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<title>Basic Formal Ontology (BFO) | Publications</title>
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<td id="header-left" nowrap="true"><a href="."><span id="logo-left">BFO</span><span id="logo-right">Basic Formal Ontology</span></h1></a></td>
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<td id="menu-left" nowrap="true"><a href="..">Home</a><a href="https://github.com/bfo-ontology/BFO/wiki">GitHub</a><a href="https://mitpress.mit.edu/building-ontologies">Guidebook</a><a href="publications.html">Publications</a><a href="fol.html">FOL</a><a href="users.html">Users</a><!--a href="/">IFOMIS</a--></td>
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<h2>Publications</h2>
<h4>Papers</h4>
<ul>
<li><a href="http://mitpress.mit.edu/books/building-ontologies-basic-formal-ontology">Robert Arp, Barry Smith and Andrew Spear: "Building Ontologies with Basic Formal Ontology", MIT Press, 2015</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/Classifying_Processes.pdf">Barry Smith: "Classifying Processes: An Essay in Applied Ontology", Ratio, 25:4 (2012), 463-488</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/Functions-in-BFO.pdf">Andrew Spear, Werner Ceusters and Barry Smith: "Functions in Basic Formal Ontology", Applied Ontology, 11:2 (2016), 103-128</a></li>
<li><a href="http://ontology.buffalo.edu/ido/Dispositions_and_IDO.pdf">Albert Goldfain, Barry Smith and Lindsay Cowell: "Dispositions and the Infectious Disease Ontology", Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010), IOS Press, 2010, 400-413</a></li>
<li><a href="https://philpapers.org/rec/TREAAO">Kerry Trentelman, Barry Smith: "An Axiomatisation of Basic Formal Ontology with Projection Functions", Advances in Ontologies, Proceedings of the Sixth Australasian Ontology Workshop (AOW 2010), ACS, 2010, 71-80</a></li>
<li><a href="https://philpapers.org/archive/SMIOCM.pdf">Barry Smith: "On Classifying Material Entities in Basic Formal Ontology", Interdisciplinary Ontology. Proceedings of the Third Interdisciplinary Ontology Meeting, Keio University Press, 2012, 1-13</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/fois2014.pdf">Selja Seppälä, Barry Smith and Werner Ceusters: "Applying the Realism-Based Ontology-Versioning Method for Tracking Changes in the Basic Formal Ontology", Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2014), IOS Press, 2014, 227-240</a></li>
<li><a href="https://philpapers.org/rec/FURDOA">Francesco Furini, Rahul Rai, Giorgio Colombo, Barry Smith and Venkat Krovi: "Development of a Manufacturing Ontology for Functionally Graded Materials", Proceedings of International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE 2016)</a></li>
<li><a href="http://ontology.buffalo.edu/medo/biodynamic.pdf">Pierre Grenon, Barry Smith and Louis Goldberg: "Biodynamic Ontology: Applying <em>BFO</em> in the Biomedical Domain"</a></li>
<li><a href="http://ontology.buffalo.edu/medo/gmds2004Norm.pdf">Thomas Bittner and Barry Smith: "Normalizing Medical Ontologies using Basic Formal Ontology"</a></li>
<li><a href="http://ontology.buffalo.edu/medo/Cologne.pdf">Jonathan Simon and Barry Smith: "Using Philosophy to Improve the Coherence and Interoperability of Applications Ontologies"</a></li>
<li><a href="http://ontology.buffalo.edu/geo/sto.pdf">Thomas Bittner: "Formal Ontologies for Space and Time"</a></li>
</ul>
<h3>WonderWeb</h3>
<ul>
<li><a href="http://www.loa.istc.cnr.it/old/Papers/D18.pdf">Claudio Masolo, Stefano Borgo, Aldo Gangemi, Nicola Guarino and Alessandro Oltramari: "WonderWeb Deliverable D18: Ontology Library"</a></li>
</ul>
<h3>Papers on Ontology and Formal Ontology</h3>
<h4>The Big Picture</h4>
<ul>
<li><a href="http://ontology.buffalo.edu/smith//articles/lfo.pdf">Barry Smith: "Logic and Formal Ontology", <i>Manuscrito</i>, 23: 2, 2000, 275-323.</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/fois1998.pdf">Barry Smith: "Basic Concepts of Formal Ontology"</a>, <i>Formal Ontology in Information Systems</i>, Amsterdam, Oxford, Tokyo, Washington, DC: IOS Press (Frontiers in Artificial Intelligence and Applications), 1998, 19-28.</li>
<li><a href="http://ontology.buffalo.edu/smith/articles/ontology_pic.pdf">Barry Smith: "Ontology", <i>Blackwell Guide to the Philosophy of Computing and Information</i>, Oxford: Blackwell, 2003, 155-166</a></li>
</ul>
<h4>On Concepts</h4>
<ul>
