Developed web services

The NBDC promotes database integration by quickly reflecting the results of discussions, investigations and collaborative research and development with associated organizations on the web services listed below.

Integbio Database Catalog

Basic information

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https://integbio.jp/dbcatalog/?lang=en

Outline

The Integbio Database Catalog collects and publishes information on domestic and international databases in the life sciences.
Information about the publishing, updating or closing of databases is not always announced in research papers, so searching the literature alone is insufficient for comprehending trends in research fields. This service compiles summary information (recorded species, URL, whether batch downloadis possible and corresponding URLs, etc.) on more than 1,950 databases (as of April 2019) and ensures the information is permanently available for comprehensive search and browsing.
Since 2017, we have been collaborating with FAIRsharing.org to exchange database information and improve its comprehensiveness.

External presentations, etc.

Introductory video

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Life Science Database Cross Search

Basic information

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https://biosciencedbc.jp/dbsearch/?lang=en

Outline

Life Science Database Cross Search is a service that enables users to conduct cross searches of various different databases. A user can use it to batch check how the name of a particular gene or species was mentioned in domestic patents and databases over the world. More than 180 databases (as of Sep. 2019) are searched with this service, and more are being progressively added.
Even though this service is specialized for life sciences, the covered research fields are diverse. Furthermore, the management organizations and locations of searched databases differ. Therefore, to enable cross searching this service carries out sharing of index data for searching and development of common search specifications with the management organizations of databases. We are also continuously making improvements in both the back end (improved calculation methods for page rank scores, adjustments based on the search log, etc.) and the front end (providing examples of search keywords, addition of search history saving function, etc.) in order to provide search results that match the intention of the viewer.

The database information searched using this service is managed and operated jointly with the following services:

External presentations, etc.

Introductory video

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Life Science Database Archive

Basic information

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https://dbarchive.biosciencedbc.jp/index-e.html

Outline

The Life Science Database Archive makes available to the public a variety of datasets produced by domestic and international researchers based on submissions from the producers of the data. We store research data, which is a shared asset for the human race, stably over the long term and keep it available to the public in a form in which it can be reused widely.
In addition to being available for bulk download, datasets can be simply viewed or searched using a browser.
With this service, we carry out the following initiatives in order to make it a model case for research data storage, sharing and publication:

  1. Provision of descriptions (metadata) of datasets in a unified format,
  2. Display of easy-to-understand terms of use using Creative Commons,
  3. Curation to provide formats and expressions that are easier for third parties to understand after careful examination of the research data by NBDC staff and consultation with the depositor when a dataset is deposited
  4. Addition of DOI to each dataset.

External presentations, etc.

Introductory video

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NBDC Human Database

Basic information

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https://humandbs.biosciencedbc.jp/en/

Outline

NBDC Human Database is a platform for promoting the sharing and use of research data on humans that takes the protection of personal information into consideration.
We conduct the following activities in cooperation with the Bioinformation and DDBJ Center at the National Institute of Genetics.

  • Development of guidelines for sharing data generated from human specimens
  • Investigation of domestic and international ethical/ legal/ social issues to harmonize rules for human data sharing
  • Submission, publication, and sharing of human data in a secure manner
  • Reviews by the Human Data Review Board on submitted data and use of controlled-access data

External presentations, etc.

Introductory video

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TogoVar

Basic information

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https://togovar.biosciencedbc.jp/

Outline

TogoVar (integrated database of Japanese genomic variation) is a database in which genome sequence differences between individuals (variants) in the Japanese population and the disease information associated with them are collected and organized.
This service provides genotype/allele on the frequencies in the Japanese population as an aggregation across research projects. JGA-NGS and JGA-SNP, which are the two available datasets, are frequencies data obtained by aggregating the individual genomic data submitted and published in the NBDC Human Database/Japanese Genotype-phenotype Archive (JGA). This service also integrates information related to genotypes and phenotypes compiled independently in a variety of different databases, and provides information to researchers studying genetics and genetic counselors so they are able to interpret variants in a one-stop, easy-to-understand manner.
This service was developed through collaborative research between NBDC and the Database Center for Life Science (DBCLS).

External presentations, etc.

Introductory video

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NBDC Group Sharing Database

Basic information

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https://gr-sharingdbs.biosciencedbc.jp/Only in Japanese

Outline

This is a platform for sharing data only for a project or group prior to the release of research data in concurrence with the publication of a report.

External presentations, etc.

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NBDC RDF Portal

Basic information

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https://integbio.jp/rdf/

Outline

The NBDC RDF Portal site provides life science databases in RDF format.
This service enables users to view overviews of RDF format life sciences data prepared by domestic research institutes. Using this service, for all datasets users can check who produced a dataset, the terms of use for a dataset, and the relationships between datasets, as well as search datasets using SPARQL language.
For the purpose of handling RDF data on a scale that is unprecedented globally, we examine back end systems and investigate and implement the datasets required for integrating and utilizing registered datasets.

External presentations, etc.

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PURL.jp

Basic information

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https://purl.biosciencedbc.jp/

Outline

This server is used to prepare and maintain Persistent Uniform Resource Locators (PURL).
PURL is a web address which functions as a permanent identifier to redirect to the original web resource. For example, by citing information on the web using PURL in the draft of a report, permanence can be guaranteed without concern for dead links within a report even if the URL of the address where the corresponding information is shown is changed after the report is published, as the PURL registrant for the corresponding information corrects the redirect destination.

External presentations, etc.

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HOWDY-R

Basic information

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https://howdy.biosciencedbc.jp/HOWDY-R/

Outline

This is an integrated database on human genome information which interrelates public databases on human genome information and enables integrated use of the information.
A keyword search displays items in each database that contain the keyword in an interrelated manner. The database interconnects outcomes related to Advanced Lifescience Information System (JST-ALIS) projects with the major public data available globally.
This is the successor site to HOWDY (http://howdy.biosciencedbc.jp/), an integrated database on human genome information.

External presentations, etc.

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TogoProt

Basic information

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https://togoprot.biosciencedbc.jp/R/

Outline

This is an integrated search system for databases related to proteins.
With a keyword search, a list of protein families is displayed on the menu first. By selecting the desired protein or family from the menu, the data and link for the protein (family) is displayed to enable the user to reach the intended database entry.

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Inquiries & opinions

Feel free to contact us if you have any questions about this website or the web-based services that NBDC provides or wish to consult with us regarding research data or databases.