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Convergence on a standard for representing clinical guidelines: work in health level seven.

Concern regarding patient safety and practice variation has focused attention on clinical guidelines as a way of influencing the behavior of health care providers in order to improve patient outcomes. Despite the abundant number of guidelines produced, their use has been limited, in part because the necessary knowledge is relatively inaccessible at the point of care. In turn, this has led researchers to make guidelines computable so that they can be employed in information systems that provide tailored decision support. A number of different efforts have been mounted to create a standard formalism. Health Level Seven (HL7) is a key international standards development organization. Ongoing work in HL7 attempts to synthesize the best aspects of these efforts, producing along the way shareable components of a guideline representation, such as a common expression language and standard data model. These shareable components require in turn an information architecture that makes available a range of patient data encoded in an appropriate format. Convergence on a standard guideline formalism will facilitate use of guidelines and thus enhance patient care.

Decision Support Systems, Clinical↗

The role of XML in medical informatics in Hungary.

Reforms in healthcare means frequent changes. The author focusing on flexible information systems and data structures in healthcare, that gives the chance to avoid costly deadlocks, incompatibilities and data chaos--keeping the financial and administrative burden of provider and reimbursement information systems at low level. He describes data and document exchange among health care providers (hospitals, GPs etc.) and the reimbursing insurance institute introducing XML (eXtensible Markup Language) technology and it's multimedia extension called SMIL (Synchronized Multimedia Integration Language) that well supports large textual and multimedia nature of data in healthcare. He presents the most frequent XML datasets for reimbursement in Hungary, the validation schemas (Data Type Definitions) and procedures, comparing the new and old data file sizes with different compressions. The comparison includes different schema file sizes, and validation times.

Humans↗

HyperCare: a prototype of an active database for compliance with essential hypertension therapy guidelines.

HyperCare is a prototype of a decision support system for essential hypertension care management. The medical knowledge implemented in HyperCare derives from the guidelines for the management of mild hypertension of the World Health Organization/International Society of Hypertension, and from the recommendations of the United States Joint National Committee on Detection, Evaluation and Treatment of High Blood Pressure. HyperCare has been implemented using Chimera, an active database language developed at the Politecnico di Milano. HyperCare proves the possibility to use active database systems in developing a medical data-intensive application where inferential elaboration of moderate complexity is required.

Databases as Topic↗

A general purpose neural network simulator system for medical data processing.

We developed a general purpose neural network simulator system for medical data processing. This system has a flexible network definition language. Users can define arbitrary hierarchical neural networks using the definition language to analyze medical data that contains some complex patterns. The learning algorithm used in this system is back propagation. Learning curves are displayed on multiple windows. This is a general purpose system, so it can be used for various kinds of medical data processing such as one dimensional signal processing or two dimensional image processing. The system can run on a standard UNIX workstation, which is faster and more powerful than most personal computers. The system needs an X window system/Motif and C compiler. These are standard system programs already available on most UNIX workstations. The source code of the system can be retrieved from our anonymous ftp site via Internet.

Algorithms↗

The relational database model and multiple multicenter clinical trials.

The Southwest Oncology Group (SWOG) chose to use a relational database management system (RDBMS) for the management of data from multiple clinical trials because of the underlying relational model's inherent flexibility and the natural way multiple entity types (patients, studies, and participants) can be accommodated. The tradeoffs to using the relational model as compared to using the hierarchical model include added computing cycles due to deferred data linkages and added procedural complexity due to the necessity of implementing protections against referential integrity violations. The SWOG uses its RDBMS as a platform on which to build data operations software. This data operations software, which is written in a compiled computer language, allows multiple users to simultaneously update the database and is interactive with respect to the detection of conditions requiring action and the presentation of options for dealing with those conditions. The relational model facilitates the development and maintenance of data operations software.

Clinical Trials as Topic↗

Design and implementation of a web-based HL7 message generation and validation system.

Health level 7 (HL7) is the standard of electronic data interchange in the health domain. We have developed a web-based message generation and validation system for testing the message format of the data exchange among hospitals and health organizations. Compared with other existing ones, this system has incorporated several novel functions that optimize medical data exchange and helps medical students in learning HL7 messages. When receiving HL7 message from another system with the hypertext transmission protocol or accepting an uploaded HL7 message file, the system shows the validation result through a web browser. In this platform, users may input and edit medical data on-line to test and generate standard HL7 messages. The system supports various data formats and is capable of transforming HL7 messages between the standard delimiter format and the extensible markup language format. This system has been successfully passed our system evaluation among 139 student users for HL7 training. Most of the users agreed that the system is helpful for medical data exchange.

