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At least 811 records · Page 45Linked to original sources

PubMed2002

The EMBL Nucleotide Sequence Database.

The EMBL Nucleotide Sequence Database (aka EMBL-Bank; http://www.ebi.ac.uk/embl/) incorporates, organises and distributes nucleotide sequences from all available public sources. EMBL-Bank is located and maintained at the European Bioinformatics Institute (EBI) near Cambridge, UK. In an international collaboration with DDBJ (Japan) and GenBank (USA), data are exchanged amongst the collaborating databases on a daily basis. Major contributors to the EMBL database are individual scientists and genome project groups. Webin is the preferred web-based submission system for individual submitters, whilst automatic procedures allow incorporation of sequence data from large-scale genome sequencing centres and from the European Patent Office (EPO). Database releases are produced quarterly. Network services allow free access to the most up-to-date data collection via FTP, email and World Wide Web interfaces. EBI's Sequence Retrieval System (SRS), a network browser for databanks in molecular biology, integrates and links the main nucleotide and protein databases plus many other specialized databases. For sequence similarity searching, a variety of tools (e.g. Blitz, Fasta, BLAST) are available which allow external users to compare their own sequences against the latest data in the EMBL Nucleotide Sequence Database and SWISS-PROT. All resources can be accessed via the EBI home page at http://www.ebi.ac.uk.

Animals↗

PubMed2000

TANCLICO: tools for the analysis of inter-departmental clinical communications.

Patient care management provided by healthcare organizations is complex, involving many different care providers. The information exchange between providers concerns a varying and considerable number of actors and a high transmission load. Based on models, used to characterize specific features of work processes, we propose a new method able to analyze and represent clinical communications inside hospitals. Software has been developed, providing tools for storing and retrieving information resulting from clinical communications. The method, together with data collected in actual situations, may constitute useful tools for health information systems developers.

Computer Communication Networks↗

PubMed2002

The Gene Resource Locator: gene locus maps for transcriptome analysis.

Since the advent of the draft human genome sequence there has been growing interest in transcriptome analysis based on genomic data. The Gene Resource Locator (GRL) assembles gene maps that include information on gene-expression patterns, cis-elements in regulatory regions and alternatively spliced transcripts. The database was constructed using customized software, and currently contains 2.2 million alignments (exon-intron structures). The alignments have been annotated and integrated into a system that encompasses approximately 90 000 EST loci sharing common exons, 8091 alternatively spliced transcript groups, 10 801 expression-profile groups, 8066 candidate regulatory regions in full-length cDNAs, and 1 million SNP loci. We have used Flash technology to build a dynamic web viewer that facilitates browsing through the millions of alignments. All of the information is available through the World Wide Web at the Gene Resource Locator web site (http://grl.gi.k.u-tokyo.ac.jp).

Alternative Splicing↗

PubMed1994

Prototyping a genetics deductive database.

We are developing a laboratory notebook system known as the Genetics Deductive Database. Currently our prototype provides storage for biological facts and rules with flexible access via an interactive graphical display. We have introduced a formal basis for the representation and reasoning necessary to order genome map data and handle the uncertainty inherent in biological data. We aim to support laboratory activities by introducing an experiment planner into our prototype. The Genetics Deductive Database is built using new database technology which provides an object-oriented conceptual model, a declarative rule language, and a procedural update language. This combination of features allows the implementation of consistency maintenance, automated reasoning, and data verification.

Animals↗

PubMed2004

ProbeLynx: a tool for updating the association of microarray probes to genes.

As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes. ProbeLynx(www.pathogenomics.ca/probelynx) is a new web service which uses current genomic sequence information to re-examine microarray probe specificity and provide annotation updates relevant to determining which gene(s) and transcript(s) are associated with a given probe. Probe sequences (either oligonucleotide- or cDNA-based) are uploaded in FASTA format and the results returned as a tab-delimited flat file for insertion into a spreadsheet application or database management system for further analysis. ProbeLynx has been initially developed to focus on arrays derived from human, mouse, chicken and bovine genomes, but may be expanded to handle other genomic datasets. ProbeLynx offers microarray users the important ability to continuously assess the potential of a probe to cross-hybridize to paralogous genes and the suitability of a given probe to investigate a transcript of interest. By also including the latest gene function annotation information in the output, ProbeLynx provides the critical first step in updating microarray data annotation.

Animals↗

PubMed2006

The integrated microbial genomes (IMG) system.

The integrated microbial genomes (IMG) system is a new data management and analysis platform for microbial genomes provided by the Joint Genome Institute (JGI). IMG contains both draft and complete JGI genomes integrated with other publicly available microbial genomes of all three domains of life. IMG provides tools and viewers for analyzing genomes, genes and functions, individually or in a comparative context. IMG allows users to focus their analysis on subsets of genes and genomes of interest and to save the results of their analysis. IMG is available at http://img.jgi.doe.gov.

