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

• 批准号: 8325682
• 负责人: PAUL Warren STERNBERG
• 金额: $ 281.53万
• 依托单位: CALIFORNIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 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/8325682
• 关键词: Aging; Agriculture; Anatomy; Animals; Behavior; Biocompatible Materials; Bioinformatics; Biological; Biological Models; Biological Process; Biomedical Research; Caenorhabditis; Caenorhabditis elegans; Cell Communication; Cell Death; Cell Differentiation process; Chromosome Mapping; Collection; Communication; Communities; Data; Data Set; Data Sources; Databases; Development; Diagnosis; Disease; Ensure; Funding; Gene Proteins; Genes; Genetic; Genome; Genomics; Human; Individual; Institutes; Internet; Knowledge; Laboratories; Link; Literature; Livestock; Malignant Neoplasms; Medical; Molecular; Molecular Genetics; Nematoda; Nicotine Dependence; Nomenclature; Online Systems; Ontology; Organism; Parasites; Phenotype; Physical Map of the Human Genome; Physiology; Reagent; Research; Research Infrastructure; Resources; Site; Slave; Source; Supervision; System; Technology; Terminology; Transcript; Universities; Washington; base; biological research; cell motility; comparative genomics; data management; functional genomics; genetic analysis; genome sequencing; member; model organisms databases; relational database; web site

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、解剖学和发育有完整描述的动物，以及关于其约22，000个基因中每个基因的一些信息。需要五年的资金来维持和扩大WormBase，这是一个模式生物数据库（MOD），完全覆盖了关于这种线虫和其他线虫的核心基因组，遗传，解剖和功能信息。这样一个数据库是必要的，使整个生物医学研究界充分利用线虫基因组序列。两个首要任务将是密集的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，生理学和行为有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，如小杆线虫遗传学中心的菌株收集，并提供与其他人维护的数据集的直接链接。数据将从现有资源、各实验室的直接贡献和文献中恢复。虽然WormBase将作为一个中心论坛，每个实验室都能够为全面了解这种后生动物有机体的全球努力做出建设性贡献，但WormBase的专业策展人将确保数据源的详细归属，并检查一致性和完整性。为了便于交流，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Web，易于使用。将使用多个关系数据库进行数据管理;将使用基于对象的Acedb数据库系统进行整合，并将使用这一整合数据库加上“从属”关系数据库来驱动网站。该项目的协调和主要的策展地点将在加州理工学院的监督下，一个C。优雅的生物学家基因组序列的编辑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。牛津大学将保留遗传命名法。 线虫（蛔虫）是人类、牲畜和农作物的主要寄生虫，将WormBase扩展到线虫基因组学的更广泛覆盖范围将促进对基于线虫的疾病的诊断和治疗的研究。研究C。秀丽线虫告诉我们正常发育的基本原理和衰老，癌症，尼古丁成瘾的分子基础，以及各种基本的生物过程，如细胞迁移，细胞分化和细胞死亡。

项目成果

nGASP--the nematode genome annotation assessment project.

• DOI: 10.1186/1471-2105-9-549
• 发表时间: 2008-12-19
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Coghlan A;Fiedler TJ;McKay SJ;Flicek P;Harris TW;Blasiar D;nGASP Consortium;Stein LD
• 通讯作者: Stein LD

WormBase 2007.

• DOI: 10.1093/nar/gkm975
• 发表时间: 2008-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Rogers A;Antoshechkin I;Bieri T;Blasiar D;Bastiani C;Canaran P;Chan J;Chen WJ;Davis P;Fernandes J;Fiedler TJ;Han M;Harris TW;Kishore R;Lee R;McKay S;Müller HM;Nakamura C;Ozersky P;Petcherski A;Schindelman G;Schwarz EM;Spooner W;Tuli MA;Van Auken K;Wang D;Wang X;Williams G;Yook K;Durbin R;Stein LD;Spieth J;Sternberg PW
• 通讯作者: Sternberg PW

WormBase: new content and better access.

• DOI: 10.1093/nar/gkl818
• 发表时间: 2007-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Bieri T;Blasiar D;Ozersky P;Antoshechkin I;Bastiani C;Canaran P;Chan J;Chen N;Chen WJ;Davis P;Fiedler TJ;Girard L;Han M;Harris TW;Kishore R;Lee R;McKay S;Müller HM;Nakamura C;Petcherski A;Rangarajan A;Rogers A;Schindelman G;Schwarz EM;Spooner W;Tuli MA;Van Auken K;Wang D;Wang X;Williams G;Durbin R;Stein LD;Sternberg PW;Spieth J
• 通讯作者: Spieth J

Modeling the evolution dynamics of exon-intron structure with a general random fragmentation process.

• DOI: 10.1186/1471-2148-13-57
• 发表时间: 2013-02-28
• 期刊: BMC evolutionary biology
• 影响因子: 3.4
• 作者: Wang L;Stein LD
• 通讯作者: Stein LD

WormBase 2012: more genomes, more data, new website.

• DOI: 10.1093/nar/gkr954
• 发表时间: 2012-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Yook K;Harris TW;Bieri T;Cabunoc A;Chan J;Chen WJ;Davis P;de la Cruz N;Duong A;Fang R;Ganesan U;Grove C;Howe K;Kadam S;Kishore R;Lee R;Li Y;Muller HM;Nakamura C;Nash B;Ozersky P;Paulini M;Raciti D;Rangarajan A;Schindelman G;Shi X;Schwarz EM;Ann Tuli M;Van Auken K;Wang D;Wang X;Williams G;Hodgkin J;Berriman M;Durbin R;Kersey P;Spieth J;Stein L;Sternberg PW
• 通讯作者: Sternberg PW