March 29, 2011
INOH release 4.0 has been released (BioPAX Level2 and Level3 formats included).
The data files are available from our download site.
Signal Transduction Pathway Data and Metabolic Pathway Data.
Moreover, all INOH pathway diagram files are now available in BioPAX Level2 and Level3 formats.
Visit Download page and get each file separately or as a single archive.
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newly curated pathways
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BMP signaling in Drosophila
PDGF signaling pathway (Mammal)
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updated pathways
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TGF-beta_BMP Diagram(MolecularVariation)
Drosophila Toll-like receptor signaling
EGF signaling pathway Diagram (D. melanogaster, C. elegans)
FGF signaling pathway
IFN gamma signaling(JAK1 JAK2 STAT1)
IL-2 signaling(JAK1 JAK3 STAT5)
IL-4 signaling(JAK1 JAK3 STAT6)
IL-7 signaling(JAK1 JAK3 STAT5)
JAK STAT MolecularVariation 1
JAK-STAT pathway and regulation pathway Diagram (Canonical, D. melanogaster)
NGF signaling pathway
TGF-beta_super_family_signaling_pathway(canonical)
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
IL-1 signaling pathway (through JNK cascade)
IL-1 signaling pathway (through NF-kappaB)
IL-1 signaling pathway (through p38 cascade)
Toll-like receptor signaling pathway (through JNK cascade)
Toll-like receptor signaling pathway (trough NF-kappaB)
Toll-like receptor signaling pathway (p38 cascade)
CD4 T cell receptor signaling (ERK cascade)
CD4 T cell receptor signaling (JNK cascade)
CD4 T cell receptor signaling (NF-kB cascade)
CD4 T cell receptor signaling
GPCR signaling (G alpha s, PKA and ERK)
Notch signaling pathway Diagram (Canonical, Mammal, D. melanogaster, C. elegans)
JAK STAT MolecularVariation 2
Fas signaling pathway
GPCR Adenosine A2A receptor signaling pathway
TNFR1 signaling pathway
Alanine,Aspartic acid and Asparagine metabolism
Aminosugars metabolism
Arginine and Proline metabolism
Butanoate metabolism
Citrate cycle
FGF8 signaling (Mouse)
FGF8 signaling (Xenopus)
FGF signaling pathway (C. elegans)
FGF signaling pathway (D. melanogaster)
Folate metabolism
Fructose and Mannose metabolism
Galactose metabolism
Glutamic acid and Glutamine metabolism
Glycine and Serine metabolism
Glycolysis and Gluconeogenesis
Hedgehog signaling pathway (Canonical, Mammal, D. melanogaster)
Histidine degradation
IFN alpha signaling(JAK1 TYK2 STAT1 STAT2 STAT3)
IL-23 signaling(JAK2 TYK2 STAT3 STAT4)
Inositol phosphate metabolism
Lysine degradation
Methionine and Cysteine metabolism
Nicotinate and Nicotinamide metabolism
Pentose phosphate cycle
Phenylalanine degradation
Porphyrin metabolism
Propanoate metabolism
Prostaglandin and Leukotriene metabolism
Purine nucleotides and Nucleosides metabolism
Pyrimidine Nucleotides and Nucleosides metabolism
Pyruvate metabolism
Steroids metabolism
Tryptophan degradation
Tyrosine metabolism
Valine,Leucine and Isoleucine degradation
Insulin receptor signaling
Insulin receptor signaling (C. elegans)
Insulin receptor signaling (D. melanogaster)
Insulin receptor signaling (Mammal)
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BioPAX Level3 Statistics
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Pathway 857
PathwayStep 773
BiochemicalPathwayStep 3196
Control 162
Catalysis 2614
Modulation 0
TemplateReactionRegulation 31
Conversion 81
BiochemicalReaction 1740
TransportWithBiochemicalReaction 0
ComplexAssembly 1108
Degradation 31
Transport 236
GeneticInteraction 0
MolecularInteraction 0
TemplateReaction 152
Complex 5801
Dna 661
DnaRegion 0
Protein 14493
Rna 218
RnaRegion 0
SmallMolecule 4415
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INOH Statistics
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-- NODE --
Diagram 102
EventCompound 4066
Event 139
Process 3348
EventRelation 542
Protein 14493
MolecularComplexCompound 5479
MolecularComplex 45
DNACompound 277
DNA 661
ChemicalSubstance 4415
RNA 218
Terminal 34
-- EDGE --
IN 6056
OUT 5131
Control 193
Catalyze 2614
Connected 3721
PASSING 3341
HomologousEvent 466
MolecularVariation 257
Identical 62
Posted by HiromiNakamura : 02:39 PM | TrackBacks
MoleculeRole Ontology Ver.2.24
The latest MoleculeRole Ontology is Ver2.24
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
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All entries 9217
Chemicals 593
Proteins 8591
Obsoletes 32
UniProt ACs 5868
GO IDs 346
InterPro ACs 32
KEGG COMPOUND IDs 588
PubMed IDs 172
MoleculeRole Ontology Release Notes
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Version: 2.24 (Mar 4, 2011)
Molecule Role is a hierarchical ontology which contains the molecular functional group names, the abstract molecule names and the concrete molecule names collected from literature manually. This classification is based on a conceptual classification of molecular roles in protein interaction and signal transduction.
