The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process

The Cell Cycle Ontology (http://www.CellCycleOntology.org) is an application ontology that automatically captures and integrates detailed knowledge on the cell cycle process. Cell Cycle Ontology is enabled by semantic web technologies, and is accessible via the web for browsing, visualizing, advanced querying, and computational reasoning. Cell Cycle Ontology facilitates a detailed analysis of cell cycle-related molecular network components. Through querying and automated reasoning, it may provide new hypotheses to help steer a systems biology approach to biological network building.

[1]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[2]  Hiroyuki Ogata,et al.  KEGG: Kyoto Encyclopedia of Genes and Genomes , 1999, Nucleic Acids Res..

[3]  Stefan Hohmann,et al.  Topics in current genetics , 2003 .

[4]  Carole A. Goble,et al.  State of the nation in data integration for bioinformatics , 2008, J. Biomed. Informatics.

[5]  Jeff Z. Pan,et al.  Resource Description Framework , 2020, Definitions.

[6]  Feng Chen,et al.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups , 2005, Nucleic Acids Res..

[7]  T. Ideker,et al.  A new approach to decoding life: systems biology. , 2001, Annual review of genomics and human genetics.

[8]  Ted Slater,et al.  Beyond data integration. , 2008, Drug discovery today.

[9]  Frank van Harmelen,et al.  Web Ontology Language , 2004 .

[10]  Thomas Yan,et al.  Practical Issues in Ontology Engineering , 2007, IC-AI.

[11]  Bernard De Baets,et al.  Structuring the Life Science Resourceome for Semantic Systems Biology: Lessons from the BioGateway Project , 2008, SWAT4LS.

[12]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[13]  H. Kitano.  Systems Biology: A Brief Overview , 2002, Science.

[14]  B. Alberts,et al.  Molecular Biology of the Cell 4th edition , 2007 .

[15]  C. Stoeckert,et al.  OrthoMCL: identification of ortholog groups for eukaryotic genomes. , 2003, Genome research.

[16]  Asunción Gómez-Pérez,et al.  METHONTOLOGY: From Ontological Art Towards Ontological Engineering , 1997, AAAI 1997.

[17]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.

[18]  Stephen P Gardner,et al.  Ontologies and semantic data integration. , 2005, Drug discovery today.

[19]  Alexander E. Kel,et al.  CYCLONET—an integrated database on cell cycle regulation and carcinogenesis , 2007, Nucleic Acids Res..

[20]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[21]  Michael Luck,et al.  Agents in bioinformatics, computational and systems biology , 2006, Briefings Bioinform..

[22]  Eva Blomqvist.  Semi-automatic Ontology Engineering Using Patterns , 2007, ISWC/ASWC.

[23]  Magdi N. Kamel,et al.  A Methodology for Developing Ontologies Using the Ontology Web Language (OWL) , 2007, ICEIS.

[24]  Robert F Murphy,et al.  Putting proteins on the map , 2006, Nature Biotechnology.

[25]  Elizabeth Pennisi.  How Will Big Pictures Emerge From a Sea of Biological Data? , 2005, Science.

[26]  Y. Zhang,et al.  IntAct—open source resource for molecular interaction data , 2006, Nucleic Acids Res..

[27]  Michael Uschold,et al.  Ontologies: principles, methods and applications , 1996, The Knowledge Engineering Review.

[28]  Steffen Staab,et al.  International Handbooks on Information Systems , 2013 .

[29]  Werner Ceusters,et al.  Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain , 2006, KR-MED.

[30]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[31]  Scott Boag,et al.  XQuery 1.0 : An XML Query Language , 2007 .

[32]  Gary An,et al.  Translational Systems Biology of Inflammation , 2008, PLoS Comput. Biol..

[33]  Diego Calvanese,et al.  The Description Logic Handbook: Theory, Implementation, and Applications , 2003, Description Logic Handbook.

[34]  Nicola Guarino,et al.  Formal Ontology and Information Systems , 1998 .

[35]  P. Bork,et al.  Evolution of Cell Cycle Control: Same Molecular Machines, Different Regulation , 2007, Cell cycle.

[36]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[37]  Ian Horrocks,et al.  The OBO to OWL Mapping, GO to OWL 1.1! , 2007, OWLED.

[38]  Evelyn Camon,et al.  Methods for gene ontology annotation. , 2007, Methods in molecular biology.

[39]  Judith A. Blake,et al.  Gene Ontology annotations: what they mean and where they come from , 2008, BMC Bioinformatics.

[40]  Peter Buneman,et al.  Challenges in Integrating Biological Data Sources , 1995, J. Comput. Biol..

[41]  Zhenjun Hu,et al.  VisANT 3.0: new modules for pathway visualization, editing, prediction and construction , 2007, Nucleic Acids Res..

[42]  John J. Tyson,et al.  Temporal Organization of the Cell Cycle , 2008, Current Biology.

[43]  Matteo Cristani,et al.  A Survey on Ontology Creation Methodologies , 2005, Int. J. Semantic Web Inf. Syst..

[44]  Bob J. Wielinga,et al.  Using explicit ontologies in KBS development , 1997, Int. J. Hum. Comput. Stud..

[45]  Stephen A. Racunas,et al.  HyBrow: a prototype system for computer-aided hypothesis evaluation , 2004, ISMB/ECCB.

[46]  U. Sauer,et al.  Getting Closer to the Whole Picture , 2007, Science.

