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 Integrated Database Project 

     Life Science Database Archive 

    •  Life Science Database Archive metadata
    •  tRNADB-CE (tRNA gene database curated manually by experts)(Archive)
    •  Open TG-GATEs(Archive)
    •  Open TG-GATEs - Pathological images(Archive)
    •  Plabrain DB(Archive)
    •  GETDB(Archive)
    •  AcEST(Archive)
    •  Dicty_cDB(Archive)
    •  Budding yeast cDNA sequencing project(Archive)
    •  Gclust Server(Archive)
    •  Dynamic Macrophage Pathway CSML Database(Archive)
    •  Yeast Interacting Proteins Database(Archive)
    •  Database for Gene expression and function of Baker's yeast(Archive)
    •  ClEST(Archive)
    •  D-HaploDB(Archive)
    •  BodyParts3D(Archive)
    •  Taxonomy Icon(Archive)
    •  RMG(Archive)
    •  Knowledge-based Oryza Molecular biological Encyclopedia(Archive)
    •  AT Atlas(Archive)
    •  TP Atlas(Archive)
    •  Q-TARO(Archive)
    •  Trypanosomes Database(Archive)
    •  GenLibi(Archive)
    •  PGDBj - Ortholog DB(Archive)
    •  KEGG MEDICUS(Archive)
    •  SEVENS(Archive)
    •  PLACE(Archive)
    •  KAIKOcDNA[Archive]
    •  RGP : RICE GENETIC MAP IN NATURE GENETICS[Archive]
    •  RPSD[Archive]
    •  SAHG[Archive]
    •  Chip-atlas[Archive]
    •  Metabolonote[Archive]
    •  SSBD[Archive]
    •  Confc[Archive]
    •  PSCDB[Archive]
    •  TMFunction[Archive]
    •  dbQSNP[Archive]
    •  DB-SPIRE[Archive]
    •  Arabidopsis Phenome Database[Archive]
    •  Togo Picture Gallery[Archive]
    •  GRIPDB[Archive]
    •  PGDBj Registered plant list, Marker list, QTL list, Plant DB link and Genome analysis methods[Archive]
    •  SKIP Stemcell Database[Archive]
    •  GENIUS II[Archive]
    •  jPOST repository metadata[Archive]
    •  Oligonucleic Acid Drug Database[Archive]
    •  Mouse Basement Membrane Bodymap[Archive]
    •  MeCab user dictionary for science technology term[Archive]
    •  CHEMTHEATRE[Archive]
    •  AOE[Archive]
    •  FANTOM5[Archive]
    •  POSSUM[Archive]
    •  Silkworm, Bombyx mori, reference transcriptome data[Archive]
    •  SPD[Archive]
  •  BodyParts3D
  •  Integbio Database Catalog
  •  NBDC RDF Portal

 Term 

  •  Gene Wiki
  •  Proteopedia
  •  Gray’s Anatomy of the Human Body
  •  PHDB(morphologydb)
  •  GeneReviews
  •  Genetics Home Reference (Conditions)
  •  Genetics Home Reference (Genes)
  •  Genetics Home Reference (Chromosomes)
  •  Genetics Home Reference (Handbooks)
  •  Genetics Home Reference (Glossary)
  •  Genetics Home Reference (Resources)
  •  biosharing.org
  •  FAIRsharing.org(standards)
  •  FAIRsharing.org(policies)
  •  FAIRsharing.org(databases)
  •  J-CHECK: Japan chemical collaborative knowledge database
  •  NITE-CHRIP: NITE Chemical Risk Information Platform
  •  NPEdia (Natural Products Encyclopedia)

 Genome/Gene/RNA 

     Genome 

    •  miyakogusa.jp
    •  Rubber Genome and Transcriptome Database
    •  BGDB
    •  O157 genome database
    •  Vibrio parahaemolyticus genome database
    •  Genome information broker
    •  Nocardia farcinica genome
    •  Streptomyces avermitilis genome database
    •  CyanoBase
    •  RhizoBase
    •  Mycoplasma penetrans genome
    •  MBGD - Microbial Genome Database for Comparative Analysis
    •  BSORF - Bacillus subtilis Genome Database
    •  KEGG VGENOME
    •  PEC(Profiling of E. coli Chromosome)
    •  Extremo Base
    •  KAIKOGAAS
    •  Swine Marker Viewer
    •  Pt_spiderBASE
    •  KEGG GENOME

     Medals 

    •  DOGAN
    •  G-compass

     Gene/Transcription 

    •  FANTOM4
    •  FLJ Human cDNA Database
    •  NEDO

      •  Entrez Gene 

    •  RefSeq
    •  FANTOM3
    •  ROUGE
    •  Bombyx Trap DataBase
    •  CiAID
    •  FANTOM5
    •  XDB
    •  Knowledge-Oriented Molecular Biological Encyclopedia (KOME)
    •  Rice Annotation Project Database (RAP-DB)
    •  RiceGAAS: Rice Genome Automated Annotation System
    •  KATANA
    •  ARTADE
    •  FioreDB
    •  Dictyostelium cDNA Database
    •  Hepatitis Virus Database (HVDB)
    •  Database for Genetic Engineering of Microalgae
    •  TADB 2.0
    •  KEGG GENES
    •  KEGG VGENES
    •  RPG - Ribosomal Protein Gene database

