Biodynamic Ontology: Applying BFO in the Biomedical Domain

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Abstract
Current approaches to formal representation in biomedicine are characterized by their focus on either the static or the dynamic aspects of biological reality. We here outline a theory that combines both perspectives and at the same time tackles the by no means trivial issue of their coherent integration. Our position is that a good ontology must be capable of accounting for reality both synchronically (as it exists at a time) and diachronically (as it unfolds through time), but that these are two quite different tasks, whose simultaneous realization is by no means trivial. The paper is structured as follows. We begin by laying out the methodological and philosophical background of our approach. We then summarize the structure and elements of the Basic Formal Ontology on which it rests, in particular the SNAP ontology of objects and the SPAN ontology of processes. Finally, we apply the general framework to the specific domain of biomedicine.
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Archival date: 2019-08-06
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The Ontology for Biomedical Investigations.Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Bug, Bill; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A.; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L. & Zheng, Jie
Flexibility and Utility of the Cell Cycle Ontology.Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De Baets, Bernard; Kuiper, Martin & Stevens, Robert
MIREOT: The Minimum Information to Reference an External Ontology Term.Courtot, Mélanie; Gibson, Frank; Lister, Allyson L.; Malone, James; Schober, Daniel; Brinkman, Ryan R. & Ruttenberg, Alan
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses.Cooper, Laurel; Walls, Ramona; Elser, Justin; Gandolfo, Maria A.; Stevenson, Dennis W.; Smith, Barry & Others,
A Terminological and Ontological Analysis of the NCI Thesaurus.Ceusters, Werner; Smith, Barry & Goldberg, Louis

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