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At least 955 records · Page 53Linked to original sources
PubMed1998

Adapting the Biomek 2000 Laboratory Automation Workstation for printing DNA microarrays.

The Biomek 2000 Laboratory Automation Workstation is used for liquid handling and other repetitive operations in many laboratories. Since it has very good spatial positioning capabilities, we have modified this workstation to deliver samples at high densities onto microscope slides to produce DNA microarrays. The workstation tool, originally designed for bacterial colony replication, was adapted to carry special printing pins and was further modified to improve its positional accuracy. Software written in the Tool Command Language was concurrently developed to control the movements of the workstation arm during the process of printing. With these modifications, the workstation can reliably deliver individual samples at a spacing of 0.5 mm, corresponding to a total of more than 3000 samples on a single slide. Arrays prepared in this way were successfully tested in hybridization experiments.

Automation↗
PubMedDate not supplied

Information object definition-based unified modeling language representation of DICOM structured reporting: a case study of transcoding DICOM to XML.

Supplement 23 to DICOM (Digital Imaging and Communications for Medicine), Structured Reporting, is a specification that supports a semantically rich representation of image and waveform content, enabling experts to share image and related patient information. DICOM SR supports the representation of textual and coded data linked to images and waveforms. Nevertheless, the medical information technology community needs models that work as bridges between the DICOM relational model and open object-oriented technologies. The authors assert that representations of the DICOM Structured Reporting standard, using object-oriented modeling languages such as the Unified Modeling Language, can provide a high-level reference view of the semantically rich framework of DICOM and its complex structures. They have produced an object-oriented model to represent the DICOM SR standard and have derived XML-exchangeable representations of this model using World Wide Web Consortium specifications. They expect the model to benefit developers and system architects who are interested in developing applications that are compliant with the DICOM SR specification.

Computer Communication Networks↗
PubMed2003

Open-source toolkit for simple XML annotation.

Use of Extensible Markup Language (XML) is increasingly prevalent among medical informatics projects. Many of these projects involve, at some point, the interaction between a researcher and specialized XML documents for the purpose of annotating the XML data. We offer a simple toolkit to assist these researchers. Our solution is a simple, yet fully functional, annotation system that can easily be adapted to the needs of the researcher. All of the materials for this toolkit are freely available.

Algorithms↗
PubMed2003

Modelling protein functional domains in signal transduction using Maude.

Modelling of protein-protein interactions in signal transduction is receiving increased attention in computational biology. This paper describes recent research in the application of Maude, a symbolic language founded on rewriting logic, to the modelling of functional domains within signalling proteins. Protein functional domains (PFDs) are a critical focus of modern signal transduction research. In general, Maude models can simulate biological signalling networks and produce specific testable hypotheses at various levels of abstraction. Developing symbolic models of signalling proteins containing functional domains is important because of the potential to generate analyses of complex signalling networks based on structure-function relationships.

Algorithms↗
PubMedDate not supplied

Temporal expressiveness in querying a time-stamp--based clinical database.

Most health care databases include time-stamped instant data as the only temporal representation of patient information. Many previous efforts have attempted to provide frameworks in which medical databases could be queried in relation to time. These, however, have required either a sophisticated database representation of time, including time intervals, or a time-stamp-based database coupled with a nonstandard temporal query language. In this work, the authors demonstrate how their previously described data retrieval application, DXtractor, can be used as a database querying application with expressive power close to that of temporal databases and temporal query languages, using only standard SQL and existing time-stamp-based repositories. DXtractor provides the ability to compose temporal queries through an interface that is understood by nonprogramming medical personnel. Not all temporal constructs are easily implemented using this framework; nonetheless, DXtractor's temporal capabilities provide a significant improvement in the temporal expressivity accessible to clinicians using standard time-stamped clinical databases.

Database Management Systems↗
PubMed2001

Using features of Arden Syntax with object-oriented medical data models for guideline modeling.

Computer-interpretable guidelines (CIGs) can deliver patient-specific decision support at the point of care. CIGs base their recommendations on eligibility and decision criteria that relate medical concepts to patient data. CIG models use expression languages for specifying these criteria, and define models for medical data to which the expressions can refer. In developing version 3 of the GuideLine Interchange Format (GLIF3), we used existing standards as the medical data model and expression language. We investigated the object-oriented HL7 Reference Information Model (RIM) as a default data model. We developed an expression language, called GEL, based on Arden Syntax's logic grammar. Together with other GLIF constructs, GEL reconciles incompatibilities between the data models of Arden Syntax and the HL7 RIM. These incompatibilities include Arden's lack of support for complex data types and time intervals, and the mismatch between Arden's single primary time and multiple time attributes of the HL7 RIM.

