Biomedical subjects
Publications and source records attributed to P Rodriguez-Tomé.
Since July 1995, the European Bioinformatics Institute (EBI) has maintained the Radiation Hybrid database (RHdb; http://www.ebi.ac. uk/RHdb ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to RHdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).
Nowadays it is possible to unravel complex information at all levels of cellular organization by obtaining multi-dimensional image information. At the macromolecular level, three-dimensional (3D) electron microscopy, together with other techniques, is able to reach resolutions at the nanometer or subnanometer level. The information is delivered in the form of 3D volumes containing samples of a given function, for example, the electron density distribution within a given macromolecule. The same situation happens at the cellular level with the new forms of light microscopy, particularly confocal microscopy, all of which produce biological 3D volume information. Furthermore, it is possible to record sequences of images over time (videos), as well as sequences of volumes, bringing key information on the dynamics of living biological systems. It is in this context that work on BioImage started two years ago, and that its first version is now presented here. In essence, BioImage is a database specifically designed to contain multi-dimensional images, perform queries and interactively work with the resulting multi-dimensional information on the World Wide Web, as well as accomplish the required cross-database links. Two sister home pages of BioImage can be accessed at http://www. bioimage.org and http://www-embl.bioimage.org
A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.
Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).
MOTIVATION: The BioCatalog is a database of information on software of interest in molecular biology and genetics. The programs are grouped by domain of interest. AVAILABILITY: The BioCatalog is freely distributed as ASCII files. It can be searched through its Web interface at http://www.ebi.ac.uk/biocat. CONTACT: biocat@ebi. ac.uk
MOTIVATION: There are a large number of genetic and physical maps, distributed at many sites. Each site offers different kinds of access methods and viewers. CORBA, the de facto standard for distributed object-oriented computing, offers new opportunities to unify the view on these maps through standard interfaces. A collaboration of Infobiogen and the EBI proposes a common IDL for maps. RESULTS: A CORBA map viewer is presented which serves as a proof of concept for the proposed IDL. It demonstrates its usefulness in the context of map viewing and its ability to handle large maps with <1000 markers. The viewer gives access to the maps of the Radiation Hybrid Database at EBI. It gives a quick overview of several large maps side by side. The marker density at each map position is displayed and different marker types can be highlighted. AVAILABILITY: Demonstration and source code at: http://sunny.ebi.ac.uk/ approximately jungfer/Mapplet CONTACT: jungfer@ebi.ac.uk
Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb, a public database for radiation hybrid data. Radiation hybrid data are used in the generation of alternative genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved genetic clusters of polymorphic STSs. The EBI is an Outstation of the European Molecular Biology Laboratory (EMBL).
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Modern biology depends on a wide range of software interacting with a large number of data sources, varying both in size, complexity and structure. The range of important databases in molecular biology and genetics makes it crucial to overcome the problems which this multiplicity presents. At EMBL-EBI we have started to use CORBA technology to support interoperability between a variety of databases, as well as to facilitate the integration of tools that access these databases. Within the Radiation Hybrid DataBase project we are confronted daily with the interoperation and linking issues. In this paper we present a CORBA infrastructure implemented to access the Radiation Hybrid DataBase.
The human genome is thought to harbor 50,000 to 100,000 genes, of which about half have been sampled to date in the form of expressed sequence tags. An international consortium was organized to develop and map gene-based sequence tagged site markers on a set of two radiation hybrid panels and a yeast artificial chromosome library. More than 16,000 human genes have been mapped relative to a framework map that contains about 1000 polymorphic genetic markers. The gene map unifies the existing genetic and physical maps with the nucleotide and protein sequence databases in a fashion that should speed the discovery of genes underlying inherited human disease. The integrated resource is available through a site on the World Wide Web at http://www.ncbi.nlm.nih.gov/SCIENCE96/.
The European Bioinformatics Institute (EBI) maintains and distributes the EMBL Nucleotide Sequence database, Europe's primary nucleotide sequence data resource. The EBI also maintains and distributes the SWISS-PROT Protein Sequence database, in collaboration with Amos Bairoch of the University of Geneva. Over fifty additional specialist molecular biology databases, as well as software and documentation of interest to molecular biologists are available. The EBI network services include database searching and sequence similarity searching facilities.