tag:www.inoh.org,2008:/inohblog/main/2 2008-02-04T09:59:06Z Integrating Network Objects with Hierarchies Movable Type 3.2-ja-2 tag:www.inoh.org,2008:/inohblog/main//2.46 2008-02-04T09:48:46Z 2008-02-04T09:59:06Z

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...

Ken Fukuda 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. INOH client is a pathway editor and a front end of our database and Java 6 is required to issue a query. But you can install the linux version on your Mac and browse pathways. 1. download Linux without Java VM from http://www.inoh.org/Web_Installers/install.htm 2. run the downloaded installer by # sh install.bin 4. cd to InohClient and edit the inoh.sh script in the bin-sample a) edit the following two variables. JAVA_HOME=... INOH_CLIENT_HOME=... b)edit the last line's ${JRE_HOME}/bin/java to fit your machine configuration. 5. start the INOH Client with # sh inoh.sh The pathway files (with .inoh extensions) are available from http://www.inoh.org/download.html#PathwayData tag:www.inoh.org,2007:/inohblog/main//2.44 2007-12-03T08:22:21Z 2007-12-03T09:50:57Z

Our new INOH Client is now available. Currently only Windows and Linux are supported. Mac OSX will be supported as soon as Apple releases Java 6 for Leopard. You can download the application from here. This version is a major...

Ken Fukuda 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. ]]> Release Notes ====================== Version 2.0.2 - Version 2 requires JRE1.6. Newly added features: - add "INOHID" and "secondaryINOHID" property. - add "External DB links Panel"(link to INOH Ontology Viewer,PubMed,UniProt,GO,and KEGG). - add "Errors Panel". -->check edge rules (ex.Catalyze edge : From Material To Process, Connected edge:between Proteins) -->check mandatory attributes. -->check attribute values and formats for CVs(ex."Organism","Citaion" of Evidence). -->check if two sequential events share the output and input entities correctly. - add edge redrawing (you do not have to delete and create a new edge to modify an existing edge) - add "Redo". - add "zoom selected" checkbox (local search and Errors panel). - change node double-click action. double-click a node object and a property edit dialog will pop-up. --> in version 1.x, double-click was yFiles' default action (get one level down of the graph hierarchy) tag:www.inoh.org,2007:/inohblog/main//2.43 2007-11-30T07:07:44Z 2007-11-30T07:25:50Z

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...

Ken Fukuda 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 ]]> 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 ]]> tag:www.inoh.org,2007:/inohblog/main//2.42 2007-10-25T01:47:52Z 2007-11-01T06:05:49Z

Paxtools persistency layer for BioPAX Level 2 specification is available from the 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...

Ken Fukuda 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.]]> Paxtools provides a complete domain object model (DOM) in Java that enables users manipulating and evaluating BioPAX. It also provides state-of-the-art persistence services based on Java Persistence API. Finally Paxtools implement a fail-fast validation framework, mitigating the cost of potential pitfalls for the developers. Paxtools was designed to be modular, lightweight and platform independent to be easily embedded into applications. [quoted from the ISMB2007 poster abstract]]]> tag:www.inoh.org,2007:/inohblog/main//2.41 2007-10-03T08:44:41Z 2007-10-03T08:52:59Z

The latest MoleculeRole Ontology is Ver2.22 MoleculeRole Ontology is an ontology for proteins. You can download it from the OBO site and from our download page. Statistics ========== All entries 8821 Chemicals 592 Proteins 8228 Obsoletes 25 UniProt ACs 5572...

Satoko Yamamoto 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]]> MoleculeRole Ontology Release Notes ===================== Version: 2.22 (Oct 3, 2007) 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 8821 Chemicals 592 Proteins 8228 Obsoletes 25 UniProt ACs 5572 GO IDs 344 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 99 tag:www.inoh.org,2007:/inohblog/main//2.40 2007-10-03T08:33:51Z 2007-10-03T08:39:21Z

The latest Event Ontology is Ver.1.62 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...

Noriko Sakai OBO site and from our download page. Statistics ========== All entries 2781 Obsoletes 37 definition 470 GO IDs 406 KEGG PATHWAY IDs 184 Reactome IDs 110 PSI-MI IDs 68]]> Event Ontology Release Notes ===================== Version: 1.62 (3rd Oct. 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 1.61 ===================== [Added terms and definitions] 1. terms related to genetic interaction (e.g., IEV_0003393:synthetic interaction) 2. subpathways related to EPO signaling pathway (e.g., IEV_0003438:Binding of EPO receptor and STAT3) 3. subpathways related to TNFR signaling pathway (e.g., IEV_0003418:Proteasome degradation of c-FLIP) 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). Statistics ========== All entries 2781 Obsoletes 37 definition 470 GO IDs 406 KEGG PATHWAY IDs 184 Reactome IDs 110 PSI-MI IDs 68 tag:www.inoh.org,2007:/inohblog/main//2.39 2007-03-31T02:47:45Z 2007-04-04T06:06:01Z

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...

