Ontology Research Group

PUBLICATIONS OF ORG RESEARCHERS

2005

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.

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

Werner Ceusters, Barry Smith and Louis Goldberg, “A Terminological and Ontological Analysis of the NCI Thesaurus”, Methods of Information in Medicine, 44 (2005), 498-507.

Objective: The National Cancer Institute Thesausus is described by its authors as “a biomedical vocabulary that provides consistent, unambiguous codes and definitions for concepts used in cancer research” and which “exhibits ontology-like properties in its construction and use”. We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. Materials and methods: We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Results: We found many mistakes and inconsistencies with respect to the termformation principles used, the underlying knowledge representation system, and missing or inappropriately assigned verbal and formal definitions. Conclusion: Version 04.08b of the NCI Thesaurus suffers from the same broad range of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent.

Barry Smith, Werner Ceusters, Anand Kumar and Cornelius Rosse, “On Carcinomas and Other Pathological Entities”, Comparative and Functional Genomics, vol. 6, issue 7/8, 2005, 379-387.

Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. Includes a classification of biomedical entities which revises the classification provided in Rosse, et al.

Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst and Dirk Siebert, “Functional Anatomy: A Taxonomic Proposal”, Acta Biotheoretica, 53(3), 2005, 153-166.

It is argued that medical science requires a classificatory system that (a) puts functions in the taxonomic center and (b) does justice ontologically to the difference between the processes which are the realizations of functions and the objects which are their bearers. We propose formulae for constructing such a system and describe some of its benefits. The arguments are general enough to be of interest to all the life sciences.

Jonathan Simon, James Fielding, Mariana Dos Santos and Barry Smith, “Formal Ontology for Natural Language Processing and the Integration of Biomedical Databases”, International Journal of Medical Informatics, 75 (3-4), 2005, 224-231.

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end LinKBase‘, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase‘ are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase‘ structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase‘ as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase‘ is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”.

Barry Smith, “The Logic of Biological Classification and the Foundations of Biomedical Ontology”, in Petr Haacutejek, Luis Valdés-Villanueva and Dag Westerståhl (ed.), Logic, Methodology and Philosophy of Science. Proceedings of the 12th International Conference, London: King’s College Publications, 2005, 505-520.

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances.

Barry Smith, “Against Fantology”, in Johann C. Marek and Maria E. Reicher (eds.), Experience and Analysis, Vienna: HPT&ÖBV, 2005, 153-170.

A dark force haunts much of what is most admirable in the philosophy of the last one hundred years. It consists, briefly put, in the doctrine to the effect that one can arrive at a correct ontology by paying attention to certain superficial (syntactic) features of first-order predicate logic as conceived by ar and Russell. More specifically, it is a doctrine to the effect that the key to the ontological structure of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of first-order logic, where ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “fantology”. Because predicate logic has exactly two syntactically different kinds of referring expressionsmdash;‘F’, ‘G’, ‘R’, etc., and ‘a’, ‘b’, ‘c’, etc.mdash;so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects), the relation between these two kinds of entity being revealed in the predicate-argument structure of atomic formulas in first-order logic.

Anand Kumar and Barry Smith, “Oncology Ontology in the NCI Thesaurus”, AIME 2005 (Artificial Intelligence in Medicine Europe), (Lecture Notes in Computer Science 3581), 213-220.

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future.

Barry Smith, Werner Ceusters and Rita Temmerman, “Wüsteria”, Medical Informatics Europe (MIE 2005), Geneva, Stud Health Technol Inform. 2005;116:647-652.

The last two decades have seen considerable efforts directed towards making Electronic Health Records interoperable through improvements in medical ontologies, terminologies and coding systems. Unfortunately, these efforts have been hampered by a number of influential ideas inherited from the work of Eugen Wüster, the father of terminology standardization and the founder of ISO TC 37. We here survey Wüster’s ideas - which see terminology work as being focused on the classification of concepts in people’s minds - and we argue that they serve still as the basis for a series of influential confusions. We argue further that an ontology based unambiguously, not on concepts, but on the classification of entities in reality can, by removing these confusions, make a vital contribution to ensuring the interoperability of coding systems and healthcare records in the future.

