WormBase: a core data resource for C elegans and other nematodes

WormBase：线虫和其他线虫的核心数据资源

基本信息

批准号：
7502984
负责人：
PAUL Warren STERNBERG
金额：
$ 275万
依托单位：
CALIFORNIA INSTITUTE OF TECHNOLOGY
依托单位国家：
美国
项目类别：
财政年份：
2000
资助国家：
美国
起止时间：
2000-07-20 至 2013-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7502984
关键词：
Ablation Age Agriculture Alleles Anatomy Animals Antibodies Architecture Base Sequence Behavior Binding Sites Bioinformatics Biological Biological Models Biological Process Biomedical Research Caenorhabditis Caenorhabditis elegans Cell Communication Cell Death Cell Differentiation process Cell physiology Cells Chromosome Mapping Code Collection Communication Communities Comparative Anatomy Compatible DNA Sequence Data Data Set Data Sources Databases Depth Detection Development Diagnosis Disease Elements Ensure Expressed Sequence Tags Funding Gene Expression Regulation Gene Proteins Gene Structure Genes Genetic Genetic Processes Genetic Recombination Genetic Variation Genome Genomics Human Hybrids Imagery Individual Institutes Internet Knock-out Knowledge Laboratories Link Literature Livestock Longevity Malignant Neoplasms Maps Medical Metabolic Methods Molecular Molecular Genetics Mutation Names Natural Language Processing Nature Nematoda Nicotine Dependence Nomenclature Online Systems Ontology Organism Paper Parasites Parasitic nematode Pathway interactions Phenotype Physical Chromosome Mapping Physiology Pliability Process Proteins Proteomics RNA Interference Reagent Regulation Research Research Infrastructure Resources Running Secure Site Slave Source Subcellular Anatomy Supervision System Techniques Technology Terminology Tertiary Protein Structure Transcript Transgenes Transgenic Organisms Universities Variant Washington Yeasts base cell motility chromatin immunoprecipitation comparative comparative genomic hybridization data integration data management data modeling design experience functional genomics gene function genetic analysis genome sequencing improved interoperability member migration model organisms databases programs research study small molecule tool transcription factor usability web interface yeast two hybrid system

项目摘要

DESCRIPTION (provided by applicant): Caenorhabditis elegans is a major model system for basic biological and biomedical research and the first animal for which there is a complete description of its genome, anatomy and development, and some information about each of its ~22,000 genes. Five years of funding is requested to maintain and expand WormBase, a Model Organism Database (MOD), with complete coverage of core genomic, genetic, anatomical and functional information about this and other nematodes. Such a database is necessary to allow the entire biomedical research community to make full use of nematode genomic sequences. The two top priorities will be intensive data curation and user interface improvement. WormBase will include up-to-date annotation of the genomic data, the current genetic and physical maps and many experimental data such as genome-scale datasets connected to the function and interactions of cells and genes, as well as development, physiology and behavior. Direct access to the sources of biological material, such as the strain collection of the Caenorhabditis Genetics Center and direct links to data sets maintained by others will be provided. Data will be recovered from the existing resources, from direct contribution of the individual laboratories, and from the literature. While WormBase will act as a central forum through which every laboratory will be able to contribute constructively to the global effort to fully comprehend this metazoan organism, WormBase professional curators will ensure detailed attribution of data sources and check consistency and integrity. To facilitate communication, WormBase will use technology, terminology and style concordant with other databases wherever possible. WormBase will maintain ontologies for nematode anatomy and phenotypes. WormBase will be Web-based and easy to use. Multiple relational databases will be used for data management; the object-based Acedb database system will be used for integration, and this integrated database plus "slave" relational databases will be used to drive the website. Coordination of the project and the main curation site will be at Caltech under the supervision of a C. elegans biologist. Curation and annotation of genomic sequence will take place at the centers - the Sanger Institute and Washington University - that generated the entire genome sequence. Oxford University will maintain genetic nomenclature. Nematodes (roundworms) are major parasites of humans, livestock and crops, and extension of WormBase to broader coverage of nematode genomics will facilitate research into the diagnosis and treatment of nematode-based disease. Studies of C. elegans have informed us of basic principles of normal development and the molecular basis of aging, cancer, nicotine addiction, as well as a variety of fundamental biological processes such as cell migration, cell differentiation and cell death.

描述（由申请人提供）：秀丽隐杆线虫是基础生物学和生物医学研究的主要模型系统，也是第一种对其基因组、解剖结构和发育以及约 22,000 个基因中每一个基因都有完整描述的动物。需要五年的资金来维护和扩展 WormBase，这是一个模式生物数据库 (MOD)，完全覆盖有关该线虫和其他线虫的核心基因组、遗传、解剖和功能信息。这样的数据库对于让整个生物医学研究界充分利用线虫基因组序列是必要的。两个首要任务将是密集数据管理和用户界面改进。 WormBase 将包括基因组数据的最新注释、当前的遗传和物理图谱以及许多实验数据，例如与细胞和基因的功能和相互作用以及发育、生理学和行为相关的基因组规模数据集。将提供对生物材料来源的直接访问，例如秀丽隐杆线虫遗传学中心的菌株收集以及与其他人维护的数据集的直接链接。数据将从现有资源、各个实验室的直接贡献以及文献中恢复。虽然 WormBase 将充当一个中心论坛，每个实验室都可以通过该论坛为全面理解这种后生动物生物体的全球努力做出建设性贡献，但 WormBase 专业管理者将确保数据源的详细归属并检查一致性和完整性。为了促进沟通，WormBase 将尽可能使用与其他数据库一致的技术、术语和风格。 WormBase 将维护线虫解剖学和表型的本体。 WormBase 将基于网络并且易于使用。将使用多个关系数据库进行数据管理；基于对象的Acedb数据库系统将用于集成，该集成数据库加上“从属”关系数据库将用于驱动网站。该项目和主要策展地点的协调将在加州理工学院进行，并由秀丽隐杆线虫生物学家监督。基因组序列的整理和注释将在产生整个基因组序列的中心——桑格研究所和华盛顿大学进行。牛津大学将保留基因命名法。线虫（蛔虫）是人类、牲畜和农作物的主要寄生虫，将 WormBase 扩展到更广泛的线虫基因组覆盖范围将有助于线虫疾病的诊断和治疗研究。对线虫的研究让我们了解了正常发育的基本原理和衰老、癌症、尼古丁成瘾的分子基础，以及细胞迁移、细胞分化和细胞死亡等多种基本生物过程。