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At least 415 records · Page 23Linked to original sources

Mining multilevel and location-aware service patterns in mobile web environments.

In this correspondence, we address the issue of efficiently mining multilevel and location-aware associated service patterns in a mobile web environment. In terms of multilevel concept, we consider the complex problem that locations and services are of hierarchical structures. We propose a new data mining method named two-dimensional multilevel (2-DML) association rules mining, which can efficiently discover the associated service request patterns by taking into account the multilevel properties of locations and services. The discovered patterns can be effectively utilized in real applications like location-based and personalized services. To the best of our knowledge, this is the first work addressing this research issue. Some variations of the 2-DML method with different properties in terms of execution efficiency and memory efficiency were also developed. Through empirical evaluation, the proposed methods are shown to deliver good performance in terms of efficiency and scalability under various system conditions.

Algorithms↗

A knowledge-based time-oriented active database approach for intelligent abstraction, querying and continuous monitoring of clinical data.

Query and interpretation of time-oriented medical data involves two subtasks: Temporal-reasoning--intelligent analysis of time-oriented data, and temporal-maintenance--effective storage, query, and retrieval of these data. Integration of these tasks into one system, known as temporal-mediator, has been proven to be beneficial to biomedical applications such as monitoring, therapy, quality assessment, visualization and exploration of time-oriented data. One potential problem in existing temporal-mediation approaches is lack of sufficient responsiveness when querying or continuously monitoring the database for complex abstract concepts that are derived from the raw data, especially regarding a large patient group. We propose a new approach: the knowledge-based time-oriented active database, a temporal extension of the active-database concept, and a merger of temporal reasoning and temporal maintenance within a persistent database framework. The approach preserves the efficiency of databases in handling data storage and retrieval, while enabling specification and performance of complex temporal reasoning using an incremental-computation approach. We implemented our approach within the Momentum system. Initial experiments are encouraging; an evaluation is underway

Algorithms↗

Computational knowledge integration in biopharmaceutical research.

An initiative to increase biopharmaceutical research productivity by capturing, sharing and computationally integrating proprietary scientific discoveries with public knowledge is described. This initiative involves both organisational process change and multiple interoperating software systems. The software components rely on mutually supporting integration techniques. These include a richly structured ontology, statistical analysis of experimental data against stored conclusions, natural language processing of public literature, secure document repositories with lightweight metadata, web services integration, enterprise web portals and relational databases. This approach has already begun to increase scientific productivity in our enterprise by creating an organisational memory (OM) of internal research findings, accessible on the web. Through bringing together these components it has also been possible to construct a very large and expanding repository of biological pathway information linked to this repository of findings which is extremely useful in analysis of DNA microarray data. This repository, in turn, enables our research paradigm to be shifted towards more comprehensive systems-based understandings of drug action.

Algorithms↗

Visualisation and navigation methods for typed protein-protein interaction networks.

Protein-protein interactions form large and complex networks. Their visualisation can aid biologists in gaining new insights about the processes in cells and is, therefore, very useful for building sophisticated research tools. Often standard force-directed graph drawing algorithms are used for the visualisation of these networks. However, currently available visual interfaces to biological databases only show general interactions and cannot cope well with more complex networks with different types of interactions. This paper presents a new approach to the visual analysis of protein-protein interaction networks. It uses a combination of circular and force-directed graph drawing algorithms to compute visual representations of protein networks depending on the type of the selected interaction. Smooth transitions between subsequent drawings enable users to explore different functional clusters in these networks without getting lost in the entire network. The visualisation system has been tested with data from the BRITE database.

Algorithms↗

EMBL-Align: a new public nucleotide and amino acid multiple sequence alignment database.