Werner Ceusters and Barry Smith, “Tracking Referents in Electronic Health Records”, Medical Informatics Europe (MIE 2005), Geneva, Stud Health Technol Inform. 2005;116:71-76.

Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in which all clinically salient particulars - from the concrete disorder on the side of the patient and the body parts in which it occurs to the concrete treatments given - should be uniquely identified. This will allow us to achieve interoperability among different systems of records at the level where it really matters: in regard to what is happening in the real world. It will also allow us to keep track of particular disorders and of the effects of particular treatments in a precise and unambiguous way. We discuss the ontological and epistemological aspects of our claim and describe a scenario for implementation within EHR systems.

Anand Kumar, Y. Lina Yip, Barry Smith, Dirk Marwede and Daniel Novotny, “An Ontology for Carcinoma Classification for Clinical Bioinformatics”, Medical Informatics Europe (MIE 2005), Stud Health Technol Inform. 2005;116:635-40.

There are a number of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications represent classes of entities which exist at various anatomical levels of granularity. We argue that in order to apply such representations to the Electronic Health Records one needs sound ontologies which take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a way that the ontologies can be used to support inferences relating to entities which exist at different anatomical levels of granularity. Our case study is the colon carcinoma, one of the most common carcinomas prevalent within the European population.

Louis J. Goldberg, Werner Ceusters, John Eisner and Barry Smith, “The Significance of SNODENT”, Medical Informatics Europe (MIE 2005), Geneva, Stud Health Technol Inform. 2005;116:737-742.

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT’s manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and maintenance. This paper builds on previous software-based methodologies designed to assess the quality of SNOMED-CT.

Barry Smith, Jose L.V. Mejino Jr., Stefan Schulz, Anand Kumar and Cornelius Rosse, “Anatomical Information Science”, in A. G. Cohn and D. M. Mark (eds.), Spatial Information Theory. Proceedings of COSIT 2005 (Lecture Notes in Computer Science), Berlin/Heidelberg/New York: Springer, 149-164.

The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts - including the map-like representations we find in familiar anatomical atlases - it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its object-domain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general.

Stephan Schulz, Philipp Daumke, Barry Smith and Udo Hahn, “How to Distinguish Parthood from Location in Bioontologies”, Proceedings of AMIA Symposium 2005, Washington DC, 669-673.

The pivotal role of the relation part-of in the description of living organisms is widely acknowledged. Organisms are open systems, which means that in contradistinction to mechanical artifacts they are characterized by a continuous flow and exchange of matter. A closer analysis of the spatial relations in biological organisms reveals that the decision as to whether a given particular is part-of a second particular or whether it is only contained-in the second particular is often controversial. We here propose a rule-based approach which allows us to decide on the basis of well-defined criteria which of the two relations holds between two anatomical objects, given that one spatially includes the other. We discuss the advantages and limitations of this approach, using concrete examples from human anatomy.

Barry Smith and Werner Ceusters, “A Methodology for the Migration of Medical Terminologies to Electronic Health Records”, Proceedings of AMIA Symposium 2005, Washington DC, 704-708.

Biomedical terminologies are focused on what is general, Electronic Health Records (EHRs) on what is particular, and it is commonly assumed that the step from the one to the other is unproblematic. We argue that this is not so, and that, if the EHR of the future is to fulfill its promise, then the foundations of both EHR architectures and biomedical terminologies need to be reconceived. We accordingly describe a new framework for the treatment of both generals and particulars in biomedical information systems that is designed: 1) to provide new opportunities for the sharing and management of data within and between healthcare institutions, 2) to facilitate interoperability among different terminology and record systems, and thereby 3) to allow new kinds of reasoning with biomedical data.

Cornelius Rosse, Anand Kumar, Jose Leonardo V. Mejino, Daniel L. Cook, Landon T. Detwiler and Barry Smith, “A Strategy for Improving and Integrating Biomedical Ontologies”, Proceedings of AMIA Symposium 2005, Washington DC, 639-643.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies in anatomy, physiology and pathology.

