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Life Science Database Archive
LSDB Archive

If a database is inadequate in terms of its description, unclear with respect to the terms of use, or is not downloadable, it may not be fully used, cited or rightly acknowledged by the (research) communities. This is even true for databases with high-quality datasets.

The Life Science Database Archive maintains and stores the datasets generated by life scientists in Japan in a long-term and stable state as national public goods. The Archive makes it easier for many people to search datasets by metadata (description of datasets) in a unified format, and to access and download the datasets with clear terms of use (see here for detailed descriptions).

In addition, the Archive provides datasets in forms friendly to different types of users in public and private institutions, and thereby supports further contribution of each research to life science.

Lifescience Database Archive

Archived Databases

 Database nameMaintenance sitePrincipal creatorDatabase classificationOrganismSummaryLicense
  RPSD rpsd National Institute of Agrobiological Sciences external link Toshimasa Yamazaki Protein Structure Rice The database of protein 3D structures of seven kinds of plants such as rice. CC BY-SA
Detail
  RGP gmap rgp gmap National Institute of Agrobiological Sciences external link Yuzo Minobe DNA marker Rice The database of DNA markers that were used to create the rice genetic map. CC BY-SA
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  PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods pgdbj_dna_marker_linkage_map Kazusa DNA Research Institute external link Satoshi Tabata Plant Genome Plant, Algae, Green algae The database of general information, DNA markers, QTLs, DB links and genome analysis methods of plants including model plants. CC BY-SA
Detail
  KAIKOcDNA kaiko_cdna National Institute of Agrobiological Sciences external link Yoshitaka Suetsugu cDNA silkworm The database of silkworm partial cDNA sequences with annotations. CC BY-SA
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  PLACE place National Institute of Agrobiological Sciences external link Kenichi Higo Regulation of Gene Expression Vascular plant The database of motifs found in plant cis-acting regulatory DNA elements based on previously published reports on vascular plants. CC BY-SA
Detail
  PGDBj - Ortholog DB pgdbj_ortholog_db Kazusa DNA Research Institute external link Akihiro Nakaya Ortholog Viridiplantae, Cyanobacteria The database of orthologous relationships of genes that are computationally determined according to similarities between amino acid sequences. CC BY-SA
Detail
  KEGG MEDICUS kegg_medicus Kanehisa Laboratory, Institute for Chemical Research, Kyoto University external link Minoru Kanehisa Drug, Disease human The database of an integrated information resource of diseases, drugs, and health-related substances, aiming to bring the genomic revolution to society. CC BY-NC-ND
Detail
  GenLibi genlibi Japan Science and Technology Agency external link Japan Science and Technology Agency Protein human, mouse, rat The database of information on genes and their related diseases and phenotypes that were obtained from the JST bibliographic information JDream II. CC BY-SA
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  The Rice Growth Monitoring for The Phenotypic Functional Analysis agritogo-rice-phenome National Institute of Agrobiological Sciences external link Tomoko Shinomura Phenotype Rice The database of phenotype analysis of rice by the system capable of imaging growth from germination to flowering. CC BY-SA
Detail
  Trypanosomes Database trypanosome The Targeted Proteins Research Program external link Hideaki Sugawara Protein trypanosoma, human The database of enzymes that are effective targets for drug development that can control trypanosomiasis. CC BY-SA
Detail
  Q-TARO qtaro National Institute of Agrobiological Sciences external link Junichi Yonemaru QTL Rice The database of Rice QTL information extracted from published research papers. CC BY-SA
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  AT Atlas atatlas The Targeted Proteins Research Program external link Hideaki Sugawara Other Molecular Biology Databases, Experimental Methodology - The database of graphical descriptions of techniques developed in the Targeted Proteins Research Program. CC BY-SA
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  TP Atlas tpatlas The Targeted Proteins Research Program external link Hideaki Sugawara Metabolic and Signaling Pathways Homo sapiens, bacteria and various model organisms The database of achievements of Targeted Proteins Research Program mapped on pathway diagrams. CC BY-SA
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  RMG rmg National Institute of Agrobiological Sciences external link Kouichi Kadowaki Genome rice The database of rice mitochondrial genome and its analysis results. CC BY-SA
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  KOME KOME National Institute of Agrobiological Sciences external link Shoshi Kikuchi cDNA rice The database of rice full-length cDNA clones that were sequenced in the rice full-length cDNA project. CC BY-SA
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  BodyParts3D BodyParts3D Database Center for Life Scienceexternal link Kousaku Okubo organ human The dictionary-type database for anatomy in which anatomical concepts are represented by 3D structure data that specify corresponding segments of a three-dimensional whole-body model for an adult human male. CC BY-SA
