Table of Contents

All Articles

• BioAssay Ontology: Modularization, Integration and Applications by Uma D. Vempati, Hande Küçük, Saminda Abeyruwan, Ubbo Visser, Ahsan Mir, Vance Lemmon, Stephan C. Schürer
• Dizeez: an online game for human gene-disease annotation by Salvatore Loguercio, Benjamin M. Good, Andrew I. Su
• A Task-Based Approach For Gene Ontology Evaluation by Erik L. Clarke, Benjamin M. Good, Andrew I. Su
• Ontology-driven visualisation of NHGRI GWAS data by Danielle Welter, Tony Burdett, Lucia Hindorff, Heather Junkins, Simon Jupp, Jackie MacArthur, Helen Parkinson
• Query Enhancement through the Practical Application of Ontology: The IEDB and OBI by Randi Vita, Jason A. Greenbaum, Alessandro Sette, OBI consortium, Bjoern Peters
• Continuous Integration of Open Biological Ontology Libraries by Christopher J. Mungall, Heiko Dietze, Seth J Carbon, Amelia Ireland, Sebastian Bauer, Suzanna Lewis
• Using Entropy Estimates for DAG-Based Ontologies by Andrew Warren, João C. Setubal
• Increased Expressivity of Gene Ontology Annotations by Christopher J. Mungall, Amelia Ireland, Valerie Wood, Midori Harris, David Hill, Paul D. Thomas, Emily Dimmer
• The Human Studies Database Project Uses the Ontology of Clinical Research to Federate Human Studies Information by Simona Carini, Samson W. Tu, Landon T. Detwiler, Karl Burke, Jim Brinkley, Ida Sim
• Automated Annotation of Abstracts for Cognitive Experiments by Chayan Chakrabarti, George F. Luger, Angie R. Laird, Jessica A. Turner
• A data-driven approach to automatic discovery of prescription drugs in cardiovascular risk management by Soroush Samadian, Benjamin M. Good, Bruce McManus, Mark D. Wilkinson
• Development of a toxicological Ontology for the OECD QSAR Toolbox by Olga Tcheremenskaia, Romualdo Benigni, Cecilia Bossa, Monika Batke, Thomas Baier, Doris Hirmann, Terry Schultz
• Analysis of MeSH and IPC as a Prerequisite for Guided Patent Search by D. Eisinger, T. Wächter, M. Bundschus, U. Wieneke, M. Schroeder
• Bottom-up curation of terminology for experimental variables: the Ontology of Experimental Variables and Values (OoEVV) by Gully A.P.C. Burns, Jessica A. Turner
• DOMEO: a web-based tool for semantic annotation of online documents by Paolo Ciccarese, Marco Ocana, Tim Clark
• Automated Assessment of High Throughput Hypotheses on Gene Regulatory Mechanisms Involved in the Gastrin Response by Sushil Tripathi, Aravind Venkatesan, Mikel Egaña Aranguren, Zahra Zavareh, Konika Chawla, Vladimir Mironov, Liv Thommesen, Torunn Bruland, Martin Kuiper, Astrid Lægreid
• Linking genes to diseases with a SNPedia-Gene Wiki mashup by Benjamin M. Good, Salvatore Loguercio, Andrew I. Su
• Using Multiple Ontologies to Annotate and Integrate Phenotype Records from Multiple Sources by Mary Shimoyama, Rajni Nigam, Melinda Dwinell
• The Vertebrate Bridging Ontology (VBO) by Ravensara Travillian, James Malone, Chao Pang, John Hancock, Peter W.H. Holland, Paul Schofield, Helen Parkinson
• The EDAM ontology for bioinformatics tools and data by Jon Ison, Matus Kalas, Steve Pettifer, Peter Rice
• "Of Mice and Men" Revisited: Basic Quality Checks for Reference Alignments Applied to the Human-Mouse Anatomy Alignment by Elena Beisswanger, Udo Hahn
• CALOHA: A new human anatomical ontology as a support for complex queries and tissue expression display in neXtProt. by Paula D. Duek, Anne Gleizes, Catherine Zwahlen, Anaïs Mottaz, Amos Bairoch, Lydie Lane
• OpenTox Predictive Toxicology Framework: toxicological ontology and semantic media wiki-based OpenToxipedia by Olga Tcheremenskaia, Romualdo Benigni, Ivelina Nikolova, Nina Jeliazkova, Sylvia E.Escher, Helvi Grimm, Thomas Baier, Vladimir Poroikov, Alexey Lagunin, Micha Rautenberg, Barry Hardy
• An Ontology of Annotation Content Structure and Provenance by Kevin M. Livingston, Michael Bada, Lawrence E. Hunter, Karin M. Verspoor
• EMO – The Enzyme Mechanism Ontology by Julius O. B. Jacobsen, Nicholas Furnham, Gemma L. Holliday
• Relating Processes and Events for Granularity-neutral Modeling by Niels Grewe
• Records and situations. Integrating contextual aspects in clinical ontologies by Stefan Schulz, Daniel Karlsson
• A Maximum-Entropy Approach for Accurate Document Annotation in the Biomedical Domain by George Tsatsaronis, Natalia Macari, Sunna Torge, Heiko Dietze, Michael Schroeder
• Vital Sign Ontology by Albert Goldfain, Barry Smith, Sivaram Arabandi, Mathias Brochhausen, William R. Hogan
• What’s new and what’s changing in ChEBI in 2011 by Janna Hastings, Paula de Matos, Adriano Dekker, Marcus Ennis, Kenneth Haug, Zara Josephs, Gareth Owen, Steve Turner, Christoph Steinbeck
• An Ontological Representation of Biomedical Data Sources and Records by Michael Bada, Kevin Livingston, Lawrence Hunter
• Processes and properties by Colin Batchelor, Janna Hastings, Christoph Steinbeck
• The State of Bio-Medical Ontologies by Matthew Horridge, Bijan Parsia, Ulrike Sattler
• Exploring Gene Ontology Annotations with OWL by Simon Jupp, Robert Stevens, Robert Hoehndorf
• An exercise in kidney factomics: From article titles to RDF knowledge base by James M. Eales, George Demetriou, Robert Stevens
• The Coriell Cell Line Ontology: Rapidly Developing Large Ontologies by Chao Pang, Tomasz Adamusiak, Helen Parkinson, James Malone

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