UNLABELLED: The submission of multiple sequence alignment data to EMBL has grown 30-fold in the past 10 years, creating a problem of archiving them. The EBI has developed a new public database of multiple sequence alignments called EMBL-Align. It has a dedicated web-based submission tool, Webin-Align. Together they represent a comprehensive data management solution for alignment data. Webin-Align accepts all the common alignment formats and can display data in CLUSTALW format as well as a new standard EMBL-Align flat file format. The alignments are stored in the EMBL-Align database and can be queried from the EBI SRS (Sequence Retrieval System) server. AVAILABILITY: Webin-Align: http://www.ebi.ac.uk/embl/Submission/align_top.html, EMBL-Align: ftp://ftp.ebi.ac.uk/pub/databases/embl/align, http://srs.ebi.ac.uk/

Amino Acid Sequence↗

Collaborative social and medical service application.

Baylor College of Medicine has five Teen Health Clinics (THC) dispersed throughout Harris county. The population served by the clinics includes inner-city adolescent boys and girls 19 years of age and under. Patients receive services such as family planning, sexually transmitted disease screening and treatment, perinatal care, counseling, and support services. Adolescents may receive services at any one of the clinics at no cost to the adolescent or their dependents. Given the geographical distribution of the clinics and the reliance on paper-based records, client services cannot be provided efficiently or expeditiously. According to the statistics developed by Clinic staff, ineffective coordination of service needs and client schedules undermine the follow-up needed for effective care. For example, a counselor will often need to balance a school schedule, clinic visits, well baby follow-up, and the Best Friends Program for a new mother. In addition, the lack of ready access to patient information impairs the ability of clinical and social service staff to provide continuity of care. In fact, some cases of client dropout are attributable to these difficulties. We have developed the Collaborative Social and Medical Service Application (CSMSA) to facilitate the provision of social and medical services to this population. The CSMSA is a domain-specific application based on a robust infrastructure known as the Ambulatory Services Architecture (ASA). This system is designed to support integrated social and ambulatory care. The ASA is a Baylor developed application framework and architecture for the computerization of the patient medical record in the ambulatory care setting. The working environment for the CSMSA user is an integrated desktop which provides an operating environment for both third-party applications and the CSMSA, as well as a fundamental set of services. The integrated desktop services include a mechanism for object organization or grouping, a facility for the management of desktop objects including disposal and storage, and an embedded search utility to assist in the location of desktop objects as well as other application objects. The access control mechanism will provide the security for the desktop environment by requiring the user to log into and out of the environment. This security mechanism will also enable/disable CSMSA tools based on the user's role at the clinic. The CSMSA is designed to provide work process, functionality and data access appropriate to the responsibilities of the user, e.g., a THC clerk may have permission to view a patient's orders but does not have the facility to create an order. Patient context is defined through a patient browser containing the master patient index or a user defined patient list. Patient encounters are managed using forms based on the process for each encounter type (e.g., initial visit). Forms are used for data entry and for queries. Data entry forms are only committed to the patient database (i.e., making the patient data available to other users who have permission to access the data) when the user approves the data. The CSMSA provides a means to suspend an entry into a chart by saving incomplete or non-committed data entry forms as part of the desktop state which is restored when the user logs into the system. CSMSA was designed to provide a robust, expandable application capable of accommodating the changes in health care and social services delivery while encompassing evolving software standards and new technology. This goal was achieved using object-oriented methodologies and technologies, combined with an object-oriented database management system as the foundation of our server to facilitate the evolution of our data model.

Adolescent↗

Detecting adverse events for patient safety research: a review of current methodologies.

Promoting patient safety is a national priority. To evaluate interventions for reducing medical errors and adverse event, effective methods for detecting such events are required. This paper reviews the current methodologies for detection of adverse events and discusses their relative advantages and limitations. It also presents a cognitive framework for error monitoring and detection. While manual chart review has been considered the "gold-standard" for identifying adverse events in many patient safety studies, this methodology is expensive and imperfect. Investigators have developed or are currently evaluating, several electronic methods that can detect adverse events using coded data, free-text clinical narratives, or a combination of techniques. Advances in these systems will greatly facilitate our ability to monitor adverse events and promote patient safety research. But these systems will perform optimally only if we improve our understanding of the fundamental nature of errors and the ways in which the human mind can naturally, but erroneously, contribute to the problems that we observe.

