tag:www.inoh.org,2011:/inohblog/main/2 2011-03-29T06:01:17Z Integrating Network Objects with Hierarchies Movable Type 3.2-ja-2 tag:www.inoh.org,2011:/inohblog/main//2.69 2011-03-29T05:39:55Z 2011-03-29T06:01:17Z

The data files are available from our download site. Signal Transduction Pathway Data and Metabolic Pathway Data. Moreover, all INOH pathway diagram files are now available in BioPAX Level2 and Level3 formats. Visit Download page and get each file separately...

Hiromi Nakamura Signal Transduction Pathway Data and Metabolic Pathway Data. Moreover, all INOH pathway diagram files are now available in BioPAX Level2 and Level3 formats. Visit Download page and get each file separately or as a single archive. ====================== newly curated pathways ====================== BMP signaling in Drosophila PDGF signaling pathway (Mammal) ================= updated pathways ================= TGF-beta_BMP Diagram(MolecularVariation) Drosophila Toll-like receptor signaling EGF signaling pathway Diagram (D. melanogaster, C. elegans) FGF signaling pathway IFN gamma signaling(JAK1 JAK2 STAT1) IL-2 signaling(JAK1 JAK3 STAT5) IL-4 signaling(JAK1 JAK3 STAT6) IL-7 signaling(JAK1 JAK3 STAT5) JAK STAT MolecularVariation 1 JAK-STAT pathway and regulation pathway Diagram (Canonical, D. melanogaster) NGF signaling pathway TGF-beta_super_family_signaling_pathway(canonical) 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 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 JNK cascade) Toll-like receptor signaling pathway (trough NF-kappaB) Toll-like receptor signaling pathway (p38 cascade) 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 signaling (G alpha s, PKA and ERK) Notch signaling pathway Diagram (Canonical, Mammal, D. melanogaster, C. elegans) JAK STAT MolecularVariation 2 Fas signaling pathway GPCR Adenosine A2A receptor signaling pathway TNFR1 signaling pathway Alanine,Aspartic acid and Asparagine metabolism Aminosugars metabolism Arginine and Proline metabolism Butanoate metabolism Citrate cycle FGF8 signaling (Mouse) FGF8 signaling (Xenopus) FGF signaling pathway (C. elegans) FGF signaling pathway (D. melanogaster) Folate metabolism Fructose and Mannose metabolism Galactose metabolism Glutamic acid and Glutamine metabolism Glycine and Serine metabolism Glycolysis and Gluconeogenesis Hedgehog signaling pathway (Canonical, Mammal, D. melanogaster) Histidine degradation IFN alpha signaling(JAK1 TYK2 STAT1 STAT2 STAT3) IL-23 signaling(JAK2 TYK2 STAT3 STAT4) Inositol phosphate metabolism Lysine degradation Methionine and Cysteine metabolism Nicotinate and Nicotinamide metabolism Pentose phosphate cycle Phenylalanine degradation Porphyrin metabolism Propanoate metabolism Prostaglandin and Leukotriene metabolism Purine nucleotides and Nucleosides metabolism Pyrimidine Nucleotides and Nucleosides metabolism Pyruvate metabolism Steroids metabolism Tryptophan degradation Tyrosine metabolism Valine,Leucine and Isoleucine degradation Insulin receptor signaling Insulin receptor signaling (C. elegans) Insulin receptor signaling (D. melanogaster) Insulin receptor signaling (Mammal)]]> ========================= BioPAX Level3 Statistics ========================= Pathway 857 PathwayStep 773 BiochemicalPathwayStep 3196 Control 162 Catalysis 2614 Modulation 0 TemplateReactionRegulation 31 Conversion 81 BiochemicalReaction 1740 TransportWithBiochemicalReaction 0 ComplexAssembly 1108 Degradation 31 Transport 236 GeneticInteraction 0 MolecularInteraction 0 TemplateReaction 152 Complex 5801 Dna 661 DnaRegion 0 Protein 14493 Rna 218 RnaRegion 0 SmallMolecule 4415 =============== INOH Statistics =============== -- NODE -- Diagram 102 EventCompound 4066 Event 139 Process 3348 EventRelation 542 Protein 14493 MolecularComplexCompound 5479 MolecularComplex 45 DNACompound 277 DNA 661 ChemicalSubstance 4415 RNA 218 Terminal 34 -- EDGE -- IN 6056 OUT 5131 Control 193 Catalyze 2614 Connected 3721 PASSING 3341 HomologousEvent 466 MolecularVariation 257 Identical 62 tag:www.inoh.org,2011:/inohblog/main//2.68 2011-03-29T03:13:37Z 2011-03-29T03:26:24Z

The latest MoleculeRole Ontology is Ver2.24 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...

