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mirri-db.sql
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234
mirri-db.sql
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-- MySQL dump 10.13 Distrib 5.5.62, for Win64 (AMD64)
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--
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-- Host: mirri-is.mirri.org Database: mirri-db
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-- ------------------------------------------------------
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-- Server version 8.0.29
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/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
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/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
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/*!40101 SET @OLD_COLLATION_CONNECTION=@@COLLATION_CONNECTION */;
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/*!40101 SET NAMES utf8 */;
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/*!40103 SET @OLD_TIME_ZONE=@@TIME_ZONE */;
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/*!40103 SET TIME_ZONE='+00:00' */;
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/*!40014 SET @OLD_UNIQUE_CHECKS=@@UNIQUE_CHECKS, UNIQUE_CHECKS=0 */;
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/*!40014 SET @OLD_FOREIGN_KEY_CHECKS=@@FOREIGN_KEY_CHECKS, FOREIGN_KEY_CHECKS=0 */;
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/*!40101 SET @OLD_SQL_MODE=@@SQL_MODE, SQL_MODE='NO_AUTO_VALUE_ON_ZERO' */;
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/*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */;
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--
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-- Table structure for table `Genomic information`
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--
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DROP TABLE IF EXISTS `Genomic information`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Genomic information` (
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`Strain_AN` text COLLATE utf8mb4_unicode_ci,
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`Marker` text COLLATE utf8mb4_unicode_ci,
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`INSDC_AN` text COLLATE utf8mb4_unicode_ci,
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`Sequence` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Geographic origin`
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--
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DROP TABLE IF EXISTS `Geographic origin`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Geographic origin` (
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`ID` text COLLATE utf8mb4_unicode_ci,
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`Country` text COLLATE utf8mb4_unicode_ci,
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`Region` text COLLATE utf8mb4_unicode_ci,
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`City` text COLLATE utf8mb4_unicode_ci,
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`Locality` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Growth media`
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--
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DROP TABLE IF EXISTS `Growth media`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Growth media` (
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`Acronym` text COLLATE utf8mb4_unicode_ci,
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`Description` text COLLATE utf8mb4_unicode_ci,
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`Full_description` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Literature`
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--
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DROP TABLE IF EXISTS `Literature`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Literature` (
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`ID` text COLLATE utf8mb4_unicode_ci,
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`Full_reference` text COLLATE utf8mb4_unicode_ci,
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`Authors` text COLLATE utf8mb4_unicode_ci,
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`Title` text COLLATE utf8mb4_unicode_ci,
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`Journal` text COLLATE utf8mb4_unicode_ci,
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`Year` text COLLATE utf8mb4_unicode_ci,
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`Volume` text COLLATE utf8mb4_unicode_ci,
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`Issue` text COLLATE utf8mb4_unicode_ci,
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`First_page` text COLLATE utf8mb4_unicode_ci,
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`Last_page` text COLLATE utf8mb4_unicode_ci,
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`Book_title` text COLLATE utf8mb4_unicode_ci,
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`Editors` text COLLATE utf8mb4_unicode_ci,
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`Publisher` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Markers`
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--
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DROP TABLE IF EXISTS `Markers`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Markers` (
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`Acronym` text COLLATE utf8mb4_unicode_ci,
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`Marker` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Ontobiotope`
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--
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DROP TABLE IF EXISTS `Ontobiotope`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Ontobiotope` (
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`ID` text COLLATE utf8mb4_unicode_ci,
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`Name` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Sexual states`
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--
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DROP TABLE IF EXISTS `Sexual states`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Sexual states` (
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`H+` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `Strains`
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--
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DROP TABLE IF EXISTS `Strains`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `Strains` (
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`Accession_number` text COLLATE utf8mb4_unicode_ci,
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`Restrictions_on_use` text COLLATE utf8mb4_unicode_ci,
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`Nagoya_protocol_restrictions_and_compliance_conditions` text COLLATE utf8mb4_unicode_ci,
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`ABS_related_files` text COLLATE utf8mb4_unicode_ci,
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`MTA_file` text COLLATE utf8mb4_unicode_ci,
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`Other_culture_collection_numbers` text COLLATE utf8mb4_unicode_ci,
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`Strain_from_a_registered_collection` text COLLATE utf8mb4_unicode_ci,
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`Risk_Group` text COLLATE utf8mb4_unicode_ci,
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`Dual_use` text COLLATE utf8mb4_unicode_ci,
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`Quarantine_in_Europe` text COLLATE utf8mb4_unicode_ci,
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`Organism_type` text COLLATE utf8mb4_unicode_ci,
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`Taxon_name` text COLLATE utf8mb4_unicode_ci,
