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Database name ⇅	DOI ⇅	Database classification ⇅	Organism ⇅	Database description ⇅	Features and manner of utilization of database ⇅	Database maintenance site ⇅	License ⇅
INOH (Integrating Network Objects with Hierarchies)	10.18908/lsdba.nbdc00107-000.V003	Metabolic and Signaling Pathways - Metabolic pathways Metabolic and Signaling Pathways - Protein-protein interactions Metabolic and Signaling Pathways - Signalling pathways		INOH database is a highly structured, manually curated database of signal transduction pathways. The database focuses on curating and encoding textual knowledge in scientific articles into a machine-processable form.	INOH database provides signal transduction pathway data which is well-annotated by the INOH ontology terms. INOH curators who have a biological background created pathways and annotated every pathway component by a set of uniquely developed ontologies. The INOH Client tool, which is a pathway navigation/editor tool, is freely downloadable. INOH pathway diagrams are freely available in INOH XML and BioPAX formats.	The Institute of Medical Science, The University of Tokyo *The original website was terminated.	CC BY-SA
PGDBj Registered plant list, Marker list, QTL list, Plant DB link & Genome analysis methods (PGDBj Marker, Map and Basic Information)	10.18908/lsdba.nbdc01194-01-000.V003	Plant Databases Nucleotide Sequence Databases Genomics Databases (non-vertabrate) Database Catalog		DNA marker and gene map are used for useful gene identification with gene analysis, genome structure comparison and application researches such as marker selective breeding and DNA fingerprinting. We have selected 65 plants (mainly horticultural crop) and aggregated and marshalled their DNA markers (65 plants), QTLs related with important agronomic trait and gene maps (45 plants) from articles and other databases. We published the results in this database. We have also aggregated, marshalled and published basic information, gene analysis method and links to related web sites about 80 plants.	Information of DNA markers and QTLs are curated manually from the published literature. The marker information includes marker sequences, genotyping methods, population and linkage map, and the results of population genetic analyses. The QTL information includes the genetic effects, chromosomal positions, and LOD scores. Website links are classified according to the content (e.g. Genome database and Expression database). User can search information about DNA marker, QTL, and website links by keywords such as marker name, agricultural trait, and classification of website links.	Kazusa DNA Research Institute	CC BY-SA
GENIUS II	10.18908/lsdba.nbdc00471-000	Protein sequence databases	Archaea (2157) Bacteria (2) Eukaryota (2759)	GENIUS II is an automated database system in which protein coding regions in complete genomes are assigned to known three-dimensional structures.		National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront *The original website was terminated.	CC BY-SA
GRIPDB (GPCRs Interaction Partners Database)	10.18908/lsdba.nbdc01665-000	Protein sequence databases - Protein sequence motifs and active sites Protein sequence databases - Databases of individual protein families Structure Databases - Protein structure	Homo Sapiens (9606)	GRIPDB provides information about GPCR oligomerization. The entries in the database are divided into two sections: (I) Experiment Information section and (II) Prediction Information section. The Experiment Information section contains (I-i) experimentally indentified GPCR oligomers and their annotations, and (I-ii) experimentally suggested interfaces for the oligomerization.The entries for the Prediction Information section provide the interface residues or regions predicted by computational methods. The details of the entries in both sections are described below.	The information in the GRIPDB, especially that about the interfaces, is useful to investigate the molecular mechanisms of signal transduction via GPCR oligomerization.	National Institute of Industrial Science and Technology (AIST), Tokyo Waterfront *The original website was terminated.	CC BY-SA
MicrobeDB.jp	10.18908/lsdba.nbdc01181-000.V002	Integrated database of microbiological	Archaea (2157) Bacteria (2) Fungi (4751)	MicrobeDB.jp is an integrated database of several microbiological datasets (e.g., genes, taxa, and environments) using semantic web technology with a gene/genome -centric approach.	MicrobeDB.jp version 2 (doi: 10.18908/lsdba.nbdc01181-000.V002) is an updated version of MicrobeDB.jp version 1 (doi: 10.18908/lsdba.nbdc01181-000.V001). Since version 1 contains microbial genome, ortholog, metagenome, and culture collection data that were obtained before 2013, we updated these data with reorganizing RDF data structures. Microbial environmental ontology and other ontologies were also updated. These ontologies were used for annotation of the data. The data format of MicrobeDB.jp version 2 are RDF and OWL. Users can use these data by (i) loading the data to Triplestore, and (ii) searching the data using SPARQL.	National Institute of Technology	CC BY-SA
Database name	DOI	Database classification	Organism	Database description	Features and manner of utilization of database	Database maintenance site	License