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Biomedical subjects

J E Rogers

Publications and source records attributed to J E Rogers.

At least 19 recordsLinked to original sources
PubMed2006

Quality assurance of medical ontologies.

OBJECTIVE: To review the literature concerning the quality assurance of medical ontologies. METHODS: scholar.google.com was searched using the search strings (+ontology +"quality assurance") and (+ontology +"evaluation/evaluating"). Relevant publications were selected by manual review. Other work already familiar to the author, or suggested by other researchers contacted by the author, were included. The papers were analysed for common themes. RESULTS: Four broad properties of an ontology were identified that may be quality-assured: philosophical validity, compliance with meta-ontological commitments, 'content correctness', and fitness for purpose. Each published methodology addressed only a subset of these properties. 'Content' may be divided into domain knowledge content, and metadata describing either the provenance of domain knowledge content, or relationships between it and lexical information (e.g. for display and retrieval). 'Correctness' (whether of domain knowledge content or metadata) may also be further subdivided into truth, completeness, parsimony and internal consistency. CONCLUSIONS: Understanding of how to assure the quality of ontologies, or evaluate their fitness for specific purposes, is improving but remains poor. A combination of methodologies is required, but tools to support a comprehensive quality assurance programme remain lacking. Perfect quality of an ontology is not provable and may not be desirable: an ontology compliant with all current philosophical theories, following necessary ontological commitments, and with entirely 'correct' content, may be too complex to be directly usable or useful. The extent to which an ontology's fitness for purpose is predicted or influenced by its other properties remains to be determined. Field studies of ontologies in use, including interrater effects, are required.

Medical Informatics↗
PubMed2004

Attitudes and access to electronic exchange of information on occupational disease.

BACKGROUND: THOR is a network of work-related disease surveillance schemes dependent on volunteer case reporting by medical specialists. Data collection and dissemination has hitherto been paper-based. AIMS: To elicit the opinion of existing reporters in THOR on electronic exchange of information and to assess the practical capabilities of the same reporters to participate in electronic communication. METHODS: A mail-based questionnaire of randomly selected THOR reporters using closed format questions. RESULTS: The response rate to the questionnaire was 66% (253/383). Almost half (47%) of the responders wanted dissemination of information solely in an electronic form, 35% favoured paper-based reports, while 16% wanted both paper and electronic reports. Two-thirds (66%) would make use of electronic archives of reports and 59% would use this facility to resolve questions by accessing accumulated data. The majority (82%) read e-mail more than once a week and 34% browsed the web as frequently. However, 5% did not have e-mail and 6% never browsed the web. Most responders judged their internet connectivity to be rapid (68%) and convenient (83%), and 91% could receive e-mail attachments. CONCLUSIONS: Most responders have the skills and infrastructure required to engage in electronic information exchange, and are favourably disposed to electronic means of communication. However it is also relevant to note that one-third of responders have a preference for the existing paper-based system.

Attitude of Health Personnel↗
PubMed2003

OpenGALEN: open source medical terminology and tools.

The GALEN programme of research into medical terminology began in 1991. In 1999 OpenGALEN was formed to provide an open source route both for disseminating the results of that programme and as a framework for its future development. Currently available open source resources include a sophisticated ontology development environment and a large open source description logic-based ontology for the medical domain.

Intellectual Property↗
PubMed2001

Nucleotide oxidation mediated by naphthalimide excited states with covalently attached viologen cosensitizers.

The ground- and excited-state interactions of polymethylene-linked 1,8-naphthalimide-viologen dyads with calf-thymus DNA have been investigated. By virtue of the covalently attached viologen, the compounds represent the first example of linked chromophore/cosensitizer systems in the photooxidation of duplex DNA. The compounds associate strongly with DNA. Analysis of ground-state spectral changes yield binding constants of 0.7-2.5 x 10(6) M-1. Upon 355 nm pulsed irradiation of the compounds in the presence of calf-thymus DNA, reduced viologen is observed within the laser pulse. Photoproducts are not observed on this time scale in the absence of DNA. Since ground-state bleaching of the naphthalimide was not observed, the results suggest that DNA nucleobases are the species being oxidized. The quantum efficiency of radical production increases with the extent of binding to DNA. Under conditions where the compounds are bound predominantly to DNA, the quantum efficiencies were found to range from 0.02 to 0.03. Although small, the values represent a substantial increase in charge-separation yield compared to 1,8-naphthalimide compounds that lack the covalently attached viologen. The mechanism of radical production and effect of number of intervening methylenes are discussed.

Animals↗
PubMed2001

Mechanisms of photoinitiated cleavage of DNA by 1,8-naphthalimide derivatives.

