Services

The NBDC provides, or supports the development and operation of the following databases, and tools etc. through joint research and development, contracted research and development, etc.

1. Database Users (Browsing)

Category Purpose and service name Logo and link Abstract

Database Integration

Full-text search databases, patent and literature in life science

Life Science Database Cross Search

Search & download life science datasets

Life Science Database Archive

Search life science database information

Integbio Database Catalog

Browse RDF data metadata and relationships

RDF Portal

Search, retrieve, format, and RDFize major databases

TogoWS

Search & reuse your own relational databases

TogoDB

Search and convert links between identifiers(IDs) of databases(DBs)

TogoID

Material

Search 3D human anatomy diagrams

BodyParts3D

Search Japanese expositions on articles in life science

FirstAuthors

Search reviews in life science

LeadingAuthors

Search manual movies for database

TogoTV

Search illustrations in life science

TogoTV TogoPic

Search materials for bioinformatics training

TogoTV AJACS

Search questions and answers in bioinformatics

LSQA

Human

Reuse analysis data of human sample

NBDC Human Database

Search variant data in Japanese human genome

TogoVar

Search gene expression and transcription start site (human and mouse)

DBKERO

Genome

Search genomes, species, phenotypes, and environment (whole genome)

TogoGenome

Search rapidly genome sequence (model organism)

GGGenome

Design guide RNAs for genome editing

CRISPRdirect

Search SNPs and phenotype in plant genomes

Plant GARDEN

Metagenome

Search metagenome and microbial genome

MicrobeDB.jp

Epigenome

Search, browse and analyze ChIP-seq data

ChIP-Atlas

Gene

Search genes by sequence or keyword

GGRNA

Enrichment analysis of disease-related genes

Gendoo

Gene Expression

Search gene expression in normal tissues and cells

RefEx

Search experimental datasets of gene expression

AOE

NGS

Search NGS raw data

DBCLS SRA

Protein

Search protein structures

PDBj

Proteome

Search proteome experimental data

jPOSTdb

Glycome

Search glycan information

GlyCosmos Portal

Drug

Search drug and drug ingredient information

KEGG MEDICUS

Disease

Search rare and intractable disease candidates by symptoms

PubCaseFinder

NLP

Search English expressions used in papers

inMeXes

Search abbreviations used in papers

Allie

Search citations and contexts of papers

Colil

SPARQL search

Add SPARQL search results to data table with GUI

TogoTable

Search your question with natural language and get results from SPARQL endpoints

LODQA

2. Developers (API)

Category Purpose and service name Logo and link Abstract

Database Integration

Retrieve life science database information

Integbio Database Catalog

Search RDF data with SPARQL

RDF Portal

Search, retrieve, format, and RDFize major databases with REST API

TogoWS

Search your own relational databases with SPARQL

TogoDB

Convert links between identifiers(IDs) of databases(DBs) with REST API

TogoID

Human

Search variant data in Japanese human genome with SPARQL

TogoVar

Search gene expression and transcription start site with SPARQL (human and mouse)

DBKERO

Genome

Reuse genomes, species, phenotypes, and environment (whole genome) in web app

TogoGenome

Search rapidly genome sequence with REST API

GGGenome

Gene

Search genes by sequence or keyword with REST API

GGRNA

Enrichment analysis of disease-related genes with REST API

Gendoo

Gene Expression

Search experimental datasets of gene expression with REST API

AOE

NGS

Search NGS raw data with REST API

DBCLS SRA

Protein

Search protein structures with SPARQL

PDBj

Proteome

Search proteome experimental data with SPARQL

jPOSTdb

Glycome

Search glycan information with SPARQL

GlyCosmos Portal

Disease

Search relevant information on rare and incurable diseases with SPARQL

PubCaseFinder

NLP

Search annotations in articles or other texts with SPARQL

PubAnnotation / TextAE

Search dictionaries for text mining

PubDictionaries

Search English expressions used in papers with REST API

inMeXes

Search abbreviations used in papers with SPARQL

Allie RDF Data Portal

Search citations and contexts of papers with SPARQL

Colil RDF Data Portal

Search the Life Science Dictionary with SPARQL

LSD RDF Data Portal

RDF coding

Convert RDB to RDF with GUI

D2RQ Mapper

Convert JSON data to JSON-LD (RDFize)

JSON2LD Mapper

Split RDF data into multiple files without collapsing blank nodes

split4blank

A guideline for RDFizing databases

RDF化ガイドライン

SPARQL search

View ratings for SPARQL endpoints

Umaka-Yummy Data

Visualize RDF data structure

Umaka Viewer

Visualize SPARQL search results and reuse them on any web page

TogoStanza

Customize and visualize SPARQL search results with JavaScript

d3sparql.js

Publish and reuse complex SPARQL queries as a REST API

SPARQList

Run complex SPARQL queries on the command line

SPANG

Search RDF data in SPARQL endpoints with GUI

Endpoint browser

Create SPARQL queries with GUI and search RDF data

SPARQL Builder

Search RDF data with SPARQL input support

SPARQL support

Search RDF data in GraphQL and get results from SPARQL endpoints

Grasp

Optimize and publish securely SPARQL endpoints

SPARQL-proxy

Define RDF data models to automatically generate SPARQL queries and diagrams

RDF config

3. Big data analysts (Bulk donwload)

Category Purpose and service name Logo and link Abstract

Database Integration

Download life sciences datasets

Life Science Database Archive

Download your own databases

TogoDB

Download RDF data

RDF Portal

Material

Download 3D human anatomy chart

BodyParts3D

Download Japanese on articles in life science

FirstAuthors

Download review in life science

LeadingAuthors

Human

Download variant data in Japanese human genome

TogoVar

Download gene expression and transcription start site (human and mouse)

DBKERO

Genome

Search genomes, species, phenotypes, and environment (whole genome) with REST API and SPARQL

TogoGenome

Epigenome

Download peak data of ChIP-seq

ChIP-Atlas

Gene Expression

Download gene expression in normal tissues and cells

RefEx

Protein

Download protein structure data

PDBj

Proteome

Download Proteome data

jPOSTrepo

4. Data owners (Publishing or converting)

Category Purpose and service name Logo and link Abstract

Database Integration

Deposit your own datasets

Life Science Database Archive

Register your own RDF data

RDF Portal

Convert your own into RDB and RDF

TogoDB

Material

Deposit your own manual movies

TogoTV

Deposit your own illustrations I life science

TogoTV TogoPic

Human

Deposit your own analysis data of human sample

NBDC Human Database

Proteome

Register proteome experimental data

jPOSTrepo

Glycome

Register your own glycan data

GlyCosmos Portal

NLP

Register annotations for articles or other texts

PubAnnotation / TextAE

Register your own dictionary for text mining

PubDictionaries

Inquiries & opinions

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