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".
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)
| 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). 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.
| 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 intracellular 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"
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".
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Tag
You can narrow the records by tags described in the items "Tag - Target" and "Tag - Information type" (with multiple selections allowed).
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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].
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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".
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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.
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Others > Link to TogoTV
You can narrow the database records of databases which are provided movies in TogoTV.
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Others > DB with batch downloadable data
You can narrow the database records of databases which have batch downloadable data.