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PubMedDate not supplied

The Asgaard project: a task-specific framework for the application and critiquing of time-oriented clinical guidelines.

Clinical guidelines can be viewed as generic skeletal-plan schemata that represent clinical procedural knowledge and that are instantiated and refined dynamically by care providers over significant time periods. In the Asgaard project, we are investigating a set of tasks that support the application of clinical guidelines by a care provider other than the guideline's designer. We are focusing on the application of the guideline, recognition of care providers' intentions from their actions, and critique of care providers' actions given the guideline and the patient's medical record. We are developing methods that perform these tasks in multiple clinical domains, given an instance of a properly represented clinical guideline and an electronic medical patient record. In this paper, we point out the precise domain-specific knowledge required by each method, such as the explicit intentions of the guideline designer (represented as temporal patterns to be achieved or avoided). We present a machine-readable language, called Asbru, to represent and to annotate guidelines based on the task-specific ontology. We also introduce an automated tool for the acquisition of clinical guidelines based on the same ontology, developed using the PROTEGE-II framework.

Artificial Intelligence↗

PubMed1997

An information infrastructure for long-term care.

Emerging trends promise to alter the way long-term care is practiced. These include: changing regulation of the nursing home industry with emphasis on outcome and assessment, a trend in medical informatics away from expert systems and toward on-line decision support and reminder systems, and the application of industrial statistical quality management techniques to the realm of human services. Emerging standards such as the Arden Syntax and Unified Medical Language Systems and technologies such as Rapid Application Development Tools will facilitate the use of modern computing to mold and implement these converging trends.

Abstracting and Indexing↗

PubMed2002

Representing nested semantic information in a linear string of text using XML.

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information.

Programming Languages↗

PubMed2001

PDL: a definition language for trend pattern representation and detection in medicine.

This paper proposes a pattern definition language, PDL, to effectively represent and manipulate trend patterns to support medical decision making in time-critical domains. Based on a modified version of SDL, a shape definitional language introduced by Agrawal, PDL extends the expressive power of SDL in the temporal domains. PDL also permits irregular length of elementary patterns to be matched in the query. This paper describes the syntax and the semantics of PDL, as well as illustrating how it can be applied in a time-critical medical domain.

Critical Care↗

PubMed2004

Description and status update on GELLO: a proposed standardized object-oriented expression language for clinical decision support.

A major obstacle to sharing computable clinical knowledge is the lack of a common language for specifying expressions and criteria. Such a language could be used to specify decision criteria, formulae, and constraints on data and action. Al-though the Arden Syntax addresses this problem for clinical rules, its generalization to HL7's object-oriented data model is limited. The GELLO Expression language is an object-oriented language used for expressing logical conditions and computations in the GLIF3 (GuideLine Interchange Format, v. 3) guideline modeling language. It has been further developed under the auspices of the HL7 Clinical Decision Support Technical Committee, as a proposed HL7 standard., GELLO is based on the Object Constraint Language (OCL), because it is vendor-independent, object-oriented, and side-effect-free. GELLO expects an object-oriented data model. Although choice of model is arbitrary, standardization is facilitated by ensuring that the data model is compatible with the HL7 Reference Information Model (RIM).

Decision Making, Computer-Assisted↗

PubMedDate not supplied

CellML: its future, present and past.

Advances in biotechnology and experimental techniques have lead to the elucidation of vast amounts of biological data. Mathematical models provide a method of analysing this data; however, there are two issues that need to be addressed: (1) the need for standards for defining cell models so they can, for example, be exchanged across the World Wide Web, and also read into simulation software in a consistent format and (2) eliminating the errors which arise with the current method of model publication. CellML has evolved to meet these needs of the modelling community. CellML is a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. In this paper we summarise the structure of CellML, its current applications (including biological pathway and electrophysiological models), and its future development--in particular, the development of toolsets and the integration of ontologies.

Algorithms↗

PubMedDate not supplied

The HL7 Clinical Document Architecture.

Many people know of Health Level 7 (HL7) as an organization that creates health care messaging standards. Health Level 7 is also developing standards for the representation of clinical documents (such as discharge summaries and progress notes). These document standards make up the HL7 Clinical Document Architecture (CDA). The HL7 CDA Framework, release 1.0, became an ANSI-approved HL7 standard in November 2000. This article presents the approach and objectives of the CDA, along with a technical overview of the standard. The CDA is a document markup standard that specifies the structure and semantics of clinical documents. A CDA document is a defined and complete information object that can include text, images, sounds, and other multimedia content. The document can be sent inside an HL7 message and can exist independently, outside a transferring message. The first release of the standard has attempted to fill an important gap by addressing common and largely narrative clinical notes. It deliberately leaves out certain advanced and complex semantics, both to foster broad implementation and to give time for these complex semantics to be fleshed out within HL7. Being a part of the emerging HL7 version 3 family of standards, the CDA derives its semantic content from the shared HL7 Reference Information Model and is implemented in Extensible Markup Language. The HL7 mission is to develop standards that enable semantic interoperability across all platforms. The HL7 version 3 family of standards, including the CDA, are moving us closer to the realization of this vision.