Using water-soluble 1,8-naphthalimide derivatives, the mechanisms of photosensitized DNA damage have been elucidated. Specifically, a comparison of rate constants for the photoinduced relaxation of supercoiled to circular DNA, as a function of dissolved halide, oxygen and naphthalimide concentration, has been carried out. The singlet excited states of the naphthalimide derivatives were quenched by chloride, bromide and iodide. In all cases the quenching products were naphthalimide triplet states, produced by induced intersystem crossing within the collision complex. Similarly, the halides were found to quench the triplet excited state of the 1,8-naphthalimide derivatives by an electron transfer mechanism. Bimolecular rate constants were < 10(5) M-1 s-1 for quenching by bromide and chloride. As expected from thermodynamic considerations quenching by iodide was 6.7 x 10(9) and 8.8 x 10(9) M-1 s-1 for the two 1,8-naphthalimide derivatives employed. At sufficiently high ground-state concentration self-quenching of the naphthalimide triplet excited state also occurs. The photosensitized conversion of supercoiled to circular DNA is fastest when self-quenching reactions are favored. The results suggest that, in the case of 1,8-naphthalimide derivatives, radicals derived from quenching of the triplet state by ground-state chromophores are more effective in cleaving DNA than reactive oxygen species or radicals derived from halogen atoms.

1-Naphthylamine↗
PubMed2000

GALEN: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

Generalised architecture for languages, encyclopedia and nomenclatures in medicine (GALEN) has developed a new generation of terminology tools based on a language independent model describing the semantics and allowing computer processing and multiple reuses as well as natural language understanding systems applications to facilitate the sharing and maintaining of consistent medical knowledge. During the European Union 4 Th. framework program project GALEN-IN-USE and later on within two contracts with the national health authorities we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures named CCAM in a minority language country, France. On one hand, we contributed to a language independent knowledge repository and multilingual semantic dictionaries for multicultural Europe. On the other hand, we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW (for classification workbench) to process French professional medical language rubrics produced by the national colleges of surgeons domain experts into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation, on one hand, we generate with the LNAT natural language generator controlled French natural language to support the finalization of the linguistic labels (first generation) in relation with the meanings of the conceptual system structure. On the other hand, the Claw classification manager proves to be very powerful to retrieve the initial domain experts rubrics list with different categories of concepts (second generation) within a semantic structured representation (third generation) bridge to the electronic patient record detailed terminology.

Abstracting and Indexing↗
PubMed2000

Having our cake and eating it too: how the GALEN Intermediate Representation reconciles internal complexity with users' requirements for appropriateness and simplicity.

Clinical terminologies are complex objects, getting more complex as the requirements on them grow, and as more complex technologies are used in their construction. But to the clinical end-user, functionality and utility is important, not inherent complexity--the simpler a clinical terminology can be for the end-user, the better. To reconcile these contradictory requirements, the GALEN Programme has developed an Intermediate Representation that allows the OpenGALEN Clinical Terminology to retain a high degree of internal complexity, whilst allowing it to be efficiently maintained, and easily used. This paper describes the elements of the Intermediate Representation, how it works, and some experience of its use.

Abstracting and Indexing↗
PubMed1999

A reference terminology for drugs.

GALEN technology for re-usable terminologies using formal classification is being applied to the creation and maintenance of a reference terminology for drugs. GALEN's techniques are being used to address specific deficiencies of existing drug classifications that make it difficult to create and maintain guidelines to support prescribing in the care of patients with chronic diseases. The reference terminology is in two parts; firstly, a re-usable and automatically-classified 'ontology' is built with GALEN technology; this describes generic drugs, their composition in terms of chemicals and chemical classes, their actions, indications and interactions. Secondly, a 'dictionary' of prescribable proprietary products is integrated with this ontology. The result is a drug resource designed to support both the traditional uses of a drug knowledge base (e.g. prescribing and messaging), and the specialized demands of guideline authoring and execution.

Artificial Intelligence↗
PubMed1999

Galen: a third generation terminology tool to support a multipurpose national coding system for surgical procedures.

GALEN has developed a new generation of terminology tools based on a language independent concept reference model using a compositional formalism allowing computer processing and multiple reuses. During the 4th framework program project Galen-In-Use we applied the modelling and the tools to the development of a new multipurpose coding system for surgical procedures (CCAM) in France. On one hand we contributed to a language independent knowledge repository for multicultural Europe. On the other hand we support the traditional process for creating a new coding system in medicine which is very much labour consuming by artificial intelligence tools using a medically oriented recursive ontology and natural language processing. We used an integrated software named CLAW to process French professional medical language rubrics produced by the national colleges of surgeons into intermediate dissections and to the Grail reference ontology model representation. From this language independent concept model representation on one hand we generate controlled French natural language to support the finalization of the linguistic labels in relation with the meanings of the conceptual system structure. On the other hand the classification manager of third generation proves to be very powerful to retrieve the initial professional rubrics with different categories of concepts within a semantic network.

Abstracting and Indexing↗
PubMed1998

Reconciling users' needs and formal requirements: issues in developing a reusable ontology for medicine.

