November 30, 2007
INOH release 2.0 has been released (BioPAX format included)
The data files are available from our download site.
======================
newly curated pathways
======================
EPO signaling pathway(JAK2 STAT1 STAT3 STAT5)
Fas signaling pathway
GPCR Adenosine A2A receptor signaling pathway
TNFR1 signaling pathway
=================
updated pathways
=================
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
=============
New ID system (INOHID)
=============
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.
===================
BioPAX Level2 enhancement
===================
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
=========================
BioPAX Level2 Statistics
=========================
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
===============
INOH Statistics
===============
-- 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 : 04:07 PM | TrackBacks
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
September 28, 2006
INOH BioPAX Level2 release update
INOH BioPAX Level2 release has been updated and is available here.
The update includes data error correction and new XREFs to various resources such as UniProt, IPR, KEGG, Reactome, GO, ChEBI.
1. (2006/09/28) For each Interaction instance that has LEFT and RIGHT property referring to the same instance, postfix "_act" was added to the RIGHT instance.
2. (2006/09/15) data error correction
In diagram file "GPCR_signaling-pertussis_toxin-.inoh", the following value of protein node "G alpha i_ADP" (GID:ll0000056 LID:id1339337698 MatID:MI0007292) was corrected.
"MoleculeRoleOntorogy" value was changed from "IMR_0000313:adenylate cyclase" to "IMR_0000319:G-alpha-i".
3. (2006/09/15) added more unificationXrefs and relationshipXrefs (UniProt, IPR, KEGG, Reactome, GO, ChEBI)
4. (2006/09/15) wrong unificationXref in several pathway/interaction instances
5. (2006/09/15) Strange use of unificationXref
Changed to the following scheme.
INOH_XREF_ID:URL
1 : http://www.biocarta.com/pathfiles/h_egfPathway.asp
2 : http://www.biocarta.com/pathfiles/h_metPathway.asp
3 : http://www.biocarta.com/pathfiles/h_ngfPathway.asp
4 : http://www.biocarta.com/pathfiles/h_pdgfPathway.asp
5 : http://www.stanford.edu/~rnusse/wntwindow.html
6. (2006/09/06) Added UniProt unificationXref inscances to protein
7. (2006/09/06) Deleted ORGANISM property from smallMolecule
8. (2006/09/06) smallMolecule instances, changed from sequenceParticipant to physicalEntityParticipant
9. (2006/09/06) relationshipXref, empty DB/ ID
10. (2006/09/06) Multiple instances with the same name "IC"
There was a file in which openControlledVocabulary instances and evidence instances had the same name "IC" (IC is an INOH evidence code that stands for Inferred by Curator).
Evidence instance name was generated automatically as EVIDENCE-CODE + "_" + XREF and instances without any XREF had only EVIDENCE-CODE for their names (for example IC)
The rule was changed to the following.Evidence instance without EVIDENCE-CODE has the name NOEVIDENCE-CODE + "_" +XREF?Evidence instance with empty XREF has the name EVIDENCE-CODE + "_" + "NOXREF". Now an instance evidence with evidence code IC and a blank XREF will have the name IC_NOXREF.
Posted by KenFukuda : 10:02 PM | TrackBacks
August 10, 2006
INOH BioPAX Level2 release
All INOH pathway diagram files are now available in BioPAX Level2 format.
Visit Download page and get each file separately or as a single archive.
Release note:
Known issues:
1. There are some instances not referred from any instances. (undeleted garbage generated during the conversion)
* Some "INOH_GID_LID"s of "unificationXref".
* "Connected_xxx" of "relationshipXref"
* "PASSING_xxx"
* Some "phsicalEntityParticipant"s
e.g.) MI0006343_IkB_NFkB0_pep(B_cell_receptor_signaling.owl)
2. Mapped to COMMENT property (should be resolved in the next level of BioPAX)
* Amino residue names (e.g. Ser), domain names (e.g. ITAM) in SequenceFeature mapped to COMMENT of sequenceFeature
* Evidence information of Material nodes mapped to COMMENT of PEP or SP
* Connected edge information mapped to COMMENT of relationshipXref class's instances "Connected_xxx"
Posted by KenFukuda : 05:12 PM | TrackBacks
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 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