January 06, 2011
Similarity Search service of INOH client is available!!
We have developed a prototype web tool that accepts a graph query, whose nodes and edges are proteins and their relations respectively or "Event" and their connections respectively, searches the pathway/network data for the similar subgraphs on INOH.
This tool is designed on the assumption that a pathway/network query is submitted through the INOH client tool.
Please install the INOH client tool and the INOH pathway dataset from this site.
Continue reading"Similarity Search service of INOH client is available!!"
Posted by HiromiNakamura : 06:46 PM | TrackBacks (0)
INOH client application new version is available!
Our new INOH Client is now available.
Windows, Max OSX and Linux are supported.
JRE 6.0 is required.
You can download INOH client application from here.
The version number is updated from 3.1.9 to 3.4.0.
Continue reading"INOH client application new version is available!"
Posted by HiromiNakamura : 06:37 PM | TrackBacks (0)
June 14, 2010
Event Ontology Ver.1.71
The latest Event Ontology is Ver.1.71
Event Ontology is an ontology of pathways.
It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
You can browse or search this ontology at INOH Ontology Viewer and download it from the OBO site and from our download page.
Statistics
==========
All entries 3775
Obsoletes 149
definition 652
GO IDs 516
KEGG Reaction IDs 596
KEGG map IDs 1179
Reactome IDs 110
PSI-MI IDs 70
Continue reading"Event Ontology Ver.1.71"
Posted by NorikoSakai : 04:15 PM | TrackBacks (0)
June 03, 2010
INOH release 3.0 has been released (BioPAX format included)
The data files are available from our download site.
Signal Transduction Pathway Data and Metabolic Pathway Data.
======================
newly curated pathways
======================
Hedgehog signaling pathway
Mammal
D.melanogaster
Canonical
Insulin signaling pathway
Mammal
D.melanogaster
C.elegans
Canonical
Jak-STAT signaling pathway
D.melanogaster
EGF signaling pathway
D.melanogaster
C.elegans
FGF signaling pathway
Mouse
Xenopus
D.melanogaster
C.elegans
IGF signaling pathway
Canonical
IL-5 signaling(JAK1 JAK2 STAT1 STAT5)
Canonical
IL-13 signaling(JAK1 TYK2 STAT6)
Canonical
IL-23 signaling(JAK2 TYK2 STAT3 STAT4)
Canonical
======================
Metabolic pathways
======================
Alanine_Aspartate_Asparagine_metabolism
Aminosugars_metabolism
Arginine_Proline_metabolism
Butanoate_metabolism
Citrate_cycle
Folate_metabolism
Fructose_Mannose_metabolism
Galactose_metabolism
Glutamate_Glutamine_metabolism
Glycine_Serine_metabolism
Glycolysis_Gluconeogenesis
Histidine_degradation
Inositol_phosphate_metabolism
Lysine_degradation
Methionine_Cysteine_metabolism
Nicotinate_Nicotinamide_metabolism
Pentose_phosphate_cycle
Phenylalanine_degradation
Porphyrin_metabolism
Propanoate_metabolism
Prostaglandin_Leukotriene_metabolism
Purine_nucleotides_nucleosides_metabolism
Pyrimidine_nucleotides_nucleosides_metabolism
Pyruvate_metabolism
Steroids_metabolism
Tryptophan_degradation
Tyrosine_metabolism
Valine_Leucine_Isoleucine_degradation
Vitamin_B6_metabolism
=================
updated pathways
=================
B cell receptor signaling
BMP2 signaling(TGF-beta_signaling MolecularVariation)
BMP2 signaling(through TAK1)
CD4 T cell receptor signaling (JNK cascade)
CD4 T cell receptor signaling (NF-kB cascade)
CD4 T cell receptor signaling (ERK cascade)
CD4 T cell receptor signaling
Drosophila IMD pathway
Drosophila Toll-like receptor signaling
EGF signaling pathway
EPO signaling pathway(JAK2 STAT1 STAT3 STAT5)
Fas signaling pathway
FGF signaling pathway
GPCR Adenosine A2A receptor signaling
GPCR Dopamine D1like receptor
GPCR GroupI metabotropic glutamate receptor
GPCR signaling (G alpha i)
GPCR signaling (G alpha q)
GPCR signaling (G alpha s, Epac and ERK)
GPCR signaling (G alpha s, PKA and ERK)
GPCR signaling (cholera toxin)
GPCR signaling (pertussis toxin)
Growth hormone signaling(JAK2 STAT5)
HGF signaling pathway
IFN alpha signaling
IFN gamma signaling(JAK1 JAK2 STAT1)
IL-10 signaling(JAK1 TYK2 STAT3)
IL-12 signaling(JAK2 TYK2 STAT4)
IL-1 signaling pathway (through JNK cascade)
IL-1 signaling pathway (through NF-kappaB)
IL-1 signaling pathway (through p38 cascade)
IL-2 signaling(JAK1 JAK3 STAT5)
IL-3 signaling(JAK1 JAK2 STAT5)
IL-4 signaling(JAK1 JAK3 STAT6)
IL-6 signaling(JAK1 JAK2 STAT3)
IL-7 signaling(JAK1 JAK3 STAT5)
Integrin signaling pathway
JAK STAT MolecularVariation 1
JAK STAT MolecularVariation 2
JAK-STAT pathway and regulation pathway
LIF signaling(JAK1 JAK2 STAT3)
NGF signaling pathway
Notch signaling pathway Diagram
PDGF signaling pathway
TGF-beta signaling(through TAK1)
TGF-beta_super_family_signaling_pathway(canonical)
Toll-like receptor signaling pathway (through ECSIT, MEKK1, MKKs, JNK cascade)
Toll-like receptor signaling pathway (through ECSIT, MEKK1, MKKs, p38 cascade)
Toll-like receptor signaling pathway (through JNK cascade)
Toll-like receptor signaling pathway (p38 cascade)
Toll-like receptor signaling pathway (trough NF-kappaB)
TNFR1 signaling pathway
TPO signaling (JAK2 STAT3)
VEGF signaling pathway
C. elegans endoderm induction Wnt signaling pathway Diagram
Canonical Wnt signaling pathway Diagram
Drosophila Wingless/Wnt signaling pathway Diagram
Mammalian Wnt signaling pathway Diagram
Xenopus axis formation Wnt signaling pathway Diagram
Continue reading"INOH release 3.0 has been released (BioPAX format included)"
Posted by HiromiNakamura : 03:50 PM | TrackBacks (0)
June 01, 2010
MoleculeRole Ontology Ver.2.23
The latest MoleculeRole Ontology is Ver2.23
MoleculeRole Ontology is an ontology for proteins/chemicals.
It is used to annotate protein family names, generic/concrete protein names and chemical names in the INOH pathway data.
You can browse or search this ontology at INOH Ontology Viewer and download it from the OBO site and from our download page.
Statistics
==========
All entries 9132
Chemicals 593
Proteins 8538
Definition 250
UniProt ACs 5823
GO IDs 347
InterPro ACs 32
KEGG COMPOUND IDs 588
PubMed IDs 160
Continue reading"MoleculeRole Ontology Ver.2.23"
Posted by SatokoYamamoto : 03:23 PM | TrackBacks (0)
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