diff --git a/schema/RaMP_MySQL_BASE_2.4.0.sql b/schema/RaMP_MySQL_BASE_2.4.0.sql new file mode 100644 index 0000000..b423ce3 --- /dev/null +++ b/schema/RaMP_MySQL_BASE_2.4.0.sql @@ -0,0 +1,387 @@ +-- MySQL dump 10.13 Distrib 8.0.21, for Win64 (x86_64) +-- +-- Host: localhost Database: ramp +-- ------------------------------------------------------ +-- Server version 8.0.28 + +/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; +/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; +/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */; +/*!50503 SET NAMES utf8 */; +/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */; +/*!40103 SET TIME_ZONE='+00:00' */; +/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */; +/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */; +/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */; +/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; + +-- +-- Table structure for table `analyte` +-- + +DROP TABLE IF EXISTS `analyte`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `analyte` ( + `rampId` varchar(30) NOT NULL, + `type` varchar(30) DEFAULT NULL, + PRIMARY KEY (`rampId`), + KEY `analyte_rampId_RampID_IDX` (`rampId`) USING BTREE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `analytehasontology` +-- + +DROP TABLE IF EXISTS `analytehasontology`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `analytehasontology` ( + `rampCompoundId` varchar(30) DEFAULT NULL, + `rampOntologyId` varchar(30) DEFAULT NULL, + KEY `analyte_ont_ramp_id_idx` (`rampCompoundId`), + KEY `analyte_ont_id_idx` (`rampOntologyId`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `analytehaspathway` +-- + +DROP TABLE IF EXISTS `analytehaspathway`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `analytehaspathway` ( + `rampId` varchar(30) DEFAULT NULL, + `pathwayRampId` varchar(30) DEFAULT NULL, + `pathwaySource` varchar(30) DEFAULT NULL, + KEY `pathwayRampID_IDX` (`pathwayRampId`) USING BTREE, + KEY `ahp_RampID_IDX` (`rampId`) USING BTREE, + KEY `ahp_path_source_IDX` (`pathwaySource`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `analytesynonym` +-- + +DROP TABLE IF EXISTS `analytesynonym`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `analytesynonym` ( + `Synonym` varchar(500) DEFAULT NULL, + `rampId` varchar(30) DEFAULT NULL, + `geneOrCompound` varchar(30) DEFAULT NULL, + `source` varchar(30) DEFAULT NULL, + KEY `analSyn_RampID_IDX` (`rampId`) USING BTREE, + KEY `analSyn_syn_IDX` (`Synonym`) USING BTREE, + KEY `idx_analytesynonym_geneOrCompound` (`geneOrCompound`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `catalyzed` +-- + +DROP TABLE IF EXISTS `catalyzed`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `catalyzed` ( + `rampCompoundId` varchar(30) DEFAULT NULL, + `rampGeneId` varchar(30) DEFAULT NULL, + `proteinType` varchar(32) DEFAULT NULL, + KEY `catal_gene_idx` (`rampGeneId`), + KEY `catal_comp_idx` (`rampCompoundId`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `chem_props` +-- + +DROP TABLE IF EXISTS `chem_props`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `chem_props` ( + `ramp_id` varchar(30) NOT NULL, + `chem_data_source` varchar(32) DEFAULT NULL, + `chem_source_id` varchar(45) DEFAULT NULL, + `iso_smiles` varchar(256) DEFAULT NULL, + `inchi_key_prefix` varchar(32) DEFAULT NULL, + `inchi_key` varchar(32) DEFAULT NULL, + `inchi` varchar(4096) DEFAULT NULL, + `mw` float DEFAULT NULL, + `monoisotop_mass` float DEFAULT NULL, + `common_name` varchar(1024) DEFAULT NULL, + `mol_formula` varchar(64) DEFAULT NULL, + KEY `prop_source_idx` (`chem_data_source`) USING BTREE, + KEY `inchi_key_idx` (`inchi_key`) USING BTREE, + KEY `inchi_key_prefix_idx` (`inchi_key_prefix`) USING BTREE, + KEY `ramp_id_idx` (`ramp_id`) USING BTREE +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Holds metabolite properties for all ramp metabolites'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `db_version` +-- + +DROP TABLE IF EXISTS `db_version`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `db_version` ( + `ramp_version` varchar(20) NOT NULL, + `load_timestamp` datetime NOT NULL DEFAULT CURRENT_TIMESTAMP, + `version_notes` varchar(256) DEFAULT NULL, + `met_intersects_json` varchar(10000) DEFAULT NULL, + `gene_intersects_json` varchar(10000) DEFAULT NULL, + `met_intersects_json_pw_mapped` varchar(10000) DEFAULT