diff options
Diffstat (limited to 'sql')
| -rwxr-xr-x | sql/map-database.sh | 15 | ||||
| -rw-r--r-- | sql/schema-original.sql | 2334 | ||||
| -rw-r--r-- | sql/schema.png | bin | 0 -> 1412091 bytes | |||
| -rw-r--r-- | sql/schema.sql | 2406 | ||||
| -rw-r--r-- | sql/schema.svg | 1430 | ||||
| -rw-r--r-- | sql/update/README.md (renamed from sql/README.md) | 0 | ||||
| -rw-r--r-- | sql/update/metadata_audit.sql (renamed from sql/metadata_audit.sql) | 0 |
7 files changed, 6185 insertions, 0 deletions
diff --git a/sql/map-database.sh b/sql/map-database.sh new file mode 100755 index 0000000..2e4d1d7 --- /dev/null +++ b/sql/map-database.sh @@ -0,0 +1,15 @@ +#! /bin/sh -e + +# This scripts visualizes schema.sql into schema.png and schema.svg. It uses +# sqlt-graph from the perl-sql-transform package. Sadly, perl-sql-transform is +# not packaged for Guix yet. We will likely deprecate this script in favor of +# a custom scheme script that does not depend on perl-sql-transform. + +skip_tables=AvgMethod,CeleraINFO_mm6,Chr_Length,DatasetMapInvestigator,DatasetStatus,Dataset_mbat,EnsemblProbe,EnsemblProbeLocation,GORef,GeneCategory,GeneIDXRef,GeneList_rn3,GeneList_rn33,GeneMap_cuiyan,GeneRIFXRef,GenoCode,GenoFile,GenoSE,H2,InfoFiles,InfoFilesUser_md5,LCorrRamin3,RatSnpPattern,Sample,SampleXRef,SnpAllRat,SnpAllele_to_be_deleted,SnpPattern,SnpSource,Vlookup,metadata_audit,pubmedsearch,temporary + +clusters="Others=AccessLog,Docs,Investigators,MachineAccessLog,News,Organizations,TableComments,TableFieldAnnotation,User,UserPrivilege,login,role,roles_users,user,user_collection,user_openids" + +flags="--db MySQL --skip-tables $skip_tables --cluster $clusters" + +sqlt-graph $flags --output-type png --output schema.png schema.sql +sqlt-graph $flags --output-type svg --output schema.svg schema.sql diff --git a/sql/schema-original.sql b/sql/schema-original.sql new file mode 100644 index 0000000..8803d8a --- /dev/null +++ b/sql/schema-original.sql @@ -0,0 +1,2334 @@ +-- MySQL dump 10.16 Distrib 10.1.41-MariaDB, for debian-linux-gnu (x86_64) +-- +-- Host: localhost Database: db_webqtl +-- ------------------------------------------------------ +-- Server version 10.5.8-MariaDB-log + +/*!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 */; +/*!40101 SET NAMES utf8mb4 */; +/*!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 `AccessLog` +-- + +DROP TABLE IF EXISTS `AccessLog`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `AccessLog` ( + `id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `accesstime` datetime /* mariadb-5.3 */ NOT NULL DEFAULT '0000-00-00 00:00:00', + `ip_address` char(20) NOT NULL DEFAULT '0.0.0.0', + PRIMARY KEY (`id`) +) ENGINE=MyISAM AUTO_INCREMENT=1366832 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `AvgMethod` +-- + +DROP TABLE IF EXISTS `AvgMethod`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `AvgMethod` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `AvgMethodId` int(5) DEFAULT NULL, + `Name` char(30) NOT NULL DEFAULT '', + `Normalization` varchar(30) DEFAULT NULL, + PRIMARY KEY (`Id`) +) ENGINE=MyISAM AUTO_INCREMENT=28 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `BXDSnpPosition` +-- + +DROP TABLE IF EXISTS `BXDSnpPosition`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `BXDSnpPosition` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `Chr` char(2) DEFAULT NULL, + `StrainId1` int(11) DEFAULT NULL, + `StrainId2` int(11) DEFAULT NULL, + `Mb` double DEFAULT NULL, + `Mb_2016` double DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `BXDSnpPosition` (`Chr`,`StrainId1`,`StrainId2`,`Mb`) +) ENGINE=MyISAM AUTO_INCREMENT=7791982 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CaseAttribute` +-- + +DROP TABLE IF EXISTS `CaseAttribute`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `CaseAttribute` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `Name` varchar(30) NOT NULL DEFAULT '', + PRIMARY KEY (`Id`) +) ENGINE=MyISAM AUTO_INCREMENT=34 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CaseAttributeXRef` +-- + +DROP TABLE IF EXISTS `CaseAttributeXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `CaseAttributeXRef` ( + `ProbeSetFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0, + `StrainId` smallint(5) unsigned NOT NULL DEFAULT 0, + `CaseAttributeId` smallint(5) NOT NULL DEFAULT 0, + `Value` varchar(100) NOT NULL DEFAULT '', + PRIMARY KEY (`ProbeSetFreezeId`,`StrainId`,`CaseAttributeId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CaseAttributeXRefNew` +-- + +DROP TABLE IF EXISTS `CaseAttributeXRefNew`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `CaseAttributeXRefNew` ( + `InbredSetId` smallint(5) unsigned NOT NULL DEFAULT 0, + `StrainId` int(8) unsigned NOT NULL DEFAULT 0, + `CaseAttributeId` smallint(5) NOT NULL DEFAULT 0, + `Value` varchar(100) NOT NULL DEFAULT '', + PRIMARY KEY (`InbredSetId`,`StrainId`,`CaseAttributeId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `CeleraINFO_mm6` +-- + +DROP TABLE IF EXISTS `CeleraINFO_mm6`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `CeleraINFO_mm6` ( + `Id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `SNPID` char(14) NOT NULL DEFAULT '', + `chromosome` char(3) DEFAULT NULL, + `MB_UCSC` double DEFAULT NULL, + `MB_celera` double DEFAULT NULL, + `allele_B6` char(4) DEFAULT NULL, + `allele_D2` char(4) DEFAULT NULL, + `allele_AJ` char(4) DEFAULT NULL, + `B6_D2` char(1) DEFAULT NULL, + `B6_AJ` char(1) DEFAULT NULL, + `D2_AJ` char(1) DEFAULT NULL, + `MB_UCSC_OLD` double DEFAULT NULL, + `allele_S1` char(4) DEFAULT NULL, + `allele_X1` char(4) DEFAULT NULL, + `flanking5` char(100) DEFAULT NULL, + `flanking3` char(100) DEFAULT NULL, + PRIMARY KEY (`Id`), + KEY `celeraIndex` (`chromosome`,`MB_celera`), + KEY `celeraIndex2` (`chromosome`,`MB_UCSC`), + KEY `chromosome_2` (`chromosome`,`MB_UCSC`), + KEY `MB_UCSC_2` (`MB_UCSC`,`chromosome`), + KEY `SNPID` (`SNPID`) +) ENGINE=MyISAM AUTO_INCREMENT=3028848 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Chr_Length` +-- + +DROP TABLE IF EXISTS `Chr_Length`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Chr_Length` ( + `Name` char(3) NOT NULL DEFAULT '', + `SpeciesId` smallint(5) unsigned NOT NULL DEFAULT 0, + `OrderId` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `Length` int(10) unsigned NOT NULL DEFAULT 0, + `Length_2016` int(10) unsigned NOT NULL DEFAULT 0, + `Length_mm8` int(10) unsigned DEFAULT NULL, + UNIQUE KEY `nameIdx` (`SpeciesId`,`Name`), + UNIQUE KEY `SpeciesIdx` (`SpeciesId`,`OrderId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `DBList` +-- + +DROP TABLE IF EXISTS `DBList`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `DBList` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `DBTypeId` smallint(5) unsigned NOT NULL DEFAULT 0, + `FreezeId` smallint(5) unsigned NOT NULL DEFAULT 0, + `Name` char(50) NOT NULL DEFAULT '', + `Code` char(50) DEFAULT NULL, + PRIMARY KEY (`Id`), + UNIQUE KEY `Cde` (`Code`), + KEY `DBIndex` (`DBTypeId`,`FreezeId`) +) ENGINE=MyISAM AUTO_INCREMENT=907 