ClaML: a standard for the electronic publication of classification coding schemes.

This paper proposes a number of revisions to CEN/TS 14463 (ClaML), which is a pre-standard mark-up language for the electronic publication of classification coding schemes. A CEN Taskforce in close collaboration with the WHO network carefully analysed 70 classifications from the healthcare domain. All were transformed in ClaML using a dedicated classification management tool. The proposal removes all formatting elements and adds a number of layout structuring elements. Several elements have been replaced by attributes to enforce internal consistency. A modest number of extensions are proposed to help users and authors in maintenance and version control. A pilot implementation has shown that ICD10 as one of the most complex traditional classifications can be adequately represented to produce quality printed output.

Three types of IS-A statement in diagnostic classifications: three types of knowledge needed for development and maintenance.

Update mechanisms for diagnostic classifications should capture changes in medical knowledge but also allow for comparability across versions. This paper provides a basis for such a mechanism by describing types of IS-A statement and types of knowledge used in the construction of diagnostic classifications. Three types of IS-A statement are used: 'A is by definition a B', 'A is probably a B' and 'A is in theory necessarily a B'. Each relates to a different type of knowledge: knowledge of linguistic conventions, of probabilities, and of empirical theories and their status, respectively. Consequently, the development and maintenance of diagnostic classifications requires a collaboration of medical terminologists and medical scientists. The role of the latter is especially important during updating. Updating is necessitated by changing probabilities and by the introduction or changing status of empirical theories. The linguistic notion of hyponymy oversimplifies the issue.

A Terminology Server for medical language and medical information systems.

GALEN is developing a Terminology Server to support the development and integration of clinical systems through a range of key terminological services, built around a language-independent, re-usable, shared system of concepts--the CORE model. The focus is on supporting applications for medical records, clinical user interfaces and clinical information systems, but also includes systems for natural language understanding, clinical decision support, management of coding and classification schemes, and bibliographic retrieval. The Terminology Server integrates three modules: the Concept Module which implements the GRAIL formalism and manages the internal representation of concept entities, the Multilingual Module which manages the mapping of concept entities to natural language, and the Code Conversion Module which manages the mapping of concept entities to and from existing coding and classification schemes. The Terminology Server also provides external referencing to concept entities, coercion between data types, and makes its services available through a uniform applications programming interface. Taken together these services represent a new approach to the development of clinical systems and the sharing of medical knowledge.

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.

Practical development of re-usable terminologies: GALEN-IN-USE and the GALEN Organisation.

Medical terminology is now playing a key role in medical software. This requires new techniques with which many clinical users, classification experts and applications developers are unfamiliar. There is a conflict in that the more re-usable techniques for terminology needed to support sharing of information among many different applications are more difficult to use for any one application. A layered approach to re-use is described which combines techniques from first generation systems and relatively easily understood second generation systems with the formal rigour of third generation systems to resolve this conflict. The methodology also provides a potentially rigorous approach to defining the relationship between terminology and structure in the electronic healthcare record architecture. It provides a natural migration pathway from existing systems to powerful re-usable multilingual terminologies.

From a time standard for medical informatics to a controlled language for health.

CEN ENV 12381 is a European Prestandard focusing on formal representation and explicit reference of temporal information in healthcare informatics and telematics. One of its merits is not just the possibility to represent natural language expressions containing time-related information in a structured way, but also to give some mechanisms on how clinical language itself can be used to convey meaning unambiguously. As such, CEN ENV 12381 introduces the notion of 'controlled language use' in the domain of healthcare. In this paper the principles behind controlled language design and use are explained. Through a detailed study of the inconsistencies and ambiguities that arise when interpreting Snomed procedure terms in the framework of the Galen-In-Use project, it is shown that most of them can be explained as a violation of sound term-formation principles. A proposal is made to develop a controlled language for health and to use it in subsequent versions of coding and classification systems. It is expected that such an endeavour will lead to a more effective application of linguistic engineering in areas such as automatic knowledge acquisition, automatic translation, and terminology validation in the domain of healthcare informatics.

Computerized assessment with primary care guidelines in The Netherlands.

To promote quality assurance and expertise in primary health care in the Netherlands the Dutch College of General Practitioners develops protocols, called standards. These standards concern medical action-taking in case of regular complaints and diseases in common practice. To improve dissemination of the standards and to develop effective and useful methods for quality assurance on the basis of the standards a project, called the Guidelines Automation Project (Richtlijnen Automatiseringsproject) was started to develop a computer program that can support quality assurance of medical action-taking in general practice on the basis of the NHG-standards. The main feature of the program is educational assessment. Other features of the program are: guidance for case data collection, stating of differential diagnoses, and disease profiles. These features also use patient case data as a starting point. In conclusion it is argued that all efforts towards an "electronic' use of protocols in the health care delivery system will fail, unless we arrive at a care record that both with respect to its structure and to its content, is being founded on sound formal principles. Several problems need to be solved first. The implementation, and exploitation of protocols, though relatively simple from a knowledge representation point of view, is not a straightforward task.

