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PubMed2005

Adding some SPICE to DAS.

UNLABELLED: The distributed annotation system (DAS) defines a communication protocol used to exchange biological annotations. It is motivated by the idea that annotations should not be provided by single centralized databases but instead be spread over multiple sites. Data distribution, performed by DAS servers, is separated from visualization, which is carried out by DAS clients. The original DAS protocol was designed to serve annotation of genomic sequences. We have extended the protocol to be applicable to macromolecular structures. Here we present SPICE, a new DAS client that can be used to visualize protein sequence and structure annotations. AVAILABILITY: http://www.efamily.org.uk/software/dasclients/spice/

Algorithms↗
PubMed2006

Protein kinase resource: an integrated environment for phosphorylation research.

The protein kinase superfamily is an important group of enzymes controlling cellular signaling cascades. The increasing amount of available experimental data provides a foundation for deeper understanding of details of signaling systems and the underlying cellular processes. Here, we describe the Protein Kinase Resource, an integrated online service that provides access to information relevant to cell signaling and enables kinase researchers to visualize and analyze the data directly in an online environment. The data set is synchronized with Uniprot and Protein Data Bank (PDB) databases and is regularly updated and verified. Additional annotation includes interactive display of domain composition, cross-references between orthologs and functional mapping to OMIM records. The Protein Kinase Resource provides an integrated view of the protein kinase superfamily by linking data with their visual representation. Thus, human kinases can be mapped onto the human kinome tree via an interactive display. Sequence and structure data can be easily displayed using applications developed for the PKR and integrated with the website and the underlying database. Advanced search mechanisms, such as multiparameter lookup, sequence pattern, and blast search, enable fast access to the desired information, while statistics tools provide the ability to analyze the relationships among the kinases under study. The integration of data presentation and visualization implemented in the Protein Kinase Resource can be adapted by other online providers of scientific data and should become an effective way to access available experimental information.

Amino Acid Sequence↗
PubMed1998

Searching for information on outcomes: do you need to be comprehensive?

The concepts of evidence-based practice and clinical effectiveness are reliant on up to date, accurate, high quality, and relevant information. Although this information can be obtained from a range of sources, computerised databases such as MEDLINE offer a fast, effective means of bringing up to date information to clinicians, as well as health service and information professionals. Common problems when searching for information from databases include missing important relevant papers or retrieving too much information. Effective search strategies are therefore necessary to retrieve a manageable amount of relevant information. This paper presents a range of strategies which can be used to locate information on MEDLINE efficiently and effectively.

Data Collection↗
PubMed2003

GLYCO-FRAGMENT: A web tool to support the interpretation of mass spectra of complex carbohydrates.

Mass spectrometry is frequently used to analyze complex oligosaccharides and glycopeptides. The spectra of glycans can be complicated and difficult to interpret without reference data. Unfortunately, no libraries of suitably pure and homogeneous standards have so far been compiled. The web-based tool GLYCO-FRAGMENT allows the generation of all theoretically possible MS relevant fragments of oligosaccharides as defined using the extended IUPAC nomenclature. The main focus of GLYCO-FRAGMENT is to support the manual assignment of all peaks contained in mass spectra of complex carbohydrates. The service is available at http://www.dkfz.de/spec/projekte/fragments/.

Carbohydrate Sequence↗
PubMed2003

The EMBL Nucleotide Sequence Database: major new developments.

The EMBL Nucleotide Sequence Database (http://www.ebi.ac.uk/embl/) incorporates, organizes and distributes nucleotide sequences from all available public sources. The database 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 to achieve optimal synchronization. Webin is the preferred web-based submission system for individual submitters, while 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) integrates and links the main nucleotide and protein databases plus many other specialized molecular biology databases. For sequence similarity searching, a variety of tools (e.g. 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↗
PubMed1980

A computerized data base system for medical diagnostic studies (Diastu).

A computerized database system (DIASTU) has been developed for the storage and selective retrieval of the results of medical diagnostic studies. The system is being used to analyze the disease process and the efficacy and yield of selected diagnostic studies. The system runs on a DEC PDP-11/60 computer. It consists of three FORTRAN IV programs linked to a general-purpose assembly language database handler. One program, DSENT, interactively modifies the information in the database. The second, DSLIST, prints all or portions of the database. The third program, DSTAT, interactively assembles the parameters for selective searches of the database and executes them. A query language is used that allows the use of time and size specifications and Boolean operators in nested loops.

Computers↗
PubMed2006

A predictive model for identifying proteins by a single peptide match.