Computer Systems↗

Systems biology markup language: Level 2 and beyond.

The SBML (systems biology markup language) is a standard exchange format for computational models of biochemical networks. We continue developing SBML collaboratively with the modelling community to meet their evolving needs. The recently introduced SBML Level 2 includes several enhancements to the original Level 1, and features under development for SBML Level 3 include model composition, multistate chemical species and diagrams.

Computational Biology↗

XML, bioinformatics and data integration.

MOTIVATION: The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML. CONTACT: Emmanuel.Barillot@infobiogen.fr

Computational Biology↗

Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus.

MOTIVATION: SBML is becoming a standard 'de-facto' to represent and store biological models. Although SBML is very useful in defining ways of exchanging and storing biological information, it is not formal enough to allow direct translation into non ambiguous formal representation languages to perform analysis and simulation of models. We here suggest to map SBML models into process calculi representations. RESULTS: We implemented and validated a tool that translates SBML descriptions into stochastic pi-calculus specifications. AVAILABILITY: Source code is freely available for academic use by contacting the authors.

Algorithms↗

Structuring healthcare knowledge bases: an analysis of explicit and implicit structures in Arden Syntax and an XML schema representation of Arden Syntax.

The Arden Syntax for Medical Logic Modules (MLMs) is an ANSI and ISO recognized standard language for representing clinical knowledge bases. We analyzed the explicit and implicit structures in Arden Syntax MLMs and developed an information model represented as an XML schema. While the explicit structures were easily represented as XML, implicit structures require further explicit definition. In any future representation format, explicit structuring must be balanced with expressiveness and usability.

Artificial Intelligence↗

Extensible markup language (XML) in health care: integration of structured reporting and decision support.

The Extensible Markup Language (XML) is a newly adopted Internet protocol for data interchange designed to bring the key features of the Standard Generalized Markup Language (SGML; ISO 8879:1986)--extensibility, complex structures, and validation--to the World Wide Web. In this paper, we describe an architecture that uses XML to mediate between disparate client-server systems for structured reporting and decision support.

Bayes Theorem↗

CytometryML, an XML format based on DICOM and FCS for analytical cytology data.

BACKGROUND: Flow Cytometry Standard (FCS) was initially created to standardize the software researchers use to analyze, transmit, and store data produced by flow cytometers and sorters. Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies. METHODS: We extended the existing mapping of FCS to the Digital Imaging and Communications in Medicine (DICOM) standard to include list-mode data produced by flow cytometry, laser scanning cytometry, and microscopic image cytometry. FCS list-mode was mapped to the DICOM Waveform Information Object. We created a collection of Extensible Markup Language (XML) schemas to express the DICOM analytical cytologic text-based data types except for large binary objects. We also developed a cytometry markup language, CytometryML, in an open environment subject to continuous peer review. RESULTS: The feasibility of expressing the data contained in FCS, including list-mode in DICOM, was demonstrated; and a preliminary mapping for list-mode data in the form of XML schemas and documents was completed. DICOM permitted the creation of indices that can be used to rapidly locate in a list-mode file the cells that are members of a subset. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language (MathML). CONCLUSIONS: The use of XML format based on DICOM for analytical cytology met most of the previously specified requirements and appears capable of meeting the others; therefore, the present FCS should be retired and replaced by an open, XML-based, standard CytometryML.

Computer Communication Networks↗

An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets.

With the recent exponential increase in protein phosphorylation sites identified by mass spectrometry, a unique opportunity has arisen to understand the motifs surrounding such sites. Here we present an algorithm designed to extract motifs from large data sets of naturally occurring phosphorylation sites. The methodology relies on the intrinsic alignment of phospho-residues and the extraction of motifs through iterative comparison to a dynamic statistical background. Results show the identification of dozens of novel and known phosphorylation motifs from recently published serine, threonine and tyrosine phosphorylation studies. When applied to a linguistic data set to test the versatility of the approach, the algorithm successfully extracted hundreds of language motifs. This method, in addition to shedding light on the consensus sequences of identified and as yet unidentified kinases and modular protein domains, may also eventually be used as a tool to determine potential phosphorylation sites in proteins of interest.

Algorithms↗

Darwin v. 2.0: an interpreted computer language for the biosciences.