Bacteriophages↗

PubMedDate not supplied

A natural language user interface for fuzzy scope queries.

This paper presents a two-agent framework to build a natural language query interface for IC information system, focusing more on scope queries in a single English sentence. The first agent, parsing agent, syntactically processes and semantically interprets natural language sentence to construct a fuzzy structured query language (SQL) statement. The second agent, defuzzifying agent, defuzzifies the imprecise part of the fuzzy SQL statement into its equivalent executable precise SQL statement based on fuzzy rules. The first agent can also actively ask the user some necessary questions when it manages to disambiguate the vague retrieval requirements. The adaptive defuzzification approach employed in the defuzzifying agent is discussed in detail. A prototype interface has been implemented to demonstrate the effectiveness.

Algorithms↗

PubMed1992

EDMUS, a European database for multiple sclerosis.

EDMUS is a minimal descriptive record developed for research purposes to document clinical and laboratory data in patients with multiple sclerosis (MS). It has been designed by a committee of the European Concerted Action for MS, organised under the auspices of the Commission of the European Communities. The software is user-friendly and fast, with a minimal set of obligatory data. Priority has been given to analytical data and the system is capable of automatically generating data, such as diagnosis classification, using appropriate algorithms. This procedure saves time, ensures a uniform approach to individual cases and allows automatic updating of the classification whenever additional information becomes available. It is also compatible with future developments and requirements since new algorithms can be entered in the programme when necessary. This system is flexible and may be adapted to the users needs. It is run on Apple and IBM-PC personal microcomputers. Great care has been taken to preserve confidentiality of the data. It is anticipated that this "common" language will enable the collection of appropriate cases for specific purposes, including population-based studies of MS and will be particularly useful in projects where the collaboration of several centres is needed to recruit a critical number of patients.

Database Management Systems↗

PubMed2005

Automatic annotation of protein function.

The annotation of protein function at genomic scale is essential for day-to-day work in biology and for any systematic approach to the modeling of biological systems. Currently, functional annotation is essentially based on the expansion of the relatively small number of experimentally determined functions to large collections of proteins. The task of systematic annotation faces formidable practical problems related to the accuracy of the input experimental information, the reliability of current systems for transferring information between related sequences, and the reproducibility of the links between database information and the original experiments reported in publications. These technical difficulties merely lie on the surface of the deeper problem of the evolution of protein function in the context of protein sequences and structures. Given the mixture of technical and scientific challenges, it is not surprising that errors are introduced, and expanded, in database annotations. In this situation, a more realistic option is the development of a reliability index for database annotations, instead of depending exclusively on efforts to correct databases. Several groups have attempted to compare the database annotations of similar proteins, which constitutes the first steps toward the calibration of the relationship between sequence and annotation space.

Artificial Intelligence↗

PubMed2002

The Ensembl genome database project.

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

Computational Biology↗

PubMed2004

Towards cooperative frameworks for modeling and integrating biological processes knowledge.

Data organization has become a strategic target for biologists due to the increasing volume of genomic data available for them. For this purpose, we need a complete knowledge model for representing biological system. In this paper, we deal with both processes for the creation and integration of shareable, reusable domain models within biology, which is a critical issue. In particular, this work introduces a new cooperative development approach for biology ontologies. This approach is based on the integration of the ontologies supplied by different human experts. Two experiments in biological domains are presented and their results discussed.

Artificial Intelligence↗

PubMed2004

An ontology of randomized controlled trials for evidence-based practice: content specification and evaluation using the competency decomposition method.

Randomized controlled trials (RCTs) are one of the least biased sources of clinical research evidence, and are therefore a critical resource for the practice of evidence-based medicine. With over 10,000 new RCTs indexed in Medline each year, knowledge systems are needed to help clinicians translate evidence into practice. Common ontologies for RCTs and other domains would facilitate the development of these knowledge systems. However, no standard method exists for developing domain ontologies. In this paper, we describe a new systematic approach to specifying and evaluating the conceptual content of ontologies. In this method, called competency decomposition, the target task for an ontology is hierarchically decomposed into subtasks and methods, and the ontology content is specified by identifying the domain information required to complete each of the subtasks. We illustrate the use of this competency decomposition approach for the content specification and evaluation of an RCT ontology for evidence-based practice.

Database Management Systems↗

PubMedDate not supplied

Computer assisted information resources navigation.

In this paper, the design and development of Computer Assisted Information Resources Navigation (CAIRN) is discussed. CAIRN system is a medical information retrieval system that allows physicians and students to store full text medical information from any resource, organize and retrieve it. The most important feature of CAIRN is its capability to assist the user, physician, student etc. in selecting documents against a submitted query in Natural Language. The retrieved documents are presented in decreasing order according to their similarity to the submitted query. The nearest neighbour method is used. An alternative similarity measure based on a new calculation of the length of documents is proposed and some experimentation with it is discussed.

