The GDB Human Genome Database Anno 1997.

The value of the Genome Database (GDB) for the human genome research community has been greatly increased since the release of version 6. 0 last year. Thanks to the introduction of significant technical improvements, GDB has seen dramatic growth in the type and volume of information stored in the database. This article summarizes the types of data that are now available in the Genome Database, demonstrates how the database is interconnected with other biomedical resources on the World Wide Web, discusses how researchers can contribute new or updated information to the database, and describes our current efforts as well as planned improvements for the future.     

Improvements to the GDB Human Genome Data Base.

Version 6.0 of the Human Genome Data Base introduces a number of significant improvements over previous releases of GDB. The most important of these are revised data representations for genes and genomic maps and a new curatorial model for the database. GDB 6.0 is the first major genomic database to provide read/write access directly to the scientific community, including capabilities for third-party annotation. The revised database can represent all major categories of genetic and physical maps, along with the underlying order and distance information used to construct them. The improved representation permits more sophisticated map queries to be posed and supports the graphical display of maps. In addition the new GDB has a richer model for gene information, better suited for supporting cross-references to databases describing gene function, structure, products, expression and associated phenotypes.     

The GDB Human Genome Data Base anno 1994.

In 1991 the Genome Data Base at Johns Hopkins University School of Medicine was selected as the central repository for mapping data from the Human Genome Project, and was funded by NIH and DOE under a three year award. GDB has now finished 28 months of Federally funded operation. During this period a great deal of progress and many internal changes have taken place. In addition, many changes have also occurred in the external environment, and GDB has adapted its strategies to play an appropriate role in those changes as well. Recognizing the central role of mapping information in the genome project, it is important that GDB respond aggressively to the increasing demands of genomic researchers, as well as formulate a program of response to a number of long standing, but still unmet, needs of that community. It is even more important that GDB provide leadership in the genome informatics enterprise. Three themes described here are dominant in our future plans and represent the essence of the major changes made in the past year. They include: enhanced data acquisition, better map representation, and full integration into the collection of genomic databases.     

SGD: Saccharomyces Genome Database.

The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic sequence, its genes and their products, the phenotypes of its mutants, and the literature supporting these data. The amount of information and the number of features provided by SGD have increased greatly following the release of the S.cerevisiae genomic sequence, which is currently the only complete sequence of a eukaryotic genome. SGD aids researchers by providing not only basic information, but also tools such as sequence similarity searching that lead to detailed information about features of the genome and relationships between genes. SGD presents information using a variety of user-friendly, dynamically created graphical displays illustrating physical, genetic and sequence feature maps. SGD can be accessed via the World Wide Web at http://genome-www.stanford.edu/Saccharomyces/     

MGD: the Mouse Genome Database

The Mouse Genome Database (MGD) (http://www.informatics.jax.org) one component of a community database resource for the laboratory mouse, a key model organism for interpreting the human genome and for understanding human biology. MGD strives to provide an extensively integrated information resource with experimental details annotated from both literature and on-line genomic data sources. MGD curates and presents the consensus representation of genotype (sequence) to phenotype information including highly detailed information about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse. Recent developments include a general implementation of database structures for controlled vocabularies and the integration of a phenotype classification system.     

RsGDB, the Rhodobacter sphaeroides Genome Database.

This report provides a summary of the sequencing project of the small chromosome (CII) of Rhodobacter sphaeroides 2.4.1(T),and introduces the first version of the genome database of this bacterium. The database organizes and describes diverse sets of biological information. The main role of the R.sphaeroides genome database (RsGDB) is to provide public access to the collected genomic information for R.sphaeroides via the World-Wide Web at http://utmmg.med.uth.tmc.edu/sphaeroides. The database allows the user access to hundreds of low redundancy R.sphaeroides sequences for further database searching, a summary of our current search results, and other allied information pertaining to this bacterium.     

The UCSC Genome Browser Database

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.     

人类基因组计划与后基因组时代

2003年4月14日生命科学诞生了一个新的重要里程碑,人类基因组计划完成,后基因组时代正式来临。着重介绍了人类基因组计划的提出、目标与任务、实施与进展等方面的基本情况,讨论了后基因组时代的时间界定,分析展望了后基因组时代与人类基因组计划密切相关的生物信息学、功能基因组学、蛋白质组学、药物基因组学等几个重要研究领域 。     

Leprosy and the Human Genome

Summary: Despite the availability of effective treatment for several decades, leprosy remains an important medical problem in many regions of the world. Infection with Mycobacterium leprae can produce paucibacillary disease, characterized by well-formed granulomas and a Th1 T-cell response, or multibacillary disease, characterized by poorly organized cellular infiltrates and Th2 cytokines. These diametric immune responses confer states of relative resistance or susceptibility to leprosy, respectively, and have well-defined clinical manifestations. As a result, leprosy provides a unique opportunity to dissect the genetic basis of human in vivo immunity. A series of studies over the past 40 years suggests that host genes influence the risk of leprosy acquisition and the predilection for different clinical forms of the disease. However, a comprehensive, cellular, and molecular view of the genes and variants involved is still being assembled. In this article, we review several decades of human genetic studies of leprosy, including a number of recent investigations. We emphasize genetic analyses that are validated by the replication of the same phenotype in independent studies or supported by functional experiments demonstrating biological mechanisms of action for specific polymorphisms. Identifying and functionally exploring the genetic and immunological factors that underlie human susceptibility to leprosy have yielded important insights into M. leprae pathogenesis and are likely to advance our understanding of the immune response to other pathogenic mycobacteria. This knowledge may inform new treatment or vaccine strategies for leprosy or tuberculosis.