NULL, + `gene_intersects_json_pw_mapped` varchar(10000) DEFAULT NULL, + `db_sql_url` varchar(256) DEFAULT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `entity_status_info` +-- + +DROP TABLE IF EXISTS `entity_status_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `entity_status_info` ( + `status_category` varchar(64) NOT NULL, + `entity_source_id` varchar(32) NOT NULL, + `entity_source_name` varchar(45) NOT NULL, + `entity_count` int NOT NULL +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='holds entity counts'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `metabolite_class` +-- + +DROP TABLE IF EXISTS `metabolite_class`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `metabolite_class` ( + `ramp_id` varchar(32) NOT NULL, + `class_source_id` varchar(32) NOT NULL, + `class_level_name` varchar(128) NOT NULL, + `class_name` varchar(128) NOT NULL, + `source` varchar(32) NOT NULL, + KEY `ramp_id_metclass_idx` (`ramp_id`), + KEY `class_source_id_metclass_idx` (`class_source_id`), + KEY `class_name_metclass_idx` (`class_name`), + KEY `class_source_metclass_idx` (`source`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='holds rampid and class source id to metabolic class levels and names'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ontology` +-- + +DROP TABLE IF EXISTS `ontology`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ontology` ( + `rampOntologyId` varchar(30) DEFAULT NULL, + `commonName` varchar(64) DEFAULT NULL, + `HMDBOntologyType` varchar(30) DEFAULT NULL, + `metCount` int DEFAULT '0', + KEY `ontol_parent_idx` (`commonName`), + KEY `ontol_ramp_id_idx` (`rampOntologyId`), + KEY `ontol_term_idx` (`HMDBOntologyType`), + KEY `ontol_metCount_idx` (`metCount`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `pathway` +-- + +DROP TABLE IF EXISTS `pathway`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `pathway` ( + `pathwayRampId` varchar(30) NOT NULL, + `sourceId` varchar(30) DEFAULT NULL, + `type` varchar(30) DEFAULT NULL, + `pathwayCategory` varchar(30) DEFAULT NULL, + `pathwayName` varchar(250) DEFAULT NULL, + PRIMARY KEY (`pathwayRampId`), + KEY `pathway_RampID_IDX` (`pathwayRampId`) USING BTREE, + KEY `idx_pathway_sourceId` (`sourceId`), + KEY `idx_pathway_type` (`type`), + KEY `idx_pathway_pathwayCategory` (`pathwayCategory`), + FULLTEXT KEY `idx_pathway_pathwayName` (`pathwayName`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ramp_data_object` +-- + +DROP TABLE IF EXISTS `ramp_data_object`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `ramp_data_object` ( + `data_key` varchar(32) NOT NULL, + `data_blob` longblob NOT NULL, + PRIMARY KEY (`data_key`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_0900_ai_ci; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reaction` +-- + +DROP TABLE IF EXISTS `reaction`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reaction` ( + `ramp_rxn_id` varchar(16) NOT NULL, + `rxn_source_id` varchar(16) NOT NULL, + `status` int NOT NULL, + `is_transport` int NOT NULL, + `direction` varchar(8) NOT NULL, + `label` varchar(256) NOT NULL, + `equation` varchar(256) NOT NULL, + `html_equation` varchar(256) NOT NULL, + `ec_num` varchar(256) DEFAULT NULL, + `has_human_prot` int NOT NULL, + `only_human_mets` int NOT NULL, + PRIMARY KEY (`ramp_rxn_id`), + KEY `reaction_src_id_idx` (`rxn_source_id`), + KEY `reaction_ec_num_idx` (`ec_num`), + KEY `reaction_has_human_prot_idx` (`has_human_prot`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='ramp primary reaction annotation table.'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reaction2met` +-- + +DROP TABLE IF EXISTS `reaction2met`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reaction2met` ( + `ramp_rxn_id` varchar(16) NOT NULL, + `rxn_source_id` varchar(16) NOT NULL, + `ramp_cmpd_id` varchar(16) NOT NULL, + `substrate_product` int NOT NULL, + `met_source_id` varchar(32) NOT NULL, + `met_name` varchar(256) DEFAULT NULL, + `is_cofactor` int NOT NULL DEFAULT '0', + KEY `rxn2met_rxn_ramp_id_idx` (`ramp_rxn_id`), + KEY `rxn2met_rxn_source_id_idx` (`rxn_source_id`), + KEY `rxn2met_met_ramp_id_idx` (`ramp_cmpd_id`), + KEY `rxn2met_subs_prod_idx` (`substrate_product`), + KEY `rxn2met_met_source_id_idx` (`met_source_id`), + KEY `rxn2met_iscofactor_idx` (`is_cofactor`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='holds reaction to metabolite mapping.'