Decision Making, Computer-Assisted↗
PubMed2002

Standard protocol for exchange of health-checkup data based on SGML: the Health-checkup Data Markup Language (HDML).

OBJECTIVES: To develop a health/medical data interchange model for efficient electronic exchange of data among health-checkup facilities. RESULTS: A Health-checkup Data Markup Language (HDML) was developed on the basis of the Standard Generalized Markup Language (SGML), and a feasibility study carried out, involving data exchange between two health checkup facilities. The structure of HDML is described. RESULTS: The transfer of numerical lab data, summary findings and health status assessment was successful. CONCLUSIONS: HDML is an improvement to laboratory data exchange. Further work has to address the exchange of qualitative and textual data.

Computer Communication Networks↗
PubMed1995

NeuroNames Brain Hierarchy.

The NeuroNames Brain Hierarchy is a structured system of neuroanatomical terminology that provides a comprehensive representation of virtually all human and nonhuman primate brain structures that are identifiable either grossly or in Niss1-stained histological sections. This system was devised for computer applications to address deficiencies in the brain terminology presented in Nomina Anatomica. English terms are listed for 783 structures in nine levels of hierarchical ranking. Abbreviations are provided for all superficial and primary volumetric structures. The substructures that constitute the total volume of every superstructure are identified. Superficial features of the brain are clearly distinguished from internal, volumetric brain structures. Structures found solely in either humans or macaques are identified. The purpose of the NeuroNames Brain Hierarchy is to bring greater standardization to the neuroanatomical terminology used by scientific investigators, clinicians, and students. This effort is consistent with the goals of the Unified Medical Language System program of the National Library of Medicine. It is hoped that the systematic construction of the NeuroNames Brain Hierarchy will facilitate use of the most widely accepted definitions of classical neuroanatomy in quantitative computerized neuroimaging applications. It should provide an accurate structural framework against which to reference the many other kinds of neuroanatomical information that are acquired by modern imaging, mapping, and histological labeling techniques.

Animals↗
PubMed1997

Applications of abduction: hypothesis testing of neuroendocrinological qualitative compartmental models.

It is difficult to assess hypothetical models in poorly measured domains such as neuroendocrinology. Without a large library of observations to constrain inference, the execution of such incomplete models implies making assumptions. Mutually exclusive assumptions must be kept in separate worlds. We define a general abductive multiple-worlds engine that assesses such models by (i) generating the worlds and (ii) tests if these worlds contain known behaviour. World generation is constrained via the use of relevant envisionment. We describe QCM, a modeling language for compartmental models that can be processed by this inference engine. This tool has been used to find faults in theories published in international refereed journals; i.e. QCM can detect faults which are invisible to other methods. The generality and computational limits of this approach are discussed. In short, this approach is applicable to any representation that can be compiled into an and-or graph, provided the graphs are not too big or too intricate (fanout < 7).

Computer Simulation↗
PubMed2004

Importing MAGE-ML format microarray data into BioConductor.

UNLABELLED: The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. AVAILABILITY: http://www.bioconductor.org. Open Source.

Database Management Systems↗
PubMed1997

The place of SGML and HTML in building electronic patient records.

The authors are concerned that, although popular, SGML (Standard Generalized Markup Language) is only one approach to capturing, storing, viewing and exchanging healthcare information and does not provide a suitable paradigm for solving most of the problems associated with paper based patient record systems. Although a discussion of the relative merits of SGML, HTML (HyperText Markup Language) may be interesting, we feel such a discussion is avoiding the real issues associated with the most appropriate way to model, represent, and store electronic patient information in order to solve healthcare problems, and therefore the medical informatics community should firstly concern itself with these issues. The paper substantiates this viewpoint and concludes with some suggestions of how progress can be made.

Computer Communication Networks↗
PubMed1995

Querying temporal clinical databases with different time granularities: the GCH-OSQL language.