Anand Kumar, Barry Smith, Domenica Pisanelli, Aldo Gangemi and Mario Stefanelli, “Clinical Guidelines as Plans: An Ontological Theory”, Methods of Information in Medicine, 45 (2), 2006, 204-210.

Objective: Clinical guidelines are special types of plans realized by collective agents. We provide an ontological theory of such plans that is designed to support the construction of a framework in which guideline-based information systems can be employed in the management of workflow in health care organizations. Method: The framework we propose allows us to represent in formal terms how clinical guidelines are realized through the actions of individuals organized into teams. We provide various levels of implementation representing different levels of conformity on the part of health care organizations. Result: Implementations built in conformity with our framework are marked by two dimensions of flexibility that are designed to make them more likely to be accepted by health care professionals than are standard guideline-based management systems. They do justice to the fact (1) that responsibilities within a health care organization are widely shared, and (2) that health care professionals may on different occasions be noncompliant with guidelines for a variety of well justified reasons. Conclusion: The advantage of the framework lies in its built-in flexibility, its sensitivity to clinical context, and its ability to use inference tools based on a robust ontology. One disadvantage lies in the complication of its implementation.

Anand Kumar, Yum Lina Yip, Barry Smith and Pierre Grenon, “Bridging the Gap between Medical and Bioinformatics: An Ontological Case Study in Colon Carcinoma”, Computers in Biology and Medicine, in press.

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma.

James J. Cimino and Barry Smith, “Introduction: International Medical Informatics Association Working Group 6 and the 2005 Rome Conference”, Journal of Biomedical Informatics, 2006; 39(3): 249-251.

Barry Smith, “From Concepts to Clinical Reality: An Essay on the Benchmarking of Biomedical Terminologies”, Journal of Biomedical Informatics, 2006; 39(3): 288-298.

It is only by fixing on agreed meanings of terms in biomedical terminologies that we will be in a position to achieve that accumulation and integration of knowledge that is indispensable to progress at the frontiers of biomedicine. Standardly, the goal of fixing meanings is seen as being realized through the alignment of terms on what are called ‘concepts’. Part I addresses three versions of the concept-based approach - by Cimino, by Wüster, and by Campbell and associates - and surveys some of the problems to which they give rise, all of which have to do with a failure to anchor the terms in terminologies to corresponding referents in reality. Part II outlines a new, realist solution to this anchorage problem, which sees terminology construction as being motivated by the goal of alignment not on concepts but on the universals (kinds, types) in reality and thereby also on the corresponding instances (individuals, tokens). We outline the realist approach, and show how on its basis we can provide a benchmark of correctness for terminologies which will at the same time allow a new type of integration of terminologies and electronic health records. We conclude by outlining ways in which the framework thus defined might be exploited for purposes of diagnostic decision-support.

Christane Fellbaum, Udo Hahn and Barry Smith, “Towards New Information Resources for Public Health - From WordNet to Medical WordNet”, Journal of Biomedical Informatics, 2006; 39(3): 321-332.

In the last two decades, WORDNET has evolved as the most comprehensive computational lexicon of general English. In this article, we discuss its potential for supporting the creation of an entirely new kind of information resource for public health, viz. MEDICAL WORDNET. This resource is not to be conceived merely as a lexical extension of the original WORDNET to medical terminology; indeed, there is already a considerable degree of overlap between WORDNET and the vocabulary of medicine. Instead, we propose a new type of repository, consisting of three large collections of (1) medically relevant word forms, structured along the lines of the existing Princeton WORDNET; (2) medically validated propositions, referred to here as medical facts, which will constitute what we shall call MEDICAL FACTNET; and (3) propositions reflecting laypersons’ medical beliefs, which will constitute what we shall call the MEDICAL BELIEFNET. We introduce a methodology for setting up the MEDICAL WORDNET. We then turn to the discussion of research challenges that have to be met in order to build this new type of information resource.

Werner Ceusters and Barry Smith, “Strategies for Referent Tracking in Electronic Health Records”, Journal of Biomedical Informatics, 2006; 39(3): 362-378.

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor - though nevertheless ontologically important - technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto.