Computer Communication Networks↗

PubMed2006

Evaluation of PROforma as a language for implementing medical guidelines in a practical context.

BACKGROUND: PROforma is one of several languages that allow clinical guidelines to be expressed in a computer-interpretable manner. How these languages should be compared, and what requirements they should meet, are questions that are being actively addressed by a community of interested researchers. METHODS: We have developed a system to allow hypertensive patients to be monitored and assessed without visiting their GPs (except in the most urgent cases). Blood pressure measurements are performed at the patients' pharmacies and a web-based system, created using PROforma, makes recommendations for continued monitoring, and/or changes in medication. The recommendations and measurements are transmitted electronically to a practitioner with authority to issue and change prescriptions. We evaluated the use of PROforma during the knowledge acquisition, analysis, design and implementation of this system. The analysis focuses on the logical adequacy, heuristic power, notational convenience, and explanation support provided by the PROforma language. RESULTS: PROforma proved adequate as a language for the implementation of the clinical reasoning required by this project. However a lack of notational convenience led us to use UML activity diagrams, rather than PROforma process descriptions, to create the models that were used during the knowledge acquisition and analysis phases of the project. These UML diagrams were translated into PROforma during the implementation of the project. CONCLUSION: The experience accumulated during this study highlighted the importance of structure preserving design, that is to say that the models used in the design and implementation of a knowledge-based system should be structurally similar to those created during knowledge acquisition and analysis. Ideally the same language should be used for all of these models. This means that great importance has to be attached to the notational convenience of these languages, by which we mean the ease with which they can be read, written, and understood by human beings. The importance of notational convenience arises from the fact that a language used during knowledge acquisition and analysis must be intelligible to the potential users of a system, and to the domain experts who provide the knowledge that will be used in its construction.

Antihypertensive Agents↗

PubMed2000

The use of XML in healthcare information management.

Extensible Markup Language (XML) is an emerging Internet standard that is gaining momentum in many industries, including healthcare. This article examines the origins of XML, its components, and some potential uses for XML in the healthcare industry. It then discusses a specific initiative to use XML as the basis for an industry-standard scheduling protocol.

Appointments and Schedules↗

PubMed2003

A native XML database design for clinical document research.

Health-care institutions are gaining an increasing interest in exploiting the data that are gathered through electronic medical records. Narrative data, generated by transcription or direct entry, represents a far greater challenge for analytic tasks. Moreover, a small number of institutions are beginning to explore deeper structuring of narrative data using natural language processing (NLP). The data produced by NLP systems has a complex, nested structure. Current electronic medical records do not have the ability to store and retrieve data of this complexity in a suitable way.

Database Management Systems↗

PubMed1992

An extended SQL for temporal data management in clinical decision-support systems.

We are developing a database implementation to support temporal data management for the T-HELPER physician workstation, an advice system for protocol-based care of patients who have HIV disease. To understand the requirements for the temporal database, we have analyzed the types of temporal predicates found in clinical-trial protocols. We extend the standard relational data model in three ways to support these querying requirements. First, we incorporate timestamps into the two-dimensional relational table to store the temporal dimension of both instant- and interval-based data. Second, we develop a set of operations on timepoints and intervals to manipulate timestamped data. Third, we modify the relational query language SQL so that its underlying algebra supports the specified operations on timestamps in relational tables. We show that our temporal extension to SQL meets the temporal data-management needs of protocol-directed decision support.

Acquired Immunodeficiency Syndrome↗

PubMed1990

Conducting a matched-pairs historical cohort study with a computer-based ambulatory medical record system.

We describe techniques for using the Computer-Stored Ambulatory Record (COSTAR) at the Massachusetts General Hospital to conduct a historical cohort study of the effect of nonsteroidal anti-inflammatory drugs (NSAIDs) on blood pressure control. A query language was used to identify patients satisfying clinical and data-availability criteria, to match these patients with clinically similar patients not exposed to NSAIDs, and to collect data from the COSTAR records of both groups of patients to determine any differences in outcome. We analyzed over 30,000 patient records to select 90 pairs of patients used in the study. This approach to clinical research uses data collected for purpose of patient care and so does not require the separate recording of patient data for clinical research. Using computer-based medical record systems with a query language allows selection and matching of patients using detailed demographic and clinical criteria. The ability to conduct such studies is an advantage of computer-based medical record systems over the paper record system.

Ambulatory Care↗

PubMed1993

Computer supported analysis of cardiovascular parameters by impedance cardiography and plethysmography.

A fully automated system for computer supported analysis of cardiovascular parameters on the basis of impedance technique, which is confined to the analysis of relative changes of stroke volume and cardiac output, has been developed and tested. The evaluation showed good agreement between automatic and manual calculation. As the whole computational procedure is done by software, which is written in a common language (BASIC), a maximum of flexibility and portability is guaranteed. Estimation of relative changes of stroke volume and cardiac output as well as peripheral blood flow is possible without any manual interaction. Extension from physiological measurement of healthy individuals to clinical application has been started.