There is a need for managing temporal clinical information given at different levels of granularity. Different time granularities are also needed in querying clinical databases. In this paper, we describe GCH-OSQL (Granular Clinical History--Object Structured Query Language), an object-oriented temporally-oriented extension of SQL. GCH-OSQL is based on an object-oriented temporal data model. It allows storage of clinical information at different and mixed granularities. GCH-OSQL deals with the valid time of clinical information. GCH-OSQL offers also a graphical user-interface. It guides different end users, from expert to naive, to formulate expressive and correct queries.

Computer Graphics↗
PubMed2005

CLAIM (CLinical Accounting InforMation)--an XML-based data exchange standard for connecting electronic medical record systems to patient accounting systems.

With the evolving and diverse electronic medical record (EMR) systems, there appears to be an ever greater need to link EMR systems and patient accounting systems with a standardized data exchange format. To this end, the CLinical Accounting InforMation (CLAIM) data exchange standard was developed. CLAIM is subordinate to the Medical Markup Language (MML) standard, which allows the exchange of medical data among different medical institutions. CLAIM uses eXtensible Markup Language (XML) as a meta-language. The current version, 2.1, inherited the basic structure of MML 2.x and contains two modules including information related to registration, appointment, procedure and charging. CLAIM 2.1 was implemented successfully in Japan in 2001. Consequently, it was confirmed that CLAIM could be used as an effective data exchange format between EMR systems and patient accounting systems.

Accounts Payable and Receivable↗
PubMed2005

Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

Database Management Systems↗
PubMed1999

HL7 document patient record architecture: an XML document architecture based on a shared information model.

The HL7 SGML/XML Special Interest Group is developing the HL7 Document Patient Record Architecture. This draft proposal strives to create a common data architecture for the interoperability of healthcare documents. Key components are that it is under the umbrella of HL7 standards, it is specified in Extensible Markup Language, the semantics are drawn from the HL7 Reference Information Model, and the document specifications form an architecture that, in aggregate, define the semantics and structural constraints necessary for the exchange of clinical documents. The proposal is a work in progress and has not yet been submitted to HL7's formal balloting process.

Humans↗
PubMed2001

Combining diagnosis and treatment using Asbru.

Traditionally, diagnosis and treatment have been seen as two distinct tasks. Consequently, most approaches to computer supported health care focus on one of the two - mostly on diagnosis or rather on the interpretation of measurements which is much better understood and formalized. However, in practice diagnosis and treatment overlap and influence each other in many ways. Combinations range from repeatedly going through the diagnosis-treatment loop over a period of time to permanent monitoring of the patients' health condition as it is done in intensive care units. In this paper we describe how to model these combinations using the clinical protocol-representation language Asbru. It implements treatment steps in a hierarchy of skeletal, time-oriented plans. Diagnosis can either be described in a declarative way in the conditions, under which treatment steps are taken or it can be modelled explicitly as plans of their own right. We demonstrate our approach using examples taken from the American Association of Paediatricians' guideline for the treatment of hyperbilirubinemia in the new-born.

Decision Making, Computer-Assisted↗
PubMed1998

Use of project ontologies and terminology servers to support software engineering.

Complex medical software imposes new requirements on the methods and tools used for maintenance. Appropriate maintenance tools can increase software reliability and quality by providing means to trace dependencies among software artifacts for reducing unexpected impacts in software caused by software changes. We have used the GRAIL concept-representation language for medical terminologies to build a project ontology that models relationships among software artifacts. Our approach involves modeling of the terminology used in software projects, which enables us to describe, classify and relate individual software artifacts. A networked repository accessible to the entire software development staff stores the conceptual model, source code and associated documents. We present an architecture for a maintenance tool, and show how developers can use GRAIL to build a project ontology.

Databases as Topic↗
PubMed1987

Acquisition of sign language by autistic children. III: Generalized descriptive phrases.

Sign language training has emerged as a viable alternative to speech for those autistic children who remain nonverbal in spite of remediation efforts. Yet the variables responsible for the acquisition of specific signing skills have not been fully investigated. The present study was undertaken to validate experimentally a portion of a general language intervention program developed by the authors. Specifically, we focused on descriptive signing that involved action-object phrases. Four autistic children were successfully taught such phrases following an intervention composed of prompting, fading, stimulus rotation, and differential reinforcement. After being trained on a small number of action-object phrases, the children displayed skill generalization to new situations. The results were discussed with respect to the likely need for added incidental teaching to bring about communicative use of the skills taught.

Adolescent↗