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`Infrasubspecific_names` text COLLATE utf8mb4_unicode_ci,
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`Comment_on_taxonomy` text COLLATE utf8mb4_unicode_ci,
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`Interspecific_hybrid` text COLLATE utf8mb4_unicode_ci,
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`Status` text COLLATE utf8mb4_unicode_ci,
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`History_of_deposit` text COLLATE utf8mb4_unicode_ci,
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`Depositor` text COLLATE utf8mb4_unicode_ci,
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`Date_of_deposit` text COLLATE utf8mb4_unicode_ci,
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`Date_of_inclusion_in_the_catalogue` text COLLATE utf8mb4_unicode_ci,
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`Collected_by` text COLLATE utf8mb4_unicode_ci,
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`Date_of_collection` text COLLATE utf8mb4_unicode_ci,
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`Isolated_by` text COLLATE utf8mb4_unicode_ci,
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`Date_of_isolation` text COLLATE utf8mb4_unicode_ci,
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`Substrate/host_of_isolation` text COLLATE utf8mb4_unicode_ci,
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`Tested_temperature_growth_range` text COLLATE utf8mb4_unicode_ci,
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`Recommended_growth_temperature` text COLLATE utf8mb4_unicode_ci,
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`Recommended_medium_for_growth` text COLLATE utf8mb4_unicode_ci,
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`Form_of_supply` text COLLATE utf8mb4_unicode_ci,
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`Other_denomination` text COLLATE utf8mb4_unicode_ci,
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`Coordinates_of_geographic_origin` text COLLATE utf8mb4_unicode_ci,
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`Altitude_of_geographic_origin` text COLLATE utf8mb4_unicode_ci,
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`Geographic_origin` text COLLATE utf8mb4_unicode_ci,
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`Isolation_habitat` text COLLATE utf8mb4_unicode_ci,
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`Ontobiotope_term_for_the_isolation_habitat` text COLLATE utf8mb4_unicode_ci,
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`GMO` text COLLATE utf8mb4_unicode_ci,
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`GMO_construction_information` text COLLATE utf8mb4_unicode_ci,
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`Mutant_information` text COLLATE utf8mb4_unicode_ci,
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`Genotype` text COLLATE utf8mb4_unicode_ci,
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`Sexual_state` text COLLATE utf8mb4_unicode_ci,
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`Ploidy` text COLLATE utf8mb4_unicode_ci,
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`Plasmids` text COLLATE utf8mb4_unicode_ci,
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`Plasmids_collections_fields` text COLLATE utf8mb4_unicode_ci,
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`Literature` text COLLATE utf8mb4_unicode_ci,
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`Plant_pathogenicity_code` text COLLATE utf8mb4_unicode_ci,
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`Pathogenicity` text COLLATE utf8mb4_unicode_ci,
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`Enzyme_production` text COLLATE utf8mb4_unicode_ci,
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`Production_of_metabolites` text COLLATE utf8mb4_unicode_ci,
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`Applications` text COLLATE utf8mb4_unicode_ci,
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`Remarks` text COLLATE utf8mb4_unicode_ci,
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`Literature_linked_to_the_sequence/genome` text COLLATE utf8mb4_unicode_ci,
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`f_id` bigint DEFAULT NULL
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) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `culture_collections`
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--
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DROP TABLE IF EXISTS `culture_collections`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `culture_collections` (
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`cc_id` int NOT NULL AUTO_INCREMENT,
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`name` varchar(250) COLLATE utf8mb4_unicode_ci NOT NULL,
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PRIMARY KEY (`cc_id`)
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) ENGINE=InnoDB AUTO_INCREMENT=2 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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--
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-- Table structure for table `file_upload`
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--
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DROP TABLE IF EXISTS `file_upload`;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
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/*!40101 SET character_set_client = utf8 */;
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CREATE TABLE `file_upload` (
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`f_id` int NOT NULL AUTO_INCREMENT,
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`filename` varchar(250) COLLATE utf8mb4_unicode_ci NOT NULL,
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`created_datetime` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
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`cc_id` int DEFAULT NULL,
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PRIMARY KEY (`f_id`),
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KEY `file_upload_FK` (`cc_id`),
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CONSTRAINT `file_upload_FK` FOREIGN KEY (`cc_id`) REFERENCES `culture_collections` (`cc_id`)
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) ENGINE=InnoDB AUTO_INCREMENT=15 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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CREATE OR REPLACE VIEW `vw_last_file` AS
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select
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`fu`.`cc_id` AS `cc_id`,
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max(`fu`.`f_id`) AS `file_id`
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from
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`file_upload` `fu`
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group by
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`fu`.`cc_id`;
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75
vw_strains_202206 source.sql
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75
vw_strains_202206 source.sql
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-- mirri.vw_strains_202206 source
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CREATE OR REPLACE VIEW `mirri`.`vw_strains_202206` AS
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with `taxonomy` as (
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select
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`zmsmt`.`_id` AS `_id`,
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`zmsmt`.`x` AS `x`,
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`zmsmt`.`y` AS `y`,
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`zmsmt`.`idx` AS `idx`,
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`zmsmt`.`idy` AS `idy`
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from
