONS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table MS_QUANT_COMPOUND
+
+CREATE TABLE MS_QUANT_COMPOUNDS (
+	ID BIGSERIAL NOT NULL,
+  MS_QUANT_CONCENTRATION_ID TECH_ID NOT NULL,
+  COMPOUND_ID TECH_ID NOT NULL,
+  CONSTRAINT FK_QUANT_COMPOUND_1 FOREIGN KEY (MS_QUANT_CONCENTRATION_ID) REFERENCES MS_QUANT_CONCENTRATIONS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table EVENTS
+
+CREATE TABLE EVENTS (
+  LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
+);
+
+GRANT SELECT ON TABLE EXPERIMENTS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE SAMPLES TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE DATA_SETS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EIC_MS_RUNS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_MS_RUNS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_PROFILES TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_CENTROIDS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANTIFICATIONS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANT_CONCENTRATIONS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANT_COMPOUNDS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EVENTS TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE SAMPLES_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MS_QUANTIFICATIONS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MS_QUANT_CONCENTRATIONS_ID_SEQ TO GROUP metabol_readonly;
+
+GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EIC_MS_RUNS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_MS_RUNS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_PROFILES TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_CENTROIDS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANTIFICATIONS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANT_CONCENTRATIONS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANT_COMPOUNDS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE SAMPLES_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MS_QUANTIFICATIONS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MS_QUANT_CONCENTRATIONS_ID_SEQ TO GROUP metabol_readwrite;
+