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PubMed1998

Self-documenting structured reports using open information standards.

Structured reporting systems use standardized data elements and predetermined data-entry formats to record observations. This article describes a system for structured data entry and reporting that generates reports encoded in the Standard Generalized Markup Language (SGML), an open, internationally accepted standard for document interchange. The structured report is self-documenting: it includes a definition of its allowable data field and values encoded as a report-specific SGML document type definition (DTD). By linking its reporting concepts with those of external vocabularies such as the UMLS Metathesaurus, this system can create open, universally comprehensible structured reports.

Data Display↗

PubMed1994

Mid-term report on the Arden Syntax in a clinical event monitor.

In implementing a clinical event monitor (CEM), a decision-support system, we worked with an existing repository of clinical data (Keystone), fed from ancillary systems using HL7. The rules are written in the Arden Syntax, an ASTM standard for expressing medical knowledge as medical logic modules (MLMs). The Arden Syntax leaves unspecified the clinical data model and deductive database access language; we briefly describe our query language and the related medical concepts dictionary (MCD). This paper gives an overview of our implementation of the Arden Syntax, the MCD and the deductive database access language, with reasons for the major design decisions. Overall, less than a quarter of the development effort has gone into the Arden compiler and interpreter; the rest has focused on accessing the data and integrating with other systems. We feel that the Arden Syntax has proved its worth in writing rules; effort should now be focused on medical vocabularies and data models.

Artificial Intelligence↗

PubMedDate not supplied

Federated healthcare record server--the Synapses paradigm.

The delivery of healthcare relies on the sharing of patient information between those who are providing for the care of the patient and this information is increasingly being expressed in terms of a 'record'. Further, it is desirable that these records are available in electronic form as Electronic HealthCare Records. As it is likely that patient records or parts of records will be stored in many different information systems and in the form of disparate record architectures, uniform access to patient records would be problematic. This paper presents an overview of the Synapses computing environment in which a Federated Healthcare Record Server provides uniform access to patient information stored in connected heterogeneous autonomous information systems and other Synapses servers. The Synapses record architecture is based on the architecture proposed by the Technical Committee 251 of the European Committee for Standardisation and the interfaces to the Synapses server are specified in the ISO standard Interface Definition Language. Synapses is a pan-European project involving a number of hospitals, software companies, universities and research institutes and is partly funded by the EU Health Telematics Programme. The overview is described in terms of the Open Distributed Processing Reference Model.

Computer Communication Networks↗

PubMed2006

A probabilistic Classifier System and its application in data mining.

The article is about a new Classifier System framework for classification tasks called BYP-CS (for BaYesian Predictive Classifier System). The proposed CS approach abandons the focus on high accuracy and addresses a well-posed Data Mining goal, namely, that of uncovering the low-uncertainty patterns of dependence that manifest often in the data. To attain this goal, BYP-CS uses a fair amount of probabilistic machinery, which brings its representation language closer to other related methods of interest in statistics and machine learning. On the practical side, the new algorithm is seen to yield stable learning of compact populations, and these still maintain a respectable amount of predictive power. Furthermore, the emerging rules self-organize in interesting ways, sometimes providing unexpected solutions to certain benchmark problems.

Algorithms↗

PubMed2006

SBMLToolbox: an SBML toolbox for MATLAB users.

SUMMARY: We present SBMLToolbox, a toolbox that facilitates importing and exporting models represented in the Systems Biology Markup Language (SBML) in and out of the MATLAB environment and provides functionality that enables an experienced user of either SBML or MATLAB to combine the computing power of MATLAB with the portability and exchangeability of an SBML model. SBMLToolbox supports all levels and versions of SBML. AVAILABILITY: SBMLToolbox is freely available from http://sbml.org/software/sbmltoolbox

Computer Simulation↗

PubMed2000

HGML: a hypertext guideline markup language.

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form.

Decision Support Systems, Clinical↗

PubMed2002

PQL: a declarative query language over dynamic biological schemata.

We introduce the PQL query language (PQL) used in the GeneSeek genetic data integration project. PQL incorporates many features of query languages for semi-structured data. To this we add the ability to express metadata constraints like intended semantics and database curation approach. These constraints guide the dynamic generation of potential query plans. This allows a single query to remain relevant even in the presence of source and mediated schemas that are continually evolving, as is often the case in data integration.

Computational Biology↗

PubMed1998

Hypertext markup language as an authoring tool for CD-ROM production.

The Hypertext Markup Language (HTML) used to create Web pages is an attractive alternative to the proprietary authoring software that is now widely used to produce multimedia content for CD-ROMs. This paper describes the advantages and limitations of HTML as a non-proprietary and cross-platform CD-ROM authoring system, and the more general advantages of HTML as data standard for biocommunications content.

Authorship↗

PubMed1990

Nonlinear phenomenon of interfacial polarization immittance of a Pt electrode.

Description of a computerized, automated method to measure the interfacial polarization immittance of a Pt electrode in nonlinear range is presented. The classical three-electrode setup is used for measurements in conjunction with a special purpose software implemented on a Unix computer using C language. A collection of data at very low frequencies (below 2 Hz) and at high input intensities with various dc biases imposed on the input are presented to show the behavior of the interface in nonlinear range. The instrument also provides on-line harmonic analysis of the output signal, by calculating the first four Fourier series coefficients, in response to a pure sinusoidal input.

