-- This is a work-in-progress schema for the GeneNetwork database. The
-- GeneNetwork database has no foreign key constraint information. This schema
-- has them manually added. But, the work is not complete, and there may be
-- errors. A visualization of this schema can be found in schema.png and
-- schema.svg.
-- 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
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UNIQUE KEY `InfoPageName` (`InfoPageName`),
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FOREIGN KEY (TissueId) REFERENCES Tissue(TissueId),
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KEY `InbredSetId` (`InbredSetId`)
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`GenbankId` varchar(1000) DEFAULT NULL,
`SNP` int(2) DEFAULT NULL,
`BlatSeq` text NOT NULL,
`TargetSeq` text DEFAULT NULL,
`UniGeneId` varchar(100) DEFAULT NULL,
`Strand_Probe` char(1) DEFAULT NULL,
`Strand_Gene` char(1) DEFAULT NULL,
`OMIM` varchar(20) DEFAULT NULL,
`comments` text NOT NULL,
`Probe_set_target_region` varchar(255) DEFAULT NULL,
`Probe_set_specificity` double DEFAULT NULL,
`Probe_set_BLAT_score` double DEFAULT NULL,
`Probe_set_Blat_Mb_start` double DEFAULT NULL,
`Probe_set_Blat_Mb_end` double DEFAULT NULL,
`Probe_set_Blat_Mb_start_2016` double DEFAULT NULL,
`Probe_set_Blat_Mb_end_2016` double DEFAULT NULL,
`Probe_set_strand` varchar(255) DEFAULT NULL,
`Probe_set_Note_by_RW` varchar(255) DEFAULT NULL,
`flag` char(1) DEFAULT NULL,
`Symbol_H` varchar(100) DEFAULT NULL,
`description_H` varchar(255) DEFAULT NULL,
`chromosome_H` char(3) DEFAULT NULL,
`MB_H` double DEFAULT NULL,
`alias_H` varchar(255) DEFAULT NULL,
`GeneId_H` varchar(20) DEFAULT NULL,
`chr_num` smallint(5) unsigned DEFAULT 30,
`name_num` int(10) unsigned DEFAULT 4294967290,
`Probe_Target_Description` varchar(225) DEFAULT NULL,
`RefSeq_TranscriptId` varchar(255) DEFAULT NULL,
`ENSEMBLGeneId` varchar(50) DEFAULT NULL,
`Chr_mm8` char(3) DEFAULT NULL,
`Mb_mm8` double DEFAULT NULL,
`Probe_set_Blat_Mb_start_mm8` double DEFAULT NULL,
`Probe_set_Blat_Mb_end_mm8` double DEFAULT NULL,
`HomoloGeneID` varchar(20) DEFAULT NULL,
`Biotype_ENS` varchar(255) DEFAULT NULL,
`ProteinID` varchar(50) DEFAULT NULL,
`ProteinName` varchar(50) DEFAULT NULL,
`UniProtID` varchar(20) DEFAULT NULL,
`Flybase_Id` varchar(25) DEFAULT NULL,
`RGD_ID` int(10) DEFAULT NULL,
`HMDB_ID` varchar(255) DEFAULT NULL,
`Confidence` int(5) DEFAULT NULL,
`ChEBI_ID` int(10) DEFAULT NULL,
`ChEMBL_ID` varchar(100) DEFAULT NULL,
`CAS_number` varchar(100) DEFAULT NULL,
`PubChem_ID` int(10) DEFAULT NULL,
`ChemSpider_ID` int(10) DEFAULT NULL,
`UNII_ID` varchar(100) DEFAULT NULL,
`EC_number` varchar(100) DEFAULT NULL,
`KEGG_ID` varchar(100) DEFAULT NULL,
`Molecular_Weight` double DEFAULT NULL,
`Nugowiki_ID` int(10) DEFAULT NULL,
`Type` varchar(255) DEFAULT NULL,
`Tissue` varchar(255) DEFAULT NULL,
`PrimaryName` varchar(255) DEFAULT NULL,
`SecondaryNames` longtext DEFAULT NULL,
`PeptideSequence` varchar(20) DEFAULT NULL,
PRIMARY KEY (`Id`),
UNIQUE KEY `ProbeSetId` (`ChipId`,`Name`),
FOREIGN KEY (HomoloGeneID) REFERENCES Homologene(HomologeneId),
KEY `Name_IDX` (`Name`),
KEY `symbol_IDX` (`Symbol`),
KEY `RefSeq_TranscriptId` (`RefSeq_TranscriptId`),
KEY `GENBANK_IDX` (`GenbankId`),
KEY `TargetId` (`TargetId`),
KEY `Position` (`Chr`),
KEY `GeneId_IDX` (`GeneId`),
FULLTEXT KEY `SEARCH_GENE_IDX` (`Symbol`,`alias`),
FULLTEXT KEY `SEARCH_FULL_IDX` (`Name`,`description`,`Symbol`,`alias`,`GenbankId`,`UniGeneId`,`Probe_Target_Description`),
FULLTEXT KEY `RefSeq_FULL_IDX` (`RefSeq_TranscriptId`)
) ENGINE=MyISAM AUTO_INCREMENT=12118724 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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/*!40101 SET character_set_client = utf8 */;
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`StrainId` smallint(5) unsigned NOT NULL DEFAULT 0,
`value` float NOT NULL,
UNIQUE KEY `DataId` (`Id`,`StrainId`),
FOREIGN KEY (StrainId) REFERENCES Strain(Id)
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
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`ProbeFreezeId` smallint(5) unsigned NOT NULL DEFAULT 0,
