The ARKdb: genome databases for farmed and other animals

The ARKdb genome databases provide comprehensive public repositories for genome mapping data from farmed species and other animals (http://www.thearkdb.org) providing a resource similar in function to that offered by GDB or MGD for human or mouse genome mapping data, respectively. Because we have attempted to build a generic mapping database, the system has wide utility, particularly for those species for which development of a specific resource would be prohibitive. The ARKdb genome database model has been implemented for 10 species to date. These are pig, chicken, sheep, cattle, horse, deer, tilapia, cat, turkey and salmon. Access to the ARKdb databases is effected via the World Wide Web using the ARKdb browser and Anubis map viewer. The information stored includes details of loci, maps, experimental methods and the source references. Links to other information sources such as PubMed and EMBL/GenBank are provided. Responsibility for data entry and curation is shared amongst scientists active in genome research in the species of interest. Mirror sites in the United States are maintained in addition to the central genome server at Roslin.

Mendel-GFDb and Mendel-ESTS: databases of plant gene families and ESTs annotated with gene family numbers and gene family names

There is no control over the information provided with sequences when they are deposited in the sequence databases. Consequently mistakes can seed the incorrect annotation of other sequences. Grouping genes into families and applying controlled annotation overcomes the problems of incorrect annotation associated with individual sequences. Two databases (http://www.mendel.ac.uk) were created to apply controlled annotation to plant genes and plant ESTs: Mendel-GFDb is a database of plant protein (gene) families based on gapped-BLAST analysis of all sequences in the SWISS-PROT family of databases. Sequences are aligned (ClustalW) and identical and similar residues shaded. The families are visually curated to ensure that one or more criteria, for example overall relatedness and/or domain similarity relate all sequences within a family. Sequence families are assigned a ‘Gene Family Number’ and a unified description is developed which best describes the family and its members. If authority exists the gene family is assigned a ‘Gene Family Name’. This information is placed in Mendel-GFDb. Mendel-ESTS is primarily a database of plant ESTs, which have been compared to Mendel-GFDb, completely sequenced genomes and domain databases. This approach associated ESTs with individual sequences and the controlled annotation of gene families and protein domains; the information being placed in Mendel-ESTS. The controlled annotation applied to genes and ESTs provides a basis from which a plant transcription database can be developed.

trEST, trGEN and Hits: access to databases of predicted protein sequences

High throughput genome (HTG) and expressed sequence tag (EST) sequences are currently the most abundant nucleotide sequence classes in the public database. The large volume, high degree of fragmentation and lack of gene structure annotations prevent efficient and effective searches of HTG and EST data for protein sequence homologies by standard search methods. Here, we briefly describe three newly developed resources that should make discovery of interesting genes in these sequence classes easier in the future, especially to biologists not having access to a powerful local bioinformatics environment. trEST and trGEN are regularly regenerated databases of hypothetical protein sequences predicted from EST and HTG sequences, respectively. Hits is a web-based data retrieval and analysis system providing access to precomputed matches between protein sequences (including sequences from trEST and trGEN) and patterns and profiles from Prosite and Pfam. The three resources can be accessed via the Hits home page (http://hits.isb-sib.ch).

Creating local bibliographic databases: new tools for evidence-based health care*

The Internet has created new opportunities for librarians to present literature search results to clinicians. In order to take full advantage of these opportunities, libraries need to create locally maintained bibliographic databases. A simple method of creating a local bibliographic database and publishing it on the Web is described. The method uses off-the-shelf software and requires minimal programming. A hedge search strategy for outcome studies of clinical process interventions is created, and Ovid is used to search MEDLINE. The search results are saved and imported into EndNote libraries. The citations are modified, exported to a Microsoft Access database, and published on the Web. Clinicians can use a Web browser to search the database. The bibliographic database contains 13,803 MEDLINE citations of outcome studies. Most searches take between four and ten seconds and retrieve between ten and 100 citations. The entire cost of the software is under $900. Locally maintained bibliographic databases can be created easily and inexpensively. They significantly extend the evidence-based health care services that libraries can offer to clinicians.

Aladdin's Magic Lamp: Developing Methods for Calibration and Geolocation Accuracy Assessment of the DMSP OLS

Nighttime satellite imagery from the Defense Meteorological Satellite Program (DMSP) Operational Linescan System (OLS) has a unique capability to observe nocturnal light emissions from sources including cities, wild fires, and gas flares. Data from the DMSP OLS is used in a wide range of studies including mapping urban areas, estimating informal economies, and estimating urban populations. Given the extensive and increasing list of applications a repeatable method for assessing geolocation accuracy, performing inter-calibration, and defining the minimum detectable brightness would be beneficial. An array of portable lights was designed and taken to multiple field sites known to have no other light sources. The lights were operated during nighttime overpasses by the DMSP OLS and observed in the imagery. A first estimate of the minimum detectable brightness is presented based on the field experiments conducted. An assessment of the geolocation accuracy was performed by measuring the distance between the GPS measured location of the lights and the observed location in the imagery. A systematic shift was observed and the mean distance was measured at 2.9km. A method for in situ radiance calibration of the DMSP OLS using a ground based light source as an active target is presented. The wattage of light used by the active target strongly correlates with the signal measured by the DMSP OLS. This approach can be used to enhance our ability to make inter-temporal and inter-satellite comparisons of DMSP OLS imagery. Exploring the possibility of establishing a permanent active target for the calibration of nocturnal imaging systems is recommended. The methods used to assess the minimum detectable brightness, assess the geolocation accuracy, and build inter-calibration models lay the ground work for assessing the energy expended on light emitted into the sky at night. An estimate of the total energy consumed to light the night sky globally is presented.

How to make a natural language interface to query databases accessible to everyone: An example

Natural Language Interfaces to Query Databases (NLIDBs) have been an active research field since the 1960s. However, they have not been widely adopted. This article explores some of the biggest challenges and approaches for building NLIDBs and proposes techniques to reduce implementation and adoption costs. The article describes {AskMe*}, a new system that leverages some of these approaches and adds an innovative feature: query-authoring services, which lower the entry barrier for end users. Advantages of these approaches are proven with experimentation. Results confirm that, even when {AskMe*} is automatically reconfigurable against multiple domains, its accuracy is comparable to domain-specific NLIDBs.

Europe on the Internet. A selection of useful websites, databases and documents for information on the European Union and the wider Europe. July 2016

No abstract.

Online literature searching and databases at the U.S. Environmental Protection Agency, Environmental Research Center, Library, Cincinnati, Ohio /

Mode of access: Internet.

Advanced quality systems : guidelines for establishing and maintaining construction quality databases /

"HRDI-12/11-06(2M)E"--P. [4] of cover.

The delay/re-read protocol for concurrency control in databases /

"UILU-ENG 83 1723"--Cover.

A characterization of globally consistent databases and their correct access paths /

"Supported in part by NSF grant MCS-80-03308."

Hardware for searching very large text databases /

Vita.