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
======================
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)

Continue reading"INOH release 4.0 has been released (BioPAX Level2 and Level3 formats included)."

Posted by HiromiNakamura : 02:39 PM | TrackBacks (0)

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
==========
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

Continue reading"MoleculeRole Ontology Ver.2.24"

Posted by SatokoYamamoto : 12:13 PM | TrackBacks (0)

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
==========
all entries 52
obsolete 2
definition 44

GO IDs 49

Continue reading"Location Ontology Ver.1.02"

Posted by NorikoSakai : 04:03 PM | TrackBacks (0)

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
==========
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

Continue reading"Event Ontology Ver.1.72"

Posted by NorikoSakai : 03:45 PM | TrackBacks (0)

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.

Continue reading"INOH client application new version is available!"

Posted by HiromiNakamura : 06:04 PM | TrackBacks (0)

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