Database
Human Genome Research Dataset Archive
| Dataset | Description |
|---|---|
| Japanese Genotype-phenotype Archive (JGA) | This restricted-access database stores datasets such as human whole-genome sequencing data, exome sequencing data, and genotype imputation panels obtained by researchers in Japan and other Asian countries. Access to the datasets requires a data use application. A list of datasets can be viewed from List of Available Research Data. After confirming the How to Use the Data, you can apply via the Data Use Application System. NCBI counterpart service: The database of Genotypes and Phenotypes (dbGaP) EBI counterpart service: European Genome-Phenome Archive (EGA) |
| Japanese Genotype-phenotype Archive Metadata (JGA-metadata) | A metadata repository of the JGA database. The metadata is public information and accessible without a data use application. Download URL: https://ddbj.nig.ac.jp/public/jga/ NIG supercomputer file path: /usr/local/shared_data/jga/ |
| Reanalysis Results of Public Human Genome Datasets | Reanalysis results of publicly available human whole-genome sequencing datasets (1000 Genomes, HGDP, KPGP, SGDP). Alignment results (CRAM) and variant detection results (gVCF, aggregate VCF) based on the GRCh38 assembly, and alignment results (CRAM) and variant detection results (gVCF) based on the CHM13 assembly are available. Download URL: https://ddbj.nig.ac.jp/public/public-human-genomes/ NIG supercomputer file path: /usr/local/shared_data/public-human-genomes/ |
Human Genome Variation Databases
| Dataset | Description |
|---|---|
| TogoVar-repository | TogoVar-repository is a public database for human variants, allele frequencies, and genotypes. Accession numbers are assigned to human variants, and data are exchanged with NCBI dbSNP, NCBI dbVar, and EBI European Variation Archive. Download URL: https://ddbj.nig.ac.jp/public/togovar/ NIG supercomputer file path: /usr/local/shared_data/togovar/ NCBI counterpart (for small variants ≤50 bp [single nucleotide polymorphisms, microsatellites, short insertions and deletions]): The Single Nucleotide Polymorphism Database (dbSNP) NCBI counterpart (for structural variants >50 bp [insertions, deletions, duplications, inversions, transposable elements, translocations, complex variants]): The Database of Genomic Structural Variation (dbVar) EBI counterpart (including non-human species): European Variation Archive (EVA) |
Annotated Sequence Databases
| Dataset | Description |
|---|---|
| DDBJ Annotated/Assembled Sequences | A database of annotated nucleotide sequences of genomes, genes, and transcripts. As a member of the INSDC (International Nucleotide Sequence Database Collaboration), DDBJ (DNA Data Bank of Japan) shares annotated and assembled nucleotide sequence data as part of the international nucleotide database. Download URL: https://ddbj.nig.ac.jp/public/ddbj_database/ddbj/ NIG supercomputer file path: TBD NCBI counterpart: NCBI GenBank NCBI counterpart (non-redundant dataset): NCBI RefSeq EBI counterpart (covers both annotated and raw sequences): European Nucleotide Archive (ENA) |
| NCBI GenBank (mirror) | NCBI GenBank data mirror provided by DDBJ Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ncbi.nih.gov/genbank/ NIG supercomputer file path: TBD |
| NCBI RefSeq (mirror) | NCBI RefSeq data mirror provided by DDBJ Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ncbi.nih.gov/ncbi_refseq/ NIG supercomputer file path: TBD |
| ENA (mirror) | ENA data mirror provided by DDBJ Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ebi.ac.uk/ NIG supercomputer file path: TBD |
Raw Sequence Databases
| Dataset | Description |
|---|---|
| DDBJ Sequence Read Archive (DRA) | A database storing raw sequence data and alignment information generated by high-throughput sequencing platforms. Download URL: https://ddbj.nig.ac.jp/public/ddbj_database/dra/ NIG supercomputer file path: /usr/local/shared_data/dra/ NCBI counterpart: NCBI Sequence Read Archive (SRA) EBI counterpart (covers both annotated and raw sequences): European Nucleotide Archive (ENA) |