Database Management Systems↗

PubMed1998

Towards semantic integration within an existing medical information system.

Talking about the problems of integration in medical information systems, the necessity to provide end users with a consistent and coherent view of patient's data, has been largely reported. In order to attempt this goal, systems need to perform semantic integration. We propose a pragmatic way to describe the semantics of the elements of a database, based on a bottom-up three steps process: 1. a back documentation of the elements of the system from their description contained in the data catalog of the database 2. a first semantic extension to transform a data catalog into a data dictionary 3. a second semantic extension to create a dictionary of the medical concepts from a data dictionary. This dictionary of concepts can be considered as the final result of "semantic integration". It contains a set of entities directly understandable by the end users. These entities are deduced or built from the elements collected and characterized in the data dictionary. This work reports the conceptual analysis and the implementation of such a data dictionary.

Database Management Systems↗

PubMed2004

BioRAT: extracting biological information from full-length papers.

MOTIVATION: Converting the vast quantity of free-format text found in journals into a concise, structured format makes the researcher's quest for information easier. Recently, several information extraction systems have been developed that attempt to simplify the retrieval and analysis of biological and medical data. Most of this work has used the abstract alone, owing to the convenience of access and the quality of data. Abstracts are generally available through central collections with easy direct access (e.g. PubMed). The full-text papers contain more information, but are distributed across many locations (e.g. publishers' web sites, journal web sites and local repositories), making access more difficult. In this paper, we present BioRAT, a new information extraction (IE) tool, specifically designed to perform biomedical IE, and which is able to locate and analyse both abstracts and full-length papers. BioRAT is a Biological Research Assistant for Text mining, and incorporates a document search ability with domain-specific IE. RESULTS: We show first, that BioRAT performs as well as existing systems, when applied to abstracts; and second, that significantly more information is available to BioRAT through the full-length papers than via the abstracts alone. Typically, less than half of the available information is extracted from the abstract, with the majority coming from the body of each paper. Overall, BioRAT recalled 20.31% of the target facts from the abstracts with 55.07% precision, and achieved 43.6% recall with 51.25% precision on full-length papers.

Abstracting and Indexing↗

PubMed2000

GXD: a Gene Expression Database for the laboratory mouse: current status and recent enhancements. The Gene Expresison Database group.

The Gene Expression Database (GXD) is a community resource of gene expression information for the laboratory mouse. The database is designed as an open-ended system that can integrate different types of expression data. New expression data are made available on a daily basis. Thus, GXD provides increasingly complete information about what transcripts and proteins are produced by what genes; where, when and in what amounts these gene products are expressed; and how their expression varies in different mouse strains and mutants. GXD is integrated with the Mouse Genome Database (MGD). Continuously refined interconnections with sequence databases and with databases from other species place the gene expression information in the larger biological and analytical context. GXD is accessible through the Mouse Genome Informatics Web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression_menu.shtm l

Alternative Splicing↗

PubMed1992

Improving dental epidemiologic data collection with computers.

A computerized dental data recording system (DDRS) was developed for the New England Elder Dental Study to improve data quality and increase field staff efficiency. The DDRS displays video screens similar to traditional paper forms to record data on coronal and root caries, dentate and denture status, subacute bacterial endocarditis screening, gingival bleeding, calculus, and periodontal attachment level. DDRS provides facilities for date and exam-component time tracking, on-line contextual comments, random record retrieval, editing, data backup, and data output in various data formats. This study compared the DDRS with a paper-form system for data entry accuracy. Dental caries and periodontal disease measurement data from 38 subjects were recorded on paper forms and independently entered using DDRS. The DDRS identified 150 illogical data errors, 39 inconsistent data errors, 7 invalid data and 34 miscellaneous data errors. Four technicians with field experience using both paper forms and DDRS reported time savings using DDRS in the field. DDRS has the potential for additional time savings by minimizing the time for data coding, cleaning, and management. Results demonstrate that DDRS could improve the quality of oral epidemiologic data by mandating strict adherence to protocols, preventing errors, and increasing field efficiency.

Computers↗

PubMed2004

[Application of the JJ1017 code to master-table of RIS database].

We are developing an open-type Radiology Information System (RIS) under the project name KPECK. Part of the RIS has already been employed in Kouri Hospital of Kansai Medical University. The RIS is based on a database of the history of clinical study and exposure. We tried using the JJ1017 (ver1.0) code for the master-table of the database. The JJ1017 code, which is standardized by JIRA and JAHIS, is used in communicating information between the RIS and medical modalities. Through construction of the database, we found a technique by which the JJ1017 code could be applied to its master-table. In coordinating the JJ1017 code with the master-table of the database, we extended various study codes and systematically coordinated them with the architecture of the database.

Database Management Systems↗