`AvgID` smallint(5) unsigned NOT NULL DEFAULT 0,
`Name` varchar(40) DEFAULT NULL,
`Name2` varchar(100) NOT NULL DEFAULT '',
`FullName` varchar(100) NOT NULL DEFAULT '',
`ShortName` varchar(100) NOT NULL DEFAULT '',
`CreateTime` date NOT NULL DEFAULT '0000-00-00',
`OrderList` int(5) DEFAULT NULL,
`public` tinyint(4) NOT NULL DEFAULT 0,
`confidentiality` tinyint(4) NOT NULL DEFAULT 0,
`AuthorisedUsers` varchar(300) NOT NULL,
`DataScale` varchar(20) NOT NULL DEFAULT 'log2',
PRIMARY KEY (`Id`),
UNIQUE KEY `FullName` (`FullName`),
UNIQUE KEY `Name` (`Name`),
FOREIGN KEY (ProbeFreezeId) REFERENCES ProbeFreeze(ProbeFreezeId),
KEY `NameIndex` (`Name2`),
KEY `ShortName` (`ShortName`),
KEY `ProbeFreezeId` (`ProbeFreezeId`),
KEY `conf_and_public` (`confidentiality`,`public`)
) ENGINE=MyISAM AUTO_INCREMENT=1006 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `ProbeSetSE`
--
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/*!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`),
FOREIGN KEY (StrainId) REFERENCES Strain(Id)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `ProbeSetXRef`
--
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/*!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`),
FOREIGN KEY (ProbeSetFreezeId) REFERENCES ProbeSetFreeze(Id),
FOREIGN KEY (ProbeSetId) REFERENCES ProbeSet(Id),
KEY `ProbeSetId1` (`ProbeSetId`),
KEY `Locus` (`Locus`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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-- Table structure for table `ProbeXRef`
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/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
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`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`),
FOREIGN KEY (ProbeFreezeId) REFERENCES ProbeFreeze(ProbeFreezeId),
FOREIGN KEY (ProbeId) REFERENCES Probe(Id)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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-- Table structure for table `Publication`
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/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `Publication` (
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`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 */;
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-- Table structure for table `PublishData`
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/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `PublishData` (
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`StrainId` smallint(5) unsigned NOT NULL DEFAULT 0,
`value` float(14,6) DEFAULT NULL,
UNIQUE KEY `DataId` (`Id`,`StrainId`),
FOREIGN KEY (StrainId) REFERENCES Strain(Id)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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-- Table structure for table `PublishFreeze`
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/*!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`),
FOREIGN KEY (InbredSetId) REFERENCES InbredSet(InbredSetId),
KEY `InbredSetId` (`InbredSetId`)
) ENGINE=MyISAM AUTO_INCREMENT=60 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `PublishSE`
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/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `PublishSE` (
`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`),
FOREIGN KEY (StrainId) REFERENCES Strain(Id)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `PublishXRef`
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/*!40101 SET @saved_cs_client = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `PublishXRef` (
`Id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`InbredSetId` smallint(5) unsigned NOT NULL DEFAULT 0,
`PhenotypeId` smallint(5) unsigned NOT NULL DEFAULT 0,
`PublicationId` smallint(5) unsigned NOT NULL DEFAULT 0,
`DataId` int(10) unsigned NOT NULL DEFAULT 0,
`mean` double DEFAULT NULL,
`Locus` char(50) DEFAULT NULL,
`LRS` double DEFAULT NULL,
`additive` double DEFAULT NULL,
`Sequence` smallint(5) unsigned NOT NULL DEFAULT 1,
`comments` text NOT NULL,
UNIQUE KEY `InbredSet` (`InbredSetId`,`Id`),