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reaction2protein` +-- + +DROP TABLE IF EXISTS `reaction2protein`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reaction2protein` ( + `ramp_rxn_id` varchar(16) NOT NULL, + `rxn_source_id` varchar(16) NOT NULL, + `ramp_gene_id` varchar(16) NOT NULL, + `uniprot` varchar(16) NOT NULL, + `protein_name` varchar(16) NOT NULL, + KEY `rxn_prot_ramp_id_idx` (`ramp_rxn_id`), + KEY `rxn2prot_source_id_idx` (`rxn_source_id`), + KEY `rxn2prot_ramp_gene_id_idx` (`ramp_gene_id`), + KEY `rxn2prot_uniprot_idx` (`uniprot`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='maps reaction ids to associated uniprot ids and their ramp ids'; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `reaction_protein2met` +-- + +DROP TABLE IF EXISTS `reaction_protein2met`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `reaction_protein2met` ( + `ramp_rxn_id` varchar(16) NOT NULL, + `rxn_source_id` varchar(16) NOT NULL, + `ramp_gene_id` varchar(16) NOT NULL, + `gene_source_id` varchar(16) NOT NULL, + `substrate_product` int NOT NULL, + `ramp_cmpd_id` varchar(16) NOT NULL, + `cmpd_source_id` varchar(45) NOT NULL, + `cmpd_name` varchar(256) DEFAULT NULL, + `is_cofactor` int NOT NULL DEFAULT '0', + KEY `rxn_p2m_rxn_ramp_id_idx` (`ramp_rxn_id`), + KEY `rxn_p2m_rxn_source_id_idx` (`rxn_source_id`), + KEY `rxn_p2m_rxn_gene_ramp_id_idx` (`ramp_gene_id`), + KEY `rxn_p2m_gene_source_id_idx` (`gene_source_id`), + KEY `rxn_subprod_idx` (`substrate_product`), + KEY `rxn_p2m_ramp_cmpd_id_idx` (`ramp_cmpd_id`), + KEY `rxn_p2m_cmpd_source_id_idx` (`cmpd_source_id`), + KEY `rxn_p2m_iscofactor_idx` (`is_cofactor`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `source` +-- + +DROP TABLE IF EXISTS `source`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `source` ( + `sourceId` varchar(30) CHARACTER SET utf8 COLLATE utf8_general_ci NOT NULL, + `rampId` varchar(30) CHARACTER SET utf8 COLLATE utf8_general_ci DEFAULT NULL, + `IDtype` varchar(30) CHARACTER SET utf8 COLLATE utf8_general_ci DEFAULT NULL, + `geneOrCompound` varchar(30) CHARACTER SET utf8 COLLATE utf8_general_ci DEFAULT NULL, + `commonName` varchar(256) CHARACTER SET utf8 COLLATE utf8_general_ci DEFAULT NULL, + `priorityHMDBStatus` varchar(32) CHARACTER SET utf8 COLLATE utf8_bin DEFAULT NULL, + `dataSource` varchar(32) CHARACTER SET utf8 COLLATE utf8_bin DEFAULT NULL, + `pathwayCount` int NOT NULL DEFAULT '0', + KEY `source_RampID_IDX` (`rampId`) USING BTREE, + KEY `source_sid_RampID_IDX` (`sourceId`) USING BTREE, + KEY `source_comName_RampID_IDX` (`commonName`) USING BTREE, + KEY `source_datasrc_IDX` (`dataSource`), + KEY `source_pathCount_IDX` (`pathwayCount`), + KEY `idx_source_geneOrCompound` (`geneOrCompound`), + KEY `idx_source_IDtype` (`IDtype`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8_bin; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `version_info` +-- + +DROP TABLE IF EXISTS `version_info`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!50503 SET character_set_client = utf8mb4 */; +CREATE TABLE `version_info` ( + `ramp_db_version` varchar(16) NOT NULL, + `db_mod_date` date NOT NULL, + `status` varchar(16) NOT NULL, + `data_source_id` varchar(32) NOT NULL, + `data_source_name` varchar(128) NOT NULL, + `data_source_url` varchar(128) NOT NULL, + `data_source_version` varchar(128) NOT NULL, + KEY `status_index` (`status`), + KEY `data_source_index` (`data_source_id`) +) ENGINE=InnoDB DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; +/*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; + +/*!40101 SET SQL_MODE=@OLD_SQL_MODE */; +/*!40014 SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS */; +/*!40014 SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS */; +/*!40101 SET CHARACTER_SET_CLIENT=@OLD_CHARACTER_SET_CLIENT */; +/*!40101 SET CHARACTER_SET_RESULTS=@OLD_CHARACTER_SET_RESULTS */; +/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; +/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; + +-- Dump completed on 2023-10-30 14:02:17 diff --git a/schema/RaMP_SQLite_BASE_2.4.0.sqlite b/schema/RaMP_SQLite_BASE_2.4.0.sqlite new file mode 100644 index 0000000..1289a5f Binary files /dev/null and b/schema/RaMP_SQLite_BASE_2.4.0.sqlite differ