Collaborative Research: ABI Development: An open infrastructure to disseminate phylogenetic knowledge

合作研究：ABI 开发：传播系统发育知识的开放基础设施

• 批准号: 1458595
• 负责人: Enrico Pontelli
• 金额: $ 31.7万
• 依托单位: New Mexico State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2020-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1458595&HistoricalAwards=false
• 关键词: Collaborative; Research; ABI; Development; open

Because phylogenies (trees) showing the evolutionary relationships of species are so useful in bioscience and biotechnology, there has been a major worldwide effort to determine trees for various groups of organisms. This information can be knitted together into a single "Tree of Life" (ToL) covering millions of species, though it is often better to think of expert ToL knowledge as a forest of overlapping source-trees. Because this body of knowledge is complex, rapidly changing, and distributed among many online resources, getting the latest knowledge is a challenge. The focus of this project is to get ToL knowledge into the hands of scientists, educators, and the public, by building a distributed system of internet services that work together with existing NSF-sponsored projects to deliver custom trees to users as quickly and easily as they currently get online driving directions. The resulting system will allow a greater range of life-sciences researchers to ask more complex and challenging questions relating to diversity and biological functions. The project will work directly with educators and with educational resources such as the Encyclopedia of Life, making it easy for millions of users to access the latest scientific knowledge of species relationships. Phylogenetic trees are useful in all areas of biology, both to organize knowledge by guiding classification and for process-based models that allow scientists to make robust inferences from comparisons of evolved entities (genes, species, etc). Phylogenetic knowledge is disseminated today via a very large number of idiosyncratic pathways, most of which are not easily traceable. While experts continue expanding the Tree of Life (ToL) knowledge, addressing gaps and conflicts, our focus is on dissemination, putting ToL knowledge in the hands of researchers, educators, and the public. The goal of this project is to design and develop an open web-service architecture for ToL delivery, with the functionality necessary to integrate into scientific workflows, including name-resolution, tree discovery, subtree extraction, and scaling of trees. The architecture will be designed as a sustainable distributed collection of services and will rely on semantically rich descriptions to facilitate composition of services and to documents the tree discovery and reuse process. The project will cultivate this system as a community resource by (1) involving partners, domain experts, and a broader phyloinformatics community in the design process; (2) partnering with other projects to involve them as service-providers or consumers; (3) developing innovative clients demonstrating quantitatively important use-cases; (4) staging a hackathon for participants to add services or develop clients. Results of the project will be accessible via www.phylotastic.org.

由于显示物种进化关系的系统发育（树）在生物科学和生物技术中非常有用，因此全世界范围内都在努力确定各种生物体的树。这些信息可以编织成一个涵盖数百万个物种的单一“生命之树”(ToL)，尽管通常最好将专家 ToL 知识视为重叠源树的森林。由于这些知识体系复杂、变化迅速，并且分布在许多在线资源中，因此获取最新知识是一项挑战。 该项目的重点是通过构建一个分布式互联网服务系统，将 ToL 知识交到科学家、教育工作者和公众手中，该系统与现有 NSF 资助的项目一起工作，以尽可能快速、轻松地向用户提供定制树。他们目前获得在线行车路线。由此产生的系统将使更多的生命科学研究人员能够提出与多样性和生物功能相关的更复杂和更具挑战性的问题。该项目将直接与教育工作者和生命百科全书等教育资源合作，使数百万用户能够轻松获取有关物种关系的最新科学知识。系统发育树在生物学的所有领域都很有用，既可以通过指导分类来组织知识，也可以用于基于过程的模型，使科学家能够从进化实体（基因、物种等）的比较中做出可靠的推论。如今，系统发育知识通过大量特殊途径传播，其中大多数途径不易追踪。虽然专家们继续扩展生命之树 (ToL) 知识、解决差距和冲突，但我们的重点是传播，将 ToL 知识交到研究人员、教育工作者和公众手中。该项目的目标是设计和开发用于 ToL 交付的开放式 Web 服务架构，具有集成到科学工作流程中所需的功能，包括名称解析、树发现、子树提取和树缩放。该架构将被设计为可持续的分布式服务集合，并将依赖于语义丰富的描述来促进服务的组合并记录树发现和重用过程。该项目将通过以下方式将该系统培育为社区资源：(1) 让合作伙伴、领域专家和更广泛的系统信息学社区参与设计过程； (2) 与其他项目合作，让其作为服务提供者或消费者； (3) 开发创新客户，展示数量上重要的用例； (4) 举办黑客马拉松，让参与者添加服务或开发客户。 该项目的结果可通过 www.phylotastic.org 获取。

项目成果

Phylotastic: Improving Access to Tree-of-Life Knowledge With Flexible, on-the-Fly Delivery of Trees

Phylotastic：通过灵活、即时的树木交付来改善对生命树知识的获取

• DOI: 10.1177/1176934319899384
• 发表时间: 2020-01
• 期刊: Evolutionary Bioinformatics
• 影响因子: 2.6
• 作者: Nguyen, Van D;Nguyen, Thanh H;Tayeen, Abu Saleh;Laughinghouse, H Dail;Sánchez;Wiggins, Jodie;Pontelli, Enrico;Mozzherin, Dmitry;O’Meara, Brian;Stoltzfus, Arlin
• 通讯作者: Stoltzfus, Arlin

Natural Language Generation from Ontologies

从本体生成自然语言

• DOI: 10.1007/978-3-030-05998-9_5
• 发表时间: 2019-01
• 期刊: Lecture notes in computer science
• 作者: Nguyen, Van;Son, Tran Cao;Pontelli, Enrico
• 通讯作者: Pontelli, Enrico

On Repairing Web Services Workflows

关于修复 Web 服务工作流程

• DOI: 10.1007/978-3-030-39197-3_3
• 发表时间: 2020-01-20
• 期刊: International Journal of Computer Applications
• 作者: T. Nguyen;Enrico Pontelli;Tran Cao Son
• 通讯作者: Tran Cao Son