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INOH specifications


Unique identifier OMICS_12653
Alternative name Integrating Network Objects with Hierarchies
Restrictions to use None
Community driven No
Data access Browse, Application programming interface
User data submission Not allowed
Maintained No


This tool is not maintained anymore.

Publication for Integrating Network Objects with Hierarchies

INOH citations


Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T PLL

Nat Commun
PMCID: 5814445
PMID: 29449575
DOI: 10.1038/s41467-017-02688-6

[…] h Signaling Pathway” (Wikipathways), “TP53 Regulates Transcription of DNA Repair Genes” (Reactome), “TCR” (NetPath), “Interleukin-4 and −13 signaling” (Reactome), and “JAK STAT MolecularVariation 2” (INOH). […]


Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method

PMCID: 5696233
PMID: 29190967
DOI: 10.18632/oncotarget.21669
call_split See protocol

[…] hese collectively allowed for the most comprehensive and up to date annotation dataset to be used. Integrated pathway databases include BioCarta [], Edinburgh Human Metabolic Network [], HumanCyc [], INOH [], KEGG [], PharmGKB [], NCI Pathway Interaction Database [], Reactome [], SMPDB [], and WikiPathways []. Functions were obtained from the Gene Ontology []. […]


Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open angle glaucoma

PLoS One
PMCID: 5338784
PMID: 28264060
DOI: 10.1371/journal.pone.0172427

[…] case cohorts (HTG, NTG and all POAG) and all control groups. InnateDB is a publicly available platform incorporating major public domain pathway databases (including KEGG, Reactome, PID, Netpath and INOH). The database contains all human and mouse genes with their associated pathways and interactions. There is also improved annotation of the innate immunity interactome via manual curation. Genes […]


Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

PMCID: 4309023
PMID: 25632107
DOI: 10.1093/database/bau126

[…] EGG and BIOCARTA by the GOLD.db database developers. Similarly, InnateDB contains its own self-annotated pathway data and the imported pathway information from other resources, such as KEGG, NetPath, INOH, REACTOME and NCI-PID. It is also worth to mention that several other primary databases, such as Uniprot, Genbank, GO database, gene expression databases (GEO, EBI-Array Express) also annotate th […]


KB Rank: efficient protein structure and functional annotation identification via text query

J Struct Funct Genomics
PMCID: 3375009
PMID: 22270457
DOI: 10.1007/s10969-012-9125-7

[…]>. The following annotations are assembled. Cellular and biochemical pathway assignments were extracted from BioCyc [], CellMap [], HumanCyc [], INOH [], and the NCI Pathway Interaction Database (PID) []. Small molecule associations were from BioCyc, BindingDB [], HumanCyc, DrugBank [], ChEBI [], ChEMBL [], and SMPDB []. SNPs3D [] and OMIM [, […]


The BioLexicon: a large scale terminological resource for biomedical text mining

BMC Bioinformatics
PMCID: 3228855
PMID: 21992002
DOI: 10.1186/1471-2105-12-397

[…] ce in Man) [], ChEBI [,], Enzyme Nomenclature [], Sequence Ontology [], RegulonDB [], CORUM [], Operon Database (ODB) [], BioThesaurus [], the NCBI taxonomy [], InterPro [], TRANSFAC [] and the IMR - INOH Protein name/family name Ontology [].By far the largest categories of terms are gene and protein names, which have been gathered from BioThesaurus []. BioThesaurus consists of several million rec […]


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INOH institution(s)
Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kashiwa, Japan; Information and Mathematical Science Laboratory, Inc., Bunkyo, Japan; INTEC Inc., Koto, Japan; Intelligent Information Infrastructure Division, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan; Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan
INOH funding source(s)
Institute for Bioinformatics Research and Development (BIRD) of Japan Science and Technology Agency (JST)

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