Cardiac Output↗

PubMedDate not supplied

Visualizing 3D data obtained from microscopy on the Internet.

The Internet is a powerful communication medium increasingly exploited by business and science alike, especially in structural biology and bioinformatics. The traditional presentation of static two-dimensional images of real-world objects on the limited medium of paper can now be shown interactively in three dimensions. Many facets of this new capability have already been developed, particularly in the form of VRML (virtual reality modeling language), but there is a need to extend this capability for visualizing scientific data. Here we introduce a real-time isosurfacing node for VRML, based on the marching cube approach, allowing interactive isosurfacing. A second node does three-dimensional (3D) texture-based volume-rendering for a variety of representations. The use of computers in the microscopic and structural biosciences is extensive, and many scientific file formats exist. To overcome the problem of accessing such data from VRML and other tools, we implemented extensions to SGI's IFL (image format library). IFL is a file format abstraction layer defining communication between a program and a data file. These technologies are developed in support of the BioImage project, aiming to establish a database prototype for multidimensional microscopic data with the ability to view the data within a 3D interactive environment.

Animals↗

PubMed1988

The expert system language GALEN.

GALEN is an expert system language based upon nonmonotonic logic and sorted higher-order quantificational logic. It is designed to permit the composition of expert systems for computerized electrocardiographic diagnosis. Using GALEN, a cardiologist will be able to supplement or replace the commercially available computer-assisted ECG diagnostic systems with diagnostic criteria of his or her own for research and clinical uses.

Diagnosis, Computer-Assisted↗

PubMed1998

The role of digital imaging and communications in medicine in an evolving healthcare computing environment: the model is the message.

The decision to use Digital Imaging and Communications in Medicine (DICOM), Health Level 7 (HL7), a common object broker such as the Common Object Request Brokering Architecture (CORBA) or ActiveX (Microsoft Corp, Redmond, WA) or any other protocol for the transfer of DICOM data depends on the requirements of a particular implementation. The selection of protocol is independent of the information model. Our goal as message standards developers is to design a data interchange infrastructure that will faithfully convey the computer-based patient record and make it available to authorized health care providers when and where it is needed for patient care. DICOM accurately and expressively represents the clinically significant properties of images and the semantics of image-related information. The DICOM data model is small and well-defined. The model can be expressed in Standard Generalized Markup Language (SGML) or Object Management Group Interface Definition Language or other common syntax-and can be implemented using any reliable communications protocol. Therefore our opinion is that the DICOM semantic data model should serve as the basis for a logically equivalent set of specifications in HL7, CORBA, ActiveX, and SGML for the interchange of biomedical images and image-related information.

Computer Communication Networks↗

PubMedDate not supplied

The medical information bus: overview of the medical device data language.

The Medical Information Bus (MIB) reference model defines a new, object-oriented Medical Device Data Language (MDDL), under development by the Institute of Electrical and Electronic Engineers Society (IEEE) P1073 MIB Standard Committee. The MDDL treats medical devices, host computers, humans and device parameters as objects, and provides a flexible and extensible language for describing and passing messages between objects. This paper describes the MDDL semantic reference model and presents an overview of the MDDL structure, within the framework of the International Standards Organization (ISO) System Management Overview (SMO) model. A simple example of how the MDDL can be used to construct a device event report is also described.

Computer Communication Networks↗

PubMed2001

Acquisition and analysis of repeating patterns in time-oriented clinical data.

OBJECTIVES: (1) Creation of an expressive language for specification of temporal patterns in clinical domains, (2) Development of a graphical knowledge-acquisition tool allowing expert physicians to define meaningful domain-specific patterns, (3) Implementation of an interpreter capable of detecting such patterns in clinical databases, and (4) Evaluation of the tools in the domains of diabetes and oncology. METHODS: We describe a constraint-based language, named CAPSUL, for specification of temporal patterns. We implemented a knowledge-acquisition tool and a temporal-pattern interpreter within Résumé, a larger temporal-abstraction architecture. We evaluated the knowledge-acquisition process with the help of domain experts. In collaboration with the Rush Presbyterian/St. Luke's Medical Center, we analyzed data of bone-marrow transplantation patients. The expert compared the detected patterns to a manual inspection of the data, with the help of an experimental information-visualization tool we are developing in a related project. RESULTS: The CAPSUL language was expressive enough during the knowledge-acquisition process to capture almost all of the patterns that the experts found useful. The patterns detected in the data by the pattern interpreter were all verified as correct. Completeness (whether all correct patterns were found) was difficult to assess, due to the size of the database. CONCLUSIONS: The CAPSUL language enables medical experts to express temporal patterns involving multiple levels of abstraction of clinical data. The ability to reuse both domain-patterns and abstract constraints seems highly useful. The Résumé interpreter, augmented by the CAPSUL semantics, finds the complex patterns within a clinical time-oriented database in a sound fashion.

Algorithms↗