A common language, or terminology, for representing what clinicians have said and done is an important requirement for individual clinical systems, and it is a pre-requisite for integrating disparate applications in a distributed telematic healthcare environment. Formal representations based on description logics or closely related formalisms are increasingly used for representing medical terminologies. GALEN's experience in using one such formalism raises two major issues, as follows: how to make ontologies based on description logics easy to use and understand for both clinicians and applications developers; what features are required of the ontology and description logic if they are to achieve their aims. Based on our experience we put forward four contentions: two relating to each of these two issues, as follows: that natural language generation is essential to make a description logic based ontology accessible to users; that the description logic based ontology should be treated as an "assembly language" and accessed via "intermediate representations" oriented to users and "perspectives" adapting it to specific applications; that independence and reuse are best supported by partitioning the subsumption hierarchy of elementary concepts into orthogonal taxonomies, each of which forms a pure tree in which the branches at each level are disjoint but nonexhaustive subconcepts of the parent concept; that the expressivity of the description logic must include support for transitive relations despite the computational cost, and that this computational cost is acceptable in practice. The authors argue that these features will be necessary, though by no means sufficient, for the development of any large reusable ontology for medicine.

Clinical Medicine↗
PubMed1998

Natural language generation of surgical procedures.

The GALEN-IN-USE project has developed a compositional scheme for the conceptual representation of surgical operative procedure rubrics. The complex representations which result are translated back to surface language by a tool for multilingual natural language generation. This generator can be adapted to the specific characteristics of the scheme by introducing particular definitions of concepts and relationships. We discuss how the generator uses such definitions to bridge between the modelling 'style' of the GALEN scheme and natural language.

Humans↗
PubMed1997

Rubrics to dissections to GRAIL to classifications.

This paper summarises the process in the GALEN-IN-USE project by which rubrics from traditional medical coding schemes are analysed into an intermediate, relatively informal conceptual representation which is then automatically translated into the GRAIL formalism and its Common Reference Model.

Europe↗
PubMed1997

Using the GRAIL language for classification management.

This paper describes a novel approach in classification management where a formal model of medical semantics is being used for manipulations on existing classification systems. The paper addresses the issue of semi-automatically making specialist classifications that are compatible with the source classification. The examples in this paper are from a limited domain. At the time of the presentation results will be shown of the present modelling work within the GALEN-In-Use project. The model will then contain several thousands of medical procedures from four different classification centres.

Classification↗
PubMed1997

Terminological systems: bridging the generation gap.

A rigorous formal description of the intended behaviour of a compositional terminology, a 'third generation' system, enables powerful semantic processing techniques to assist in the building of a large terminology. Use of an intermediate representation derived from such a formalism, but simplified to resemble a 'second generation' system, enables authors to work in an simpler and more familiar environment, avoiding many of the technical complications of the 'third generation' system.

Classification↗
PubMed1996

Rubella reimmunization: comparative analysis of the immunoglobulin G response to rubella virus vaccine in previously seronegative and seropositive individuals.

Rubella virus (RV)-specific immunoglobulin G (IgG) antibodies were studied in military recruits undergoing unselected immunization with live attenuated measles, mumps, and rubella virus (MMR) vaccine. Three different whole-RV enzyme immunoassays (EIAs) and an epitope-specific EIA with a synthetic peptide (BCH-178c) representing a heutralization domain on the RV E1 envelope protein were used. Before vaccination, 84.2, 87.7, and 84.5% of the subjects tested (n = 399) were found to be seropositive (> 10 IU/ml or assay equivalent) by the three whole-RV EIAs, respectively, while only 82.5% were seropositive by the BCH-178c EIA. Although prevaccination seropositivity rates were similar for the whole-RV EIAs (sensitivity, 94 to 100%), many sera considered seropositive by the whole-RV EIAs had E1 peptide EIA antibody levels of < 10 IU/ml (sensitivity, 77.4 to 80.7%). One month after vaccination, 97.8, 97.2, and 93.5% of the subjects who were followed (n = 356) were seropositive by the three whole-RV EIAs, respectively, while 89% had BCH-178c peptide-specific IgG titers of > 10 IU/ml. After vaccination, depending on the assay used, up to 20.6% of initially seropositive individuals exhibited a greater than fourfold increase in RV-specific IgG, while up to 47.3% showed a greater than twofold increase. Increased antibody titers after vaccination (seroboosting) were most frequently associated with low levels of BCH-178c peptide-specific IgG before vaccination. RV protein-specific IgG was also studied by immunoblot assays in a subset (n = 56) of individuals receiving the MMR vaccine. Of these, 89.4 and 91.1% exhibited RV protein (E1, E2, and C protein)-specific IgG before and after vaccination, respectively. Seroboosting (two- to fourfold increase in EIA titers of individuals seropositive by the whole-RV EIA before vaccination) was usually accompanied by a shift in the IgG immunoblot pattern from a single (E1) to multiple (E1-E1, E1-C, or E1-E2-C) specificities, suggesting exposure of new epitopes as a result of viral replication.

Adolescent↗