Database Management Systems↗

MODBASE, a database of annotated comparative protein structure models, and associated resources.

MODBASE (http://salilab.org/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on the MODELLER package for fold assignment, sequence-structure alignment, model building and model assessment (http:/salilab.org/modeller). MODBASE uses the MySQL relational database management system for flexible querying and CHIMERA for viewing the sequences and structures (http://www.cgl.ucsf.edu/chimera/). MODBASE is updated regularly to reflect the growth in protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different data sets. The largest data set contains 1,26,629 models for domains in 659,495 out of 1,182,126 unique protein sequences in the complete Swiss-Prot/TrEMBL database (August 25, 2003); only models based on alignments with significant similarity scores and models assessed to have the correct fold despite insignificant alignments are included. Another model data set supports target selection and structure-based annotation by the New York Structural Genomics Research Consortium; e.g. the 53 new structures produced by the consortium allowed us to characterize structurally 24,113 sequences. MODBASE also contains binding site predictions for small ligands and a set of predicted interactions between pairs of modeled sequences from the same genome. Our other resources associated with MODBASE include a comprehensive database of multiple protein structure alignments (DBALI, http://salilab.org/dbali) as well as web servers for automated comparative modeling with MODPIPE (MODWEB, http://salilab. org/modweb), modeling of loops in protein structures (MODLOOP, http://salilab.org/modloop) and predicting functional consequences of single nucleotide polymorphisms (SNPWEB, http://salilab. org/snpweb).

Amino Acid Sequence↗

[Computer programs SAN and EPID: family analysis and epidemiology of multifactorial diseases].

SAN software, a database management system, is elaborated. It is subject-oriented to family analysis in the genetics of multifactorial traits (diseases). The software allows creating and maintaining a family-oriented database and using the inputted information to calculate relative risk of disease, heritability, and correlations between several diseases or forms, with both actual frequency of the trait (prevalence) and probability of new cases (incidence). If appropriate data on sibships or nuclear families are available, one can calculate an empirical estimation of the risk of repeated cases of the disease in a family in relation to family anamnesis in different methods of sampling, sex-related morbidity, and varying age of onset. The database may also be used independently as a card index. The software allows one to represent pedigrees graphically, highlighting the desired set of traits. As application program, EPID, was developed, aimed at calculation and graphical presentation of age-related estimations of prevalence and incidence, as well as of the population risk of an individual to develop a disease within a time interval from birth to a certain age (accumulated morbidity).

Causality↗

A Paradox-based data collection and management system for multi-center randomized clinical trials.

We have developed a Paradox-based data collection and management system for large-scale multi-site randomized clinical trials. The system runs under Windows operating system and integrates Symantec pcAnywhere32 telecommunications software for data transmission and remote control sessions, PKZIP utility for the compression/decompression of transmitted data, and Stat/Transfer for exporting the centralized Paradox database for analyses. We initially developed this system for VA Cooperative Study #399 'The Effect of Antiarrhythmic Therapy in Maintaining Stability of Sinus Rhythm in Atrial Fibrillation', which collects over 1000 variables on 706 patients at 20 sites. Patient intake for this 5-year study began in March of 1998. We have also developed an enhanced version of this system, which is being used in the NIH-funded 'Glucosamine/Chondroitin Arthritis Intervention Trial (GAIT)' that collects over 1200 variables on 1588 patients at 13 sites. Patient intake for this 4-year study began in October of 2000.

Data Collection↗

OQAFMA Querying agent for the Foundational Model of Anatomy: a prototype for providing flexible and efficient access to large semantic networks.

