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

由于显示物种进化关系的系统发育图(树)在生物科学和生物技术中非常有用，因此全世界都在努力为不同的有机体群体确定树。这些信息可以被编织成一棵覆盖数百万个物种的单一“生命树”(TOL)，尽管通常更好的做法是将TOL专家知识视为一片重叠来源树的森林。由于这一知识体系复杂、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建立一个分布式的互联网服务系统，与现有的NSF赞助项目合作，将知识掌握在科学家、教育工作者和公众手中，以向用户提供定制树，就像他们目前获得在线驾驶方向一样快速和轻松。由此产生的系统将允许更多的生命科学研究人员提出与多样性和生物功能有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教育资源合作，如生命百科全书，使数百万用户很容易获得关于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，使科学家能够通过对进化实体(基因、物种等)的比较做出强有力的推断。今天，系统发育知识是通过非常大量的特殊途径传播的，其中大多数都不容易追踪。当专家们继续扩展生命之树(TOL)知识，解决差距和冲突时，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一个开放的网络服务体系结构，用于TOL的交付，具有整合到科学工作流程中所需的功能，包括名称解析、树发现、子树提取和树的缩放。该体系结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养为社区资源：(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，使他们成为服务提供者或消费者；(3)开发从数量上重要的用例演示的创新客户；(4)为参与者举办黑客马拉松，以增加服务或开发客户。该项目的结果将通过www.Phylotastic.org获得。

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.