Satoko Yamamoto INOH Ontology Viewer and download it from the OBO site and from our download page. Statistics ========== All entries 9217 Chemicals 593 Proteins 8591 Obsoletes 32 UniProt ACs 5868 GO IDs 346 InterPro ACs 32 KEGG COMPOUND IDs 588 PubMed IDs 172]]> http://www3.interscience.wiley.com/cgi-bin/fulltext/109860932/HTMLSTART) Statistics ========== All entries 9217 Chemicals 593 Proteins 8591 Obsoletes 32 UniProt ACs 5868 GO IDs 346 InterPro ACs 32 KEGG COMPOUND IDs 588 PubMed IDs 172]]> tag:www.inoh.org,2011:/inohblog/main//2.61 2011-03-23T07:03:46Z 2011-03-23T07:05:52Z

The latest Location Ontology is Ver.1.02 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...

Noriko Sakai 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: 1.02 (23th Mar, 2011) Changes from version 1.01 ===================== change the synonym type. Statistics ========== all entries 52 obsolete 2 definition 44 GO IDs 49 tag:www.inoh.org,2011:/inohblog/main//2.60 2011-03-23T06:45:07Z 2011-03-23T06:53:01Z

The latest Event Ontology is Ver.1.72 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...

Noriko Sakai INOH Ontology Viewer and download it from the OBO site and from our download page. Statistics ========== All entries 3828 Obsoletes 149 definition 681 IMR IDs 5765 GO IDs 539 KEGG Reaction IDs 618 KEGG map IDs 1192 Reactome IDs 136 PSI-MI IDs 71]]> Event Ontology Release Notes ===================== Version: 1.72 (23th Mar, 2011) 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 1.71 ===================== 1. add the terms related to BMP signaling pathway and PDGF signaling pathway. 2. link the INOH MoleculeRole ontology ID to the terms related to molecular interaction. 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 3828 Obsoletes 149 definition 681 IMR IDs 5765 GO IDs 539 KEGG Reaction IDs 618 KEGG map IDs 1192 Reactome IDs 136 PSI-MI IDs 71 tag:www.inoh.org,2011:/inohblog/main//2.59 2011-03-10T09:04:42Z 2011-03-10T09:07:38Z

Our new INOH Client is now available. Windows, Max OSX and Linux are supported. JRE 6.0 is required. You can download INOH client application from here. The version number is updated from 3.4.0 to 3.5.3....

Hiromi Nakamura here. The version number is updated from 3.4.0 to 3.5.3.]]> Release Notes ====================== Version 3.5.3 Newly added and improved features: - improved the node and edge's SVGs. - added Protein nodes (pink node, green node, orange node, purple node, and the phosphorylated and modified nodes of these nodes). - improved "Erros" check. The "Passing edge" was able to be pulled only between nodes of the same type. - "Overview Area" and "Magnifier View Area" is fixed 100% zoom. bug fixes: - layout problem after the server search. tag:www.inoh.org,2011:/inohblog/main//2.58 2011-01-06T09:46:12Z 2011-03-30T09:49:00Z

We have developed a prototype web tool that accepts a graph query, whose nodes and edges are proteins and their relations respectively or "Event" and their connections respectively, searches the pathway/network data for the similar subgraphs on INOH. This tool...