Functional Genomics Databases
| Dataset | Description |
|---|---|
| Genomic Expression Archive (GEA) | A repository of microarray- and sequence-based functional genomics data compliant with MIAME (Minimum Information About a Microarray Experiment). Download URL: https://ddbj.nig.ac.jp/public/ddbj_database/gea/ NIG supercomputer file path: /usr/local/shared_data/gea/ |
Protein Sequence and Biomolecular Structure Databases
| Dataset | Description |
|---|---|
| Uniprot mirror | Uniprot data mirror provided by DDBJ. A resource for protein sequences and functional information, provided by ELIXIR. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.uniprot.org/ NIG supercomputer file path: TBD |
| Protein Data Bank Japan (PDBj) mirror | PDBj data mirror provided by DDBJ. A structural database of biomolecules, provided by Institute for Protein Research, Osaka University. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.pdbj.org/ NIG supercomputer file path: TBD |
| World Wide Protein Data Bank (wwPDB) mirror | wwPDB data mirror provided by DDBJ. An archive of three-dimensional structural data of biomolecules (proteins, DNA, RNA), provided by the wwPDB. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/pdb/ NIG supercomputer file path: TBD |
Metabolomics Databases
| Dataset | Description |
|---|---|
| MetaboBank | A public repository that accepts submissions of metabolomics data. Download URL: https://ddbj.nig.ac.jp/public/metabobank/ NIG supercomputer file path: /usr/local/shared_data/metabobank/ |
Biological Taxonomy Databases
| Dataset | Description |
|---|---|
| NCBI Taxonomy mirror | NCBI Taxonomy data mirror provided by DDBJ. The standard nomenclature and classification repository of the International Nucleotide Sequence Database Collaboration (INSDC), which consists of GenBank, ENA (EMBL), and DDBJ. It contains organism names and taxonomic lineages used in the nucleotide and protein sequence databases of INSDC. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ncbi.nih.gov/ncbi_taxonomy/ NIG supercomputer file path: TBD |
Metadata Databases
| Dataset | Description |
|---|---|
| DDBJ BioProject | A database for organizing research projects and their associated data. By referencing a BioProject accession number, datasets can be grouped by project. DDBJ BioProject issues accession numbers with the prefix ‘PRJDB’ for registered projects. Public project data is shared with EBI and NCBI. Download URL: https://ddbj.nig.ac.jp/public/ddbj_database/bioproject/ NIG supercomputer file path: /usr/local/shared_data/bioproject/ NCBI counterpart: NCBI BioProject |
| NCBI BioProject (mirror) | NCBI BioProject data mirror provided by DDBJ. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ncbi.nih.gov/ncbi_bioproject/ NIG supercomputer file path: TBD |
| DDBJ BioSsample | A database that centrally manages biological sample information used to obtain experimental data registered in the DDBJ primary databases. Examples of BioSamples include cell lines, tissue biopsies, organisms, and environmental samples. Sample data are shared with EBI and NCBI BioSample databases. Download URL: https://ddbj.nig.ac.jp/public/ddbj_database/biosample/ NIG supercomputer file path: /usr/local/shared_data/biosample/ NCBI counterpart: NCBI BioSample |
| NCBI BioSample mirror | NCBI BioSample data mirror provided by DDBJ. Download URL: https://ddbj.nig.ac.jp/public/mirror_database/ftp.ncbi.nih.gov/ncbi_biosample/ NIG supercomputer file path: TBD |
Databases for Data Linkage
| Dataset | Description |
|---|---|
| DDBJ, Linked Data (DDBJ-LD) | Linked data provided by the DDBJ Center. Download URL: https://ddbj.nig.ac.jp/public/rdf/ NIG supercomputer file path: /usr/local/shared_data/rdf/ |
