INOH Pathway Database: March 2007 Archives

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March 31, 2007

INOH release 1.5 has been released (BioPAX format included)

Additional curation and bug fixes to BioPAX level2 export has been done.
The data is available from our download site.

==========
Statistics
==========
BioPAX Level2 instances:
control 105
catalysis 451
conversion 133
biochemicalReaction 469
complexAssembly 688
transport 124
physicalEntityParticipant 2479
sequenceParticipant 5104
pathway 332
pathwayStep 1670
complex 1621
dna 143
protein 2606
rna 60
smallMolecule 126

==============================================
newly curated data
==============================================
1. 440 complexes with detailed subunit structure information (e.g. IKK complex, IFNalphaR)
2. 33 events and 7 cascades (e.g. degradation of I-KappaB, JNK cascade, CD28 signaling)

B cell receptor signaling
BMP2 signaling(through TAK1)
BMP2 signaling(TGF-beta_signaling MolecularVariation)
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
Drosophila IMD pathway
Drosophila Toll-like receptor signaling
Growth hormone signaling(JAK2 STAT5)
IFN alpha signaling(JAK1 TYK2 STAT1)
IFN alpha signaling(JAK1 TYK2 STAT1 STAT2)
IFN alpha signaling(JAK1 TYK2 STAT1 STAT3)
IFN alpha signaling(JAK1 TYK2 STAT3)
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(JAK2 STAT5)
IL-4 signaling(JAK1 JAK3 STAT6)
IL-6 signaling(JAK1 JAK2 STAT3)
IL-7 signaling(JAK1 JAK3 STAT5)
JAK STAT MolecularVariation 1
JAK STAT MolecularVariation 2
LIF signaling(JAK1 JAK2 STAT3)
TGF-beta signaling(through TAK1)
TPO signaling(JAK2 STAT3)
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)

=============================
updated pathways
=============================
EGF signaling pathway
FGF signaling pathway
GPCR Dopamine D1like receptor
GPCR GroupI metabotropic glutamate receptor
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)
HGF signaling pathway
Integrin signaling pathway
JAK-STAT pathway and regulation pathway
NGF signaling pathway
PDGF signaling pathway
TGF-beta_super_family_signaling_pathway(canonical)
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

==========
Statistics
==========
-- BioPAX Level2 instances --
control 105
catalysis 451
conversion 133
biochemicalReaction 469
complexAssembly 688
transport 124
physicalEntityParticipant 2479
sequenceParticipant 5104
pathway 332
pathwayStep 1670
complex 1621
dna 143
protein 2606
rna 60
smallMolecule 126

-- NODE --
Diagram 58
EventCompound 1694
Event 71
Process 1431
EventRelation 318
Protein 7676
MolecularComplexCompound 3121
MolecularComplex 44
DNACompound 160
DNA 402
ChemicalSubstance 341
RNA 90
Terminal 30

-- EDGE --
IN 2540
OUT 1933
Control 106
Catalyze 455
Connected 2377
PASSING 1301
HomologousEvent 187
MolecularVariation 182
Identical 11

======================
bug fix(BioPAX level2)
======================
1. relationshipXref instance changed to publicationXref
2. changed the use of XREF in control class. Instance of relationshipXref instead of unificationXref is used for INOH EventOntology reference.
3. Avoid instance sharing for physicalEntityParticipant

======================
known issues
======================
There are still some unexpected instance dupilcation/sharing.

Posted by KenFukuda : 11:47 AM | TrackBacks

March 29, 2007

MoleculeRole Ontology Ver.2.21

The latest MoleculeRole Ontology is Ver2.21

MoleculeRole Ontology is an ontology for proteins.

You can download it from the OBO site and from our download page.

Statistics
==========
All entries 8649
Chemicals 592
Proteins 8056
Obsoletes 25

UniProt ACs 5465
GO IDs 329
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 81

MoleculeRole Ontology Release Notes
=====================
Version: 2.21 (Mar 28, 2006)

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 8649
Chemicals 592
Proteins 8056
Obsoletes 25

UniProt ACs 5465
GO IDs 329
InterPro ACs 32
KEGG COMPOUND IDs 587
PubMed IDs 81

Posted by SatokoYamamoto : 11:35 AM | TrackBacks

March 28, 2007

Event Ontology Ver.1.61

The latest Event Ontology is Ver.1.61

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 2723
Obsoletes 21
definition 455

GO IDs 400
KEGG PATHWAY IDs 184
Reactome IDs 110
PSI-MI IDs 53

Event Ontology Release Notes
=====================
Version: 1.61 (28th Mar. 2007)

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 1.60
=====================
[Added terms and definitions]

1. terms related to MAPKKK cascade (e.g., IEV_0003381:Phosphorylation of MKK4 by TAK1)
2. terms related to IL-1 signaling, TLR signaling (e.g., IEV_0003384:Phosphorylation of TAB2 and TAK1)
3. definitions related to Metabolic pathway (e.g., IEV_0001411:Glutamate metabolism)
4. 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).