     Polymorphism 

    •  gwas
    •  Keio Mutation Databases
    •  PharmGKB
    •  MMDBJ
    •  VegMarks

     Functional RNA 

    •  snoOPY
    •  tRNADB-CE

 Gene Expression/Transcription 

     Transcription Motif 

    •  DBTGR
    •  FlyFactorSurvey
    •  Mouse DNA Microarray
    •  ATTED-II
    •  PPDB
    •  PLACE
    •  DBTBS
    •  Full-Toxoplasma
    •  DBTSS
    •  JASPAR

     EST 

    •  MAGEST
    •  SilkBase
    •  Full-Anopheles
    •  Full-Tsetse
    •  ZFIN
    •  FlyBase
    •  Wormbase
    •  RGP Rice cDNA Sequence Database
    •  MiBASE
    •  PHYSCObase
    •  Full-Babesia
    •  Full-Cryptosporidium
    •  KaFTom
    •  Full-Echinococcosis

     Microarray 

    •  Mouse DNA Microarray
    •  COXPRESdb
    •  AtGenExpress
    •  MacroArray Analysis Page of Bradyrhizobium japonicum
    •  Transcriptome analysis of 2 component system in Eschericia coli
    •  CIBEX

     SAGE/CAGE/ATAC-PCR/iAFLP 

    •  CGED - Cancer Gene Expression Database
    •  CAGE

 Protein 

     Sequence/Family 

    •  PIR
    •  Aaindex
    •  UniProt
    •  Deinococci Genome Database
    •  TRIP Database

     Domain/Motif/Structure 

    •  VIPERdb
    •  PepBase
    •  GENIUS II
    •  Biological Magnetic Resonance Data Bank (BMRB)
    •  ProNuc
    •  3DinSight
    •  ConfC
    •  DB-SPIRE
    •  OLIGAMI
    •  Protein Quaternary Structure
    •  eF-site
    •  RESOPS
    •  PSCDB
    •  REFOLDdb

     Function/Localize 

    •  InGap
    •  KEGG ENZYME
    •  RPG - Ribosomal Protein Gene database
    •  Protein Mutant Database
    •  EzCatDB
    •  3DPL

     Expression 

    •  Two-Dimensional Electrophoresis Database of HSG cells proteins
    •  Rice Proteome Database (RiceProDB)

     Interaction 

    •  GLIDA
    •  TraP
    •  Genomic Object Net Pathway Database (GON)
    •  Het-PDB Navi.
    •  ProNuc
    •  Signaling Pathway Database (SPAD)
    •  Hintdb
    •  HitPredict

 Pathway/Interaction/Reaction 

  •  COXPRESdb
  •  GLIDA
  •  Genome Network Project
  •  PHDB(PHML Model Database)
  •  PHDB(timeseriesdb)
  •  REPAIRtoire
  •  ReSpect
  •  AtMetExpress LC-MS
  •  KEGG
  •  KEGG REACTION
  •  KEGG COMPOUND
  •  KEGG RPAIR
  •  Genomic Object Net Pathway Database (GON)
  •  Signaling Pathway Database (SPAD)
  •  MS-MS Fragment Viewer
  •  PCIDB

 Glyco/Lipid 

  •  KEGG GLYCAN
  •  Glycoconjugate Data Bank
  •  LipidBank
  •  GlyTouCan
  •  SuperSweet
  •  MeKO

 Cell/Organ 

  •  FABA - Ascidian Body Atlas
  •  RefDIC
  •  CITRES
  •  Plant Organelles Database
  •  RIKEN BRC Arabidopsis activation (T-DNA)-tagged lines
  •  SASSC Quick search
  •  TOMATO (National BioResource Project)
  •  The Plant Organelles Database 2 Organelles Movie Database
  •  LIPS
  •  SCMD - Saccharomyces cerevisiae Morphological Database
  •  RIKEN BRC Japan Collection of Microorganisms
  •  CELLPEDIA (Repository database for current knowledge about human cells)

 Development 

  •  3D MR Microscopic Images of Kyoto Collection of Human Embryos
  •  Mouse Basement Membrane Bodymap

 Medical/Drug 

     Medical 

    •  KEGG DISEASE
    •  gwas
    •  CGED - Cancer Gene Expression Database
    •  OMIM
    •  MedlinePlus
    •  MedlinePlus-Medical Encyclopedia (medlineplus_ency)
    •  EU Clinical Trials Register
    •  The New England Journal of Medicine（NEJM）

     Dental 

    •  Two-Dimensional Electrophoresis Database of HSG cells proteins

     Pharmaceutical 

    •  KEGG DRUG
    •  PharmGKB
    •  MedlinePlus Drugs & Supplements

     Anatomy 

    •  BodyParts3D
    •  Gray’s Anatomy of the Human Body
    •  PHDB(morphologydb)

 Environment 

     Farm 

    •  VegMarks
    •  Asian-Pacific Alien Species Database

     Environment 

    •  ChemTHEATRE

 Encyclopedia/Taxonomy 

     Encyclopedia 

    •  Digital Atlas of Actinomycetes
    •  Japanese Ant Image Database (日本産アリ類画像データベース)
    •  e-Foram Stock
    •  Asian-Pacific Alien Species Database

     Classification 

    •  KEGG BRITE
    •  KEGG ORTHOLOGY
    •  Type Collection Database
    •  Virus-Host DB