The development of large semantic networks, such as the UMLS, which are intended to support a variety of applications, requires a flexible and efficient query interface for the extraction of information. Using one of the source vocabularies of UMLS as a test bed, we have developed such a prototype query interface. We first identify common classes of queries needed by applications that access these semantic networks. Next, we survey StruQL, an existing query language that we adopted, which supports all of these classes of queries. We then describe the OQAFMA Querying Agent for the Foundational Model of Anatomy (OQAFMA), which provides an efficient implementation of a subset of StruQL by pre-computing a variety of indices. We describe how OQAFMA leverages database optimization by converting StruQL queries to SQL. We evaluate the flexibility and efficiency of our implementation using English queries written by anatomists. This evaluation verifies that OQAFMA provides flexible, efficient access to one such large semantic network, the Foundational Model of Anatomy, and suggests that OQAFMA could be an efficient query interface to other large biomedical knowledge bases, such as the Unified Medical Language System.

Abstracting and Indexing↗

How (not) to protect genomic data privacy in a distributed network: using trail re-identification to evaluate and design anonymity protection systems.

The increasing integration of patient-specific genomic data into clinical practice and research raises serious privacy concerns. Various systems have been proposed that protect privacy by removing or encrypting explicitly identifying information, such as name or social security number, into pseudonyms. Though these systems claim to protect identity from being disclosed, they lack formal proofs. In this paper, we study the erosion of privacy when genomic data, either pseudonymous or data believed to be anonymous, are released into a distributed healthcare environment. Several algorithms are introduced, collectively called RE-Identification of Data In Trails (REIDIT), which link genomic data to named individuals in publicly available records by leveraging unique features in patient-location visit patterns. Algorithmic proofs of re-identification are developed and we demonstrate, with experiments on real-world data, that susceptibility to re-identification is neither trivial nor the result of bizarre isolated occurrences. We propose that such techniques can be applied as system tests of privacy protection capabilities.

Algorithms↗

Web-based information retrieval system for the prediction of metabolic pathways.

Analysis of metabolic pathways is a central topic in understanding the relationship between genotype and phenotype. The rapid accumulation of biological data provides the possibility of studying metabolic pathways both at the genomic and metabolic levels. Our motivation is to develop a conceptual framework and computational system that will allow retrieval of metabolic information and prediction of metabolic pathways. In this paper, we introduce a metabolic pathway prediction framework that extracts metabolic information from biological databases via the Internet, and builds metabolic pathways with data sources of genes, sequences, enzymes, metabolites, etc. It provides an easy-to-use interface to retrieve, display, and manipulate metabolic information. The system has been implemented into PathAligner, available at http://bibiserv.techfak.uni-bielefeld. de/pathaligner/.

Computer Simulation↗

Towards shared patient records: an architecture for using routine data for nationwide research.

Ubiquitous information is currently one of the most challenging slogans in medical informatics research. An adequate architecture for shared electronic patient records is needed which can use data for multiple purposes and which is extensible for new research questions. We introduce eardap as architecture for using routine data for nationwide clinical research in a multihospital environment. eardap can be characterized as terminology-based. Main advantage of our approach is the extensibility by new items and new research questions. Once the definition of items for a research question is finished, a consistent, corresponding database can be created without any informatics skills. Our experiences in pediatric oncology in Germany have shown the applicability of eardap. The functions of our core system were in routine clinical use in several hospitals. We validated the terminology management system (TMS) and the module generation tool with the basic data set of pediatric oncology. The multiple usability depends mainly on the quality of item planning in the TMS. High quality harmonization will lead to a higher amount of multiply used data. When using eardap, special emphasis is to be placed on interfaces to local hospital information systems and data security issues.

Biomedical Research↗

Implementing a MIRC query interface for a database driven teaching file.

This paper describes the authors' experience with integrating an existing database-driven teaching file with the RSNA (Radiological Society of North America) Medical Imaging Resource Center (MIRC). MIRC is the product of an RSNA-sponsored initiative to enable medical institutions to share their electronic medical content (images, text, and multimedia) by creating a distributed repository accessible from the Internet. An existing database-driven teaching file, developed by the authors and used extensively by the University of California San Francisco (UCSF) Department of Radiology since 1998, was retrofitted to include an interface for handling broadcast queries initiated by a MIRC query service. These queries take place through the exchange of XML documents via HTTP. After all the storage services have responded, the results are collated by the query service and presented to the user. The teaching file and MIRC interface were developed using the 4th Dimension Relational Database Management System (RDBMS). The integration process primarily involved mapping the "MIRCdocument" schema to the teaching file's schema, translating the actual MIRC query into the internal query language of the database and extending the access control mechanisms of the teaching file to allow public access. A working implementation of the interface required only 3 days of development time, with refinements taking place over several months. Interface development was greatly aided by MIRC's use of well-established Internet standards. This project has demonstrated the feasibility of implementing a MIRC interface on an existing teaching file server.