Electrodes↗

PubMed2004

The Digital electronic Guideline Library (DeGeL): a hybrid framework for representation and use of clinical guidelines.

We propose to present a poster (and potentially also a demonstration of the implemented system) summarizing the current state of our work on a hybrid, multiple-format representation of clinical guidelines that facilitates conversion of guidelines from free text to a formal representation. We describe a distributed Web-based architecture (DeGeL) and a set of tools using the hybrid representation. The tools enable performing tasks such as guideline specification, semantic markup, search, retrieval, visualization, eligibility determination, runtime application and retrospective quality assessment. The representation includes four parallel formats: Free text (one or more original sources); semistructured text (labeled by the target guideline-ontology semantic labels); semiformal text (which includes some control specification); and a formal, machine-executable representation. The specification, indexing, search, retrieval, and browsing tools are essentially independent of the ontology chosen for guideline representation, but editing the semi-formal and formal formats requires ontology-specific tools, which we have developed in the case of the Asbru guideline-specification language. The four formats support increasingly sophisticated computational tasks. The hybrid guidelines are stored in a Web-based library. All tools, such as for runtime guideline application or retrospective quality assessment, are designed to operate on all representations. We demonstrate the hybrid framework by providing examples from the semantic markup and search tools.

Artificial Intelligence↗

PubMed2003

Bioinformatics data distribution and integration via Web Services and XML.

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

Computational Biology↗

PubMed2003

GELLO: an object-oriented query and expression language for clinical decision support.

GELLO is a purpose-specific, object-oriented (OO) query and expression language. GELLO is the result of a concerted effort of the Decision Systems Group (DSG) working with the HL7 Clinical Decision Support Technical Committee (CDSTC) to provide the HL7 community with a common format for data encoding and manipulation. GELLO will soon be submitted for ballot to the HL7 CDSTC for consideration as a standard.

Decision Making, Computer-Assisted↗

PubMed2006

Direct volumetric rendering based on point primitives in OpenGL.

The aim of this project is to present a renderization by software algorithm of acquired volumetric data. The algorithm was implemented in Java language and the LWJGL graphical library was used, allowing the volume renderization by software and thus preventing the necessity to acquire specific graphical boards for the 3D reconstruction. The considered algorithm creates a model in OpenGL, through point primitives, where each voxel becomes a point with the color values related to this pixel position in the corresponding images.

Algorithms↗

PubMed2005

Distribution of immunodeficiency fact files with XML--from Web to WAP.

BACKGROUND: Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. METHODS: Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. RESULTS: IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at http://bioinf.uta.fi/idr/. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. CONCLUSION: The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at http://bioinf.uta.fi/idml/.

Database Management Systems↗

PubMed2004

An enzyme mechanism language for the mathematical modeling of metabolic pathways.

MOTIVATION: As a first step toward the elucidation of the systems biology of complex biological systems, it was our goal to mathematically model common enzyme catalytic and regulatory mechanisms that repeatedly appear in biological processes such as signal transduction and metabolic pathways. RESULTS: We describe kMech, a Cellerator language extension that describes a suite of enzyme mechanisms. Each enzyme mechanism is parsed by kMech into a set of fundamental association-dissociation reactions that are translated by Cellerator into ordinary differential equations that are numerically solved by Mathematica. In addition, we present methods that use commonly available kinetic measurements to estimate rate constants required to solve these differential equations.

Algorithms↗

PubMed1997

Work environment of blind computer specialists in Japan.

This study aimed at investigating the circumstances in the workplace of computer specialists with visual impairment in Japan through telephone interviews. The results indicate that developments in assistive technology and personal support for blind computer specialists are insufficient, due to the complexity of the Japanese language. In particular the spread of graphical user interface is threatening to blind specialists. Although assistive technology and personal assistance are indispensable for the blind to read or create printed documents, this environment has not been appropriately prepared at this time. The opportunity of retraining and providing new information to the blind specialists, in addition to providing funds and personal services, are necessary for implementing their jobs.

Adult↗

PubMed2003

The challenge of negation in health care searches and queries.

This poster deals with exclusionary queries implemented using the database language SQL and the VA FileMan database system and the retrieval searches involving negated concepts in medical narratives. The poster describes and presents error patterns and designing database queries, underlying comprehension issues regarding negative statements and queries, strategies and software for avoiding false positives in searches, and makes practical recommendations on identifying potential sources of error and avoiding incorrect or misleading results.

Delivery of Health Care↗

PubMed1996

Supporting temporal queries on clinical relational databases: the S-WATCH-QL language.

Due to the ubiquitous and special nature of time, specially in clinical datábases there's the need of particular temporal data and operators. In this paper we describe S-WATCH-QL (Structured Watch Query Language), a temporal extension of SQL, the widespread query language based on the relational model. S-WATCH-QL extends the well-known SQL by the addition of: a) temporal data types that allow the storage of information with different levels of granularity; b) historical relations that can store together both instantaneous valid times and intervals; c) some temporal clauses, functions and predicates allowing to define complex temporal queries.

Anesthesiology↗