Electrocardiogram digitization: a practical perspective on the usefulness of a new tool to convert paper electrocardiograms into digital waveform.
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Artificial Intelligence↗
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Results for “Information Retrieval Systems”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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Biomedical databases: protecting privacy and promoting research.
When combined with medical information, large electronic databases of information that identify individuals provide superlative resources for genetic, epidemiology and other biomedical research. Such research resources increasingly need to balance the protection of privacy and confidentiality with the promotion of research. Models that do not allow the use of such individual-identifying information constrain research; models that involve commercial interests raise concerns about what type of access is acceptable. Researchers, individuals representing the public interest and those developing regulatory guidelines must be involved in an ongoing dialogue to identify practical models.
Computer Security↗
CARDIOMEDIA: a communicable multimedia medical record on Intranet and digital optical memory card.
As part of French health reform, French physicians were computerised by the end of 1998. A specific Intranet network will be used to communicate medical data between the health professionals. The objectives of the CARDIOMEDIA project were to develop and evaluate the feasibility of a coronary multimedia data record stored on an optical card and communicable on Intranet within the hospital. Patients treated by angioplasty at the University Hospital of Rennes participated in the experiment. In general, patients are treated in the University Hospital and are followed up by another health care provider closer to their home. The patient leaves the University Hospital with his card, which is directly available elsewhere for emergency or for consultation. This approach is assumed to reduce the number of examinations and to offer a better patient follow-up. The CARDIOMEDIA card is a specialised record including various data types: text, images, image sequences of coronarography and ECG signals. For this purpose an optical card with its large memory is very convenient. We used the DICOM format for image exchange and management. It is combined with CARDIOMEDIA specific compressing software. For the multimedia record the HTML format and web Intranet method are chosen. This provides an intuitive interface which can combine various data types and helper applications like a DICOM image viewer.
Angioplasty↗
Hierarchical data security in a Query-By-Example interface for a shared database.
Whenever a shared database resource, containing critical patient data, is created, protecting the contents of the database is a high priority goal. This goal can be achieved by developing a Query-By-Example (QBE) interface, designed to access a shared database, and embedding within the QBE a hierarchical security module that limits access to the data. The security module ensures that researchers working in one clinic do not get access to data from another clinic. The security can be based on a flexible taxonomy structure that allows ordinary users to access data from individual clinics and super users to access data from all clinics. All researchers submit queries through the same interface and the security module processes the taxonomy and user identifiers to limit access. Using this system, two different users with different access rights can submit the same query and get different results thus reducing the need to create different interfaces for different clinics and access rights.
Computer Security↗
SEMEDA: ontology based semantic integration of biological databases.
MOTIVATION: Many molecular biological databases are implemented on relational Database Management Systems, which provide standard interfaces like JDBC and ODBC for data and metadata exchange. By using these interfaces, many technical problems of database integration vanish and issues related to semantics remain, e.g. the use of different terms for the same things, different names for equivalent database attributes and missing links between relevant entries in different databases. RESULTS: In this publication, principles and methods that were used to implement SEMEDA (Semantic Meta Database) are described. Database owners can use SEMEDA to provide semantically integrated access to their databases as well as to collaboratively edit and maintain ontologies and controlled vocabularies. Biologists can use SEMEDA to query the integrated databases in real time without having to know the structure or any technical details of the underlying databases. AVAILABILITY: SEMEDA is available at http://www-bm.ipk-gatersleben.de/semeda/. Database providers who intend to grant access to their databases via SEMEDA are encouraged to contact the authors.
Computational Biology↗
Design of a description language for generating wrapper to collect biological data.
The biological data are scattered in various areas with various formats and they are changing continuously. Therefore, data integration becomes an important issue to provide researcher a dynamic access of data. In the data integration process, the method of extracting heterogeneous data dynamically from the data source is an essential part. Data extraction method using wrapper can provide flexibility and extensibility to an integration system.
Computational Biology↗
BIAS: Bioinformatics Integrated Application Software.
MOTIVATION: We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. AVAILABILITY: BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. CONTACT: hallett@mcb.mcgill.ca.
Computational Biology↗
A model diagram layout extension for SBML.
MOTIVATION: Since the knowledge about processes in living cells is increasing, modelling and simulation techniques are used to get new insights into these complex processes. During the last few years, the SBML file format has gained in popularity and support as a means of exchanging model data between the different modelling and simulation tools. In addition to specifying the model as a set of equations, many modern modelling tools allow the user to create and to interact with the model in the form of a reaction graph. Unfortunately, the SBML file format does not provide for the storage of this graph data along with the mathematical description of the model. RESULTS: Therefore, we developed an extension to the SBML file format that makes it possible to store such layout information which describes position and size of objects in the graphical representation. AVAILABILITY: The complete specification can be found on (http://projects.villa-bosch.de/bcb/sbml/ (SBML Layout Extension documentation, 2005). Additionally, a complete implementation exists as part of libSBML (2006, http://www.sbml.org/software/libsbml/).
Cell Physiological Phenomena↗
Seeing data: new methods for understanding information.
