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At least 685 records · Page 38Linked to original sources

PubMed2005

PLATCOM: a Platform for Computational Comparative Genomics.

MOTIVATION: As more whole genome sequences become available, comparing multiple genomes at the sequence level can provide insight into new biological discovery. However, there are significant challenges for genome comparison. The challenge includes requirement for computational resources owing to the large volume of genome data. More importantly, since the choice of genomes to be compared is entirely subjective, there are too many choices for genome comparison. For these reasons, there is pressing need for bioinformatics systems for comparing multiple genomes where users can choose genomes to be compared freely. RESULTS: PLATCOM (Platform for Computational Comparative Genomics) is an integrated system for the comparative analysis of multiple genomes. The system is built on several public databases and a suite of genome analysis applications are provided as exemplary genome data mining tools over these internal databases. Researchers are able to visually investigate genomic sequence similarities, conserved gene neighborhoods, conserved metabolic pathways and putative gene fusion events among a set of selected multiple genomes. AVAILABILITY: http://platcom.informatics.indiana.edu/platcom

Chromosome Mapping↗

PubMed1994

Clinical databases and critical care research.

Clinical investigators who seek to exploit electronic databases for clinical research need to be aware of the strengths and limitations of the data stored in these systems. Generic issues are examined that can arise from the use of any electronic database, as well as more specific and unique issues that need to be resolved before a comprehensive medical-record database can be realized. Specific suggestions are provided that can be employed by the critical care director who seeks to exploit the rich clinical data available in electronic form for clinical research.

Critical Care↗

PubMed2000

Computerized cochlear implant database system.

In an environment of clinical governance with increased demands for accountability it is very important that accurate, reliable and secure data records be maintained for easy retrieval, analysis and presentation when required. A database is a very versatile tool for this purpose. We describe here our experience in designing a database for cochlear implant patients in Cambridge, together with guidance for prospective designers in their chosen sub-specialty.

Cochlear Implantation↗

PubMed2005

Beyond the clause: extraction of phosphorylation information from medline abstracts.

MOTIVATION: Phosphorylation is an important biochemical reaction that plays a critical role in signal transduction pathways and cell-cycle processes. A text mining system to extract the phosphorylation relation from the literature is reported. The focus of this paper is on the new methods developed and implemented to connect and merge pieces of information about phosphorylation mentioned in different sentences in the text. The effectiveness and accuracy of the system as a whole as well as that of the methods for extraction beyond a clause/sentence is evaluated using an independently annotated dataset, the Phospho.ELM database. The new methods developed to merge pieces of information from different sentences are shown to be effective in significantly raising the recall without much difference in precision.

Artificial Intelligence↗

PubMed2004

MyWEST: my Web Extraction Software Tool for effective mining of annotations from web-based databanks.

MOTIVATION: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank. RESULTS: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms. AVAILABILITY: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/

Algorithms↗

PubMed1993

[The optimization of the data base of a voluntary health care cooperative for the study of postoperative morbidity in benign prostatic hypertrophy].

BACKGROUND: Investigation in health care services by data bases (DB) is undergoing an important increase in numerous countries. Several of the most relevant epidemiologic studies on the postsurgical morbidity and mortality of benign hypertrophy of the prostate (BHP) have used DB. The aim of this study was to prepare and optimize the DB of a health cooperative (Asistencia Sanitaria Colegial). METHODS: Since 1981 the DB contains sociodemographic variables, data concerning visits to general practitioners and specialists, complementary examinations and hospitalizations. The coding system was specifically developed by the cooperative. The study base was made up of all the policies of the members between January 1981 and December 1988 (101,400 males). To identify the policies 14 codes potentially related with BHP were initially chosen and all the policies containing any of these codes were selected, with the manual analysis of 204 policies being thereby performed. RESULTS: The total number of policies initially selected for the study was 3,157. Manual revision discarded the use of 9 of the 14 codes used in the first selection. In agreement with the 5 codes able to define diseases of prostatic gland and to the file in which they appeared the policies were classified as probable diseases of prostatic gland (n = 1,007, 31.9%), possible (n = 805, 25.5%) and improbable (n = 1,345, 42.5%). Likewise, the strategy to follow for the selection of a cohort of BHP cases was defined. CONCLUSIONS: The manual analysis of policies evidenced a remarkable coherence and exhaustiveness of the information registered. The principal difficulties found with the data base used were the lack of a sole diagnosis and the coding system used in addition to the impossibility of automatically controlling the assistance received by the patients outside the cooperative system. The availability of a data base such as that herein described with a well defined large population and with accessible sociodemographic and health care information justifies collaborative efforts among health care administrators, clinicians, computer scientists and epidemiologists.

Community Health Centers↗

PubMed1998

Web-based digital radiology teaching file: facilitating case input at time of interpretation.

