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. 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".

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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)

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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)

Item	Description	Comment
Basics
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; 1.[Active] 2.[Inactive] 3.[Suspended] 4.[Closed] 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
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
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).
• Please note that the following tags may be changed or new tags are added as needed.

Tag	Description	EDAM, UBERON, ChEBI	Label in EDAM, UBERON, ChEBI
Target: the items on which the database contains information
Genome/Gene	DB for genomes or genes	EDAM / topic:3053	Genetics
cDNA/EST	DB for cDNAs or ESTs	EDAM / data:3134	Gene transcript report
Genetic variation	DB for genetic variations	EDAM / topic:0199	Genetic variation
Epigenetics	DB for epigenetics	EDAM / topic:3295	Epigenetics
DNA	DB for DNA	EDAM / topic:0654	DNA
RNA	DB for RNA	EDAM / topic:0099	RNA
Protein	DB for proteins	EDAM / topic:0078	Protein
Carbohydrate	DB for carbohydrates	CHEBI:16646	carbohydrate
Lipid	DB for lipids	CHEBI:18059	lipid
Metabolite	DB for metabolites	CHEBI:25212	metabolite
Chemical compound	DB for chemical compounds	CHEBI:24431	chemical entity
Drug	DB for drugs	CHEBI:23888	drug
Cell/Organelle	DB for cells or organelles	CL_0000000	cell
Organism	DB for organisms, ranging from their parts to populations	EDAM / data:2530	Organism report
Health/Disease	DB for health or disease	EDAM / topic:0634	Pathology
Information type: the type of information available
Phenotype	DB for phenotypes or traits	EDAM / data:0920	Genotype/phenotype report
Bioresource	DB for bioresources	EDAM / topic:3277	Sample collections
Method	DB for experimental or analytical methods	EDAM / data:2531	Protocol
Ontology/Terminology/Nomenclature	DB for ontology, terminology or nomenclature	EDAM / topic:0089	Ontology and terminology
Environment	DB for environments	EDAM / data:3736	Ecological data
Sequence	DB for sequences of nucleic acids or amino acids	EDAM / data:2044	Sequence
3D structure	DB for 3D structures	EDAM / data:0883	Structure
Chemical structure	DB for chemical structures	EDAM / data:0883	Structure
Expression	DB for expression or accumulation of transcripts or proteins	EDAM / data:2603	Expression data
Localization (ex-Distribution)	DB for localization	GO:0051179	localization
Geographic location (ex-Distribution)	DB for geographic location	EDAM / data:3720	Geographic location
Interaction/Pathway	DB for interactions or pathways	EDAM / topic:0602	Molecular interactions, pathways and networks
Taxonomy	DB for classification of organisms	EDAM / data:1872	Taxonomic classification
Classification	DB for classification of molecules	EDAM / operation:2990	Classification
Image/Movie	DB for images or movies	EDAM / data:2968	Image
Bibliography/Documents	DB for collections of bibliographies or documents	EDAM / data:2526	Text data
Portal	DB for collections of databases or bioinformatic tools	-	-
Repository	DB 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"

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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.

• Keyword

  You can search by keyword.

• Exact match of DB name

  You can perform an exact match search for database names.

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 two types of statuses : [Suspended] or [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.