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November 30, 2007
INOH release 2.0 has been released (BioPAX format included)
The data files are available from our download site.
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newly curated pathways
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EPO signaling pathway(JAK2 STAT1 STAT3 STAT5)
Fas signaling pathway
GPCR Adenosine A2A receptor signaling pathway
TNFR1 signaling pathway
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updated pathways
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BMP2 signaling(through TAK1)
BMP2 signaling(TGF-beta_signaling MolecularVariation)
B cell receptor signaling
CD4 T cell receptor signaling (JNK cascade)
CD4 T cell receptor signaling (NF-kB cascade)
CD4 T cell receptor signaling
Drosophila IMD pathway
Drosophila Toll-like receptor signaling
EGF signaling pathway
FGF signaling pathway
GPCR Dopamine D1like receptor signaling pathway
GPCR GroupI metabotropic glutamate receptor signaling pathway
GPCR signaling (cholera toxin)
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 (pertussis toxin)
Growth hormone signaling(JAK2 STAT5)
HGF signaling pathway
IFN gamma signaling(JAK1 JAK2 STAT1)
IL-10 signaling(JAK1 TYK2 STAT3)
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
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 (trough NF-kappaB)
Toll-like receptor signaling pathway (p38 cascade)
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
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New ID system (INOHID)
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INOHID,secondaryINOHID have been introduced.
Mapping table of old MatID and INOHID is available from here.
INOHID starts with P/I/M followed by an integer.
Each letter ("P"/"I"/"M") stands for a pathway object, interaction, physicalEntity respectively.
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BioPAX Level2 enhancement
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Based on the UriCvNamespace Proposal for BioPAX Level2, the BioPAX main file loads an extension ontology to add properties not available in Level2. (further documentation : INOH worked examples for this proposal)
added new property pathway -MOLECULAR-VARIATION -> pathway,pathwayStep
added new property pathway -HOMOLOGOUS-EVENT -> pathway,pathwayStep
added new property pathwayStep -MOLECULAR-VARIATION -> pathway,pathwayStep
added new property pathwayStep -HOMOLOGOUS-EVENT -> pathway,pathwayStep
added new property control -CONTROLLER-EVENT -> pathway,pathwayStep
added new property control -CONTROLLED-EVENT -> pathway,pathwayStep
added new property physicalEntityParticipant -GENERIC-EVIDENCE -> evidence
added new property physicalEntityParticipant -LOCATIONONTOLOGY-EVIDENCE -> evidence
added new property sequenceFeature -SEQUENCE-FEATURE-EVIDENCE -> evidence
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BioPAX Level2 Statistics
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pathway 363
pathwayStep 1849
control 107
catalysis 527
modulation 0
conversion 131
biochemicalReaction 538
transportWithBiochemicalReaction 0
complexAssembly 756
transport 141
complex 2633
dna 386
protein 5428
rna 77
smallMolecule 255
physicalEntityParticipant 4338
sequenceParticipant 9170
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INOH Statistics
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-- NODE --
Diagram 62
EventCompound 1853
Event 76
Process 1566
EventRelation 323
Protein 8660
MolecularComplexCompound 3576
MolecularComplex 41
DNACompound 163
DNA 416
ChemicalSubstance 374
RNA 94
Terminal 31
-- EDGE --
IN 2741
OUT 2088
Control 107
Catalyze 527
Connected 2689
PASSING 1440
HomologousEvent 186
MolecularVariation 191
Identical 11
Posted by KenFukuda : November 30, 2007 04:07 PM
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