Changes from version 2.1x
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KEGG metabolic pathway related molecules (500~ chemicals and 300~ proteins) were added.
Changes from version 2.0x
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Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in an automatic way, using UniProt ACs manually collected in Molecule Role.
Changes from version 1.xx
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The ontologies and definitions are provided together in a single OBO format flat file. This data is NOT also available in the GO flat file format as an ontology file and a definitions file.
Protein sequences (=UniProt ACs) in the DbXrefs of protein leaf-class entries have been separated as new protein leaf-class entries. The parents-children relationship type is "sequence_of". The relationships of "Concrete-Names (e.g. ERK1)" and protein sequences (e.g. P27361) have been defined explicitly.
More information about MoleculeRole Ontology
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Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi, Ken Ichiro Fukuda. The Molecule Role Ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature. Comparative and Functional Genomics 2004 Volume 5, Issue 6-7, p 528-536. (http://www3.interscience.wiley.com/cgi-bin/fulltext/109860932/HTMLSTART)
Statistics
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All entries 9217
Chemicals 593
Proteins 8591
Obsoletes 32
UniProt ACs 5868
GO IDs 346
InterPro ACs 32
KEGG COMPOUND IDs 588
PubMed IDs 172
Posted by SatokoYamamoto : 12:13 PM | TrackBacks
March 23, 2011
Location Ontology Ver.1.02
The latest Location Ontology is Ver.1.02
Location Ontology is an ontology of cellular location.
You can browse or search this ontology at INOH Ontology Viewer and download it from our download page.
Statistics
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all entries 52
obsolete 2
definition 44
GO IDs 49
Location Ontology Release Notes
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Version: 1.02 (23th Mar, 2011)
Changes from version 1.01
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change the synonym type.
Statistics
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all entries 52
obsolete 2
definition 44
GO IDs 49
Posted by NorikoSakai : 04:03 PM | TrackBacks
Event Ontology Ver.1.72
The latest Event Ontology is Ver.1.72
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
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All entries 3828
Obsoletes 149
definition 681
IMR IDs 5765
GO IDs 539
KEGG Reaction IDs 618
KEGG map IDs 1192
Reactome IDs 136
PSI-MI IDs 71
Event Ontology Release Notes
=====================
Version: 1.72 (23th Mar, 2011)
Event Ontology is an ontology that organizes the concepts and terms of pathway objects such as sub-pathways, biological processes and experimental environments appearing in the cellular pathway (e.g. signal transductions, disease pathways, metabolic pathways, etc.) The concepts in the Event Ontology were manually extracted from scientific articles and text books. Each concept has a link to Gene Ontology if possible.
Changes from version 1.71
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1. add the terms related to BMP signaling pathway and PDGF signaling pathway.
2. link the INOH MoleculeRole ontology ID to the terms related to molecular interaction.
3. etc.
More information about Event Ontology
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Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event Ontology: A Pathway-Centric Ontology for Biological Processes. Pacific Symposium on Biocomputing 11:152-163(2006).
Statistics
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All entries 3828
Obsoletes 149
definition 681
IMR IDs 5765
GO IDs 539
KEGG Reaction IDs 618
KEGG map IDs 1192
Reactome IDs 136
PSI-MI IDs 71
Posted by NorikoSakai : 03:45 PM | TrackBacks
March 10, 2011
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 3.4.0 to 3.5.3.
Release Notes
======================
Version 3.5.3
Newly added and improved features:
- improved the node and edge's SVGs.
- added Protein nodes (pink node, green node, orange node, purple node, and the phosphorylated and modified nodes of these nodes).
- improved "Erros" check.
The "Passing edge" was able to be pulled only between nodes of the same type.
- "Overview Area" and "Magnifier View Area" is fixed 100% zoom.
bug fixes:
- layout problem after the server search.
Posted by HiromiNakamura : 06:04 PM | TrackBacks