Quality control in management of pain.

Since 1987 several pain clinics in The Netherlands have started with some kind of computer-assisted recording of data, mainly for purposes of quality control. However, this has not yet led to routinely generated reports about the quality of these clinics because a consensus on how to assess quality in pain-treatment is missing. Using classical system-development methods a global specification for an information system for quality assessment was defined on which a prototype application was based. Various changes were adopted into this prototype, which ultimately resulted in explicit requirements stating: 1. Which data to record, 2. What organisational prerequisites to fulfil for such a system, 3. The user-interface, and 4. Interactions with other information systems. The final application was implemented in a number of pain clinics where its usefulness in quality control is currently assessed.

GALEN ten years on: tasks and supporting tools.

The GALEN technology has matured over more than a decade of use. We describe a set of software tools and associated methodologies that together are supporting ontological engineering in a production, rather than a research setting.

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.

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.

Bi-phasic composition of trans-root electrical potential in roots of Plantago species: involvement of spatially separated electrogenic pumps.

The effect of oxygen on the trans-root potential (TRP) of excised roots in Plantago media L. and P. maritima L. was investigated. Two distinct reactions were found. In some experiments (type A roots) the reaction of TRP to anoxia was bi-phasic, and this reaction fits well into a model, assuming the presence of two spatially separated proton pump sites in the roots: one at the plasmalemma of epidermal and cortical cells and the other at the symplast/xylem interface. The two pumps work in opposite directions. In other experiments (type B roots) no hyperpolarization as a response to anoxia at the inner symplast membrane was observed. There is evidence that the inner pump is also present in these roots, but only in an inactive or electroneutral state. It is concluded that O2-deficiency prevails more often in the central part of the root than in epidermal and cortical cells, when roots are brought gradually under anoxia. This causes the pump located at the symplast/xylem interface to be inhibited more quickly than the other at decreasing O2-concentrations in the bathing solution.

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.

Photosynthetic HCO(3) Utilization and OH Excretion in Aquatic Angiosperms: LIGHT-INDUCED pH CHANGES AT THE LEAF SURFACE.

The utilization of HCO(3) (-) as carbon source for photosynthesis by aquatic angiosperms results in the production of 1 mole OH(-) for each mole CO(2) assimilated. The OH(-) ions are subsequently released to the medium. In several Potamogeton and Elodea species, the site of the HCO(3) (-) influx and OH(-) efflux are spatially separated. Described here are light- and dark-induced pH changes at the lower and upper epidermis of the leaves of Potamogeton lucens, Elodea densa, and Elodea canadensis.In the light, two phases could be discerned. During the first phase, the pH increased at both sides of the leaves. This pH increase apparently resulted from CO(2) fixation. During the second, so-called polar phase, the pH at the upper side increased further, but the pH at the lower side dropped below the pH of the ambient solution. The pH drop at the lower epidermis indicates that the K(+) influx exceeds the net CO(2) (HCO(3) (-) + CO(2)) influx slightly. This may result either from a proton pump driving an extra K(+) influx or from CO(2) diffusion from the cells into the outer medium previously taken up as HCO(3) (-). In the dark, a CO(2) gush was observed at both sides. During the polar phase, the upper side becomes electrically negative with respect to the lower side. Subsequent depolarization in the dark revealed that this potential difference consisted of a fast and a slow component.

Integrated decision support system/image archive for histological typing of breast cancer using a relation oriented inference system.

Histological typing of invasive breast cancer according to the World Health Organisation criteria is prognostically relevant, because some histological subtypes have a markedly better prognosis. However, reproducibility of histological typing is not high because of the absence of strict typing criteria, variations in the application of the typing criteria and the usually limited illustration of the relevant criteria. The aim of this study was to develop an expert system based on highly structured histological typing criteria, integrated with high-quality microscope images to illustrate the typing criteria. This system should be useful as a decision support system in the diagnosis of breast cancers and should increase the reproducibility of histological typing. Criteria for typing were extracted from textbooks and, based on experience, these criteria were structured and implemented in the Relation Oriented Inference System (ROIS), in which information can be structured by defining relations. Illustrative black and white images were digitized and integrated into the shell. The performance of the resulting decision support system was evaluated by a group of six pathologists using a set of slides covering the spectrum of the most frequently occurring histological types of invasive breast cancer. The pathologists first assessed histological type according to standard morphological procedures. The cases were then reassessed with the decision support system available for consultation. The use of the decision support system appeared to influence the previously assessed histological type in about half of the cases. Using the decision support system, histological typing was more uniform and more in accord with a 'gold standard' set by two experts.(ABSTRACT TRUNCATED AT 250 WORDS)