Olivier Bodenreider, Barry Smith, Anand Kumar and Anita Burgun, “Investigating Subsumption in SNOMED CT: An Exploration into Large Description Logic-Based Biomedical Terminologies”, Artificial Intelligence in Medicine, submitted.

Patricia L. Whetzel1, Ryan R. Brinkman, Helen C. Causton, Liju Fan, Jennifer Fostel, Gilberto Fragoso, Mervi Heiskanen, Tina Hernandez-Boussard, Norman Morrison, Helen Parkinson, Philippe Rocca-Serra, Susanna-Assunta Sansone, Daniel Schober, Barry Smith, Robert Stevens, Chris Stoeckert, Chris Taylor, Joe White, “The Development of FuGO - An Ontology for Functional Genomics Experiments”, Omics: A Journal of Integrative Biology, in press.

The development of the Functional Genomics Experiment Ontology (FuGO) is a collaborative, international effort which will provide a resource for annotating functional genomics experiments, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain terms that are both universal to functional genomics experiments and those that are domain specific.In this way, the ontology will serve as the ‘semantic glue’ to provide a common understanding of data across these disparate data sources.In addition, FuGO will reference out to existing mature ontologies in order to avoid the need to duplicate these resources, but in such a way as to enable their ease of use in annotation.This project is in the beginning stages of development and the paper will describe the efforts to initiate the project, the scope and organization of the project, the work accomplished to date and the challenges encountered as well as describe future plans.

Rubin DL, Lewis SE, Mungall CJ, Misra S, Westerfield M, Ashburner M, Sim I, Chute CG, Solbrig H, Storey MA, Smith B, Richter JD, Noy NF and Musen MA, “The National Center for Biomedical Ontology: Advancing Biomedicine through Structured Organization of Scientific Knowledge”, Omics: A Journal of Integrative Biology (in press).

Werner Ceusters and Barry Smith, “Referent Tracking for Treatment Optimisation inSchizophrenic Patients”, Journal of Web Semantics, in press.

The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients in the spirit of guideline-based medicine. We take this algorithm as our starting point in investigating how artifacts of this sort can benefit from the facilities of high-quality ontologies. The IPAP algorithm exists thus far only in a form suitable for use by human beings. We draw on the resources of Basic Formal Ontology (BFO) in order to show how such an algorithm can be enhanced in such a way that it can be used in Semantic Web and related applications. We found that BFO provides a framework that is able to capture in a rigorous way all the types of entities represented in the IPAP schizophrenia algorithm in way which yields a computational tool that can be used by software agents to perform monitoring and control of schizophrenic patients. We discuss the issues involved in building an application ontology for this purpose, issues which are important for any Semantic Web application in the life science and healthcare domains.

Jacob KÖhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith, “Quality Control for Terms and Definitions in Ontologies and Taxonomies”, BMC Bioinformatics, forthcoming.

Ontologies and taxonomies are among the most important computational resources formolecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. We present computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation.

Werner Ceusters and Barry Smith, “Referent Tracking for Treatment Optimisation in Schizophrenic Patients: A Case Study in Applying Philosophical Ontology to Diagnostic Algorithms”, Journal of Web Semantics, forthcoming.

Steffen Schulze-Kremer and Barry Smith, “Ontologies for the Life Sciences”, Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, New York and London: John Wiley and Sons, vol. 4, 2005.

Maureen Donnelly, Thomas Bittner and Cornelius Rosse, “A Formal Theory for Spatial Representation and Reasoning in Biomedical Ontologies”, Artificial Intelligence in Medicine, Vol. 36, Nr. 1, 2006, 1-27.

Thomas Bittner and Maureen Donnelly, “Computational Ontologies of Parthood, Componenthood, and Containment”, In L. Kaelbling (ed.): Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence, 2005, 382-387.

Maureen Donnelly and Thomas Bittner, (2005). Spatial relations between classes of individuals. In D. Mark and T. Cohn (eds.): Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information Science. International Conference (COSIT 2005), 182-199.

Alexander Sorokine and Thomas Bittner, “Understanding Taxonomies of Ecosystems: A Case Study”, In: Fisher, P. (ed.): Developments in Spatial Data Handling. Springer, Berlin, 2005, 559-572.