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `DBType` +-- + +DROP TABLE IF EXISTS `DBType`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `DBType` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `Name` char(30) NOT NULL DEFAULT '', + PRIMARY KEY (`Id`) +) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `DatasetMapInvestigator` +-- + +DROP TABLE IF EXISTS `DatasetMapInvestigator`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `DatasetMapInvestigator` ( + `Id` mediumint(9) NOT NULL AUTO_INCREMENT, + `DatasetId` int(6) NOT NULL, + `InvestigatorId` int(6) NOT NULL, + PRIMARY KEY (`Id`) +) ENGINE=MyISAM AUTO_INCREMENT=2403 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `DatasetStatus` +-- + +DROP TABLE IF EXISTS `DatasetStatus`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `DatasetStatus` ( + `DatasetStatusId` int(5) NOT NULL, + `DatasetStatusName` varchar(20) DEFAULT NULL, + UNIQUE KEY `DatasetStatusId` (`DatasetStatusId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Dataset_mbat` +-- + +DROP TABLE IF EXISTS `Dataset_mbat`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Dataset_mbat` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `switch` int(1) DEFAULT NULL, + `species` varchar(255) DEFAULT NULL, + `cross` varchar(255) DEFAULT NULL, + `tissue` varchar(255) DEFAULT NULL, + `database` varchar(255) DEFAULT NULL, + `database_LongName` varchar(255) DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=MyISAM AUTO_INCREMENT=16 DEFAULT CHARSET=utf8; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Datasets` +-- + +DROP TABLE IF EXISTS `Datasets`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Datasets` ( + `DatasetId` int(6) NOT NULL AUTO_INCREMENT, + `DatasetName` varchar(255) DEFAULT NULL, + `GeoSeries` varchar(30) DEFAULT NULL, + `PublicationTitle` longtext DEFAULT NULL, + `Summary` longtext DEFAULT NULL, + `ExperimentDesign` longtext DEFAULT NULL, + `AboutCases` longtext DEFAULT NULL, + `AboutTissue` longtext DEFAULT NULL, + `AboutPlatform` longtext DEFAULT NULL, + `AboutDataProcessing` longtext DEFAULT NULL, + `Contributors` longtext DEFAULT NULL, + `Citation` longtext DEFAULT NULL, + `Acknowledgment` longtext DEFAULT NULL, + `Notes` longtext DEFAULT NULL, + `InvestigatorId` int(5) NOT NULL, + `DatasetStatusId` int(5) NOT NULL, + PRIMARY KEY (`DatasetId`), + UNIQUE KEY `DatasetId` (`DatasetId`) +) ENGINE=MyISAM AUTO_INCREMENT=301 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Docs` +-- + +DROP TABLE IF EXISTS `Docs`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Docs` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `entry` varchar(255) NOT NULL, + `title` varchar(255) NOT NULL, + `content` text NOT NULL, + PRIMARY KEY (`id`) +) ENGINE=MyISAM AUTO_INCREMENT=10 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `EnsemblChip` +-- + +DROP TABLE IF EXISTS `EnsemblChip`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `EnsemblChip` ( + `Id` int(11) NOT NULL, + `ProbeSetSize` int(11) NOT NULL, + `Name` varchar(40) NOT NULL, + `Type` enum('AFFY','OLIGO') DEFAULT NULL +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `EnsemblProbe` +-- + +DROP TABLE IF EXISTS `EnsemblProbe`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `EnsemblProbe` ( + `Id` int(11) NOT NULL, + `ChipId` int(11) NOT NULL, + `ProbeSet` varchar(40) DEFAULT NULL, + `Name` varchar(40) DEFAULT NULL, + `length` int(11) NOT NULL, + KEY `EnsemblProbeId` (`Id`), + KEY `EnsemblProbeName` (`Name`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `EnsemblProbeLocation` +-- + +DROP