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.

Archived Databases

  Database name Maintenance site Principal creator Database classification Organism Summary License
  Database name Maintenance site Principal creator Database classification Organism Summary License
Mutant Panel Mutant Panel National Agriculture and Food Research Organization (NARO) Akio Miyao Plant databases Rice

Database of rice (Nipponbare) Tos17 insertion mutant lines

CC BY-SA Detail
JEDI System/ OCEANS DB JEDI System/ OCEANS DB Hidekatsu Yamasaki Marine environmental monitoring data Marine plankton The physical, chemical, biological and engineering data observed by OCEANS of JEDI System Detail
Index to Chromosome numbers in Asteraceae Index to Chromosome numbers in Asteraceae Watanabe, Kuniaki Literature Asterales

This database collects published data about Asterales needed for elucidating, classification, phylogeny, and evolution.

CC BY-SA Detail
NBDC NikkajiRDF NBDC NikkajiRDF Japan Science and Technology Agency external link - Chemical substance -

RDF data of Japan Chemical Substance Dictionary (Nikkaji) described by standard ontologies.

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16S RNA sequence set for metagenomic analysis 16S RNA sequence set for metagenomic analysis Graduate School of Integrated Sciences for Life, Hiroshima University Hidemasa Bono RNA data

16S RNA sequence set for metagenomic analysis using kraken2.

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jPOST database jPOST database jPost team Yasushi Ishihama Proteomics -

jPOSTdb is a database containing re-analysis results with unified criteria for proteome data from jPOST repository.

CC0 Detail
LigandBox LigandBox Technology Research Association for Next generation natural products chemistryExternal link Yoshifumi Fukunishi - -

The 'ready-to-dock' database of small chemical compounds, for virtual drug screening on computer docking studies.

CC BY-SA Detail
ChemTHEATRE ChemTHEATRE Center for Marine Environmental Studies, Ehime Universityexternal link Kei Nakayama Monitoring of chemical substances -

ChemTHEATRE is the database that stores monitoring data on all chemical substances.

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.

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RefEx RefEx Database Center for Life Scienceexternal link Ono, Hiromasa Gene Expression human, mouse, rat

The database of gene expression data in each tissue.

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Oligonucleic Acid Drug Database Oligonucleic Acid Drug Database Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)外部リンク Kazuhiko FUKUI Nucleic Acid Drug -

The database focuses on nucleic acid drugs known as biopharmaceuticals and displays information on approved drugs and those in four clinical trial phases.

CC BY-SA Detail
jPOST repository jPOST repository jPOSTチーム Yasushi Ishihama Proteomics -

The repository of mass spectrometry (MS) raw data, peak lists and analyzed data.

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SPD SPD National Agriculture and Food Research Organization (NARO)external link Setsuko Komatsu Proteomics Glycine max

SPD is the database of proteome, transcriptome and metabolome from soybeans under flood stress.

CC BY-SA Detail
Silkworm, Bombyx mori, reference transcriptome data Silkworm, Bombyx mori, reference transcriptome data - Kakeru Yokoi Microarray Bombyx mori

The reference transcriptomic data from new reference genome data and RNAseq data of multiple tissues in Bombyx mori P50T strain.

CC BY-SA Detail
GGGenome dataset GGGenome dataset Database Center for Life Scienceexternal link Yuki Naito Nucleotide sequence -

It is the dataset for search in GGGenome, a tool for fast and sensitive search for genomic and transcript sequence.

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MeCab user dictionary for science technology term MeCab user dictionary for science technology term National Bioscience Database Center external link Yuka Tateisi dictionary -

We have made a user dictionary of morphological analysis engine MeCab headwords and synonyms of JST Thesaurus (2015 edition) .

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AOE AOE Database Center for Life Scienceexternal link Hidemasa Bono Microarray data -

AOE is an index of public gene expression database.

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FANTOM5 FANTOM5 RIKEN Center for Integrative Medical Sciencesexternal link Yoshihide Hayashizaki Expression human, mouse, dog, rat, rhesus monkey, chicken

The database on activities of transcripts and transcription factors in various cell species of human and mouse.

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PoSSuM PoSSuM Molecular Profiling Research Center for Drug Discovery (molprof), The National Institute of Advanced Industrial Science and Technology (AIST)external link Kentaro Tomii Small molecules -

A database for detecting similar small-molecule binding sites on proteins

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First Author's First Author's Database Center for Life Science外部リンク Keisuke Iida Literature -

Open access and online review articles written by Japanese authors who published their research outcomes in some top journals.

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Leading Author's Leading Author's Database Center for Life Science外部リンク Keisuke Iida Literature -

The collection of review articles written by Japanese authors who lead several biological research areas.

