BFO Meets Critics - Revision history

Phismith at 12:06, 19 April 2015

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	Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe] Conference, Madrid, May 27-29, 2015		Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe] Conference, Madrid, May 27-29, 2015

	This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] ~~with~~ MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.		This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] by MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.

	*Speakers:		*Speakers:

Phismith at 14:58, 15 March 2015

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	Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe Conference], Madrid, May 27-29, 2015		Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe] Conference, Madrid, May 27-29, 2015

	This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.		This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.

Phismith at 14:51, 15 March 2015

2015-03-15T14:51:52Z

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	Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe Conference], Madrid, May 27-29, 2015		Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe Conference], Madrid, May 27-29, 2015

			This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.

	*Speakers:		*Speakers:
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	*Respondent: '''Barry SMITH''' (Philosophy and Biomedical Informatics, University at Buffalo)		*Respondent: '''Barry SMITH''' (Philosophy and Biomedical Informatics, University at Buffalo)
	*Moderator: '''Ronald CORNET''' (Medical Informatics, Academic Medical Center, Amsterdam, Netherlands)		*Moderator: '''Ronald CORNET''' (Medical Informatics, Academic Medical Center, Amsterdam, Netherlands)

	This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.

	~~'''Keywords''': Biological Ontologies, Data Curation, Medical Informatics~~

	'''1. Introduction'''		'''1. Introduction'''

Phismith at 14:50, 15 March 2015

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	'''1. Introduction'''		'''1. Introduction'''

	Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a ~~variety~~ of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.		Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a [http://ifomis.uni-saarland.de/bfo/users large number] of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.

	'''2. Ontological realism'''		'''2. Ontological realism'''

Phismith at 14:50, 15 March 2015

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	'''Keywords''': Biological Ontologies, Data Curation, Medical Informatics		'''Keywords''': Biological Ontologies, Data Curation, Medical Informatics

	'''1. Introduction ~~of the topic~~'''		'''1. Introduction'''

	Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.		Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.

Phismith at 14:49, 15 March 2015

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	'''1. Introduction of the topic'''		'''1. Introduction of the topic'''

	Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.		Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.

	'''2. Ontological realism'''		'''2. Ontological realism'''

	BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/ Schulz, et al.], these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.		BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/ Schulz, et al.], these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.
	The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.		The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.

	'''3. Panel organization'''		'''3. Panel organization'''

	The panel will begin with a brief summary of the book by Smith, to be followed by criticisms from the panelists, concluding with responses from Smith and with contributions from the audience. It is designed to be of general interest to biomedical informaticians, including those who have little technical knowledge of ontology. We will work to ensure also that the panel has a certain theatrical quality. The panelists will be invited to formulate their criticisms in a way that is maximally provocative. Smith will not receive notice of their criticisms in advance.		The panel will begin with a brief summary of the book by Smith, to be followed by criticisms from the panelists, concluding with responses from Smith and with contributions from the audience. It is designed to be of general interest to biomedical informaticians, including those who have little technical knowledge of ontology. We will work to ensure also that the panel has a certain theatrical quality. The panelists will be invited to formulate their criticisms in a way that is maximally provocative. Smith will not receive notice of their criticisms in advance.

Phismith at 14:48, 15 March 2015

2015-03-15T14:48:55Z

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	Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.		Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.

			'''2. Ontological realism'''
	BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/ Schulz, et al.], these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.		BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/ Schulz, et al.], these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.
	The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.		The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.

	'''2. ~~Organization~~'''		'''3. Panel organization'''
	The panel will begin with a brief summary of the book by Smith, to be followed by criticisms from the panelists, concluding with responses from Smith and with contributions from the audience. It is designed to be of general interest to biomedical informaticians, including those who have little technical knowledge of ontology. We will work to ensure also that the panel has a certain theatrical quality. The panelists will be invited to formulate their criticisms in a way that is maximally provocative. Smith will not receive notice of their criticisms in advance.		The panel will begin with a brief summary of the book by Smith, to be followed by criticisms from the panelists, concluding with responses from Smith and with contributions from the audience. It is designed to be of general interest to biomedical informaticians, including those who have little technical knowledge of ontology. We will work to ensure also that the panel has a certain theatrical quality. The panelists will be invited to formulate their criticisms in a way that is maximally provocative. Smith will not receive notice of their criticisms in advance.