<li><a href="http://ontology.buffalo.edu/bfo/BeyondConcepts.pdf">Barry Smith: "Beyond Concepts: Ontology as Reality Representation"</a>, Achille Varzi and Laure Vieu (eds.), <i>Formal Ontology in Information Systems. Proceedings of the Third International Conference</i> (FOIS 2004), Amsterdam: IOS Press, 2004, 73-84. </li>
<li><a href="http://hem.passagen.se/ijohansson/information4.PDF">Ingvar Johansson: "Bioinformatics and Biological Reality"</a></li>
</ul>
<h4>Ontology Terminology</h4>
<ul>
<li><a href="http://ontology.buffalo.edu/bfo/Terminology_for_Ontologies.pdf">Barry Smith, Waclaw Kusnierczyk, Daniel Schober and Werner Ceusters: "Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain"</a>, Barry Smith, Waclaw Kusnierczyk, Daniel Schober, Werner Ceusters, "Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain", O. Bodenreider, ed., <i>Proceedings of KR-MED</i> (CEUR, 222), 2006, 57-66.</li>
</ul>
<h4>Dissertations</h4>
<ul>
<li><a href="documents/seyed-shapiro-fois-2012.pdf">Patrice Seyed and Stuart Shapiro: "A Method for Evaluating Ontologies - Introducing the BFO-Rigidity Decision Tree Wizard"</a></li>
</ul>
<h3>Best Ontology Practices</h3>
<ul>
<li><a href="http://ontology.buffalo.edu/medo/Database_Integration.pdf">Barry Smith, Jacob Köhler and Anand Kumar: "On the Application of Formal Principles to Life Science Data: A Case Study in the Gene Ontology"</a>, in <i>Proceedings of DILS 2004</i> (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994), Berlin: Springer, 2004, 79-94.</li>
<li><a href="http://ontology.buffalo.edu/medo/NCIT.pdf">Werner Ceusters , Barry Smith, Louis Goldberg: "A Terminological and Ontological Analysis of the NCI Thesaurus"</a>, in <i>Proceedings of DILS 2004</i> (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics 2994), Berlin: Springer, 2004, 79-94.</li>
<li><a href="http://www.biomedcentral.com/content/pdf/1471-2105-7-212.pdf">Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith: "Quality Control for Terms and Definitions in Ontologies and Taxonomies"</a>, <i>BMC Bioinformatics</i>, 2006, 7: 212, PMC1482721</li>
<li><a href="http://ontology.buffalo.edu/bfo/Versioning.pdf">Werner Ceusters and Barry Smith: "A Realism-Based Approach to the Evolution of Biomedical Ontologies"</a>, <i>Proceedings of the Annual AMIA Symposium</i>, Washington DC, 2006, 121-125. PMC1839444</li>
<li><a href="http://ontology.buffalo.edu/bfo/west.pdf">Barry Smith: "Against Idiosyncrasy in Ontology Development"</a>, B. Bennett and C. Fellbaum (Eds.), Formal Ontology in Information Systems (FOIS 2006), Amsterdam: IOS Press, 2006, 15-26</li>
</ul>
<h3>Specific Ontological Issues</h3>
<h4>Taxonomy and Classification</h4>
<ul>
<li><a href="http://ontology.buffalo.edu/bio/logic_of_classes.pdf">Barry Smith: "The Logic of Biological Classification and the Foundations of Biomedical Ontology"</a></li>
<li><a href="http://hem.passagen.se/ijohansson/information7.pdf">Ingvar Johansson: "Four Kinds of 'Is_A' Relations"</a></li>
</ul>
<h4>Relations</h4>
<ul>
<li><a href="http://ontology.buffalo.edu/bfo/IUC.pdf">Thomas Bittner, Maureen Donnelly and Barry Smith: "Individuals, Universals and Collections: On the Foundational Relations of Ontology"</a></li>
<li><a href="http://ontology.buffalo.edu/medo/isa.pdf">Barry Smith and Cornelius Rosse: "The Role of Foundational Relations in the Alignment of Biomedical Ontologies"</a></li>
<li><a href="http://genomebiology.com/content/pdf/gb-2005-6-5-r46.pdf">Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L. Rector and Cornelius Rosse: "Relations in Biomedical Ontologies"</a></li>
<li><a href="http://www.ifomis.org/Home/DerivationBookVersion1-2.pdf">Mathias Brochhausen: "The Derives_From Relation in Biomedical Ontologies"</a></li>
<li>More about <a href="http://obo.sourceforge.net/relationship">"Relations in Biomedical Ontologies"</a></li>
</ul>
<h4>Ontological Topics</h4>
<ul>
<li><a href="http://www.ontosverlag.com/index.php?page=shop.product_details&flypage=flypage.tpl&product_id=108&category_id=13&option=com_virtuemart&Itemid=1&lang=en">Katherine Munn, Barry Smith (Eds.): "Applied Ontology: An Introduction"</a></li>
<li><a href="http://ontology.buffalo.edu/smith/book/P&M">Barry Smith (Ed.) "Parts and Moments: Studies in Logic and Formal Ontology"</a></li>
<li><a href="http://ontology.buffalo.edu/bfo/Tendencies.pdf">Ludger Jansen: "Tendencies and other Realizables in Medical Information Sciences</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/Mereotopology1.pdf">Barry Smith: "Mereotopology: A Theory of Parts and Boundaries"</a></li>
