About

 

What is Integbio Database Catalog?

Integbio Database Catalog provides whereabouts information (URL), database description, biological species and other attributes (metadata) of Japanese and international life science databases to make it easier for users to find databases they need. This catalog has been developed as a part of the integration of life science databases promoted by four ministries in Japan: the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), The Ministry of Health, Labor, and Welfare (MHLW), the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and the Ministry of Economy, Trade, and Industry of Japan (METI). See integbio.jp for details regarding our efforts toward the integration of life science databases.


Scope of this catalog

We already merged the following four ministries' existing database lists into Integbio Database Catalog according to the uniformed description items we defined for this catalog (See "Description items of database records" below). We continue to expand the catalog toward our goal of covering all life science databases developed within Japan across ministries and disciplines.

 

Existing database lists merged into this catalog

  • Database Catalog (National Bioscience Database Center [NBDC])

    - This service was developed by the Database Center for Life Science (DBCLS) as a part of the "Integrated Database Project" funded by MEXT and is now being provided by NBDC since April 1st, 2011.

    - Some of the contents of “Database Catalog” are based on a report that investigated the situation of life science databases published in 2008 to the Council for Science and Technology Policy funded by the Special Coordination Funds for the promotion of Science and Technology.

  • WINGpro (NBDC)
  • MEDALS Database Catalog (METI Database portal for Life Science)
  • AgrID Database Catalog (AgrID - Agrigenomics Information Database) *Japanese version only
  • National Institute of Biomedical Innovation database list (National Institute of Biomedical Innovation) *Japanese version only

As for databases in countries other than Japan, this catalog deals mainly with databases published in academic journals.


Creation of database records

Database records of this catalog are created by the project members, based on publicly available information.

Description items of database records (Example: KNApSAck Family)

ItemDescriptionComment
Basics
Database name Name of the database  
Alternative name Alternative name of the database  
URL URL of the database  
Database maintenance site Site maintaining the database  
Country/Region Country or region name where the database maintenance site is located We use the term "Global" for a case that it is difficult to assign a specific country because the database is maintained by consortium, etc..
Database description Database descirption *English version is now in preparation.
Organism(s) covered NCBI Taxonomy names and IDs covered by the database  
Category - Target Category to indicate targets for this database such as genome and protein See the list of categories below.
Category - Information type Category to indicate information types for this database such as sequence and structure See the list of categories below.
Reference(s) - PubMed ID PubMed IDs for papers related to the database Please note that this item is basically for literatures reported about database development but also can include ones related other topics.
Language(s) Languages in which the contents of the database are displayed  
Operational status Operational status for the database Three types of statuses are provided;
1.【Active】
2.【Inactive】
3.【Closed】
The status information is updated automatically on a daily basis except for the status【Closed】.
Extensions
Link to LSDB Archive Link to LSDB Archive You can download the whole dataset through this LSDB Archive.
Link to MEDALS Database catalog Link to MEDALS Database catalog of the METI database portal for life science  
Links to downloadable data Links to downloadable data of the database This download sites are in the original database
Metadata of downloadable data Links to metadata of the downloadable data  
Terms of use of downloadable data Links to terms of use of the downloadable data  
About the database record
Date of creation of this record Date of creation of this English record  
Last update date of this record Last update date of this English record  

List of categories

  • Categories are assigned to each database manually by NBDC staff members (with multiple selections allowed).
  • When a database is not available for reasons such as website closures, the categories may be assigned based on descriptions of the database records.
  • We refer to existing category or keyword systems already used by other database catalog services, including BioMed Central Databases for making the following categories.
  • Please note that the following categories may be changed or new categories are added as needed.
CategoryDescription
Target: the items on which the database contains information
Genome Whole genome sequences or structures
Gene Sequences, properties and functions of genes
cDNA cDNA sequences and librariess
Tag sequence (nucleic acid) Sequences and libraries for tag sequences (EST, STS, SAGE, etc.)
Polymorphism Genetic variations (SNP, etc.)
Other DNA Structures, properties and functions of DNA, which do not fall under any categories above
RNA Sequences, structures, properties and functions of RNA
Protein Sequences, structures, properties and functions of proteins
Enzyme As for "Protein" and "RNA", but with a focus on catalytic molecules
Other biomolecule Structures, properties and functions of biomolecules that do not fall under the categories of DNA, RNA, Protein or Enzyme (including glycan-related molecules, lipids and secondary metabolites)
Drug/Chemical Information about chemicals such as drugs and low-molecular-weight compounds
Cell Structures, properties and functions of cells
Organism Features and properties of species/individuals of organisms
Health/Disease
  • Disease phenotypes and epidemiology, the genetic basis of disease and animal models of human disease
  • Information about health and nutrition
Others Not under any categories above
Under survey Difficult to assign categories for reasons such as website closures
Information type: the type of information available
Sequence Amino acid and nucleotide sequence data
Structure Chemical and three-dimensional structures of biological and biologically active molecules
Gene expression Localization and levels of gene expression in cells, tissues and whole organisms
Interaction/Pathway
  • The physical or genetic interactions between molecules
  • A series of chemical reactions occuring within a cell
Phylogeny/Classification Evolutionary relationships and classifications of molecules and organisms
Image/Movie Visual materials of research or educational value
Ontology/ Terminology/Nomenclature
  • Source databases for the development and management of controlled vocabularies and ontologies
  • Nomenclatures of processes, molecules and organisms
Journal article/Report/Bibliography
  • Article repositories, protocols, manuals and reports of survey
  • Bibliographic databases
Bioresource Bioresources and stock centers for DNA clones, cells and whole organisms
Others Not under any categories above
Under survey Difficult to assign categories for reasons such as website closures

Search functions

Integbio Database Catalog provides the following search functions to make it eaiser for users to find the database records.


Search the records

You can search the contents of the database records by keyword.

Narrow the records by...

You can narrow the database records by the following conditions based on each description item of the database record. Please refer to Creation of database records for the description items of the database records.

  • Organism covered

    You can narrow the records based on NCBI taxonomy entries described in the item "Organism covered".

  • Category

    You can narrow the records by categories described in the items "Category - Target" and "Category - Information type" (with multiple selections allowed).

  • Operational status

    You can narrow the records by three types of statuses : [Active], [Inactive], [Closed]. The status information is updated automatically on a daily basis except for the status [Closed].

  • Region

    You can narrow the records by two types of conditions: [Japan] and [Countries other than Japan] based on country or region names described in the item "Country/Region".

  • Others > DB in LSDB Archive

    You can narrow the database records which have links to LSDB Archive. You can download the whole datasets through LSDB Archive.

  • Others > DB with batch downloadable data

    You can narrow the database records of databases which have batch downloadable data.