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  Taxonomy Icon taxonomy-icon National Bioscience Database Center external link Kousaku Okubo Images - A collection of icons (illustrations) of biological species that is free to use and distribute. CC BY
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  Society Catalog lsdb-academycatalog National Bioscience Database Center external link Shoko Kawamoto Catalog - The database of information of the academic societies in Japan (organization name, website URL, contact address, etc.) CC BY-SA
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  tRNADB-CE tRNADB-CE Bioinformatics Laboratory, Information Engineering, Niigata Universityexternal link Takashi Abe RNA sequences prokaryotes The most accurate curated database of tRNA genes in the world. Data is reviewed by several experts. CC BY-SA
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  Open TG-GATEs Pathological Image Database open-tggates-pathological-images National Institute of Biomedical Innovation external link Toxicogenomics Project / Toxicogenomics Informatics Project Toxicogenomics database rat The database of high-resolution whole slide digital pathological images of liver and kidney pathological specimens which were obtained through animal tests using 160 compounds. CC BY-SA
Detail
  Open TG-GATEs open-tggates National Institute of Biomedical Innovation external link Toxicogenomics Project / Toxicogenomics Informatics Project Toxicogenomics database human, rat The database of gene expression and toxicity when exposing rats and rat and human liver cells to 170 compounds. CC BY-SA
Detail
  ClEST clest Symbiotic Evolution and Biological Functions Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) external link Minoru Moriyama cDNA bedbug The database of expressed sequence tags (EST) of unique organs and whole bodies of the bedbug, Cimex lectularius. CC BY-SA
Detail
  DGBY DGBY National Food Research Institute, National Agriculture and Food Research Organization (NARO) external link Akira Ando Expression Yeast This database compiles the transcriptomics and phenomics data about the stress tolerance of baker's yeast. CC BY-SA
Detail
  D-HaploDB D-HaploDB Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University external link Kenshi Hayashi Polymorphism human This database presents true haplotypes and LD structures of Japanese genome, determined using DNA samples obtained from complete hydatidiform moles. CC BY-SA
Detail
  Plabrain DB Plabrain DB Laboratory for Molecular Developmental Biology Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University external link Kiyokazu Agata Expression, Localization planaria The database for planarian nervous system analysis, including results of the gene expression profiling of single cells, the gene expression analysis by whole-mount in situ hybridization and the analysis by Immunohistochemical staining. CC BY-SA
Detail
  GETDB - Gal4 Enhancer Trap Insertion Database GETDB - Gal4 Enhancer Trap Insertion Database Kyoto Institute of Technologyexternal link Shigeo Hayashi Expression fruit fly The database compiles insertion points of Gal4 enhancer trap and patterns of enhancer activity in fruit fly. CC BY-SA
Detail
  AcEST AcEST Tokyo Metropolitan Universityexternal link Takeshi Kanegae cDNA fern The database of Adiantum capillus-veneris EST clones and annotations of them. CC BY-SA
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  Dicty_cDB Dicty_cDB University of Tsukubaexternal link Hideko Urushihara cDNA cellular slime mold The database of Dictyostelium discoideum cDNA sequences and annotations (results of blast search, motif search, prediction of product localization, expression profile, alignment to the genome, and so on) CC BY-SA
Detail
  Gclust Server Gclust Server The University of Tokyoexternal link Naoki Sato Protein sequences 95 species The database of protein sequence clusters in 95 species. They are obtained from the comparison of all-against-all blast search results. CC BY-SA
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  Budding yeast cDNA sequencing project Budding yeast cDNA sequencing project The University of Tokyoexternal link Takashi Ito cDNA budding yeast The database of budding yeast 5'cDNA full length clones. CC BY-SA
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  Yeast Interacting Proteins Database Yeast Interacting Proteins Database The University of Tokyoexternal link Takashi Ito Protein-protein interactions budding yeast The database of budding yeast protein-protein interactions obtained from Y2H. CC BY-SA
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  DMPD (Dynamic Macrophage Pathway CSML Database DMPD (Dynamic Macrophage Pathway CSML Database) The University of Tokyoexternal link Satoru Miyano Metabolic and Signaling Pathways mammals The database of pathways associated with differentiation and activation of macrophage. CC BY-SA
Detail
  Gene Name Thesaurus Database Center for Life Scienceexternal link Kousaku Okubo Dictionary 9 species (human, mouse, rat, zebrafish, fruit fly, nematode, budding yeast, fission yeast, Bacillus subtilis) Gene names and gene family names were collected for 9 different organisms (including human, mouse, rat, zebrafish, fruit fly, nematode, budding yeast, fission yeast, Bacillus subtilis), and associated with parallel relationship (synonym) and hierarchical relationship (family name). Acronym notations and IDs of typical gene/genome databases are also treated as names. CC BY-SA
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