<li><a href="http://ontology.buffalo.edu/bfo/SQU.pdf">Fabian Neuhaus, Pierre Grenon, Barry Smith: "A Formal Theory of Substances, Qualities, and Universals"</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/chisholm/chisholm.pdf">Barry Smith: "Boundaries: An Essay in Mereotopology"</a></li>
<li><a href="http://home.arcor.de/metaphysicus/Texte/tendencies%20WSPI2006%20proc.pdf">Ludger Jansen: "The Ontology of Tendencies and Medical Information Science"</a></li>
<li><a href="documents/schneider-fois2010.pdf">Luc Schneider: "Revisiting the Ontological Square"</a></li>
<li><a href="http://www.biomedcentral.com/1471-2105/11/289">Lars Vogt: "Spatio-structural granularity of biological material entities"</a>
<li><a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194171">Johannes Röhl and Ludger Jansen: "Representing Dispositions"</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/greensboro.html">Barry Smith: "On Substances, Accidents and Universals: In Defence of a Constituent Ontology", Philosophical Papers, 26 (1997), 105-127</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/SNAP_SPAN.pdf">Pierre Grenon and Barry Smith: "SNAP and SPAN: Towards Dynamic Spatial Ontology", Spatial Cognition and Computation, 4: 1 (March 2004), 69-103</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/cornucopia.pdf">Barry Smith and Pierre Grenon: "The Cornucopia of Formal-Ontological Relations", Dialectica 58: 3 (2004), 279-296</a></li>
<li><a href="http://genomebiology.com/2005/6/5/R46">Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan Rector and Cornelius Rosse: "Relations in Biomedical Ontologies", Genome Biology (2005), 6 (5), R46</a></li>
<li><a href="http://www.acsu.buffalo.edu/~bittner3/Publications_files/Bittner-NA-2006-28.pdf">Thomas Bittner, Maureen Donnelly and Barry Smith: "A Spatio-Temporal Ontology for Geographic Information Integration", International Journal for Geographical Information Science, 23 (6), 2009, 765-798</a></li>
<li><a href="http://iospress.metapress.com/content/1551884412214u67/fulltext.pdf">Barry Smith and Werner Ceusters: "Ontological Realism as a Methodology for Coordinated Evolution of Scientific Ontologies", Applied Ontology, 5 (2010), 139-188</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/fois1998.pdf">Barry Smith: "The Basic Tools of Formal Ontology", in Nicola Guarino (ed.), Formal Ontology in Information Systems Amsterdam, Oxford, Tokyo, Washington, DC: IOS Press (Frontiers in Artificial Intelligence and Applications), 1998, 19-28</a></li>
<li><a href="http://ontology.buffalo.edu/bfo/Against_Fantology.pdf">Barry Smith: "Against Fantology", in Johann C. Marek and Maria E. Reicher (eds.), Experience and Analysis, Vienna: HPT&ÖBV, 2005, 153-170</a></li>
<li><a href="http://ontology.buffalo.edu/smith/articles/realizables.pdf">Robert Arp and Barry Smith: "Function, Role, and Disposition in Basic Formal Ontology", Proceedings of Bio-Ontologies Workshop (ISMB 2008), Toronto, 45-48</a></li>
<li><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0018794">Lars Vogt, Peter Grobe, Björn Quast and Thomas Bartolomaeus: "Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology"</a></li>
<li><a href="http://link.springer.com/article/10.1186/s13326-016-0058-0">Patrick Ray, Alexander Cox, Mark Jensen, Travis Allen, William Duncan, Alexander Diehl: "Representing Vision and Blindness"</a></li>
<li>More about <a href="http://ontology.buffalo.edu/smith/articles/fiat.htm">Fiat Objects</a></li>
<li>More about <a href="http://ontology.buffalo.edu/smith/articles/vagueness.htm">Granular Partitions</a></li>
</ul>
<h4>Miscellaneous</h4>
<ul>
<li><a href="http://www.disi.unige.it/person/MascardiV/Download/DISI-TR-06-21.pdf">Viviana Mascardi, Valentina Cordi and Paolo Rosso: "A Comparison of Upper Ontologies"</a></li>
<li><a href="http://www.meteck.org/files/swt09/DolceliteBFOinDLandMSyntax.pdf">Maria Keet: "Examples: DOLCE and BFO in DL and Manchester syntax"</a></li>
<li><a name="salmen"/><a href="http://ontology.buffalo.edu/smith/articles/STIDS_2011.pdf">David Salmen, Tatiana Malyuta, Alan Hansen, Shaun Cronen and Barry Smith: "Integration of Intelligence Data through Semantic Enhancement"</a> (see <a href="users#militaryontology">project<a/>)</li>
</ul>
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