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IMPS 2005 ANNUAL MEETING OF THE PSYCHOMETRIC SOCIETY, Tilburg University, The Netherlands http://labs.systemsbiology.net/bolouri/software/BioTapestry/BioTapestry Longabaugh WJ, Davidson EH, Bolouri H.: Computational representation of developmental genetic regulatory networks. Dev Biol. 283(1):1-16 (2005) http://www.copasi.org/ Copasi Kummer, U., R. Gauges, et al. (2006). Modeling, simulating, and analyzing biochemical systems with Copasi. International Conference for Systems Biology, Yokohoma, 2006 http://pybios.molgen.mpg.de/ PyBioS http://www.sysbio.pl/stocks/ STOCKS Kierzek AM.: STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm. Bioinformatics 18(3):470-81 (2002) http://www.ihop-net.org/UniPub/iHOP/ iHOP Hoffmann R, Valencia A.: Implementing the iHOP concept for navigation of biomedical literature. Bioinformatics 21 Suppl 2:ii252-ii258 (2005) http://obo.sourceforge.net/ OBO - Open Biomedical Ontologies http://www.geneontology.org/ GO - Gene Ontology Gene Ontology Consortium.: The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34(Database issue):D322-6 (2006) http://obo.sourceforge.net/cgi-bin/detail.cgi?cellCL - Cell Ontology Bard J, Rhee SY, Ashburner M.: An ontology for cell types. Genome Biol. 6(2):R21 (2005) http://obo.sourceforge.net/cgi-bin/detail.cgi?sequenceSO - Sequence Ontology Eilbeck K, Lewis SE, Mungall CJ, et al.: The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6(5):R44 (2005) http://obo.sourceforge.net/cgi-bin/detail.cgi?attribute_and_valuePATO - Phenotype Ontology http://fugo.sourceforge.net/ FuGO - Functional Genomics Investigation Ontology http://sig.biostr.washington.edu/projects/fm/index.htmlFMA - Foundational Model of Anatomy Shapiro LG, Chung E, Detwiler LT, et al.: Processes and problems in the formative evaluation of an interface to the Foundational Model of Anatomy knowledge base. J Am Med Inform Assoc. 12(1):35-46 (2005) http://obo.sourceforge.net/relationship/ OBO_REL - Relation Ontology Smith B, Ceusters W, Klagges B, et al.: Relations in biomedical ontologies. Genome Biol. 6(5):R46 (2005) http://www.mged.org/Workgroups/MAGE/mage-ml.htmlMAGE-ML Spellman PT, Miller M, Stewart J, et al.: Design and implementation of microarray gene expression markup language (MAGE-ML). 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Proteomics. 4(2):490-1 (2004) http://www.agml.org/ AGML Stanislaus R, Jiang LH, Swartz M, et al.: An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results. BMC Bioinformatics 5:9 (2004) http://www1.biz.biglobe.ne.jp/~jhupo/index-e.htmHUP-ML Kamijo K, Mizuguchi H, Kenmochi A, et al.: An XML Format For Proteomics Database to Accelerate Collaboration Among Researchers. AO HUPO workshop in Tsukuba (2002) From: http://www1.biz.biglobe.ne.jp/~jhupo/HUP-ML/hup-ml.htm http://www.biopax.org/ BioPAX Luciano JS.: PAX of mind for pathway researchers. Drug Discov Today. 10(13):937-42 (2005) http://sbgn.org/ SBGN Expression Proteomic / Mass Metabolomic / PMID Phenotypic data Data Spec Metabonomic Data 16381918 * 16381917 * 14681444 * 15608251 * 15374875 * * 15608240 * * 16381916 * * 16381915 * * 14681421 * * 16100408 * * 15208715 * * * 12519949 * * 10779484 * 15075390 * 15608262 * 14647278 * 11752297 * 11934741 * 14681484 * 15068665 * 11752296 * NA * 14681442 * 11125075 * 12463803 * 14681424 * 14744116 * * 10424174 * 15378751 * 16381945 * 14681486 * 14976030 * 12824418 * * 14681440 * 8481818 * 15085804 * 15608266 * 16041671 * 15174122 * 15274128 * 16127175 * 16381951 * * 16381952 * * 16404815 * 15613389 * * 14681450 8594593 12584128 12519995 16381840 NA 15556481 11752324 14681366 16381958 15608156 16381825 16381926 11752348 15608232 14681455 11911893 16082366 12519993 11752321 14525934 15531608 15608231

16381923 15608197 16381885 16381854

11984561

12620107 14597658 12027436 NA 15980487 16000016

15105280 10902182 NA 9888852 15593410 NA 14871872

12538248 12438191 15642112 15142756 12611808 16381960 15072998 15273159 14683609 NA 16527832 14683609 14583116

12651737 15852513

12386006 15217809 15637632 8660575

15604106

12362430

11395441 12794268 16672256 NA 16574696 15087311 15972011 NA 15907831 NA

11934747 16204114

16381878 15693950 15892872

15492037 15892874 12225585 11726920 16333295 14755292 14760721 15005801 NA 15993813 Gene Biochemical / Interaction Metabolic Signalling Regulatory Kinetic Data Networks Pathways Pathways Databases

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Quantitative Network / model Simulation Model Text Mining Data visualisation Tools Repository network visualisation network visualisation network visualisation network visualisation network visualisation network visualisation

network visualisation

network visualisation network visualisation network visualisation network visualisation network visualisation network visualisation network visualisation model visualisation model visualisation model visualisation model visualisation * model visualisation * model visualisation * model visualisation * model visualisation * model visualisation * model visualisation * model visualisation * * model visualisation * model visualisation * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Ontology Standards Notes

Database currently under development Chemical ontology

Modelling standard Modelling standard * Gene product ontology Cell type ontology Sequence ontology Phenotypic ontology Func. genomics ontology Anatomical ontology Relationships ontology Microarray standard Microarray standard Biochemical standard Interaction standard Proteomic standard Proteomic standard Proteomic standard Pathway standard Network standard