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February 17, 2006
INOH pathway data release 1.0 is now available.
With additional 22 pathway files to the original release of February 1st, now INOH pathway data release 1.0 is available from our download site.
You can also view, edit and search the pathways with our pathway editor INOH client.
The data are in .inoh XML format. Please see the format specification for technical details.
We are currently working on BioPAX versions of our pathway data.
The BioPAX level will be BioPAX level3 or higher.
This is the list of pathways added today:
==============================================================
B cell receptor signaling
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 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)
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 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)
Notch signaling pathway Diagram
Statistics of INOH pathway data release 1.0
==============================================================
-- NODE --
Protein 5654
MolecularComplexCompound 2176
EventCompound 1619
Process 1379
MolecularComplex 463
DNA 396
ChemicalSubstance 319
EventRelation 313
DNACompound 157
Event 124
RNA 89
Diagram 57
Terminal 16
-- EDGE --
IN 2429
OUT 1811
Connected 1518
PASSING 1323
Catalyze 407
HomologousEvent 187
MolecularVariation 148
Control 101
Identical 2
Posted by SatokoYamamoto : 09:10 PM | TrackBacks
February 08, 2006
Event Ontology Ver.1.59
The latest Event Ontology is Ver.1.59
Event Ontology is an ontology of pathways.
It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 2665
Obsoletes 22
definition 291
GO IDs 253
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Event Ontology Release Notes
=====================
Version: 1.59 (8th Feb. 2006)
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 1.57
=====================
[Added terms]
1. terms related to molecular interaction (e.g., IEV_0002674:Formylation)
2. terms related to genetic interaction (e.g., IEV_0002683:suppression)
3. terms related to Nervous system development (e.g., IEV_0002707:Neural tube formation)
4. subpathways related to TPO signaling pathway (e.g., IEV_0002658:Binding of TPO receptor and STAT3)
5. etc.
More information about Event Ontology
---------------------
Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event ontology: a pathway-centric ontology for biological processes, Proc. Pacific Symposium on Biocomputing, 2006. (in press)
Statistics
==========
All entries 2665
Obsoletes 22
definition 291
GO IDs 253
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Posted by NorikoSakai : 04:05 PM | TrackBacks
February 01, 2006
INOH pathway data released!!!
We are happy to annouce the first release of 35 INOH pathway files.
You can view, edit and search the pathways with our pathway editor INOH client.
You can also download the data files from here.
The data are in .inoh XML format. Please see the format specification for technical details.
We are currently working on BioPAX versions of our pathway data.
The BioPAX level will be BioPAX level3 or higher.
This is the list of pathways released today:
==============================================================
BMP2 signaling(through TAK1) 198.6KB 06/02/01
BMP2 signaling(TGF-beta_signaling MolecularVariation) 639.6KB 06/02/01
Drosophila IMD pathway 966.9KB 06/02/01
Drosophila Toll-like receptor signaling 1.5MB 06/02/01
EGF signaling pathway 456.7KB 06/02/01
FGF signaling pathway 463.2KB 06/02/01
Growth hormone signaling(JAK2 STAT5) 295.6KB 06/02/01
HGF signaling pathway 751.7KB 06/02/01
IFN alpha signaling(JAK1 TYK2 STAT1) 308.8KB 06/02/01
IFN alpha signaling(JAK1 TYK2 STAT1 STAT2) 449.3KB 06/02/01
IFN alpha signaling(JAK1 TYK2 STAT1 STAT3) 392.8KB 06/02/01
