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  1. The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration.Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J. Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J. Mungall, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Nigam Shah, Patricia L. Whetzel & Suzanna Lewis - 2007 - Nature Biotechnology 25 (11):1251-1255.
    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...)
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  2. The Ontology for Biomedical Investigations.Anita Bandrowski, Ryan Brinkman, Mathias Brochhausen, Matthew H. Brush, Bill Bug, Marcus C. Chibucos, Kevin Clancy, Mélanie Courtot, Dirk Derom, Michel Dumontier, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Frank Gibson, Alejandra Gonzalez-Beltran, Melissa A. Haendel, Yongqun He, Mervi Heiskanen, Tina Hernandez-Boussard, Mark Jensen, Yu Lin, Allyson L. Lister, Phillip Lord, James Malone, Elisabetta Manduchi, Monnie McGee, Norman Morrison, James A. Overton, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H. Scheuermann, Daniel Schober, Barry Smith, Larisa N. Soldatova, Christian J. Stoeckert, Chris F. Taylor, Carlo Torniai, Jessica A. Turner, Randi Vita, Patricia L. Whetzel & Jie Zheng - 2016 - PLoS ONE 11 (4):e0154556.
    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...)
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  3. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.Chris F. Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R. Brinkman, Adam Michael Clark, Eric W. Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M. Hancock, Nigel W. Hardy, Henning Hermjakob, Randall K. Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novere, Jim Leebens-Mack, Suzanna E. Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M. Reecy, Donald G. Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H. Scheuermann, Daniel Schober, Barry Smith & Jason Snape - 2008 - Nature Biotechnology 26 (8):889-896.
    Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...)
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    Overcoming the ontology enrichment bottleneck with Quick Term Templates.Philippe Rocca-Serra, Alan Ruttenberg, Martin J. O'Connor, Patricia L. Whetzel, Daniel Schober, Jay Greenbaum, Mélanie Courtot, Ryan R. Brinkman, Susanna Assunta Sansone & Richard Scheuermann - 2011 - Applied ontology 6 (1):13-22.
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