Ken Fukuda 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. tag:www.inoh.org,2007:/inohblog/main//2.38 2007-03-29T02:35:39Z 2007-04-04T06:06:24Z

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...

Satoko Yamamoto 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 tag:www.inoh.org,2007:/inohblog/main//2.37 2007-03-28T10:11:36Z 2007-03-30T10:28:17Z

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...

Noriko Sakai 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). Statistics ========== All entries 2723 Obsoletes 21 definition 455 GO IDs 400 KEGG PATHWAY IDs 184 Reactome IDs 110 PSI-MI IDs 53 tag:www.inoh.org,2007:/inohblog/main//2.36 2007-01-23T05:56:00Z 2007-01-23T05:59:57Z

INOH will be down from Feb 3 to Feb 5. Our host server at the Human Genome Center (HGC) will be shutdown due to scheduled system maintenance. ------------------------------------------------------------------------- NOTICE Due to the system maintenance and the electricity supply facilities maintenance...

Ken Fukuda INOH will be down from Feb 3 to Feb 5. Our host server at the Human Genome Center (HGC) will be shutdown due to scheduled system maintenance. ------------------------------------------------------------------------- NOTICE Due to the system maintenance and the electricity supply facilities maintenance , we will turn down all Supercomputers at HGC Until the maintenance of Supercomputers is completed, you will be unable to login the Supercomputers nor to use Web service during the following period: February 3, 2007 9:00 - February 5, 2007 9:00 The e-mail service will be stopped the following period: February 3, 2007 12:30 - February 3, 2007 17:00 The e-mail service will be temporarily suspended for 10-15min during 5-10pm. Sorry for any inconveniences that it may cause. System Administrator Super Computer System Human Genome Center tag:www.inoh.org,2006:/inohblog/main//2.35 2006-11-01T07:59:44Z 2006-11-01T08:04:44Z

The latest MoleculeRole Ontology is Ver2.20 MoleculeRole Ontology is an ontology for proteins. You can download it from the OBO site and from our download page. Statistics ========== All entries 8457 Chemicals 592 Proteins 7864 Obsoletes 23 UniProt ACs 5286...

Satoko Yamamoto OBO site and from our download page. Statistics ========== All entries 8457 Chemicals 592 Proteins 7864 Obsoletes 23 UniProt ACs 5286 GO IDs 322 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 78]]> MoleculeRole Ontology Release Notes ===================== Version: 2.20 (Nov 1, 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 8457 Chemicals 592 Proteins 7864 Obsoletes 23 UniProt ACs 5286 GO IDs 322 InterPro ACs 32 KEGG COMPOUND IDs 587 PubMed IDs 78 tag:www.inoh.org,2006:/inohblog/main//2.34 2006-09-28T13:02:04Z 2006-09-30T13:24:34Z

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....

Ken Fukuda 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. tag:www.inoh.org,2006:/inohblog/main//2.30 2006-08-23T01:19:37Z 2007-04-03T10:21:55Z

The latest Event Ontology is Ver.1.60 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....

Ken Fukuda The latest Event Ontology is Ver.1.60 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. Event Ontology Release Notes ===================== Version: 1.60 (23th Aug. 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 1.59 ===================== [Added terms and definitions] 1. terms related to molecular interaction (e.g., IEV_0002721:enzymatic reaction) 2. definitions related to pathway (e.g., IEV_0000208:IKK-NF-kappaB cascade) 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 2666 Obsoletes 21 definition 299 GO IDs 259 KEGG PATHWAY IDs 173 Reactome IDs 110 PSI-MI IDs 53 tag:www.inoh.org,2006:/inohblog/main//2.29 2006-08-10T08:12:55Z 2006-08-10T08:29:39Z

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....

Ken Fukuda 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" tag:www.inoh.org,2006:/inohblog/main//2.24 2006-05-12T07:35:20Z 2006-05-12T07:38:43Z

The latest INOH Client is Ver1.0.6 INOH Client Tool is a Java Application to edit and search our pathway data. User's manual Download Release Notes ====================== Version 1.0.6 bug fixes in "Type" edit slot of "SequenceFeature" Version 1.0.5 mouse-wheel support:...

Hiromi Nakamura User's manual Download Release Notes ====================== Version 1.0.6 bug fixes in "Type" edit slot of "SequenceFeature" Version 1.0.5 mouse-wheel support: Scroll Wheel - Pan vertically Ctrl+Scroll Wheel - Zoom ]]>