RESUMEN
dictyBase (http://www.dictybase.org), the model organism database for Dictyostelium, aims to provide the broad biomedical research community with well integrated, high quality data and tools for Dictyostelium discoideum and related species. dictyBase houses the complete genome sequence, ESTs, and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome to provide a 'reference genome' in the Amoebozoa clade. We highlight several new features in the present update: (i) new annotations; (ii) improved interface with web 2.0 functionality; (iii) the initial steps towards a genome portal for the Amoebozoa; (iv) ortholog display; and (v) the complete integration of the Dicty Stock Center with dictyBase.
Asunto(s)
Bases de Datos Genéticas , Dictyostelium/genética , Amebozoos/genética , Genoma de Protozoos , Internet , Anotación de Secuencia Molecular , Proteínas Protozoarias/química , Proteínas Protozoarias/genética , Integración de SistemasRESUMEN
dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome. This dictyBase update describes the annotations and features implemented since 2006, including improved strain and phenotype representation, integration of predicted transcriptional regulatory elements, protein domain information, biochemical pathways, improved searching and a wiki tool that allows members of the research community to provide annotations.
Asunto(s)
Bases de Datos Genéticas , Dictyostelium/genética , Animales , Dictyostelium/metabolismo , Genes Protozoarios , Genómica , Fenotipo , Regiones Promotoras Genéticas , Estructura Terciaria de Proteína , Proteínas Protozoarias/químicaRESUMEN
xanthusBase (http://www.xanthusbase.org) is the official model organism database (MOD) for the social bacterium Myxococcus xanthus. In many respects, M.xanthus represents the pioneer model organism (MO) for studying the genetic, biochemical, and mechanistic basis of prokaryotic multicellularity, a topic that has garnered considerable attention due to the significance of biofilms in both basic and applied microbiology research. To facilitate its utility, the design of xanthusBase incorporates open-source software, leveraging the cumulative experience made available through the Generic Model Organism Database (GMOD) project, MediaWiki (http://www.mediawiki.org), and dictyBase (http://www.dictybase.org), to create a MOD that is both highly useful and easily navigable. In addition, we have incorporated a unique Wikipedia-style curation model which exploits the internet's inherent interactivity, thus enabling M.xanthus and other myxobacterial researchers to contribute directly toward the ongoing genome annotation.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Myxococcus xanthus/genética , Enciclopedias como Asunto , Genoma Bacteriano , Internet , Modelos Biológicos , Interfaz Usuario-ComputadorRESUMEN
dictyBase (http://dictybase.org) is the model organism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the Dictyostelium genome will facilitate the annotation of other genomes.
Asunto(s)
Bases de Datos Genéticas , Dictyostelium/genética , Genoma de Protozoos , Animales , Bancos de Muestras Biológicas , Genómica , Internet , Modelos Animales , Proteínas Protozoarias/química , Proteínas Protozoarias/genética , Programas Informáticos , Integración de Sistemas , Interfaz Usuario-ComputadorRESUMEN
Our aim was to identify asthmatic patients as cases, and healthy patients as controls, for genome-wide association studies (GWAS), using readily available data from electronic medical records. For GWAS, high specificity is required to accurately identify genotype-phenotype correlations. We developed two algorithms using a combination of diagnoses, medications, and smoking history. By applying stringent criteria for source and specificity of the data we achieved a 95% positive predictive value and 96% negative predictive value for identification of asthma cases and controls compared against clinician review. We achieved a high specificity but at the loss of approximately 24% of the initial number of potential asthma cases we found. However, by standardizing and applying our algorithm across multiple sites, the high number of cases needed for a GWAS could be achieved.