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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
Event Ontology Release Notes
=====================
Version: 1.71 (14th Jun, 2010)
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 1.70
=====================
1. add the terms related to PDGF signaling pathway.
2. link the KEGG Reaction ID to the terms related to Metabolic pathway.
3. etc.
More information about Event Ontology
---------------------
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
==========
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
Posted by NorikoSakai : 04:15 PM | TrackBacks
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
=========================
BioPAX Level2 Statistics
=========================
pathway 755
pathwayStep 3560
control 144
catalysis 2517
modulation 0
conversion 192
biochemicalReaction 1634
transportWithBiochemicalReaction 0
complexAssembly 970
transport 203
complex 5005
dna 575
protein 13041
rna 169
smallMolecule 4265
physicalEntityParticipant 9534
sequenceParticipant 13788
===============
INOH Statistics
===============
-- NODE --
Diagram 101
EventCompound 3655
Event 99
Process 2999
EventRelation 443
Protein 13041
MolecularComplexCompound 4726
MolecularComplex 45
DNACompound 234
DNA 575
ChemicalSubstance 4265
RNA 169
Terminal 32
-- EDGE --
IN 5470
OUT 4663
Control 144
Catalyze 2517
Connected 3427
PASSING 3013
HomologousEvent 269
MolecularVariation 240
Identical 50
Posted by HiromiNakamura : 03:50 PM | TrackBacks
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
MoleculeRole Ontology Release Notes
=====================
Version: 2.23 (Apr 28, 2010)
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
=====================
KEGG metabolic pathway related molecules (500~ chemicals and 300~ proteins) were added.
Changes from version 2.0x
=====================
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
=====================
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
---------------------
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
==========
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
Posted by SatokoYamamoto : 03:23 PM | TrackBacks
Event Ontology Ver.1.70
The latest Event Ontology is Ver.1.70
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 3756
Obsoletes 149
definition 653
GO IDs 516
KEGG IDs 825
Reactome IDs 110
PSI-MI IDs 70
Event Ontology Release Notes
=====================
Version: 1.70 (28th Apr, 2010)
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 1.62
=====================
1. add the terms related to IGF signaling pathway, EGF signaling pathway, FGF signaling pathway, insulin signaling pathway, Hedgehog signaling pathway and metabolic pathway.
2. add the location where events take place to the terms for "moleculer interaction".
3. add three new relationship types --regulates, negatively_regulates and positively_regulates.
4. remove the terms for the annotation of events whose biological process is unknown.
5. etc.
More information about Event Ontology
---------------------
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
==========
All entries 3756
Obsoletes 149
definition 653
GO IDs 516
KEGG IDs 825
Reactome IDs 110
PSI-MI IDs 70
Posted by NorikoSakai : 03:22 PM | TrackBacks
Location Ontology Ver.1.01
The latest Location Ontology is Ver.1.01
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
Location Ontology Release Notes
=====================
Version: 1.01 (28th Apr, 2010)
Changes from version 1.00
=====================
add the terms related to cilium.
Statistics
==========
all entries 52
obsolete 2
definition 44
GO IDs 49
Posted by NorikoSakai : 03:20 PM | TrackBacks