Biomedical subjects

Jeremy Rogers

Publications and source records attributed to Jeremy Rogers.

6 recordsLinked to original sources

PubMed2006

An Ontology driven collaborative development for biomedical terminologies: from the French CCAM to the Australian ICHI coding system.

The CCAM French coding system of clinical procedures was developed between 1994 and 2004 using, in parallel, a traditional domain expert's consensus method on one hand, and advanced methodologies of ontology driven semantic representation and multilingual generation on the other hand. These advanced methodologies were applied under the framework of an European Union collaborative research project named GALEN and produced a new generation of biomedical terminology. Following the interest in several countries and in WHO, the GALEN network has tested the application of the ontology driven tools to the existing reduced Australian ICHI coding system for interventions presently under investigation by WHO to check its ability and appropriateness to become the reference international coding system for procedures. The initial results are presented and discussed in terms of feasibility and quality assurance for sharing and maintaining consistent medical knowledge and allowing diversity in linguistic expressiveness of end users.

Australia↗

PubMed2005

Granularity, scale and collectivity: when size does and does not matter.

Bridging levels of "granularity" and "scale" are frequently cited as key problems for biomedical informatics. However, detailed accounts of what is meant by these terms are sparse in the literature. We argue for distinguishing two notions: "size range," which deals with physical size, and "collectivity," which deals with aggregations of individuals into collections, which have emergent properties and effects. We further distinguish these notions from "specialisation," "degree of detail," "density," and "connectivity." We argue that the notion of "collectivity"--molecules in water, cells in tissues, people in crowds, stars in galaxies--has been neglected but is a key to representing biological notions, that it is a pervasive notion across size ranges--micro, macro, cosmological, etc.--and that it provides an account of a number of troublesome issues including the most important cases of when the biomedical notion of parthood is, or is not, best represented by a transitive relation. Although examples are taken from biomedicine, we believe these notions to have wider application.

Animals↗

PubMed2005

A linkable identity privacy algorithm for HealthGrid.

The issues of confidentiality and privacy have become increasingly important as Grid technology is being adopted in public sectors such as healthcare. This paper discusses the importance of protecting the confidentiality and privacy of patient health/medical records, and the challenges exhibited in enforcing this protection in a Grid environment. It proposes a novel algorithm to allow traceable/linkable identity privacy in dealing with de-identified medical records. Using the algorithm, de-identified health records associated to the same patient but generated by different healthcare providers are given different pseudonyms. However, these pseudonymised records of the same patient can still be linked by a trusted entity such as the NHS trust or HealthGrid manager. The paper has also recommended a security architecture that integrates the proposed algorithm with other data security measures needed to achieve the desired security and privacy in the HealthGrid context.

Algorithms↗

PubMed2005

Semantic Clarification of the Representation of Procedures and Diseases in SNOMED((R))CT.

SNOMED((R)) CT is emerging as a reference terminology for the entire health care process. It claims to be founded on logic-based modeling principles. In this work we analyze a special encoding scheme for SNOMED disease and procedure entities, the so-called relationship groups which had been devised in order to avoid ambiguities in entity definitions. We show that these artifacts may represent hidden mereological relations. We also report discrepancies encountered between the defined semantics of many SNOMED((R)) CT entity terms and their intuitive meaning, and inconsistencies detected between the definition of some complex composed entities and the definition of their top-level parents. As a result we formulate recommendations for improvements of SNOMED((R)) CT.

Humans↗

PubMed2004

Models and inference methods for clinical systems: a principled approach.

Previous papers have argued for the existence of three different models in many clinical information systems--for the medical record, for inference in guidelines, and for concepts and re-usable facts. This paper presents a principled approach to deciding which information belongs in each model based on the nature of the queries or inference to be performed: necessary or contingent, open or closed world, algorithmic vs heuristic. It then discusses an important class of systems--"ontologically indexed knowledge bases"--and issues of metadata within this framework.

Abstracting and Indexing↗

PubMed2002

Scale and context: issues in ontologies to link health- and bio-informatics.

Bridging levels of scale and context are key problems for integrating Bio- and Health Informatics. Formal, logic-based ontologies using expressive formalisms are naturally "fractal" and provide new methods to support these aims. The basic notion of composition can be used to bridge scales; axioms can be used to carry implicit information; specific context markers can be included in definitions; and a hierarchy of semantic links can be used to represent subtle differences in point of view. Experience with OpenGALEN, the UK Drug Ontology and new experiments with the Gene Ontology and Foundational Model of Anatomy suggest that these are powerful tools provide practical solutions.

Medical Informatics↗