TABLE IF EXISTS `EnsemblProbeLocation`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `EnsemblProbeLocation` ( + `Chr` char(2) NOT NULL, + `Start` int(11) NOT NULL, + `Start_2016` int(11) DEFAULT NULL, + `End` int(11) NOT NULL, + `End_2016` int(11) DEFAULT NULL, + `Strand` int(11) NOT NULL, + `MisMataches` int(11) DEFAULT NULL, + `ProbeId` int(11) NOT NULL, + KEY `EnsemblLocationProbeId` (`ProbeId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GORef` +-- + +DROP TABLE IF EXISTS `GORef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GORef` ( + `id` int(11) NOT NULL AUTO_INCREMENT, + `goterm` varchar(255) DEFAULT NULL, + `genes` text DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=MyISAM AUTO_INCREMENT=17510 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Genbank` +-- + +DROP TABLE IF EXISTS `Genbank`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Genbank` ( + `Id` varchar(20) NOT NULL DEFAULT '', + `Sequence` text DEFAULT NULL, + `SpeciesId` smallint(5) unsigned NOT NULL DEFAULT 0, + PRIMARY KEY (`Id`), + KEY `Id` (`Id`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneCategory` +-- + +DROP TABLE IF EXISTS `GeneCategory`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneCategory` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `Name` char(255) NOT NULL DEFAULT '', + PRIMARY KEY (`Id`), + KEY `name_idx` (`Name`) +) ENGINE=MyISAM AUTO_INCREMENT=22 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneChip` +-- + +DROP TABLE IF EXISTS `GeneChip`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneChip` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `GeneChipId` int(5) DEFAULT NULL, + `GeneChipName` varchar(200) DEFAULT NULL, + `Name` char(30) NOT NULL DEFAULT '', + `GeoPlatform` char(15) DEFAULT NULL, + `Title` varchar(100) DEFAULT NULL, + `SpeciesId` int(5) DEFAULT 1, + `GO_tree_value` varchar(50) DEFAULT NULL, + PRIMARY KEY (`Id`) +) ENGINE=MyISAM AUTO_INCREMENT=67 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneChipEnsemblXRef` +-- + +DROP TABLE IF EXISTS `GeneChipEnsemblXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneChipEnsemblXRef` ( + `GeneChipId` int(11) NOT NULL, + `EnsemblChipId` int(11) NOT NULL +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneIDXRef` +-- + +DROP TABLE IF EXISTS `GeneIDXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneIDXRef` ( + `mouse` int(11) NOT NULL DEFAULT 0, + `rat` int(11) NOT NULL DEFAULT 0, + `human` int(11) NOT NULL DEFAULT 0, + KEY `mouse_index` (`mouse`), + KEY `rat_index` (`rat`), + KEY `human_index` (`human`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneList` +-- + +DROP TABLE IF EXISTS `GeneList`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneList` ( + `SpeciesId` int(5) unsigned NOT NULL DEFAULT 1, + `Id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `GeneSymbol` varchar(15) DEFAULT NULL, + `GeneDescription` text DEFAULT NULL, + `Chromosome` varchar(10) DEFAULT NULL, + `TxStart` double DEFAULT NULL, + `TxStart_2016` double DEFAULT NULL, + `TxEnd` double DEFAULT NULL, + `TxEnd_2016` double DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `GeneID` varchar(10) DEFAULT NULL, + `NM_ID` varchar(15) DEFAULT NULL, + `kgID` varchar(10) DEFAULT NULL, + `GenBankID` varchar(15) DEFAULT NULL, + `UnigenID` varchar(15) DEFAULT NULL, + `ProteinID` varchar(15) DEFAULT NULL, + `AlignID` varchar(10) DEFAULT NULL, + `exonCount` int(7) NOT NULL DEFAULT 0, + `exonStarts` text DEFAULT