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PubMed2006

Hybrid specification, storage, retrieval and runtime application of clinical guidelines.

Clinical guidelines are a major tool in improving the quality of medical care. However, most guidelines are in free text, are not machine-comprehensible and are not easily accessible to clinicians at the point of care. We have designed and implemented a web-based, modular, distributed architecture, the Digital Electronic Guideline Library (DeGeL), which facilitates gradual conversion of clinical guidelines from text to a formal representation in the chosen target guideline ontology. The architecture supports guideline classification, semantic markup, context-sensitive search, browsing, run-time application and retrospective quality assessment. The DeGeL hybrid meta-ontology includes elements common to all guideline ontologies, such as semantic classification and domain knowledge; it also includes four content-representation formats: free text, semi-structured text, semi-formal representation and a formal representation. These formats support increasingly sophisticated computational tasks. Guidelines can thus be in a hybrid representation in which guidelines, and even parts of the same guideline, might exist at different formalisation levels. We have also developed and rigorously evaluated a methodology and an associated web-based tool, Uruz, for gradually structuring and semi-formalising free-text clinical guidelines. Finally, we have designed, implemented and evaluated a new approach, the hybrid runtime application model, for supporting runtime application of clinical guidelines that are not necessarily in a machine-comprehensible format; in particular, when the guideline is in a semi-formal representation and the patient's data are either in an electronic medical record or in a paper format. The tool implementing this new approach, the Spock module, is customised at this point to the Asbru guideline specification language and exploits the hybrid structure of guidelines in DeGeL. The Spock module also exploits our temporal-abstraction mediator to the patient record, IDAN, and our interactive intelligent-visualisation tool, KNAVE-II.

Decision Support Systems, Clinical↗
PubMed2000

High-throughput functional annotation of novel gene products using document clustering.

Gene products differentially expressed in healthy vs. diseased tissues may be considered drug targets since the change in their expression level can be related to the cause and progression of the disease studied. A significant portion of the proteins produced by these genes will be unknown and consequently their function must be characterised. The experimental elucidation of biochemical function must be supported by computational tools which can help predicting the possible function of a given protein from its amino acid sequence. We have designed a high-throughput system which automatically analyses amino acid sequences deduced from differentially represented cDNA clones. The system attempts to assign a biological function to protein sequences by carrying out searches in sequence databanks and by locating functionally relevant motifs in the query sequences. The results delivered by the various prediction methods consist of the annotations of matching sequences and/or motifs, which are free-format texts written by humans and therefore may describe the same concept with synonymous words. It is desirable to present the results in such a way that the annotations describing the same biological function are grouped together. To this end we devised an algorithm that enables the hierarchical clustering of free-format documents based on their contents. The system is capable of detecting and flagging conflicting annotations, and will speed up the interpretation of the function prediction results.

Algorithms↗
PubMedDate not supplied

Using ICPC in a computer-based primary care information system.

INTRODUCTION: Although the framework of the episode of care offers much promise in examining the process of primary health care, the development of episode-oriented, automated data sources has proceeded slowly. Experience with the International Classification of Primary Care (ICPC) in the European Community has confirmed its usefulness in creating and analyzing episodes of care, but it has seen little use in the United States. We describe the development of a Primary Care Information System (PCIS), which employs ICPC to create episodes of care from routinely collected clinical data. METHODS: The PCIS is a partially computerized medical information system running on a standard Macintosh microcomputer. The PCIS integrates ICPC, ICD-9-CM, and CPT-4 coding structures to provide episode-oriented data for clinical, administrative, research, and reimbursement needs. The performance of the PCIS was assessed based on five major issues: clinician cooperation, data-entry accuracy, validity of episode data, cost, and perceived value to users. RESULTS: The data collection and entry process required minimal additional effort from clinicians and data-entry personnel, and data-entry accuracy exceeded published estimates for other primary care data sources. Data management costs of about $1 per encounter compare favorably to published estimates for other office-based clinical information systems. The major problem seen during pilot testing was inaccurate tracking of episode boundaries through changes in providers and consequent changes in labels for problems and diagnoses. This problem has been addressed in development of the second-generation PCIS. CONCLUSION: The combination of an episode-oriented framework such as ICPC and a flexible medical information system provides a promising platform for the study of the content and process of primary health care.

Family Practice↗
PubMed1991

Automated analysis of medical text. II. Cognitive strategy.

In a previous paper, the authors described three paradigms applicable to automated medical text analysis. In this paper, the relative importance of the three paradigms is discussed, viz. the relative value of the linguistic word categorization, the semantic paradigm, and the medical fact delineation. The strategy adopted was to limit the linguistic disambiguation and apply probabilistic rules, in order to speed up the analytic process.

Algorithms↗
PubMed2000

Content-based retrieval in picture archiving and communication systems.

A COntent-Based Retrieval Architecture (COBRA) for picture archiving and communication systems (PACS) is introduced. COBRA improves the diagnosis, research, and training capabilities of PACS systems by adding retrieval by content features to those systems. COBRA is an open architecture based on widely used health care and technology standards. In addition to regular PACS components, COBRA includes additional components to handle representation, storage, and content-based similarity retrieval. Within COBRA, an anatomy classification algorithm is introduced to automatically classify PACS studies based on their anatomy. Such a classification allows the use of different segmentation and image-processing algorithms for different anatomies. COBRA uses primitive retrieval criteria such as color, texture, shape, and more complex criteria including object-based spatial relations and regions of interest. A prototype content-based retrieval system for MR brain images was developed to illustrate the concepts introduced in COBRA.