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`mirri`.`zy_mirri_strains_mirri_taxonomy_737` `zmsmt`)
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select
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`s`.`name` AS `MIRRI Accession number`,
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`s`.`mirri_accession_number` AS `Accession number`,
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`s`.`restriction_on_use` AS `Restrictions on use`,
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`s`.`nagoya` AS `Nagoya protocol restrictions and compliance conditions`,
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`s`.`abs_url` AS `ABS related files`,
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`s`.`mta_url` AS `MTA url`,
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`s`.`mta_text` AS `MTA text`,
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`s`.`strains_from_reg_collection` AS `Strain from a Registered Collection`,
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`s`.`risk_group` AS `Risk Group`,
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`s`.`dual_use` AS `Dual use`,
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`s`.`quarantine_europe` AS `Quarantine in Europe`,
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trim(leading ';' from concat((case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 2), '¶',-(1)) = '2') then ';Algae' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 3), '¶',-(1)) = '2') then ';Archaea' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 4), '¶',-(1)) = '2') then ';Bacteria' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 5), '¶',-(1)) = '2') then ';Cyanobacteria' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 6), '¶',-(1)) = '2') then ';Filamentous Fungi' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 7), '¶',-(1)) = '2') then ';Phage' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 8), '¶',-(1)) = '2') then ';Plasmid' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 9), '¶',-(1)) = '2') then ';Virus' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 10), '¶',-(1)) = '2') then ';Yeast' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 11), '¶',-(1)) = '2') then ';Microalgae' else '' end))) AS `Organism type`,
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`t`.`name` AS `Taxon name`,
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`s`.`infra_subsp_name` AS `Infrasubspecific names`,
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`s`.`comment_taxonomy` AS `Comment on taxonomy`,
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`s`.`type_description` AS `Type`,
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`s`.`status` AS `Status`,
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`s`.`history` AS `History of deposit`,
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`s`.`depositor` AS `Depositor`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`deposited_date`, 7, 2), '/', substr(`s`.`deposited_date`, 5, 2), '/', substr(`s`.`deposited_date`, 1, 4)))) AS `Date of deposit`,
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`s`.`collector` AS `Collected by`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`collection_date`, 7, 2), '/', substr(`s`.`collection_date`, 5, 2), '/', substr(`s`.`collection_date`, 1, 4)))) AS `Date of collection`,
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`s`.`isolator` AS `Isolated by`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`isolation_date`, 7, 2), '/', substr(`s`.`isolation_date`, 5, 2), '/', substr(`s`.`isolation_date`, 1, 4)))) AS `Date of isolation`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`catalogue_date`, 7, 2), '/', substr(`s`.`catalogue_date`, 5, 2), '/', substr(`s`.`catalogue_date`, 1, 4)))) AS `Date of inclusion in the catalogue`,
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`s`.`tested_growth_temp` AS `Tested temperature growth range`,
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`s`.`growth_temp` AS `Recommended growth temperature`,
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NULL AS `Recommended medium for growth`,
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trim(leading ';' from concat((case when (substring_index(substring_index(`s`.`form_supply`, '¶', 2), '¶',-(1)) = '2') then 'Agar' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 3), '¶',-(1)) = '2') then ';Cryo' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 4), '¶',-(1)) = '2') then ';Dry Ice' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 5), '¶',-(1)) = '2') then ';Liquid Culture Medium' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 6), '¶',-(1)) = '2') then ';Lyo' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 7), '¶',-(1)) = '2') then ';Oil' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 8), '¶',-(1)) = '2') then ';Water' else '' end))) AS `Form of supply`,
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`s`.`other_denomination` AS `Other denomination`,
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`s`.`coordinates` AS `Coordinates of geographic origin`,
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`s`.`origin_id` AS `Country`,
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`s`.`locality_of_origin` AS `Geographic origin`,
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`s`.`gmo` AS `GMO`,
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NULL AS `GMO construction information`,
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`s`.`mutant` AS `Mutant information`,
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`s`.`genotype` AS `Genotype`,
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`s`.`literature_doi` AS `Literature`,
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`s`.`sexual_state` AS `Sexual state`,
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`s`.`ploidy` AS `Ploidy`,
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`s`.`interspecific_hybrid` AS `Interspecific hybrid`,
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`s`.`pathogenicity` AS `Pathogenicity`,
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`s`.`enzyme_production` AS `Enzyme production`,
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`s`.`metabolites_production` AS `Production of metabolites`,
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||||
`s`.`applications` AS `Applications`,
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||||
`s`.`remarks` AS `Remarks`,
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`s`.`plasmids` AS `Plasmids`,
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`s`.`plasmids_collections` AS `Plasmids collections fields`,
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`s`.`substrate_of_isolation` AS `Substrate/host of isolation`,
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`s`.`isolation_habitat` AS `Isolation habitat`,
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`s`.`ontobiotope` AS `Ontobiotope term for the isolation habitat`,
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NULL AS `Genomic sequences and accession numbers`,
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NULL AS `Literature linked to the sequence/genome`,
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NULL AS `Link to other sites`,
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NULL AS `QPS`,
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NULL AS `Axenic culture`
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from
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((`mirri`.`mirri_strains` `s`
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left join `taxonomy` `tu` on
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((`tu`.`x` = `s`.`_id`)))
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left join `mirri`.`mirri_taxonomy` `t` on
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((`t`.`_id` = `tu`.`y`)));
|
||||
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