NULL, + `exonEnds` text DEFAULT NULL, + `cdsStart` double DEFAULT NULL, + `cdsStart_2016` double DEFAULT NULL, + `cdsEnd` double DEFAULT NULL, + `cdsEnd_2016` double DEFAULT NULL, + `TxStart_mm8` double DEFAULT NULL, + `TxEnd_mm8` double DEFAULT NULL, + `Strand_mm8` char(1) DEFAULT NULL, + `exonCount_mm8` int(7) DEFAULT NULL, + `exonStarts_mm8` text DEFAULT NULL, + `exonEnds_mm8` text DEFAULT NULL, + `cdsStart_mm8` double DEFAULT NULL, + `cdsEnd_mm8` double DEFAULT NULL, + `Chromosome_mm8` varchar(10) DEFAULT NULL, + `Info_mm9` text DEFAULT NULL, + `RGD_ID` int(10) DEFAULT NULL, + UNIQUE KEY `geneId` (`SpeciesId`,`Id`), + KEY `geneSymbol` (`GeneSymbol`), + KEY `geneSymbol2` (`SpeciesId`,`GeneSymbol`), + KEY `Loc1` (`SpeciesId`,`Chromosome`,`TxStart`), + KEY `Loc2` (`SpeciesId`,`Chromosome`,`TxEnd`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneList_rn3` +-- + +DROP TABLE IF EXISTS `GeneList_rn3`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneList_rn3` ( + `id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `ProbeSet` varchar(16) DEFAULT NULL, + `geneSymbol` varchar(15) DEFAULT NULL, + `geneID` varchar(10) DEFAULT NULL, + `kgID` varchar(10) DEFAULT NULL, + `geneDescription` text DEFAULT NULL, + `genBankID` varchar(15) DEFAULT NULL, + `unigenID` varchar(15) DEFAULT NULL, + `score` int(4) DEFAULT NULL, + `qStart` int(3) DEFAULT NULL, + `qEnd` int(3) DEFAULT NULL, + `qSize` int(3) DEFAULT NULL, + `identity` varchar(7) DEFAULT NULL, + `chromosome` varchar(8) DEFAULT NULL, + `strand` char(1) DEFAULT NULL, + `txStart` double DEFAULT NULL, + `txEnd` double DEFAULT NULL, + `txSize` double DEFAULT NULL, + `span` int(7) DEFAULT NULL, + `specificity` double DEFAULT NULL, + `sequence` text DEFAULT NULL, + `flag` int(1) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `geneSymbol` (`geneSymbol`), + KEY `Loc1` (`chromosome`,`txStart`), + KEY `Loc2` (`chromosome`,`txEnd`) +) ENGINE=MyISAM AUTO_INCREMENT=14917 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneList_rn33` +-- + +DROP TABLE IF EXISTS `GeneList_rn33`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneList_rn33` ( + `id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `geneSymbol` varchar(15) DEFAULT NULL, + `txStart` double DEFAULT NULL, + `txEnd` double DEFAULT NULL, + `exonCount` int(7) DEFAULT NULL, + `NM_ID` varchar(15) DEFAULT NULL, + `chromosome` varchar(8) DEFAULT NULL, + `strand` char(1) DEFAULT NULL, + `cdsStart` double DEFAULT NULL, + `cdsEnd` double DEFAULT NULL, + `exonStarts` text DEFAULT NULL, + `exonEnds` text DEFAULT NULL, + `kgID` varchar(10) DEFAULT NULL, + PRIMARY KEY (`id`), + KEY `geneSymbol` (`geneSymbol`), + KEY `Loc1` (`chromosome`,`txStart`), + KEY `Loc2` (`chromosome`,`txEnd`) +) ENGINE=MyISAM AUTO_INCREMENT=9790 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneMap_cuiyan` +-- + +DROP TABLE IF EXISTS `GeneMap_cuiyan`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneMap_cuiyan` ( + `id` bigint(20) NOT NULL AUTO_INCREMENT, + `TranscriptID` varchar(255) DEFAULT NULL, + `GeneID` varchar(255) DEFAULT NULL, + `Symbol` varchar(255) DEFAULT NULL, + PRIMARY KEY (`id`) +) ENGINE=MyISAM AUTO_INCREMENT=10537 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `GeneRIF` +-- + +DROP TABLE IF EXISTS `GeneRIF`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `GeneRIF` ( + `Id` int(10) unsigned NOT NULL DEFAULT 0, + `versionId` smallint(5) unsigned NOT NULL DEFAULT 0, + `symbol` varchar(30) NOT NULL DEFAULT '', + `PubMed_ID` varchar(255) DEFAULT