	'''3. Short biographies of panelists'''		'''4. Short biographies of panelists'''
	*Ronald Cornet publishes on a variety of topics in medical informatics, ontology, description logic, and knowledge representation, and his works play an important role especially in the study of medical terminology systems.		*Ronald Cornet publishes on a variety of topics in medical informatics, ontology, description logic, and knowledge representation, and his works play an important role especially in the study of medical terminology systems.
	*Robert Hoehndorf is a prominent contributor to ontologies in biology, and has published papers also in knowledge representation, semantic integration, semantic interoperability and phenotype informatics. His Leipzig thesis of 2009 introduces the biological core ontology GFO-Bio, which grew in turn out of the General Formal Ontology which is in some respects an early version of BFO.		*Robert Hoehndorf is a prominent contributor to ontologies in biology, and has published papers also in knowledge representation, semantic integration, semantic interoperability and phenotype informatics. His Leipzig thesis of 2009 introduces the biological core ontology GFO-Bio, which grew in turn out of the General Formal Ontology which is in some respects an early version of BFO.

Phismith at 14:47, 15 March 2015

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	Panel Session at the [www.mie2015.es/ Medical Informatics Europe Conference], Madrid, May 27-29, 2015		Panel Session at the [http://www.mie2015.es/ Medical Informatics Europe Conference], Madrid, May 27-29, 2015

	*Speakers:		*Speakers:

Phismith at 14:47, 15 March 2015

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	'''1. Introduction of the topic'''		'''1. Introduction of the topic'''
	Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.		Since 2006 the Basic Formal Ontology (BFO) has been serving as upper level architecture in a variety of biological and biomedical ontology initiatives as part of a strategy to enhance interoperability of data and information systems. Starting with the Open Biomedical Ontologies (OBO) Foundry, and now extending to include the Neuroscience Information Framework (NIF) Standard Ontologies, the IDO suite of Infectious Disease Ontologies, the cROP Common Reference Ontologies for Plants, and the VIVO-ISF (Integrated Semantic Framework) Ontologies, BFO is supporting the creation of what is intended to serve as a robust landscape of interoperable ontologies in biomedicine.
	BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by Schulz, et al., these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.
			BFO is built on the basis of a realist methodology, and many elements of this methodology are incorporated into the ontology itself, including the distinction between the types or universals which serve as the objects of scientific theory, and the instances of these types which are observed in the lab or clinic. This realist methodology has been used in turn as the basis of a series of criticisms of the so-called ‘concept orientation’ in medical terminology research, as also of a series of influential initiatives in the field of medical standards and ontologies, including HL7 RIM, SNOMED CT, and the National Cancer Institute Thesaurus. As documented by [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3920035/ Schulz, et al.], these criticisms have contributed to a paradigm shift away from what are called ‘concept representations’ and towards ontologies in the medical terminology field. At the same time, some have criticized the realist methodology, claiming for example that it leads to overcomplexity, or that it is superfluous.
	The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.		The proposed panel is devoted to such criticisms. It takes as its starting point the publication of a new book-length introduction to BFO and beginners’ guide to ontology building in biology and biomedicine, which will be published by MIT Press in early 2015. The publisher’s summary of this work is provided below.

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	*Stefan Schulz has published a series of critical papers on BFO and related topics, including the role of realism in medical terminology research. He is also a leading figure in SNOMED CT research, in medical text and data mining, and formal methods in ontology.		*Stefan Schulz has published a series of critical papers on BFO and related topics, including the role of realism in medical terminology research. He is also a leading figure in SNOMED CT research, in medical text and data mining, and formal methods in ontology.
	*Barry Smith has published many papers in ontology.		*Barry Smith has published many papers in ontology.

	~~Building Ontologies with Basic Formal Ontology~~

	~~Robert Arp, Barry Smith, and Andrew Spear~~

	~~Cambridge, MA: MIT Press, forthcoming, spring 2015~~

	In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to new disciplinary fields such as biomedical informatics. Applied ontology offers a strategy for organizing scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use.
	After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO) now used by over 130 ontology projects throughout the world, and offers examples of domain ontologies that utilize BFO. The book also describes the Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. The work is designed to be of interest not only to biomedical ontologists working in genomics and other fields where ontologies have become a standard research tool, but also to philosophers interested in the foundations of ontology and to computer scientists interested in the ways ontologies are being used as computational artifacts.

Phismith at 14:45, 15 March 2015

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	This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.		This panel will take the form of an author meets critics session prompted by the publication of the book [http://ontology.buffalo.edu/smith/BFO-book.pdf Building Ontologies with Basic Formal Ontology] with MIT Press in 2015. The panel will feature Barry Smith, a principal developer of BFO and one of the authors of this book, together with three prominent figures in the biomedical ontology field. Smith will present a brief summary of the book, which will be followed by critical remarks by the other panelists. It will conclude with Smith’s responses to these criticisms followed by questions to all panelists from the audience.

	Keywords. Biological Ontologies, Data Curation, Medical Informatics		'''Keywords''': Biological Ontologies, Data Curation, Medical Informatics

	'''1. Introduction of the topic'''		'''1. Introduction of the topic'''