MOTIVATION: Tandem mass-spectrometry of trypsin digests, followed by database searching, is one of the most popular approaches in high-throughput proteomics studies. Peptides are considered identified if they pass certain scoring thresholds. To avoid false positive protein identification, > or = 2 unique peptides identified within a single protein are generally recommended. Still, in a typical high-throughput experiment, hundreds of proteins are identified only by a single peptide. We introduce here a method for distinguishing between true and false identifications among single-hit proteins. The approach is based on randomized database searching and usage of logistic regression models with cross-validation. This approach is implemented to analyze three bacterial samples enabling recovery 68-98% of the correct single-hit proteins with an error rate of < 2%. This results in a 22-65% increase in number of identified proteins. Identifying true single-hit proteins will lead to discovering many crucial regulators, biomarkers and other low abundance proteins. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed1982

Implementation of a free-format request profile in a system for retrieving references to scientific publications.

A process is described whereby a set of instructions in free format can be used to control a search of a data file in an efficient manner. The implications of the effectiveness of this process are considered in relation to a system for the storage and retrieval of references to published works in a typical scientific research establishment. Details of this system have been described earlier.

Computers↗
PubMed1997

Organisation, transmission, manipulation of pathological human organs on the WWW.

The paper describes an integrated methodology for the development of a WWW computer system which addresses issues of the organisation, retrieval and manipulation of 3D volumetric models of pathological human organs. The library of organs is distributed on the WWW since medical expertise and needs are typically expensive resources and also because many pathological conditions are often restricted to local diffusion. Users are provided with a WWW viewer for interactive manipulation of the models of the organs. The system supports low-cost MS-Windows 32 platforms and requires no specialised hardware. Early results demonstrate that the compression techniques employed provide near real-time response for retrieval/manipulation, not only over high-speed expensive network lines, but also over low/medium network connections.

Computer Communication Networks↗
PubMed2000

Structuring the pre-search reference interview: a useful technique for handling clinical questions.

OBJECTIVES: To explore whether structuring a literature search request form according to an evidence-based medicine (EBM) anatomy elicits more information, improves precision of search results, and is acceptable to participating librarians. METHODS: Multicenter before-and-after study involved six different libraries. Data from 195 minimally structured forms collected over four months (Phase 1) were compared with data from 185 EBM-structured forms collected over a further four-month period following a brief training intervention (Phase 2). Survey of librarians' attitudes toward using the EBM-structured forms was conducted early during Phase 2. RESULTS: 380 request forms, EBM-structured and minimally structured, were analyzed using SPSS. A statistically significant Pearson correlation was found between use of the EBM-structured form and complexity of the search strategy (P = 0.002). The correlation between clinical requests handled by the EBM-structured form and fewer items retrieved was also statistically significant (P = 0.028). However, librarians rated minimally structured forms more highly than EBM-structured forms against all dimensions except informativeness. CONCLUSIONS: Although use of the EBM-structured forms is associated with more precise searches and more detailed search strategies, considerable work remains on making these forms acceptable to both librarians and users. Nevertheless, with increased familiarity and improved training, information retrieval benefits could be translated into more effective search practice.

Data Interpretation, Statistical↗
PubMed1975

Use of a computer for producing microbiological reports and for data storage and processing.

A simple 'fail-safe' system is described that produces microbiology reports on a computer teleprinter and stores results on the magnetic tapes and discs of a computer for instant retrieval and epidemiological analysis. The system, which has been in operation for over a year, involves the use of a modified conventional NCR request form. The top portion, which is completed manually by the laboratory staff, is coded by writing numbers in hatched boxes. The data thus written on to the bottom portion are transcribed by punch operators on to paper tape and this data input is verified by double punching. The reports are normally produced automatically by the computer terminal telprinter, but in case of mechanical failure the manually completed request forms can be returned to wards and outpatient departments. The system permits a wide choice of options for epidemiological analysis, and six programmes are described, one of which produces a digest of the overall percentage antibiotic sensitivities of organisms from various sites.

Computers↗
PubMed2002

Olfactory Receptor Database: a metadata-driven automated population from sources of gene and protein sequences.

The Olfactory Receptor Database (ORDB; http://senselab.med.yale.edu/senselab/ordb) is a central repository of olfactory receptor (OR) and olfactory receptor-like gene and protein sequences. To deal with the very large OR gene family, we have constructed an algorithm that automatically downloads sequences from web sources such as GenBank and SWISS-PROT into the database. The algorithm uses hypertext markup language (HTML) parsing techniques that extract information relevant to ORDB. The information is then correlated with the metadata in the ORDB knowledge base to encode the unstructured text extracted into the structured format compliant with the database architecture, entity attribute value with classes and relationship (EAV/CR), which supports the SenseLab project as a whole. Three population methods: batch, automatic and semi-automatic population are discussed. The data is imported into the database using extensible markup language (XML).

Algorithms↗