RIKEN Metabolome MetaDatabase is an integrated metabolome data repository based on the semantic web.

SPARQL
endpoint RIKEN
Database
Directory

1

Faceted Navigation (for databases with metadata)

  • Species
  • Theme
  • Publisher
  • DataType
BFOhttp://metadb.riken.jp/metabo/ontology/BFO

The Basic Formal Ontology (BFO)
(Original site: http://ifomis.uni-saarland.de/bfo/)

BIBOhttp://metadb.riken.jp/metabo/ontology/BIBO

Bibliographic Ontology
(Original site: http://bibliontology.com/)

CELLhttp://metadb.riken.jp/metabo/ontology/CELL

CELL

CHMOhttp://metadb.riken.jp/metabo/ontology/CHMO

Chemical Methods Ontology
(Original site: http://purl.obolibrary.org/obo/chmo.owl)

ChEBIhttp://metadb.riken.jp/metabo/ontology/ChEBI

Chemical Entities of Biological Interest (ChEBI)
(Original site: http://www.ebi.ac.uk/chebi/)

DDBJ-DRAhttp://metadb.riken.jp/metabo/ontology/DDBJ-DRA

DDBJ-DRA

EFOhttp://metadb.riken.jp/metabo/ontology/EFO

Experimental Factor Ontology
(Original site: https://www.ebi.ac.uk/efo/)

ENVOhttp://metadb.riken.jp/metabo/ontology/ENVO

Environment Ontology
(Original site: http://purl.bioontology.org/ontology/ENVO)

EOhttp://metadb.riken.jp/metabo/ontology/EO

Plant Environment Ontology

FALDOhttp://metadb.riken.jp/metabo/ontology/FALDO

Feature Annotation Location Description Ontology
(Original site: https://github.com/JervenBolleman/FALDO)

GOhttp://metadb.riken.jp/metabo/ontology/GO

Gene Ontology (GO)
(Original site: http://geneontology.org)

GR_taxhttp://metadb.riken.jp/metabo/ontology/GR_tax

Gramine Taxonomy Ontology

IAOhttp://metadb.riken.jp/metabo/ontology/IAO

Information Artifact Ontology
(Original site: http://purl.obolibrary.org/obo/iao)

ISAhttp://metadb.riken.jp/metabo/ontology/ISA

Investigation/Study/Assay
(Original site: http://isa-tools.org/)

LUhttp://metadb.riken.jp/metabo/ontology/LU

Left Unit Ontology
(Original site: http://metadb.riken.jp/db/LU)

MCCVhttp://metadb.riken.jp/metabo/ontology/MCCV

Microbial Culture Collection Vocabulary (MCCV)
(Original site: http://bioportal.bioontology.org/ontology/MCCV?p=classes&conceptid=root)

MEOhttp://metadb.riken.jp/metabo/ontology/MEO

Metagenome and Microbes Environmental Ontology
(Original site: http://bioportal.bioontology.org/ontologies/MEO)

MMOhttp://metadb.riken.jp/metabo/ontology/MMO

Measurement Method Ontology
(Original site: http://sourceforge.net/projects/phenoonto/)

MPOhttp://metadb.riken.jp/metabo/ontology/MPO

Microbial Phenotype Ontology (MPO)
(Original site: http://bioportal.bioontology.org/ontologies/MPO/?p=summary)

NCBITaxonhttp://metadb.riken.jp/metabo/ontology/NCBITaxon

NCBI Organismal Classification (NCBITaxon)
(Original site: http://wiki.obofoundry.org/wiki/index.php/NCBITaxon:Main_Page)

OBIhttp://metadb.riken.jp/metabo/ontology/OBI

Ontology for Biomedical Investigations
(Original site: http://purl.obolibrary.org/obo/obi)

PATOhttp://metadb.riken.jp/metabo/ontology/PATO

Phenotypic Quality (PATO)
(Original site: http://wiki.obofoundry.org/wiki/index.php/PATO:Main_Page)

PCThttp://metadb.riken.jp/metabo/ontology/PCT

PCT

POhttp://metadb.riken.jp/metabo/ontology/PO

Plant Ontology
(Original site: http://planteome.org)

ROhttp://metadb.riken.jp/metabo/ontology/RO

OBO-relation ontology (RO)
(Original site: https://code.google.com/p/obo-relations/)

SIOhttp://metadb.riken.jp/metabo/ontology/SIO

Semanticscience Integrated Ontology
(Original site: http://semanticscience.org)

SOhttp://metadb.riken.jp/metabo/ontology/SO

The Sequence Ontology
(Original site: http://www.sequenceontology.org/)

STATOhttp://metadb.riken.jp/metabo/ontology/STATO

Statistics Ontology
(Original site: http://stato-ontology.org/)

TOhttp://metadb.riken.jp/metabo/ontology/TO

Trait Ontology (TO)

UOhttp://metadb.riken.jp/metabo/ontology/UO

Units of Measurement (UO)
(Original site: https://code.google.com/p/unit-ontology/)

About RIKEN Meta Database

This database portal site is used to provide information on RIKEN's various life science databases to order to help researchers around the world make full use of RIKEN's research results.

The database provides life-science data in the bases of standardized metadata techniques including semantic web and Resource Description Framework (RDF).

W3C Dataset Descriptions: HCLS Community Profile
HCLSProfile_MataDB_ALL.ttl

Long-term recommendations for RIKEN's life sciences database platform (final report)

The direction and implementation guidelines for RIKEN databases and metadata maintenance have been discussed at the Database Working Group established within the Bioinformatics Exploratory Committee which examines technologies related to RIKEN's bioinformatics. The result of the discussion was summarized as 'Long-term recommendations for RIKEN's life sciences database platform (final report)'. The RIKEN MetaDatabase has been developed and published based on this recommendation.

Download the PDF file: LongTermRecommendataions_e.pdf