UNIQUE KEY `record` (`InbredSetId`,`PhenotypeId`,`PublicationId`,`Sequence`),
UNIQUE KEY `PhenotypeId` (`PhenotypeId`),
UNIQUE KEY `DataId` (`DataId`),
FOREIGN KEY (InbredSetId) REFERENCES InbredSet(InbredSetId),
FOREIGN KEY (PhenotypeId) REFERENCES Phenotype(Id),
FOREIGN KEY (PublicationId) REFERENCES Publication(Id),
KEY `InbredSetId` (`InbredSetId`),
KEY `Locus` (`Locus`),
KEY `PublicationId` (`PublicationId`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `RatSnpPattern`
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/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `RatSnpPattern` (
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`SnpId` int(12) NOT NULL,
`BN` char(1) DEFAULT NULL,
`F344` char(1) DEFAULT NULL,
`ACI` char(1) DEFAULT NULL,
`BBDP` char(1) DEFAULT NULL,
`FHH` char(1) DEFAULT NULL,
`FHL` char(1) DEFAULT NULL,
`GK` char(1) DEFAULT NULL,
`LE` char(1) DEFAULT NULL,
`LEW` char(1) DEFAULT NULL,
`LH` char(1) DEFAULT NULL,
`LL` char(1) DEFAULT NULL,
`LN` char(1) DEFAULT NULL,
`MHS` char(1) DEFAULT NULL,
`MNS` char(1) DEFAULT NULL,
`SBH` char(1) DEFAULT NULL,
`SBN` char(1) DEFAULT NULL,
`SHR` char(1) DEFAULT NULL,
`SHRSP` char(1) DEFAULT NULL,
`SR` char(1) DEFAULT NULL,
`SS` char(1) DEFAULT NULL,
`WAG` char(1) DEFAULT NULL,
`WLI` char(1) DEFAULT NULL,
`WMI` char(1) DEFAULT NULL,
`WKY` char(1) DEFAULT NULL,
`ACI_N` char(1) DEFAULT NULL,
`BN_N` char(1) DEFAULT NULL,
`BUF_N` char(1) DEFAULT NULL,
`F344_N` char(1) DEFAULT NULL,
`M520_N` char(1) DEFAULT NULL,
`MR_N` char(1) DEFAULT NULL,
`WKY_N` char(1) DEFAULT NULL,
`WN_N` char(1) DEFAULT NULL,
PRIMARY KEY (`Id`),
UNIQUE KEY `SnpId` (`SnpId`)
) ENGINE=MyISAM AUTO_INCREMENT=4711685 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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-- Table structure for table `Sample`
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/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `Sample` (
`Id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
`StrainId` smallint(5) unsigned NOT NULL DEFAULT 0,
`Name` varchar(30) DEFAULT NULL,
`Age` smallint(6) NOT NULL DEFAULT 0,
`Sex` enum('F','M') NOT NULL DEFAULT 'F',
`CreateTime` date NOT NULL DEFAULT '2001-01-01',
`TissueType` varchar(30) DEFAULT NULL,
`FromSrc` varchar(10) DEFAULT NULL,
`ImageURL` varchar(100) DEFAULT NULL,
`CELURL` varchar(120) DEFAULT NULL,
`DATURL` varchar(100) DEFAULT NULL,
`CHPURL` varchar(100) DEFAULT NULL,
`RPTURL` varchar(100) DEFAULT NULL,
`EXPURL` varchar(100) DEFAULT NULL,
`TXTURL` varchar(100) DEFAULT NULL,
PRIMARY KEY (`Id`),
UNIQUE KEY `Name` (`StrainId`,`Name`,`CreateTime`)
) ENGINE=MyISAM AUTO_INCREMENT=252 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
--
-- Table structure for table `SampleXRef`
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/*!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`
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DROP TABLE IF EXISTS `SnpAll`;
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/*!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`),
FOREIGN KEY (SpeciesId) REFERENCES Species(SpeciesId),
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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-- Table structure for table `SnpAllRat`
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`SnpName` char(30) DEFAULT NULL,
`Chromosome` char(2) DEFAULT NULL,
`Position` double DEFAULT NULL,
`Alleles` char(5) DEFAULT NULL,
`Source` char(35) DEFAULT NULL,
`ConservationScore` double DEFAULT NULL,
`Domain` varchar(50) DEFAULT NULL,
`Gene` varchar(30) DEFAULT NULL,
`Transcript` varchar(50) DEFAULT NULL,
`Function` varchar(50) DEFAULT NULL,
PRIMARY KEY (`Id`),
KEY `SnpName` (`SnpName`),
KEY `Position` (`Chromosome`,`Position`),
KEY `Source` (`Source`)
) ENGINE=MyISAM AUTO_INCREMENT=97663615 DEFAULT CHARSET=latin1;
/*!40101 SET character_set_client = @saved_cs_client */;
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-- Table structure for table `SnpAllele_to_be_deleted`
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`Info` char(255) DEFAULT NULL,
PRIMARY KEY (`Id`)
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