OBJECTIVE: Our goal was to develop a software system that allows easy and rapid input of digital radiology images and text reports, at the time of interpretation, into an easily searchable electronic teaching file database using the Internet and the World-Wide Web protocols, servers, and browsers. CONCLUSION: Using the Internet, the World-Wide Web, and our software system, we can rapidly input digital radiology images and associated text reports into an easily searchable database accessed by privileged users. This inexpensive and simple method for building a digital teaching file database allows cross-platform access for users who have a Web browser.

Computer Communication Networks↗

PubMed2005

Human-centered design of a distributed knowledge management system.

Many healthcare technology projects fail due to the lack of consideration of human issues, such as workflow, organizational change, and usability, during the design and implementation stages of a project's development process. Even when human issues are considered, the consideration is typically on designing better user interfaces. We argue that human-centered computing goes beyond a better user interface: it should include considerations of users, functions and tasks that are fundamental to human-centered computing. From this perspective, we integrated a previously developed human-centered methodology with a Project Design Lifecycle, and we applied this integration in the design of a complex distributed knowledge management system for the Biomedical Engineer (BME) domain in the Mission Control Center at NASA Johnson Space Center. We analyzed this complex system, identified its problems, generated systems requirements, and provided specifications of a replacement prototype for effective organizational memory and knowledge management. We demonstrated the value provided by our human-centered approach and described the unique properties, structures, and processes discovered using this methodology and how they contributed in the design of the prototype.

Artificial Intelligence↗

PubMed2003

The vaccine data link in Nha Trang, Vietnam: a progress report on the implementation of a database to detect adverse events related to vaccinations.

Real, perceived and unknown adverse events secondary to vaccinations are a source of concern for care providers of children. In the USA large linked databases have provided helpful information regarding the safety of vaccines. Very little prospectively collected data on vaccine safety is available from resource poor countries, but safety concerns may be even more relevant in such settings. Vaccine manufacturers do not have to pass the same rigorous safety standards as vaccine manufacturers in rich countries. Vaccines, which protect against cholera, Japanese encephalitis, rabies or typhoid fever are predominantly used in resource poor, tropical countries and frequently do not undergo vigorous post marketing surveillance. New vaccines specifically suited for resource poor countries are sometimes marketed without the scrutiny of vigilant, independent regulatory authorities. We describe here the design and implementation of a large linked database for a semi-rural province in central Vietnam. The design overcomes several problems inherent in data bases of medical events and vaccinations in developing countries. Assigning a permanent identification (ID) number to each resident avoids the ambiguities of ID numbers based on the address. The distribution and use of medical identification cards with a permanent ID number assists in the unambiguous identification of vaccinees and patients. Medical records of all admissions are coded according to International Classification of Diseases (ICD-10) and transcribed into a computer system. Because these processes are novel the data collected by the study will be validated. Project staff will check records on vaccinations and hospital admissions through household visits at regular intervals. Data describing vaccinations and medical events are linked to the data collected by the project staff in a computer system. Based on the validation of the data we hope to optimize this model. Once we find the model working it is planned export this vaccine data safety link to other settings of similar economic status.

Database Management Systems↗

PubMed2004

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

MOTIVATION: The presence or absence of metabolic pathways and structures provide a context that makes protein annotation far more reliable. Compiling such information across microbial genomes improves the functional classification of proteins and provides a valuable resource for comparative genomics. RESULTS: We have created a Genome Properties system to present key aspects of prokaryotic biology using standardized computational methods and controlled vocabularies. Properties reflect gene content, phenotype, phylogeny and computational analyses. The results of searches using hidden Markov models allow many properties to be deduced automatically, especially for families of proteins (equivalogs) conserved in function since their last common ancestor. Additional properties are derived from curation, published reports and other forms of evidence. Genome Properties system was applied to 156 complete prokaryotic genomes, and is easily mined to find differences between species, correlations between metabolic features and families of uncharacterized proteins, or relationships among properties. AVAILABILITY: Genome Properties can be found at http://www.tigr.org/Genome_Properties SUPPLEMENTARY INFORMATION: http://www.tigr.org/tigr-scripts/CMR2/genome_properties_references.spl.

Chromosome Mapping↗

PubMed2006

WholePathwayScope: a comprehensive pathway-based analysis tool for high-throughput data.

BACKGROUND: Analysis of High Throughput (HTP) Data such as microarray and proteomics data has provided a powerful methodology to study patterns of gene regulation at genome scale. A major unresolved problem in the post-genomic era is to assemble the large amounts of data generated into a meaningful biological context. We have developed a comprehensive software tool, WholePathwayScope (WPS), for deriving biological insights from analysis of HTP data. RESULT: WPS extracts gene lists with shared biological themes through color cue templates. WPS statistically evaluates global functional category enrichment of gene lists and pathway-level pattern enrichment of data. WPS incorporates well-known biological pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) and Biocarta, GO (Gene Ontology) terms as well as user-defined pathways or relevant gene clusters or groups, and explores gene-term relationships within the derived gene-term association networks (GTANs). WPS simultaneously compares multiple datasets within biological contexts either as pathways or as association networks. WPS also integrates Genetic Association Database and Partial MedGene Database for disease-association information. We have used this program to analyze and compare microarray and proteomics datasets derived from a variety of biological systems. Application examples demonstrated the capacity of WPS to significantly facilitate the analysis of HTP data for integrative discovery. CONCLUSION: This tool represents a pathway-based platform for discovery integration to maximize analysis power. The tool is freely available at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Computer Graphics↗

PubMed1999

A computer-assisted drug prescription system: the model and its implementation in the ATM knowledge base.