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Mouse Basement Membrane Bodymap Mouse Basement Membrane Bodymap Japan Science and Technology Agency external link Kiyotoshi Sekiguchi Protein localizations and targeting mouse

This is a database of body-wide localizations of basement membrane proteins in developing mouse embryos.

CC BY-SA Detail
Nikkaji-InChI Mapping Table Nikkaji-InChI Mapping Table Japan Science and Technology Agency external link - Chemical substance -

Mapping data of Nikkaji No., InChI and InChIKey in Nikkaji (Japan Chemical Substance Dictionary).

CC BY Detail
INOH INOH The Institute of Medical Science, The University of Tokyoexternal link Toshihisa Takagi Metabolic and Signaling Pathways Model species (Homo sapiens, Mus musculus, Rattus norvegicus) etc.

The database is a highly structured, manually curated database of signal transduction pathways.

CC BY-SA Detail
PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods 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
GENIUS II GENIUS II National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront external link Suwa Makiko Protein Sequence Bacteria, Archaea, Eukaryota The database in which protein coding regions in genomes are assigned to three-dimensional structures. CC BY-SA Detail
GRIPDB GRIPDB National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront external link Wataru Nemoto Protein Structure human The database provides information about GPCR oligomerization. CC BY-SA Detail
MicrobeDB.jp MicrobeDB.jp National Institute of Technology外部リンク Ken Kurokawa Genome Information Archaea, Bacteria, Fungi

The database is integrating various microbiological knowledge centered on genome information.

CC BY-SA Detail
Togo Picture Gallery Togo Picture Gallery Database Center for Life Science外部リンク Hiromasa Ono Image Collection -

The database of useful images for life science which are published without a fee.

CC BY Detail
TogoTV TogoTV Database Center for Life Science外部リンク Hiromasa Ono Movie Collection -

The database of tutorial videos expounding how to use biological databases and tools.

CC BY Detail
SKIP Stemcell Database SKIP Stemcell Database Center for Medical Genetics, School of medicine, Keio University外部リンク Kenjiro KOSAKI Gene, Disease human The database aggregates information on human stem cell samples owned by many institutions. 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
Arabidopsis Phenome Database Arabidopsis Phenome Database RIKEN BioResource Center外部リンク Hiroshi Masuya Phenotype Arabidopsis thaliana The database is Arabidopsis Phenome Database that consist of “RIKEN Phenome Integration of Arabidopsis Mutants”and“Database of Curated Plant Phenome”. CC BY-SA Detail
DB-SPIRE DB-SPIRE National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront external link Tamotsu Noguchi Protein Structure - This database has the positional information in the amino acid motif structure. The information is identified by experiments or sequence analysis. CC BY-SA Detail
dbQSNP dbQSNP Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu Universityexternal link Kenshi Hayashi Polymorphism human SNP discovery and determination of their allele frequency in various sample groups using pooled DNA-quantitative fluorescent SSCP analysis CC BY-SA Detail
TMFunction TMFunction National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront external link Michael Gromiha Protein Structure - TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins. CC BY-SA Detail
PSCDB PSCDB Graduate School of Information Science Nagoya University外部リンク Amemiya Takayuki Protein Structure - This database is to represent the relationship between protein structural change and ligand binding. CC BY-SA Detail
ConfC ConfC National Institute of Industrial Science and Technology (AIST), Tokyo Waterfrontexternal link Tamotsu Noguchi Protein structure, Small molecules, Nucleic acid structure - This database extracts this dynamic information from the protein structure being obtained now. CC BY-SA
Detail
SSBD SSBD RIKENexternal link Shuichi Onami Dynamic database mouse, zebrafish, fruit fly, nematode, E. coli

The database of collecting and sharing quantitative data of biological dynamics , which are generated from experimental measurement or computer simulation.

CC BY-SA Detail
ChIP-Atlas ChIP-Atlas Department of Drug Discovery Medicine, Kyoto University Graduate School of Medicineexternal link Shinya Oki Expression human, mouse, fruit fly, nematode, budding yeast, rat

The database of the result of analysis processed from the entire ChIP-Seq data archived in Sequence Read Archive.

CC BY-SA Detail
Metabolonote Metabolonote Kazusa DNA Research Instituteexternal link Nozomu Sakurai Experimental Metadata (Materials and Methods) whole organism A database specified for managing information on experimental methods (metadata) which is accompanied with the experimental data obtained from metabolomics studies. CC BY-SA
Detail
eSOL eSOL The Targeted Proteins Research Programexternal link Hideki Taguchi Protein properties E. coli

Database of solubilities of all E.coli proteins translated by using an in vitro translation system, and of chaperone effects on their aggregation.

