Publications

Louis Goldberg

Werner Ceusters Barry Smith	Referent Tracking for Digital Rights Management Digital Rights Management covers the description, identification, trading, protection, monitoring and tracking of all forms of rights over both tangible and intangible assets, including management of relationships between rights holders in a digital environment. The Digital Object Identifier (DOI) system provides a framework for the persistent identification of content in its broadest interpretation. Although the system has been very well designed to manage object identifiers, some important questions related to the assignment of identifiers are left open. The paradigm of a referent tracking system (RTS) recently advanced in the healthcare and life sciences environment is able to fill these gaps. This is demonstrated by pointing out inconsistencies in the DOI models and by showing how they can be corrected using an RTS.
Barry Smith Werner Ceusters	An Ontology-Based Methodology for the Migration of Biomedical Terminologies to Electronic Health Records 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 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 work still needs to be done in reconceiving the foundations of both EHR architectures and medical terminologies. We describe a new framework for the treatment of both generals and particulars in biomedical informatics 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.	Accepted for AMIA 2005
Werner Ceusters Barry Smith	Strategies for Referent Tracking in Electronic Health Records The goal of referent tracking is to create an ever-growing pool of data relating to concrete entities in reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their body parts, diseases, therapies, lesions, and so forth insofar as these are relevant to their diagnosis and treatment. Within a referent tracking system, all such entities are referred to 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 requires primarily a different mindset from that which has prevailed hitherto.	Draft for IMIA WG6 2005 Conference Proceedings
Barry Smith Werner Ceusters Bert Klagges Jacob Köhler Anand Kumar Jane Lomax Chris Mungall Fabian Neuhaus Alan Rector Cornelius Rosse	Relations in Biomedical Ontologies The background to this paper is the recognition that many biological and medical ontologies can be improved by adopting tools and methods that bring a greater degree of logical and ontological rigour. We describe one endeavour along these lines, which is part of the current reform efforts of the Open Biomedical Ontologies (OBO) consortium and which has implications for ontology construction in the life sciences generally. OBO ontologies consist of controlled vocabularies which can be conceived as graph-theoretical structures organized by means of links or edges called ‘relations’. Unfortunately too little attention has been paid to the nature of such relations and of the relata which they join together. How, exactly, should part_of or located_in be defined in order to ensure maximally reliable curation of each single ontology while at the same time guaranteeing maximal leverage in building a solid base for life-science knowledge integration in general? We describe a rigorous methodology for providing answers to such questions and illustrate its use in the construction of a simple and easily extendible list of ten relations of a type familiar to those working in the bio-ontological field. This list forms the core of the new OBO Relation Ontology. What is distinctive about our methodology is that, while the relations are each provided with rigorous formal definitions, these definitions can at the same time be formulated in such a way that the underlying technical details remain invisible to ontology authors and curators.	Genome Biology 2005, 6:R46 doi:10.1186/gb-2005-6-5-r46
Barry Smith Werner Ceusters Rita Temmerman	Wüsteria The last two decades have seen considerable efforts directed towards making electronic healthcare records interoperable through advances in record architectures and 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 the father of terminology standardization Eugen Wüster, founder of ISO TC 37. We survey these ideas, which see terminology work as being focused on the classification of concepts in people’s minds, and we argue that they have formed the basis for a series of still influential confusions. We argue that an ontology based unambiguously on the classification of entities (both universals and particulars) in reality can, by removing these confusions, make a vital contribution to assuring the interoperability of coding systems and healthcare records in the future.	Accepted for MIE 2005
Werner Ceusters Barry Smith	Tracking Referents in Electronic Healthcare Records Electronic Healthcare Records (EHCRs) 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 EHCR regime in which all the particulars to which reference is made in clinical statements 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 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 EHCR systems.	Accepted for MIE 2005
Lowell Vizenor Barry Smith Werner Ceusters	Foundation for the Electronic Health Record: An Ontological Analysis of the HL7’s Reference Information Model Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task remains of ensuring that the right sorts of information reach the right sorts of people. In what follows we defend the thesis that efforts to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations, and that the communication of healthcare information and knowledge needs to rest on a sound ontology of social interaction. We illustrate this thesis in relation to the HL7 RIM, which is one centrally important tool for communication in the healthcare domain.
Werner Ceusters Barry Smith Georges De Moor	Ontology-Based Integration of Medical Coding Systems and Electronic Patient Records In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories.
Werner Ceusters Barry Smith Louis Goldberg	A Terminological and Ontological Analysis of the NCI Thesaurus 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 OWLrepresentation (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. Conclusion: Version 04.08b of the NCI Thesaurus suffers from the same broad range of inconsistencies that we have 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.	Accepted by Meth Info Med
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