Computer-Assisted Instruction↗

Interhospital network system using the worldwide web and the common gateway interface.

We constructed an interhospital network system using the worldwide web (WWW) and the Common Gateway Interface (CGI). Original clinical images are digitized and stored as a database for educational and research purposes. Personal computers (PCs) are available for data treatment and browsing. Our system is simple, as digitized images are stored into a Unix server machine. Images of important and interesting clinical cases are selected and registered into the image database using CGI. The main image format is 8- or 12-bit Joint Photographic Experts Group (JPEG) image. Original clinical images are finally stored in CD-ROM using a CD recorder. The image viewer can browse all of the images for one case at once as thumbnail pictures; image quality can be selected depending on the user's purpose. Using the network system, clinical images of interesting cases can be rapidly transmitted and discussed with other related hospitals. Data transmission from relational hospitals takes 1 to 2 minutes per 500 Kbyte of data. More distant hospitals (e.g., Rakusai Hospital, Kyoto) takes 1 minute more. The mean number of accesses our image database in a recent 3-month period was 470. There is a total about 200 cases in our image database, acquired over the past 2 years. Our system is useful for communication and image treatment between hospitals and we will describe the elements of our system and image database.

CD-ROM↗

The goal of PACS in Nagoya University Hospital.

In Nagoya University Hospital, a Radiology Intelligent Information System (RIIS) is under construction which will be linked with the Hospital Intelligent Information System (HIIS). RIIS is composed of the radiation oncology information system and the diagnostic radiology information system which is named Imaging Diagnosis Intelligent Information System (IDIIS). IDIIS consists of three parts: (a) the Imaging Diagnosis Management System (IDMS); (b) the Picture Archiving and Communication System (PACS); (c) the Report Generation Support System for Imaging Diagnosis (RGSS-ID). Artificial intelligence methodology is applied to RGSS-ID and IDMS which includes the ordering and scheduling system of diagnostic imaging. IDIIS has an important role to improve the quality of patient care and medical education as well as image management and is an essential component for the implementation of HIIS.

Computer Systems↗

A hybrid method for relation extraction from biomedical literature.

PURPOSE: Over recent years, there has been a growing interest in extracting entities and relations from biomedical literature. There are a vast number of systems and approaches being proposed to extract biological relations, but none of them achieves satisfactory results. These methodologies are either parsing-based or pattern-based, which are not competent to handle the grammatical complexities of biomedical texts, or too complicated to be adapted. It is well known that appositive, coordinative propositions and such grammatical structures are extremely common in biomedical texts, particularly in full texts. However, these problems are still untouched for most of researchers. METHODS: In this paper, we have proposed a new approach, which is hybrid with both shallow parsing and pattern matching, to extract relations between proteins from scientific papers of biomedical themes. In the method, appositive and coordinative structures are interpreted based on the shallow parsing analysis, with both syntactic and semantic constraints. Then long sentences are splitted into sub-ones, from which relations are extracted by a greedy pattern matching algorithm, along with automatically generated patterns. RESULTS: Our approach is experimented to extract protein-protein interactions from full biomedical texts, and has achieved an average F-score of 80% on individual verbs, and 66% on all verbs. With the help of shallow parsing analysis, pattern matching is improved remarkably. Compared with the traditional pattern matching algorithm, our approach achieves about 7% improvement of both precision and F-score. In contrast to other systems, our approach achieves performance comparable to the best. A demo system has been available at http://spies.cs.tsinghua.edu.cn.

Abstracting and Indexing↗