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Life Science Database Archive
Search across metadata and databases:
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.

2013/2/22  BLAST service for sequences in the archived databases has been released.

Lifescience Database Archive

Archived Databases

 Database nameMaintenance sitePrincipal creatorDatabase classificationOrganismSummaryLicense
  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
Detail
  tRNADB-CE tRNADB-CE Nagahama Institute of Bio-Science and Technologyexternal 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
Detail
  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
Detail
  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
Detail
  Budding yeast cDNA sequencing project Budding yeast cDNA sequencing project The University of Tokyoexternal link Takashi Ito Genome (non-vertebrate) - Fungal genome budding yeast The database of budding yeast 5'cDNA full length clones. CC BY-SA
Detail
  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
Detail
  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
  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
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
Detail