Mining Information from Echinoderm Genomes and the Scientific Literature
从棘皮动物基因组和科学文献中挖掘信息
基本信息
- 批准号:10715580
- 负责人:
- 金额:$ 14.94万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2023
- 资助国家:美国
- 起止时间:2023-09-22 至 2028-06-30
- 项目状态:未结题
- 来源:
- 关键词:AllyAnimalsAntibodiesArchitectureBibliographyBiologicalBiological ModelsBiologyCollaborationsCommunitiesComparative StudyDataDatabasesDevelopmentDevelopmental ProcessEchinoBaseEchinodermataEmbryoEmbryonic DevelopmentEnsureEvolutionFAIR principlesFoundationsFutureGene ExpressionGene Expression ProfileGenesGenetic TranscriptionGenomeGenomicsGoalsGrantGuide RNAHeartHuman DevelopmentIndividualLinkLiteratureMiningMissionModelingModernizationNamesOntologyOrganismPaperPlayPublicationsPublishingReagentRegulator GenesRegulatory ElementResearchResearch PersonnelResourcesRoleSea UrchinsTimeTissuesVertebral columnVertebratesWorkXenBasebiological researchdata managementgene regulatory networkhuman diseaseimprovedjournal articlelife historymembermodel organismmodel organisms databasesprogramsscientific organizationtool
项目摘要
SUMMARY CURATION
Mining Information from Echinoderm Genomes and the Scientific Literature
Echinoderms (sea urchins and their allies) are valuable models for analysis of the genomic control of
embryonic development. For example, the most complete gene regulatory networks (GRNs) for development
that we have for any animal have recently been solved for sea urchin embryos. Comparative studies across
echinoderms are elucidating the evolution of gene regulatory programs. Data on genes, genomes, and gene
expression are fundamental to all aspects of modern developmental biological research. Effective access to
these data has become vital not only to members of the echinoderm research community but to a broader
audience studying developmental processes in many model systems. The activities of Echinobase are
essential in order to ultimately apply this scientific information to human development and disease.
Model organism databases enhance the value of research by consolidating and storing data, integrating
different types of information and representing it in useful ways, and linking similar kinds of data across
organisms. Echinobase was created to enhance the value of scientific data related to the genes and genomes
of sea urchins and other echinoderms and to serve as a centralized, definitive resource for information related
to these important model organisms. The Curate Component (Curate) plays a central role in the overall
mission of Echinobase by identifying, extracting, and organizing scientific data. All of our curation efforts are
supported through a close collaboration with Xenbase, which provides a suite of data entry, storage, and
analysis tools that are well-suited to our needs.
During this project period, Curate has three major goals: 1) to curate echinoderm genomes, including the
provision of accurate, orthology-based names to echinoderm genes and the improved annotation of current
echinoderm gene models; 2) to curate an extensive scientific literature related to echinoderm development,
including the ongoing assembly of a bibliography of published papers that serves as a backbone to which all
curated biological data are attributed, and the curation of a wealth of information from these papers related to
gene expression patterns, morpholinos, antibodies, guide RNAs (gRNAs), and cis-regulatory elements (CREs);
3) to enhance the current echinoderm developmental ontology, which provides a foundation for almost all of
our curation efforts, by expanding the ontology to include representatives of additional classes of echinoderms
and additional life history stages and by incorporating into Echinobase additional static content derived from
the developmental ontology. By achieving these goals, Curate will vastly enhance the utility of Echinobase to
the community of researchers who study echinoderm development and ensure that echinoderm-related
information is readily accessible to biologists who work with other model organisms, including vertebrates.
总结策展
从棘皮动物基因组和科学文献中挖掘信息
棘皮动物(海胆及其盟友)是分析基因组控制的有价值的模型
胚胎发育。例如,最完整的发育基因调控网络(GRN)
我们最近已经解决了对海胆胚胎的任何动物的问题。比较研究
棘皮动物正在阐明基因调控程序的进化。关于基因、基因组和基因的数据
表达是现代发育生物学研究各个方面的基础。有效访问
这些数据不仅对棘皮动物研究界的成员至关重要,而且对更广泛的领域也至关重要。
观众研究许多模型系统中的发育过程。 Echinobase 的活动是
对于最终将这些科学信息应用于人类发展和疾病至关重要。
模式生物数据库通过整合和存储数据、整合
不同类型的信息并以有用的方式表示它,并将类似类型的数据链接起来
有机体。 Echinobase 的创建是为了提高与基因和基因组相关的科学数据的价值
海胆和其他棘皮动物的信息,并作为相关信息的集中、权威的资源
这些重要的模式生物。 Curate 组件(Curate)在整体中起着核心作用
Echinobase 的使命是识别、提取和组织科学数据。我们所有的策展努力都是
通过与 Xenbase 的密切合作提供支持,Xenbase 提供了一套数据输入、存储和
非常适合我们需求的分析工具。
在此项目期间,Curate 有三个主要目标:1)管理棘皮动物基因组,包括
为棘皮动物基因提供准确的、基于直系学的名称,并改进当前的注释
棘皮动物基因模型; 2) 整理与棘皮动物发育相关的广泛科学文献,
包括正在收集已发表论文的参考书目,作为所有研究的支柱
整理的生物数据被归因,并且从这些论文中整理出与以下相关的大量信息
基因表达模式、吗啉代、抗体、引导RNA (gRNA) 和顺式调控元件(CRE);
3)增强当前棘皮动物发育本体论,这为几乎所有的
我们的管理工作,通过扩大本体论来包括其他棘皮动物类别的代表
和额外的生命史阶段,并通过将来自 Echinobase 的额外静态内容纳入其中
发展本体论。通过实现这些目标,Curate 将极大地增强 Echinobase 的实用性
研究棘皮动物发育并确保与棘皮动物相关的研究人员群体
研究其他模式生物(包括脊椎动物)的生物学家很容易获得信息。
项目成果
期刊论文数量(0)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
数据更新时间:{{ journalArticles.updateTime }}
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CHARLES A. ETTENSOHN其他文献
CHARLES A. ETTENSOHN的其他文献
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{{ truncateString('CHARLES A. ETTENSOHN', 18)}}的其他基金
Enhanced Echinobase: A Community Genomics Research Resource For The Future
增强型 Echinobase:未来的社区基因组学研究资源
- 批准号:
10715578 - 财政年份:2023
- 资助金额:
$ 14.94万 - 项目类别:
Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database
挖掘科学文献并构建泛棘皮动物基因表达数据库
- 批准号:
10241292 - 财政年份:2018
- 资助金额:
$ 14.94万 - 项目类别:
Enhanced Echinobase: A Community Genome Resource for the Future
增强型 Echinobase:未来的社区基因组资源
- 批准号:
10241290 - 财政年份:2018
- 资助金额:
$ 14.94万 - 项目类别:
Enhanced Echinobase: A Community Genome Resource for the Future
增强型 Echinobase:未来的社区基因组资源
- 批准号:
10442594 - 财政年份:2018
- 资助金额:
$ 14.94万 - 项目类别:
Mining the Scientific Literature and Building a Pan-Echinoderm Gene Expression Database
挖掘科学文献并构建泛棘皮动物基因表达数据库
- 批准号:
10442596 - 财政年份:2018
- 资助金额:
$ 14.94万 - 项目类别:
Enhanced Echinobase: A Community Genome Resource for the Future
增强型 Echinobase:未来的社区基因组资源
- 批准号:
9789691 - 财政年份:2018
- 资助金额:
$ 14.94万 - 项目类别:
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