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Artificial Intelligence↗
Browsers to support awareness and social interaction.
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Awareness↗
DICOM structured report document type definition.
The Digital Imaging and Communications in Medicine (DICOM) standard recently introduced rules for the encoding, transmission and storage of the structured diagnostic report. This medical document can be stored and communicated with the images. It has a structure and may contain text, with links to other data such as images, waveforms and spatial or temporal coordinates. The prompt availability of the radiology report is crucial for implementing a Patient Electronic Record. Using the extensible markup language (XML) to encode the radiology report broadens its accessibly. This paper presents a document type definition (DTD) that accurately models the DICOM structured report content, structure, and constraints.
Abstracting and Indexing↗
The Citizen Health System (CHS): a modular medical contact center providing quality telemedicine services.
In the context of the Citizen Health System (CHS) project, a modular Medical Contact Center (MCC) was developed, which can be used in the monitoring, treatment, and management of chronically ill patients at home, such as diabetic or congestive heart failure patients. The virtue of the CHS contact center is that, using any type of communication and telematics technology, it is able to provide timely and preventive prompting to the patients, thus, achieving better disease management. In this paper, we present the structure of the CHS system, describing the modules that enable its flexible and extensible architecture. It is shown, through specific examples, how quality of healthcare delivery can be increased by using such a system.
Database Management Systems↗
The emergency department triage of community-acquired pneumonia project data and documentation systems: a model for multicenter clinical trials.
Multicenter clinical trials are complex undertakings that require significant resources to ensure efficient, high quality research. This paper describes the goals, design, and implementation of a multicenter clinical trial database management system to support this aim. A large number of study sites or patients, and the goal of automatically generating large portions of data management infrastructure from common metadata, motivated the development of the system. This paper also describes extensions for a generalized project documentation system, and discusses plans for further extensions and improvements based on observed strengths, limitations, and anticipated technological change.
Community-Acquired Infections↗
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities.
BACKGROUND: Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. RESULTS: We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. CONCLUSION: Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.
Abstracting and Indexing↗
Dynamic tables: an architecture for managing evolving, heterogeneous biomedical data in relational database management systems.
Data sparsity and schema evolution issues affecting clinical informatics and bioinformatics communities have led to the adoption of vertical or object-attribute-value-based database schemas to overcome limitations posed when using conventional relational database technology. This paper explores these issues and discusses why biomedical data are difficult to model using conventional relational techniques. The authors propose a solution to these obstacles based on a relational database engine using a sparse, column-store architecture. The authors provide benchmarks comparing the performance of queries and schema-modification operations using three different strategies: (1) the standard conventional relational design; (2) past approaches used by biomedical informatics researchers; and (3) their sparse, column-store architecture. The performance results show that their architecture is a promising technique for storing and processing many types of data that are not handled well by the other two semantic data models.
Computational Biology↗
Axiope tools for data management and data sharing.
Many areas of biological research generate large volumes of very diverse data. Managing this data can be a difficult and time-consuming process, particularly in an academic environment where there are very limited resources for IT support staff such as database administrators. The most economical and efficient solutions are those that enable scientists with minimal IT expertise to control and operate their own desktop systems. Axiope provides one such solution, Catalyzer, which acts as flexible cataloging system for creating structured records describing digital resources. The user is able specify both the content and structure of the information included in the catalog. Information and resources can be shared by a variety of means, including automatically generated sets of web pages. Federation and integration of this information, where needed, is handled by Axiope's Mercat server. Where there is a need for standardization or compatibility of the structures usedby different researchers this canbe achieved later by applying user-defined mappings in Mercat. In this way, large-scale data sharing can be achieved without imposing unnecessary constraints or interfering with the way in which individual scientists choose to record and catalog their work. We summarize the key technical issues involved in scientific data management and data sharing, describe the main features and functionality of Axiope Catalyzer and Axiope Mercat, and discuss future directions and requirements for an information infrastructure to support large-scale data sharing and scientific collaboration.
Animals↗
From paper charts to the spoken electronic medical record.
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Database Management Systems↗
Mining association rules from a pediatric primary care decision support system.
The purpose of this study was to apply an unsupervised data mining algorithm to a database containing data collected at the point of care for clinical decision support. The data set was taken from the Child Health Improvement Program (CHIP), a preventive services tracking and reminder system in use at the University of North Carolina. The database contains over 30,000 visits. We used a previously described pattern discovery algorithm to extract 2nd and 3rd order association rules from the data and reviewed the literature two see if the associations had been described before. The algorithm discovered 16 2nd order associations and 103 3rd order associations. The 3rd order associations contained no new information. The 2nd order associations demonstrated a covariance among a range of health risk behaviors. Additionally, the algorithm discovered that both tobacco smoke exposure and chronic cardiopulmonary disease are associated with failure on developmental screens. These relationships have been described before and have been attributed to underlying poverty. The work demonstrates the ability of unsupervised data mining by rule association on sparse clinical data to discover clinically important associations. However, many associations may be previously known or explained by confounding variables.
Algorithms↗