Humans↗
PubMed1997

Partitioning of genetic variation between regulatory and coding gene segments: the predominance of software variation in genes encoding introvert proteins.

In considering genetic variation in eukaryotes, a fundamental distinction can be made between variation in regulatory (software) and coding (hardware) gene segments. For quantitative traits the bulk of variation, particularly that near the population mean, appears to reside in regulatory segments. The main exceptions to this rule concern proteins which handle extrinsic substances, here termed extrovert proteins. The immune system includes an unusually large proportion of this exceptional category, but even so its chief source of variation may well be polymorphism in regulatory gene segments. The main evidence for this view emerges from genome scanning for quantitative trait loci (QTL), which in the case of the immune system points to a major contribution of pro-inflammatory cytokine genes. Further support comes from sequencing of major histocompatibility complex (Mhc) class II promoters, where a high level of polymorphism has been detected. These Mhc promoters appear to act, in part at least, by gating the back-signal from T cells into antigen-presenting cells. Both these forms of polymorphism are likely to be sustained by the need for flexibility in the immune response. Future work on promoter polymorphism is likely to benefit from the input from genome informatics.

Animals↗
PubMed1994

The role of standards in creating a health information infrastructure.

In the belief that the existence of a variety of standards is an absolute necessity for health care professional workstations to work, this paper provides a detailed overview of the standards efforts of a number of groups. According to the International Standards Organization (ISO) Reference Model, workstations require a full level of standards from the physical level through and beyond the applications level. Rapidly changing technology challenges acceptance of standards at the lower levels. Current recommendations include fiberoptic media using certain protocols. Other standards in these lower levels also have support. At the applications level, data messaging standards are being developed by six groups. The consensus standards body for the United States is coordinating the efforts of these groups in order to produce a harmonized effort, and is coordinating the effort with Europe for an international effort. Work on the development of the full set of standards necessary for workstation implementations is lagging. Accelerating the process is mandatory if we are to achieve the necessary seamless interoperability required by workstations for ubiquitous intelligent communications between the workstations and the sources of data.

Database Management Systems↗
PubMed1994

Functional requirements as an integral part of the design and development process: summary and recommendations.

The Health Care Professional Workstation (HCPW) provides a portal to the health care system as a whole. Through this portal the health care professional must be able to carry out a wide variety of tasks in an integrated fashion. Traditional health care information systems have not been designed to support this kind of use, so the functional requirements development process must be capable of leading to an architecture and components for a system that will support such use. A variety of approaches may be employed to develop functional requirements, which may be used singly or in combination. Recommendations for this activity center on domain delineation, evaluation efforts to establish the most effective approaches, detailed functional requirement development, evaluation of the developed functional requirements, creation of shared resources, and education and training in the use of the tools and methodologies.

Database Management Systems↗
PubMed1989

Querying medical databases in an environment offering logical data independence.

Medical information systems are becoming popular. Furthermore, their use is expected to be expanded in future. In order to easily extract information from the underlying databases, easy to use man-machine interfaces are required. This paper concerns the doctor interface of the ARPIA medical information system based on a relational database management system. The whole system is currently used inside the Outpatient Pediatric Clinic of the Catholic University of Rome, Italy. The interface provides logical data independence towards the underlying relational database. The paper contains some background about this kind of interfaces, and also, it sketches the software architecture of the implemented prototype.

Database Management Systems↗
PubMed1995

Introduction to the Bioelectronic Devices Project in Japan.

The Bioelectronic Devices Project was organized in Japan as a 10-year national project and it has been working toward developing fundamental key technologies for designing and assembling innovative information-processing devices by realizing the excellent functions specifically found in molecular assemblies and information processing of living organisms. The project is now in the third year of the second phase (the 8th year of its 10-year duration) and researchers have been trying to elucidate the specific characters of the prototype devices. The outline of this challenging project is given with the latest experimental results.

Electron Transport↗
PubMed1996

Developing a database of published reports of randomised clinical trials in pain research.

A database of randomised clinical trials (RCTs) in pain research published from 1950 to 1990 was created following an extensive literature search. By applying a refined MEDLINE search strategy from 1966 to 1990 and by hand-searching more than 1,000,000 pages of a total of 40 biomedical journals published during the period 1950-1990, more than 8000 RCTs were identified. The RCTs were published in more than 800 journals and over 85% appeared between 1976 and 1990. If the trend of the last 15 years persists, a total of more than 15 000 RCTs will be published in pain relief by the year 2000. A detailed description of methods to ensure efficient use of resources during the identification, retrieval and management of the information in pain relief and other fields is given. Emphasis is made on the importance of refining MEDLINE search strategies, on the use of volunteers to hand-search journals and on careful monitoring of each of the steps of the process. The potential uses of the database to guide clinical and research decisions are discussed.

Databases, Bibliographic↗
PubMed1995

A case study in ontology library construction.

The goal of our work is to facilitate the development of medical knowledge-based systems by providing a library of reusable ontologies. The availability of such a library reduces the amount of knowledge acquisition required to create knowledge bases of new applications, and makes it easier to connect a knowledge-based system to existing data bases. This article presents a case study in constructing such a library. The emphasis is on studying the principles that underly the internal structure of the library as well as on the process of constructing and using the library. We envision that, in the future, application ontologies can be constructed by the selection and refinement of generic ontologies and domain ontologies from such a library.

Artificial Intelligence↗