Informatisation of drug prescription is an important topic in medical informatics. For several years now, computerized drug databases have been implemented. Usually only a small part of the prescriptions can be stored in prescription systems because of the format of the included information; prescriptions contain essentially free text without any structure and homogeneity of the used vocabulary. In this article a model is presented for knowledge representation in a computerized drug prescription system. The model should be applicable to clinical practice and be didactic for medical students. The problem of standardization of terminology had to be solved. A computer-assisted drug prescription program has been developed. The next step is its validation by clinicians. The program can also be used in a consultation mode.

Database Management Systems↗

PubMed2006

A comprehensive dictionary of protein accession codes for complete protein accession identifier alias resolving.

In mass spectrometry-based proteomics, protein identification results usually consist of peptide sequences and database-dependent accession identifiers of the matching proteins. Often certain annotations are only available in particular databases that in turn must be queried by a certain identifier. In order to simplify and unify the tracing of identified proteins back to their original annotation information, a system capable of set-oriented mapping the different accession identifiers of proteins derived from multiple sequence database sources has been developed. This allows unification of the access to protein information and tracing to other online resources providing additional information as well as resolving cross-references of protein identifications. The interface of seqDB is available via http://www.protein-ms.de following the link to seqDB.

Database Management Systems↗

PubMed2003

MASV--Multiple (BLAST) Annotation System Viewer.

UNLABELLED: Multiple (BLAST) Annotation System Viewer (MASV) is a tool designed to aid in the annotation of genomic sequences. MASV enables the researcher to compare and analyse differences in annotation and analysis, resulting from changes in databases, analysis program parameters and results. This provides a unique capability for the user to conduct further bioinformatics analysis from the information obtained. AVAILABILITY: http://cbbc.murdoch.edu.au/projects/masv/

Abstracting and Indexing↗

PubMed2004

BRAGI: linking and visualization of database information in a 3D viewer and modeling tool.

BRAGI is a well-established package for viewing and modeling of three-dimensional (3D) structures of biological macromolecules. A new version of BRAGI has been developed that is supported on Windows, Linux and SGI. The user interface has been rewritten to give the standard 'look and feel' of the chosen operating system and to provide a more intuitive, easier usage. A large number of new features have been added. Information from public databases such as SWISS-PROT, InterPro, DALI and OMIM can be displayed in the 3D viewer. Structures can be searched for homologous sequences using the NCBI BLAST server.

Amino Acid Sequence↗

PubMed2002

ASPD (Artificially Selected Proteins/Peptides Database): a database of proteins and peptides evolved in vitro.

ASPD is a new curated database that incorporates data on full-length proteins, protein domains and peptides that were obtained through in vitro directed evolution processes (mainly by means of phage display). At present, the ASPD database contains data on 195 selection experiments, which were described in 112 original papers. For each experiment, the following information is given: (i) description of the target for binding, (ii) description of the protein or peptide which serves as the template for library construction and description of the native protein which binds the target, (iii) links to the major proteomic databases (SWISS-PROT, PDB, PROSITE and ENZYME), (iv) keywords referring to the biological significance of the experiment, (v) aligned sequences of proteins or peptides retrieved through in vitro evolution and relevant native or constructed sequences, (vi) the number of rounds of selection/amplification and (vii) the number of occurrences of clones with each sequence. The literature data include a full reference, a link to the MEDLINE database and the name of the corresponding author with his email address. ASPD has a user-friendly interface which allows for simple queries using the names of proteins and ligands, as well as keywords describing the biological role of the interaction studied, and also for queries based on authors' names. It is also possible to access the database by means of the SRS system, allowing complex queries. There is a BLAST search tool against the ASPD for looking directly for homologous sequences. Research tools of the ASPD allow the analysis of pairwise correlations in the sequences of proteins and peptides selected against one target. The URL for the ASPD database is http://www.sgi.sscc.ru/mgs/gnw/aspd/.

Animals↗

PubMed2002

Phase4: automatic evaluation of database search methods.

It has become standard to evaluate newly devised database search methods in terms of sensitivity and selectivity and to compare them with existing methods. This involves the construction of a suitable evaluation scenario, the execution of the methods, the assessment of their performances, and the presentation of the results. Each of these four phases and their smooth connection usually imposes formidable work. To relieve the evaluator of this burden, a system has been designed with which evaluations can be effected rapidly. It is implemented in the programming language Python whose object-oriented features are used to offer a great flexibility in changing the evaluation design. A graphical user interface is provided which offers the usual amenities such as radio- and checkbuttons or file browsing facilities.

Data Interpretation, Statistical↗

PubMed2005

The GATO gene annotation tool for research laboratories.

Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

Biomedical Research↗