Thomas Bittner, Maureen Donnelly and Stefan Winter, “Ontology and Semantic Interoperability”, in: D. Prosperi and S. Zlatanova (ed.), Large-scale 3D Data Integration: Problems and Challenges, London: CRCPress, 2005.

Alexander Sorokine and Thomas Bittner, 2005 “Understanding Taxonomies of Ecosystems: A Case Study”, in: Fisher, P. (ed.): Developments in Spatial Data Handling, Springer, Berlin, 2005, 559-572.

Thomas Bittner and Maureen Donnelly, “Computational ontologies of parthood, componenthood, and containment”, in: L. Kaelbling (ed.): Proceedings of the Nineteenth International Joint Conference on Artificial Intelligence, 2005, 382-387.

Maureen Donnelly, 2005. “Relative Places”, Applied Ontology, Vol. 1, Nr. 1, 55-75.

Maureen Donnelly, 2005. “Containment relations in anatomical ontologies”, Proceedings of AMIA Symposium 2005, Washington DC, 206-210.

David Hershenov, “Do Dead Bodies Pose a Problem for the Biological Account of Identity?” Mind, vol. 114. 2005, 453-477.

David Hershenov, “Persons as Proper Parts of Organisms” Theoria 2005,1, 29-37.

Neil Williams, “Static and Dynamic Dispositions”, Synthese, 146 (3), 2005, 303-324.

2006 and forthcoming

Barry Smith and David Mark, “Geographical Categories: An Ontological Retrospective”, in Peter Fisher (ed.), Classics from the International Journal of Geographical Information Science, London: Taylor and Francis, 2006, 507-512.

Mark A. Musen, Suzanna Lewis and Barry Smith, “Wrestling with SUMO and bio-ontologies”, Nature Biotechnology, 24, 1 (2006), p. 21.

Barry Smith and Werner Ceusters, “Ontology as the Core Discipline of Biomedical Informatics: Legacies of the Past and Recommendations for the Future Direction of Research”, forthcoming in Computing, Philosophy, And Cognitive Science, Gordana Dodig Crnkovic and Susan Stuart (eds.), Cambridge: Cambridge Scholars Press, 2006.

Barry Smith and Chris Menzel, “[Draft:] Ontology and Information Science”, Stanford Encyclopedia of Philosophy, in preparation.

Werner Ceusters, Peter Elkin and Barry Smith “Referent Tracking: The Problem of Negative Findings”, (MIE 2006), Stud Health Technol Inform., in press.

Barry Smith and Werner Ceusters “HL7 RIM: An Incoherent Standard”, (MIE 2006), Stud Health Technol Inform., in press.

David Hershenov, “The Death of a Person.” The Journal of Medicine and Philosophy. 31:1.April 2006, in press.

David Hershenov, “How a Hylomorphic Metaphysics Constrains the Abortion Debate” National Catholic Bioethics Quarterly, forthcoming.

David Hershenov, Coming Into and Going Out of Existence (special issue of The Monist), LaSalle: The Hegeler Institute, forthcoming.

Alexander Sorokine, Thomas Bittner and Chris Renscher, “Ontological investigation of ecosystem hierarchies and formal theory for multiscale ecosystem classifications”, Geoinformatica, to appear.

Alan Rector, Jeremy Rogers and Thomas Bittner, “Granularity, scale and collectivity: When size does and does not matter”, Journal of Biomedical Informatics, to appear.

Stefan Schulz, Anand Kumar and Thomas Bittner, “Biomedical ontologies: What part-of is and isn’t”, Journal of Biomedical Informatics, to appear.

Robert Arp, “Philosophical Ontology, Domain Ontology, and Formal Ontology,” Key Terms in Logic, (Continuum Press), to appear.

Robert Arp, as editor with George Terzis, Information and Living Systems: Essays in Philosophy of Biology, (MIT Press), in preparation.

Robert Arp, as editor with Francisco Ayala, Contemporary Debates in Philosophy of Biology, (Blackwell), in preparation.

Robert Arp, as editor with Alexander Rosenberg, Philosophy of Biology: An Anthology, (Blackwell) in preparation.