[47]  Daniel L. Rubin,et al.  Biomedical ontologies: a functional perspective , 2007, Briefings Bioinform..

[48]  Bernard De Baets,et al.  ONTO-PERL: An API for supporting the development and analysis of bio-ontologies , 2008, Bioinform..

[49]  Robert Stevens,et al.  The Manchester OWL Syntax , 2006, OWLED.

[50]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[51]  G Stix,et al.  The mice that warred. , 2001, Scientific American.

[52]  Xiaoshu Wang,et al.  From XML to RDF: how semantic web technologies will change the design of 'omic' standards , 2005, Nature Biotechnology.

[53]  Mark A. Musen,et al.  OBO to OWL: a protégé OWL tab to read/save OBO ontologies , 2007, Bioinform..

[54]  James A. Hendler,et al.  The Semantic Web: A new form of Web content that is meaningful to computers will unleash a revolution of new possibilities , 2001 .

[55]  J. Davies,et al.  Molecular Biology of the Cell , 1983, Bristol Medico-Chirurgical Journal.

[56]  Kimberly Van Auken,et al.  WormBase: a multi-species resource for nematode biology and genomics , 2004, Nucleic Acids Res..

[57]  Barry Smith,et al.  Biodynamic ontology: applying BFO in the biomedical domain. , 2004, Studies in health technology and informatics.

[58]  Jacky L. Snoep,et al.  BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..

[59]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[60]  K. Dolinski,et al.  Use and misuse of the gene ontology annotations , 2008, Nature Reviews Genetics.

[61]  Andrea Splendiani,et al.  RDFScape: Semantic Web meets Systems Biology , 2008, BMC Bioinformatics.

[62]  Jacky L. Snoep,et al.  From isolation to integration, a systems biology approach for building the Silicon Cell. , 2005 .

[63]  Asunción Gómez-Pérez,et al.  Ontological Engineering: With Examples from the Areas of Knowledge Management, e-Commerce and the Semantic Web , 2004, Advanced Information and Knowledge Processing.

[64]  L. Jensen,et al.  The more the merrier: comparative analysis of microarray studies on cell cycle‐regulated genes in fission yeast , 2006, Yeast.

[65]  Ivan Merelli,et al.  A data integration approach for cell cycle analysis oriented to model simulation in systems biology , 2007, BMC Systems Biology.

[66]  M A Musen,et al.  BioPortal: ontologies and data resources with the click of a mouse. , 2008, AMIA ... Annual Symposium proceedings. AMIA Symposium.

[67]  Deborah L. McGuinness,et al.  OWL Web ontology language overview , 2004 .

[68]  Aldo Gangemi,et al.  Ontology Design Patterns , 2005 .

[69]  P. Bork,et al.  Co-evolution of transcriptional and post-translational cell-cycle regulation , 2006, Nature.

[70]  Elena Tsiporkova,et al.  A Cell-Cycle Knowledge Integration Framework , 2006, DILS.

[71]  Robert Stevens,et al.  Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology , 2008, BMC Bioinformatics.

[72]  Sean Bechhofer,et al.  Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL , 2007, BMC Bioinformatics.

[73]  Judith A. Blake,et al.  Beyond the data deluge: Data integration and bio-ontologies , 2006, J. Biomed. Informatics.

[74]  Yin Chen,et al.  OBO Explorer: an editor for open biomedical ontologies in OWL , 2008, Bioinform..

[75]  Elizabeth Chang,et al.  Mediating Databases and The Semantic Web: A Methodology for Building Domain Ontology from Databases and Existing Ontologies , 2007, SWWS.

[76]  Robert Stevens,et al.  Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language , 2008, OWLED.

[77]  Volker Haarslev,et al.  Applying OWL Reasoning to Genomic Data , 2007 .

[78]  John Quackenbush,et al.  Data standards: a call to action. , 2006, Omics : a journal of integrative biology.

[79]  Rafael Valencia-García,et al.  Combining Semantic Web technologies with Multi-Agent Systems for integrated access to biological resources , 2008, J. Biomed. Informatics.

[80]  Gene Ontology Consortium.  The Gene Ontology (GO) database and informatics resource , 2003 .

[81]  Qiong Gao,et al.  Resources for integrative systems biology: from data through databases to networks and dynamic system models , 2006, Briefings Bioinform..

[82]  P. Bork,et al.  Dynamic Complex Formation During the Yeast Cell Cycle , 2005, Science.

[83]  C. M. Sperberg-McQueen,et al.  Extensible markup language , 1997 .

[84]  Diego Calvanese,et al.  The Description Logic Handbook , 2007 .

[85]  Alan F. Scott,et al.  Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders , 2002, Nucleic Acids Res..

[86]  Christopher G Chute,et al.  National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. , 2006, Omics : a journal of integrative biology.

[87]  Torulf Mollestad,et al.  Additional Gene Ontology structure for improved biological reasoning , 2006, Bioinform..

[88]  Bijan Parsia,et al.  Ontology Performance Profiling and Model Examination: First Steps , 2007, ISWC/ASWC.

[89]  Midori A. Harris,et al.  BIOINFORMATICS APPLICATIONS NOTE doi:10.1093/bioinformatics/btm112 Databases and ontologies OBO-Edit—an ontology editor for biologists , 2007 .

[90]  Ivan Merelli,et al.  The cell cycle DB: a systems biology approach to cell cycle analysis , 2007, Nucleic Acids Res..

[91]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt) , 2004, Nucleic Acids Res..