Hiromi Nakamura the INOH client tool and the INOH pathway dataset from this site.]]> Usage: In the INOH client, 0) Set your mail address to get the link URL of the results from "Tool" -> "Settings" -> "Similarity search" tab, 1) Open one of the INOH pathway diagrams. 2) Select a region of nodes and edges that you are interested in. 3) From menu, select "Search" -> "Similarity Search" -> "MoleculeRole Ontology" or "Event Ontology". After that, your web browser will open and show the similarity-search page with your query. And you will get the submit notice mail from INOH with access URL for your similarity-search page. tag:www.inoh.org,2011:/inohblog/main//2.57 2011-01-06T09:37:51Z 2011-01-06T09:43:29Z

Our new INOH Client is now available. Windows, Max OSX and Linux are supported. JRE 6.0 is required. You can download INOH client application from here. The version number is updated from 3.1.9 to 3.4.0....

Hiromi Nakamura here. The version number is updated from 3.1.9 to 3.4.0. ]]> Release Notes ====================== Version 3.4.0 Newly added and improved features: - added "Similarity-search". - added "Copy & Paste", "Up", and "Down" in "SequenceFeature edit" and "Evidence edit". - added "ID search ( Node & Edge)". - added "EC" in the XREF field become linkable. - improved "Change node type" and "Change edge type" in "Object". - enabled "Overview Area" and "Magnifier View Area" to close. - "MoleculeRoleOntology" field is changed from Two or more input to singular input. - improved "Erros" check. bug fixes: - "Use regular expression" in "Find local". tag:www.inoh.org,2010:/inohblog/main//2.55 2010-06-14T07:15:37Z 2010-06-16T08:42:39Z

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...

Noriko Sakai 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 tag:www.inoh.org,2010:/inohblog/main//2.54 2010-06-03T06:50:46Z 2010-06-03T07:02:43Z

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...

Hiromi Nakamura 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 tag:www.inoh.org,2010:/inohblog/main//2.53 2010-06-01T06:23:16Z 2010-06-03T05:03:42Z

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...

Satoko Yamamoto 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]]> 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]]> tag:www.inoh.org,2010:/inohblog/main//2.52 2010-06-01T06:22:17Z 2010-06-04T03:59:42Z

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...

Noriko Sakai 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 tag:www.inoh.org,2010:/inohblog/main//2.56 2010-06-01T06:20:51Z 2010-06-22T06:58:45Z

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...

Noriko Sakai 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 tag:www.inoh.org,2010:/inohblog/main//2.51 2010-04-28T06:07:03Z 2010-04-28T06:14:46Z

Our new INOH Client is now available. Windows, Max OSX and Linux are supported. JRE 6.0 is required. You can download INOH client application from here. The version number is updated from 2.2.2 to 3.1.9....

Hiromi Nakamura here. The version number is updated from 2.2.2 to 3.1.9.]]> Release Notes ====================== Version 3.1.9 Newly added features: - added "Font" , specify the default font in "Tool --> Settings". - added "Organism" , specify the default value of Organism property in "Tool --> Settings". - added "Change node type" and "Change edge type" in "Object". - added "Overview Area" and "Magnifier View Area". The Overview Area is placed on the top right side of the screen. Overview of the diagram you are currently editing is displayed in this area. The Magnifier View Area is placed on the bottom right side of the screen. Magnified view of the diagram you are currently editing is displayed in this area. - added "Reduced View Mode". The reduced view that focused on molecular transition in the normal view, and these modes can be easily switched back and forth. tag:www.inoh.org,2010:/inohblog/main//2.50 2010-04-09T03:25:58Z 2010-04-09T04:48:10Z

Bug fix in "MatID"(ID of INOH). ID of objects that have the same biological identity was not equal. Update "MatID" of objects. The data files are available from our download site. As soon as we release INOH pathway data 3.0....

Hiromi Nakamura site. As soon as we release INOH pathway data 3.0.]]> tag:www.inoh.org,2009:/inohblog/main//2.49 2009-05-14T07:39:47Z 2009-05-14T07:53:26Z

Our new INOH Client is now available. Windows, Max OSX and Linux are supported. JRE 6.0 is required. You can download INOH client application from here. The version number is updated from 2.0.2 to 2.2.2....

Hiromi Nakamura here. The version number is updated from 2.0.2 to 2.2.2.]]> Release Notes ====================== Version 2.2.2 JRE 6 is required. Newly added features: - supported Mac OSX. - bug fix in "Ontology viewer links". - bug fix in "Check error". - ServerURI changed. http://www.inoh.org/axis/services/InohWebService --> http://www.inoh.org/axis2/services/InohWebService2