MOTIVATION: We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems. RESULTS: This second release improves Darwin version 1.6 in several ways: it now contains (1) a larger set of libraries touching most of the classical problems from computational biology (pairwise alignment, all versus all alignments, tree construction, multiple sequence alignment), (2) an expanded set of general purpose algorithms (search algorithms for discrete problems, matrix decomposition routines, complex/long integer arithmetic operations), (3) an improved language with a cleaner syntax, (4) better on-line help, and (5) a number of fixes to user-reported bugs. AVAILABILITY: Darwin is made available for most operating systems free of char ge from the Computational Biochemistry Research Group (CBRG), reachable at http://chrg.inf.ethz.ch. CONTACT: darwin@inf.ethz.ch

Algorithms↗

The Chronus II temporal database mediator.

Clinical databases typically contain a significant amount of temporal information. This information is often crucial in medical decision-support systems. Although temporal queries are common in clinical systems, the medical informatics field has no standard means for representing or querying temporal data. Over the past decade, the temporal database community has made a significant amount of progress in temporal systems. Much of this research can be applied to clinical database systems. This paper outlines a temporal database mediator called Chronus II. Chronus II extends the standard relational model and the SQL query language to support temporal queries. It provides an expressive general-purpose temporal query language that is tuned to the querying requirements of clinical decision support systems. This paper describes how we have used Chronus II to tackle a variety of clinical problems in decision support systems developed by our group.

Database Management Systems↗

A distributed computing system for magnetic resonance imaging: Java-based processing and binding of XML.

Recently we have developed a Java-based heterogeneous distributed computing system for the field of magnetic resonance imaging (MRI). It is a software system for embedding the various image reconstruction algorithms that we have created for handling MRI data sets with sparse sampling distributions. Since these data sets may result from multi-dimensional MRI measurements our system has to control the storage and manipulation of large amounts of data. In this paper we describe how we have employed the extensible markup language (XML) to realize this data handling in a highly structured way. To that end we have used Java packages, recently released by Sun Microsystems, to process XML documents and to compile pieces of XML code into Java classes. We have effectuated a flexible storage and manipulation approach for all kinds of data within the MRI system, such as data describing and containing multi-dimensional MRI measurements, data configuring image reconstruction methods and data representing and visualizing the various services of the system. We have found that the object-oriented approach, possible with the Java programming environment, combined with the XML technology is a convenient way of describing and handling various data streams in heterogeneous distributed computing systems.

Magnetic Resonance Imaging↗

Automatic filters for the detection of coherent structure in spatiotemporal systems.

Most current methods for identifying coherent structures in spatially extended systems rely on prior information about the form which those structures take. Here we present two approaches to automatically filter the changing configurations of spatial dynamical systems and extract coherent structures. One, local sensitivity filtering, is a modification of the local Lyapunov exponent approach suitable to cellular automata and other discrete spatial systems. The other, local statistical complexity filtering, calculates the amount of information needed for optimal prediction of the system's behavior in the vicinity of a given point. By examining the changing spatiotemporal distributions of these quantities, we can find the coherent structures in a variety of pattern-forming cellular automata, without needing to guess or postulate the form of that structure. We apply both filters to elementary and cyclical cellular automata (ECA and CCA) and find that they readily identify particles, domains, and other more complicated structures. We compare the results from ECA with earlier ones based upon the theory of formal languages and the results from CCA with a more traditional approach based on an order parameter and free energy. While sensitivity and statistical complexity are equally adept at uncovering structure, they are based on different system properties (dynamical and probabilistic, respectively) and provide complementary information.

Automation↗

A multiple-ontology customizable search interface for retrieval of clinical guidelines.

A major problem in the effective use of clinical guidelines is fast and accurate access at the point of care. Thus, we are developing a digital electronic guideline library (DeGeL) and a set of tools for incremental conversion of free-text guidelines into increasingly machine-comprehensible representations, which support automated application. Even if guidelines are represented in electronic fashion, care providers need to be able to quickly retrieve the guidelines that best fit the clinical situation at hand. We describe Vaidurya, a search and retrieval engine that exploits the hybrid nature of guideline representation in the DeGeL architecture. Vaidurya can use not only free-text keywords, but also multiple semantic indices along which the guidelines are classified, and the mark up of guidelines in DeGeL, using the semantic roles of one or more guideline-representation languages (ontologies). Vaidurya offers a wide variety of querying options, in order to enable different types of users to query the guideline library in a manner that is both efficient and user friendly. We describe the customizable query interface, in which each user can create their own personal query interface.

Expert Systems↗