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. From 2017, we started to collaborate between FAIRsharing with the view to transmit information of databases developed in Japan to the world and to get information of databases developed in other countries. For more information on FAIRsharing, please refer to the "Relevant Resources".

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. Moreover, we also collect information of databases those are developed in other countries by cooperation between FAIRsharing and Integbio Database Catalog.

* In the Integbio Database Catalog, there are two types of record, which are the records created and maintained by Integbio Database Catalog and the records derived from FAIRsharing.org's records. Please note that: these two types of record comply with different licenses. It is needed for users to read 'Terms of Use' before use. Users can distinguish these two types of record in the 'Record source' item on each 'Database Record' page.


Existing database lists merged into this catalog

  • Database Catalog (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
  • FAIRsharing.org_Databases (FAIRsharing.org)

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)

ID NBDC ID Database ID of NBDC
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 description  
Organism(s) covered NCBI Taxonomy names and IDs covered by the database  
Tag - Target Tag to indicate targets for this database such as genome and protein See the list of tags below.
Tag - Information type Tag to indicate information types for this database such as sequence and structure See the list of tags below.
Reference(s) (PubMed ID/DOI) PubMed ID / DOI 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;
The status information is updated automatically on a daily basis except for the status [Suspended] and [Closed].
Link(s) to Downloadable data Links to downloadable data of the database This download sites are in the original database
Link(s) to Metadata of downloadable data Links to metadata of the downloadable data  
Link(s) to Terms of use Link to a page described license of the database  
Link(s) to How to use Link to a page described "How to use" about the database  
Contact information of database Link to a page described contact information of the database, or the e-mail address Please convert '[at]' into '@', and '[dot]' into '.' in e-mail address.
Link(s) to API / SPARQL endpoint Link to a page described API / SPARQL endopoint those are provided or recommended by the database maintainer  
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  
Link to TogoTV Link to TogoTV of the Database Center for Life Science (DBCLS) TogoTV provides movies related to Databases.
Link to FAIRsharing Link to FAIRsharing  
Similar databases Names of databases showed the analogy It was the result of our similarity analysis.
About the database record
Record maintainer Record maintainer For record maintainer information of the records derived from FAIRshariing, see the corresponding part in the record in FAIRshariing.
Record source Source of the record Integbio Database Catalog or FAIRsharing.org (date of the data downloaded from the FAIRsharing)
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  
Record license License of this record (database information) Note that this license is not for database itself

List of tags

  • Tags 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 tags may be assigned based on descriptions of the database records.
  • The Vocabulary for Integbio Database Catalog provides a set of vocabularies that describe individual databases collected in the Integbio Database Catalog. Contributors*
  • For each tag, the same meaning from the three ontologies EDAM, UBERON, and ChEBI are listed together. However, ontology-derived tags are not assigned to tags that describe the nature of the DB (portal, repository). Contributors**
  • The "Distribution" tag has been split into two tags, "Localization" and "Geographic Distribution" (2023.12.30). Existing records that have been assigned "Distribution" will be addressed in due course.
  • Please note that the following tags may be changed or new tags are added as needed.
Target: the items on which the database contains information
Genome/GeneDB for genomes or genesEDAM / topic:3053Genetics
cDNA/ESTDB for cDNAs or ESTsEDAM / data:3134Gene transcript report
Genetic variationDB for genetic variationsEDAM / topic:0199Genetic variation
EpigeneticsDB for epigeneticsEDAM / topic:3295Epigenetics
DNADB for DNAEDAM / topic:0654DNA
RNADB for RNAEDAM / topic:0099RNA
ProteinDB for proteinsEDAM / topic:0078Protein
CarbohydrateDB for carbohydratesCHEBI:16646carbohydrate
LipidDB for lipidsCHEBI:18059lipid
MetaboliteDB for metabolitesCHEBI:25212metabolite
Chemical compoundDB for chemical compoundsCHEBI:24431chemical entity
DrugDB for drugsCHEBI:23888drug
Cell/OrganelleDB for cells or organellesCL_0000000cell
OrganismDB for organisms, ranging from their parts to populationsEDAM / data:2530Organism report
Health/DiseaseDB for health or diseaseEDAM / topic:0634Pathology
Information type: the type of information available
PhenotypeDB for phenotypes or traitsEDAM / data:0920Genotype/phenotype report
BioresourceDB for bioresourcesEDAM / topic:3277Sample collections
MethodDB for experimental or analytical methods EDAM / data:2531Protocol
Ontology/Terminology/NomenclatureDB for ontology, terminology or nomenclatureEDAM / topic:0089Ontology and terminology
EnvironmentDB for environmentsEDAM / data:3736Ecological data
SequenceDB for sequences of nucleic acids or amino acidsEDAM / data:2044Sequence
3D structureDB for 3D structuresEDAM / data:0883Structure
Chemical structureDB for chemical structuresEDAM / data:0883Structure
ExpressionDB for expression or accumulation of transcripts or proteinsEDAM / data:2603Expression data
Localization (ex-Distribution)DB for intracellular localizationGO:0051179localization
Geographic location (ex-Distribution)DB for geographic locationEDAM / data:3720Geographic location
Interaction/PathwayDB for interactions or pathwaysEDAM / topic:0602Molecular interactions, pathways and networks
TaxonomyDB for classification of organismsEDAM / data:1872Taxonomic classification
ClassificationDB for classification of moleculesEDAM / operation:2990Classification
Image/MovieDB for images or moviesEDAM / data:2968Image
Bibliography/DocumentsDB for collections of bibliographies or documentsEDAM / data:2526Text data
PortalDB for collections of databases or bioinformatic tools--
RepositoryDB with repository function or repository site of data--
  • Contributors*: "Asuka Bando", "Hideki Hatanaka", "Hiroshi Masuya", "Issaku Yamada", "Mari Minowa", "Norio Kobayashi", "Shuichi Kawashima", "Takatomo Fujisawa", "Tomoe Nobusada", "Toshiaki Katayama"
  • Contributors**: "Saya Katagiri", "Takahiro Ide", "Takatomo Fujisawa", "Tomoe Nobusada", "Yasutomo Yamamoto", "Yuka Tateishi"

Search functions

Integbio Database Catalog provides the following search functions to make it easier 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".

  • Tag

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

  • Operational status

    You can narrow the records by four types of statuses : [Active], [Inactive], [Suspended] or [Closed]. The status information is updated automatically on a daily basis except for the status [Suspended] and [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 > Link to TogoTV

    You can narrow the database records of databases which are provided movies in TogoTV.

  • Others > DB with batch downloadable data

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