http://www.inoh.org/inohblog/main/ Integrating Network Objects with Hierarchies en Copyright 2010 Mon, 14 Jun 2010 16:15:37 +0900 http://www.sixapart.com/movabletype/?v=3.2-ja-2 http://blogs.law.harvard.edu/tech/rss 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]]> http://www.inoh.org/inohblog/main/2010/06/event_ontology_ver171_1.html http://www.inoh.org/inohblog/main/2010/06/event_ontology_ver171_1.html OntologyData Mon, 14 Jun 2010 16:15:37 +0900 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 ]]> http://www.inoh.org/inohblog/main/2010/06/inoh_release_30_has_been_relea_1.html http://www.inoh.org/inohblog/main/2010/06/inoh_release_30_has_been_relea_1.html PathwayData Thu, 03 Jun 2010 15:50:46 +0900 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://www.inoh.org/inohblog/main/2010/06/moleculerole_ontology_ver223.html http://www.inoh.org/inohblog/main/2010/06/moleculerole_ontology_ver223.html OntologyData Tue, 01 Jun 2010 15:23:16 +0900 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]]> http://www.inoh.org/inohblog/main/2010/06/event_ontology_ver170_1.html http://www.inoh.org/inohblog/main/2010/06/event_ontology_ver170_1.html OntologyData Tue, 01 Jun 2010 15:22:17 +0900 INOH Ontology Viewer and download it from our download page. Statistics ========== all entries 52 obsolete 2 definition 44 GO IDs 49]]> http://www.inoh.org/inohblog/main/2010/06/location_ontology_ver101.html http://www.inoh.org/inohblog/main/2010/06/location_ontology_ver101.html OntologyData Tue, 01 Jun 2010 15:20:51 +0900 here. The version number is updated from 2.2.2 to 3.1.9.]]> http://www.inoh.org/inohblog/main/2010/04/inoh_client_application_new_ve_2.html http://www.inoh.org/inohblog/main/2010/04/inoh_client_application_new_ve_2.html Software Wed, 28 Apr 2010 15:07:03 +0900 site. As soon as we release INOH pathway data 3.0.]]> http://www.inoh.org/inohblog/main/2010/04/inoh_release_25_has_been_relea.html http://www.inoh.org/inohblog/main/2010/04/inoh_release_25_has_been_relea.html PathwayData Fri, 09 Apr 2010 12:25:58 +0900 here. The version number is updated from 2.0.2 to 2.2.2.]]> http://www.inoh.org/inohblog/main/2009/05/inoh_client_application_new_ve_1.html http://www.inoh.org/inohblog/main/2009/05/inoh_client_application_new_ve_1.html Software Thu, 14 May 2009 16:39:47 +0900 here. And JRE 6 is required. INOH client supports Windows, Mac OSX and Linux.]]> http://www.inoh.org/inohblog/main/2009/05/keyword_search_and_pathway_ret.html http://www.inoh.org/inohblog/main/2009/05/keyword_search_and_pathway_ret.html Information Thu, 14 May 2009 16:27:02 +0900 "Pathway retrieval Search" service of INOH client stops for system renewal now. We are sorry for inconvenience, and thanks your cooperation. http://www.inoh.org/inohblog/main/2009/01/pathway_retrieval_search_servi_1.html http://www.inoh.org/inohblog/main/2009/01/pathway_retrieval_search_servi_1.html Information Wed, 07 Jan 2009 13:16:20 +0900 INOH client 2.0.2 does not officially support Mac OSX because some of its features require Java 6, which has not been made available from Apple yet. But if you only do browsing then you can use the linux version on your mac. See detailes in the "more" section bellow. http://www.inoh.org/inohblog/main/2008/02/inoh_client_mac_osx_support.html http://www.inoh.org/inohblog/main/2008/02/inoh_client_mac_osx_support.html Software Mon, 04 Feb 2008 18:48:46 +0900 here. This version is a major update and the version number is updated from 1.0.6 to 2.0.2. ===IMPORTANT!!!=== delete the "frame.layout" file in the .inoh directory of your home (e.g. Windows:C:\Documents and Settings\user-name,Linux:/home/user-name) before installing version 2.x. If not, panel pane will not appear correctly in your client. ]]> http://www.inoh.org/inohblog/main/2007/12/inoh_client_application_new_ve.html http://www.inoh.org/inohblog/main/2007/12/inoh_client_application_new_ve.html Mon, 03 Dec 2007 17:22:21 +0900 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 ]]> http://www.inoh.org/inohblog/main/2007/11/inoh_release_20_has_been_relea.html http://www.inoh.org/inohblog/main/2007/11/inoh_release_20_has_been_relea.html PathwayData Fri, 30 Nov 2007 16:07:44 +0900 BioPAX sourceforge CVS. Paxtools is a Domain Object Model(DOM) for BioPAX, providing software tools such as editors, exporters, importers, visualization tools and analysis algorithms with an API for manipulating BioPAX models. The Paxtools core model is developed at CBIO, MSKCC and the persistency layer is developed by INOH database. #NOTE: Currently we only have a "dev" version in the CVS. [documents] Find out here how to set up your Paxtools with a backbone DBMS. The javadoc for the Paxtools Level2 persistency layer API is available here. You can also get the pdf file of the paxtools poster abstract at ISMB 2007 here.]]> http://www.inoh.org/inohblog/main/2007/10/paxtools_level2_persistency_la.html http://www.inoh.org/inohblog/main/2007/10/paxtools_level2_persistency_la.html Software Thu, 25 Oct 2007 10:47:52 +0900 OBO site and from our download page. Statistics ========== All entries 8821 Chemicals 592 Proteins 8228 Obsoletes 25 UniProt ACs 5572 GO IDs 344 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 99]]> http://www.inoh.org/inohblog/main/2007/10/moleculerole_ontology_ver222.html http://www.inoh.org/inohblog/main/2007/10/moleculerole_ontology_ver222.html OntologyData Wed, 03 Oct 2007 17:44:41 +0900