Development of DictyBase, an online informatics resource

开发在线信息资源 DictyBase

基本信息

批准号：
7267057
负责人：
REX L CHISHOLM
金额：
$ 48.81万
依托单位：
NORTHWESTERN UNIVERSITY AT CHICAGO
依托单位国家：
美国
项目类别：
财政年份：
2002
资助国家：
美国
起止时间：
2002-08-01 至 2010-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7267057
关键词：
Address Amoeba genus Animal Model Antidepressive Agents Arts Binding Bioinformatics Biological Biological Process Biology Budgets Class Code Collaborations Communities Complement Computer software Data Data Set Databases Deposition Development Dictyostelium Documentation Educational Materials Elements Evolution Expressed Sequence Tags Funding Gene Expression Generations Generic Drugs Genes Genome Genomics Goals Growth Health Housing Human Immune response Individual Information Retrieval Investments Knowledge Laboratories Link Literature Location Malignant Neoplasms Manuals Metabolic Pathway MicroRNAs Modeling Mutagenesis Neoplasm Metastasis Numbers Ontology Orthologous Gene Parasites Pathway interactions Pharmaceutical Preparations Phenotype Physarum Positioning Attribute Procedures Proteins Protocols documentation Range Recording of previous events Research Research Infrastructure Research Personnel Resource Informatics Resources Science Sequence Analysis Signal Pathway Software Tools Source Standards of Weights and Measures Structure Students Synteny System Tertiary Protein Structure Testing Time Training Trees United States National Institutes of Health Update Wound Healing Writing base cell motility comparative genome database genome sequencing improved insight knowledge of results model organisms databases network models programs promoter repository research study response scaffold tool tumor

项目摘要

DESCRIPTION (provided by applicant): dictyBase is a new model organism database whose development began in July 2002. The goal of dictyBase is to use the recently completed sequence of the Dictyostelium genome to organize biological knowledge derived using Dictyostelium as an experimental system. dictyBase was largely built using the database schema and code from existing model organism databases and the Generic Model Organism Database project (GMOD). It was officially launched in July 2003 and has been accessed over 600,000 times by more than 100,000 individual IP addresses. It has become an indispensable resource for investigators using Dictyostelium or seeking to use its complement of genes in comparative genomics studies. During the first funding cycle manual curation of the Dictyostelium genome improved the gene models produced by the automated sequence analysis pipeline in approximately 18% of the genes that were reviewed. Specific aims for this application are to continue the manual curation effort, to provide expert support to dictyBase users, to provide resources that facilitate research using Dictyostelium, to expand the types of data available through the database, to establish links to databases holding other Dictyostelium data, and to begin to develop the infrastructure to hold and curate the genome sequences of other amoebae. Because of its location in the evolutionary history, detailed curation of Dictyostelium genes and experimental results will give insights into the function and evolution of many genes and biological process important for fundamental understanding of biology important for human health. Examples of this include identifying genes required for growth of intracellular parasites, characterizing the mechanisms responsible for cell migration that will increase our understanding of wound healing, generation of immune responses and tumor metastasis and the identification of genes responsible for response to drugs such as antidepressants and cancer chemotherapeutics. As the number of genomes being sequenced increases, analysis of these new genomes is heavily dependent on the body of knowledge resulting from a few well characterized and carefully annotated genomes. dictyBase provides a unique complement to existing genome databases because of the body of knowledge available for Dictyostelium, its position in the evolutionary tree, the research tools available and the strength of ongoing Dictyostelium research.

描述（由申请人提供）：dictybase是一个新的模型生物数据库，其发展始于2002年7月。dictybase的目的是使用dictyostelium基因组的最近完成的序列来组织使用dictyostelium作为实验系统得出的生物学知识。 DICTYBASE在很大程度上是使用现有模型有机体数据库和通用模型有机体数据库项目（GMOD）的数据库架构和代码构建的。它于2003年7月正式推出，已通过超过100,000个单独的IP地址访问超过600,000次。对于使用Dictyostelium或试图在比较基因组学研究中使用其基因的补体的研究人员来说，它已成为必不可少的资源。在第一个融资周期中，dictyostelium Genome的手动策划改善了大约18％的综述基因中自动序列分析管道产生的基因模型。该应用程序的具体目的是继续手动策划，向DictyBase用户提供专家支持，提供促进使用Dictyostelium的研究的资源，以扩大通过数据库可用的数据类型，以建立持有其他Dictyostyostelium数据的数据库的链接，并开始开发其他基础结构以持有和策划其他Amoebae的基础序列。由于其在进化史中的位置，详细策划了Dictyostelium基因和实验结果将洞悉许多基因的功能和进化，而生物学过程对于对生物学对人类健康至关重要的基本理解很重要。其中的例子包括鉴定细胞内寄生虫生长所需的基因，表征了负责细胞迁移的机制，这将增加我们对伤口愈合的理解，免疫反应和肿瘤转移的产生以及对抗抑郁药和癌症化学治疗剂等药物反应的基因的鉴定。随着测序的基因组数量的增加，对这些新基因组的分析在很大程度上取决于少数表征和精心注释的基因组所产生的知识体。 Dictybase为现有基因组数据库提供了独特的补充，因为具有可用于Dictyostelium的知识，其在进化树中的位置，可用的研究工具以及正在进行的Dictyostelium Research的强度。