IFN alpha signaling(JAK1 TYK2 STAT3) 351.8KB 06/02/01
IFN gamma signaling(JAK1 JAK2 STAT1) 308.2KB 06/02/01
IL-10 signaling(JAK1 TYK2 STAT3) 363.3KB 06/02/01
IL-12 signaling(JAK2 TYK2 STAT4) 314.1KB 06/02/01
IL-2 signaling(JAK1 JAK3 STAT5) 327.9KB 06/02/01
IL-3 signaling(JAK2 STAT5) 296.7KB 06/02/01
IL-4 signaling(JAK1 JAK3 STAT6) 332.3KB 06/02/01
IL-6 signaling(JAK1 JAK2 STAT3) 352.3KB 06/02/01
IL-7 signaling(JAK1 JAK3 STAT5) 364.6KB 06/02/01
Integrin signaling pathway 785KB 06/02/01
JAK STAT MolecularVariation 3.1MB 06/02/01
JAK-STAT pathway and regulation pathway 872KB 06/02/01
LIF signaling(JAK1 JAK2 STAT3) 503.6KB 06/02/01
NGF signaling pathway 446KB 06/02/01
PDGF signaling pathway 437.3KB 06/02/01
TGF-beta signaling(through TAK1) 189.1KB 06/02/01
TGF-beta_super_family_signaling_pathway(canonical) 684.7KB 06/02/01
TPO signaling(JAK2 STAT3) 310.8KB 06/02/01
VEGF signaling pathway 495.5KB 06/02/01
C. elegans endoderm induction Wnt signaling pathway Diagram 1.2MB 06/02/01
Canonical Wnt signaling pathway Diagram 928.2KB 06/02/01
Drosophila Wingless/Wnt signaling pathway Diagram 1.4MB 06/02/01
Mammalian Wnt signaling pathway Diagram 1.9MB 06/02/01
Xenopus axis formation Wnt signaling pathway Diagram 1.6MB 06/02/01
Posted by KenFukuda : 09:37 PM | TrackBacks
Location Ontology Ver1.00
Location Ontology is a cellular compartment ontology.
Location Ontology Release Notes
=====================
Version: 1.00 (Dec 12, 2005)
Statistics
==========
all entries 49
obsolete 2
definition 42
GO IDs 47
Posted by KenFukuda : 07:20 PM | TrackBacks
Event Ontology Ver.1.58
The latest Event Ontology is Ver.1.58
Event Ontology is an ontology of pathways.
It classifies pathways, sub-pathways and other biological phenomena to form a DAG structure.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 2659
Obsoletes 22
definition 207
GO IDs 202
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Event Ontology Release Notes
=====================
Version: 1.58 (29th Nov. 2005)
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 1.57
=====================
[Added terms]
1. terms related to molecular interaction (e.g., IEV_0002674:Formylation)
2. terms related to genetic interaction (e.g., IEV_0002683:suppression)
3. terms related to Nervous system development (e.g., IEV_0002707:Neural tube formation)
4. subpathways related to TPO signaling pathway (e.g., IEV_0002658:Binding of TPO receptor and STAT3)
5. etc.
More information about Event Ontology
---------------------
Tatsuya Kushida, Toshihisa Takagi and Ken Ichiro Fukuda, Event ontology: a pathway-centric ontology for biological processes, Proc. Pacific Symposium on Biocomputing, 2006. (in press)
Statistics
==========
All entries 2659
Obsoletes 22
definition 207
GO IDs 202
KEGG PATHWAY IDs 173
Reactome IDs 110
PSI-MI IDs 51
Posted by KenFukuda : 03:27 PM | TrackBacks
MoleculeRole Ontology Ver.2.10
The latest MoleculeRole Ontology is Ver2.10
MoleculeRole Ontology is an ontology for proteins.
You can download it from the OBO site and from our download page.
Statistics
==========
All entries 7184
Chemicals 85
Proteins 7098
Obsoletes 18
UniProt ACs 4582
GO IDs 314
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 64
MoleculeRole Ontology Release Notes
=====================
Version: 2.10 (Dec 27, 2005)
Molecule Role is a hierarchical ontology which contains molecular functional group names, abstract molecule names and 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 2.0x
=====================
Over 13,000 synonyms were added from EntrezGene, HGNC, FlyBase, OMIM, MGI and RGD database in 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 7184
Chemicals 85
Proteins 7098
Obsoletes 18
UniProt ACs 4582
GO IDs 314
InterPro ACs 31
KEGG COMPOUND IDs 85
PubMed IDs 64
Posted by KenFukuda : 03:12 PM | TrackBacks