NULL, + `SpeciesId` smallint(5) unsigned NOT NULL DEFAULT 1, + `comment` text DEFAULT NULL, + `email` varchar(50) DEFAULT NULL, + `createtime` datetime /* mariadb-5.3 */ NOT NULL DEFAULT '0000-00-00 00:00:00', + `user_ip` varchar(20) DEFAULT NULL, + `weburl` varchar(255) DEFAULT NULL, + `initial` varchar(10) DEFAULT NULL, + `display` tinyint(4) DEFAULT 1, + `reason` varchar(100) NOT NULL DEFAULT '', + PRIMARY KEY (`Id`,`versionId`), + KEY `name_idx` (`symbol`), + KEY `status` (`display`), + KEY `timestamp` (`createtime`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; 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+/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ProbeSetSE` +-- + +DROP TABLE IF EXISTS `ProbeSetSE`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `ProbeSetSE` ( + `DataId` int(10) unsigned NOT NULL DEFAULT 0, + `StrainId` smallint(5) unsigned NOT NULL DEFAULT 0, + `error` float NOT NULL, + UNIQUE KEY `DataId` (`DataId`,`StrainId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ProbeSetXRef` +-- + +DROP TABLE IF EXISTS `ProbeSetXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `ProbeSetXRef` ( + `ProbeSetFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0, + `ProbeSetId` int(10) unsigned NOT NULL DEFAULT 0, + `DataId` int(10) unsigned NOT NULL DEFAULT 0, + `Locus_old` char(20) DEFAULT NULL, + `LRS_old` double DEFAULT NULL, + `pValue_old` double DEFAULT NULL, + `mean` double DEFAULT NULL, + `se` double DEFAULT NULL, + `Locus` char(20) DEFAULT NULL, + `LRS` double DEFAULT NULL, + `pValue` double DEFAULT NULL, + `additive` double DEFAULT NULL, + `h2` float DEFAULT NULL, + UNIQUE KEY `ProbeSetId` (`ProbeSetFreezeId`,`ProbeSetId`), + UNIQUE KEY `DataId_IDX` (`DataId`), + KEY `ProbeSetId1` (`ProbeSetId`), + KEY `Locus` (`Locus`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `ProbeXRef` +-- + +DROP TABLE IF EXISTS `ProbeXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `ProbeXRef` ( + `ProbeFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0, + `ProbeId` int(10) unsigned NOT NULL DEFAULT 0, + `DataId` int(10) unsigned NOT NULL DEFAULT 0, + UNIQUE KEY `ProbeId` (`ProbeFreezeId`,`ProbeId`), + UNIQUE KEY `DataId_IDX` (`DataId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `Publication` +-- + +DROP TABLE IF EXISTS `Publication`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `Publication` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `PubMed_ID` int(10) unsigned DEFAULT NULL, + `Abstract` text DEFAULT NULL, + `Authors` text NOT NULL, + `Title` varchar(255) DEFAULT NULL, + `Journal` varchar(255) DEFAULT NULL, + `Volume` varchar(255) DEFAULT NULL, + `Pages` varchar(255) DEFAULT NULL, + `Month` varchar(255) DEFAULT NULL, + `Year` varchar(255) NOT NULL DEFAULT '0', + PRIMARY KEY (`Id`), + UNIQUE KEY `Name` (`PubMed_ID`), + KEY `PubMed_ID` (`PubMed_ID`), + FULLTEXT KEY `Abstract1` (`Abstract`), + FULLTEXT KEY `Title1` (`Title`), + FULLTEXT KEY `Authors1` (`Authors`), + FULLTEXT KEY `SEARCH_FULL_IDX` (`Abstract`,`Title`,`Authors`) +) ENGINE=MyISAM AUTO_INCREMENT=26076 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `PublishData` +-- + +DROP TABLE IF EXISTS `PublishData`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `PublishData` ( + `Id` int(10) unsigned NOT NULL DEFAULT 0, + `StrainId` smallint(5) unsigned NOT NULL DEFAULT 0, + `value` float(14,6) DEFAULT NULL, + UNIQUE KEY `DataId` (`Id`,`StrainId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `PublishFreeze` +-- + +DROP TABLE IF EXISTS `PublishFreeze`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `PublishFreeze` ( + `Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT, + `Name` varchar(100) NOT NULL DEFAULT '', + `FullName` varchar(100) NOT NULL DEFAULT '', + `ShortName` varchar(100) NOT NULL DEFAULT '', + `CreateTime` date NOT NULL DEFAULT '2001-01-01', + `public` tinyint(4) NOT NULL DEFAULT 0, + `InbredSetId` smallint(5) unsigned DEFAULT 1, + `confidentiality` tinyint(3) DEFAULT 0, + `AuthorisedUsers` varchar(100) DEFAULT NULL, + PRIMARY KEY (`Id`), + KEY `InbredSetId` (`InbredSetId`) +) ENGINE=MyISAM AUTO_INCREMENT=60 DEFAULT CHARSET=latin1; 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+/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `SampleXRef` +-- + +DROP TABLE IF EXISTS `SampleXRef`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `SampleXRef` ( + `SampleId` smallint(5) unsigned NOT NULL DEFAULT 0, + `ProbeFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0, + PRIMARY KEY (`ProbeFreezeId`,`SampleId`) +) ENGINE=MyISAM DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `SnpAll` +-- + +DROP TABLE IF EXISTS `SnpAll`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `SnpAll` ( + `Id` int(20) unsigned NOT NULL AUTO_INCREMENT, + `SpeciesId` smallint(5) unsigned DEFAULT 1, + `SnpName` char(30) DEFAULT NULL, + `Rs` char(30) DEFAULT NULL, + `Chromosome` char(2) DEFAULT NULL, + `Position` double DEFAULT NULL, + `Position_2016` double DEFAULT NULL, + `Alleles` char(5) DEFAULT NULL, + `Source` char(35) DEFAULT NULL, + `ConservationScore` double DEFAULT NULL, + `3Prime_UTR` text DEFAULT NULL, + `5Prime_UTR` text DEFAULT NULL, + `Upstream` text DEFAULT NULL, + `Downstream` text DEFAULT NULL, + `Intron` char(1) DEFAULT NULL, + `Non_Splice_Site` text DEFAULT NULL, + `Splice_Site` text DEFAULT NULL, + `Intergenic` char(1) DEFAULT NULL, + `Exon` char(1) DEFAULT NULL, + `Non_Synonymous_Coding` text DEFAULT NULL, + `Synonymous_Coding` text DEFAULT NULL, + `Start_Gained` text DEFAULT NULL, + `Start_Lost` text DEFAULT NULL, + `Stop_Gained` text DEFAULT NULL, + `Stop_Lost` text DEFAULT NULL, + `Unknown_Effect_In_Exon` text DEFAULT NULL, + `Domain` varchar(50) DEFAULT NULL, + `Gene` varchar(30) DEFAULT NULL, + `Transcript` varchar(50) DEFAULT NULL, + PRIMARY KEY (`Id`), + KEY `SnpName` (`SnpName`), + KEY `Rs` (`Rs`), + KEY `Position` (`Chromosome`,`Position`), + KEY `Source` (`Source`) +) ENGINE=InnoDB AUTO_INCREMENT=84086331 DEFAULT CHARSET=latin1; 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PRIMARY KEY (`Id`), + FOREIGN KEY (SpeciesId) REFERENCES Species(SpeciesId), + FOREIGN KEY (MappingMethodId) REFERENCES MappingMethod(Id), + KEY `Name` (`Name`), + KEY `SpeciesId` (`SpeciesId`), + KEY `Id` (`Id`), + KEY `InbredSetCode` (`InbredSetCode`) +) ENGINE=MyISAM AUTO_INCREMENT=83 DEFAULT CHARSET=latin1; +/*!40101 SET character_set_client = @saved_cs_client */; + +-- +-- Table structure for table `IndelAll` +-- + +DROP TABLE IF EXISTS `IndelAll`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8 */; +CREATE TABLE `IndelAll` ( + `Id` int(10) unsigned NOT NULL AUTO_INCREMENT, + `SpeciesId` smallint(5) unsigned DEFAULT 1, + `SourceId` smallint(5) unsigned DEFAULT NULL, + `Name` char(30) DEFAULT NULL, + `Chromosome` char(2) DEFAULT NULL, + `Mb_start` double DEFAULT NULL, + `Mb_start_2016` double DEFAULT NULL, + `Strand` char(1) DEFAULT NULL, + `Type` char(15) DEFAULT NULL, + `Mb_end` double DEFAULT NULL, + `Mb_end_2016` double 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