CC BY-SA Detail
SAHG SAHG National Institute of Industrial Science and Technology (AIST), Tokyo Waterfrontexternal link Chie Motono Protein structure, Human ORFs, Protein sequence human SAHG is a comprehensive database of predicted structures of all human proteins. CC BY-SA Detail
fRNAdb fRNAdb National Institute of Industrial Science and Technology (AIST), Tokyo Waterfrontexternal link Toutai Mituyama RNA sequences 32,978 species The database that hosts a large collection of non-coding transcripts including annotated/non-annotated sequences. CC BY-SA
Detail
CREATE portal CREATE portal Kazusa DNA Research Instituteexternal link Hisashi Koga Proteomics mouse The database consists of InGaP and InCeP. InGap is the analysis of 274 mKIAA genes' expressions based on antibody preparation. InCep is the analysis of 50 mKIAA proteins' interactions. CC BY-SA
Detail
RPD RPD National Institute of Agrobiological Sciencesexternal link Setsuko Komatsu Proteome Rice The information on proteins identified from several organs and organelles of rice on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) reference maps. CC BY-SA Detail
JSNP JSNP Institute of Medical Science, University of Tokyoexternal link - Polymorphism human

A database of about 197,000 polymorphisms in Japanese population, with annotations such as genes, positions, amino acid substitutions

CC BY-SA Detail
RED II INAHO RED II INAHO National Institute of Agrobiological Sciencesexternal link Shoshi Kikuchi Plant databases - Rice, Microarray, Gene Expression Rice RED II INAHO is the database that analyzed the gene expression of rice using a 60-mer oligonucleotide microarray. CC BY-SA Detail
RED RED National Institute of Agrobiological Sciencesexternal link Shoshi Kikuchi Plant databases - Rice, Microarray, Gene Expression Rice RED is the database that aggregates the gene expression data analyzed with 8987EST array in the Rice Genome Project. CC BY-SA Detail
ASTRA ASTRA National Institute of Advanced Industrial Science and Technology external link Hideki Nagasaki Nucleotide Sequence Databases - Gene structure, introns and exons, splice sites 6 species (human, mouse, fruit fly, nematode, thale cress, rice) The database represents classified patterns of alternative splicing (AS) and alternative transcriptional initiation (ATI) in six eukaryotic genomes. CC BY-SA
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RMOS RMOS National Institute of Agrobiological Sciences external link Shoshi Kikuchi Experimental Methodology Rice Comprehensive information around the constitution of the Microarrays on Rice Microarray Project CC BY-SA
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RGP physicalmap RGP physicalmap National Institute of Agrobiological Sciences external link Takuji Sasaki YAC clone Rice Physical mapping of rice YAC clones selected with the RGP DNA markers. CC BY-SA Detail
RGP caps RGP caps National Institute of Agrobiological Sciences external link Takuji Sasaki DNA marker Rice The database of DNA markers (STS and CAPS markers) that were developed to detect polymorphism in Rice. CC BY-SA Detail
RGP estmap2001 RGP estmap2001 National Institute of Agrobiological Sciences external link Takuji Sasaki EST Rice The database of EST sites that were used to create the YAC-based rice transcript map. CC BY-SA Detail
RGP gmap2000 RGP gmap2000 National Institute of Agrobiological Sciences external link Takuji Sasaki DNA marker Rice The database of RFLP markers that were used to create the year 2000 version of the high-density rice genetic map. CC BY-SA Detail
TMBETA-GENOME TMBETA-GENOME National Institute of Advanced Industrial Science and Technology external link Michael Gromiha Protein Archaea, Bacteria, Eukaryota The database of transmembrane β-barrel proteins in complete genomes. CC BY-SA
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RGP gmap98 RGP gmap98 National Institute of Agrobiological Sciences external link Takuji Sasaki DNA marker Rice The database of RFLP markers that were used to create the high-density rice genetic map. CC BY-SA Detail
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 Detail
KAIKOcDNA KAIKOcDNA National Institute of Agrobiological Sciences external link Yoshitaka Suetsugu cDNA silkworm The database of silkworm partial cDNA sequences with annotations. CC BY-SA
Detail
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
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 Detail
The Rice Growth Monitoring for The Phenotypic Functional Analysis The Rice Growth Monitoring for The Phenotypic Functional Analysis 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 Trypanosomes Database 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
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Q-TARO Q-TARO 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 AT Atlas 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 TP Atlas 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 Detail
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 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
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 Detail
Society Catalog Society Catalog 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 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 TG-GATEs Pathological Image Database 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
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Open TG-GATEs Open TG-GATEs 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
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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
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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
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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
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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 - Dictyostelium cDNA Database Dicty_cDB - Dictyostelium cDNA Database 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
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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 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
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Gene Name Thesaurus 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.

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