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

由于显示物种进化关系的树在生物科学和生物技术中非常有用，因此世界范围内一直在努力确定各种生物群体的树。这些信息可以编织成一棵覆盖数百万物种的“生命之树”（ToL），尽管将专家ToL知识视为重叠源树的森林通常更好。由于这一知识体系非常复杂，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。 该项目的重点是将ToL知识交到科学家、教育工作者和公众手中，方法是建立一个分布式互联网服务系统，与现有的NSF赞助的项目一起工作，向用户提供自定义树，就像他们目前在线获取驾驶方向一样快速方便。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合作，并与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。系统发生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断。今天，系统发生学知识通过大量的特殊途径传播，其中大多数不容易追踪。在专家们继续扩大生命之树（ToL）知识，解决差距和冲突的同时，我们的重点是传播，将ToL知识交给研究人员，教育工作者和公众。该项目的目标是设计和开发一个开放的Web服务架构，用于ToL交付，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，子树提取和树的缩放。该体系结构将被设计为一个可持续的分布式服务集合，并将依赖于语义丰富的描述，以促进服务的组合，并记录树的发现和重用过程。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信息学社区参与设计过程;（2）与其他项目合作，让他们作为服务提供者或消费者参与进来;（3）开发创新客户端，展示量化的重要用例;（4）为参与者举办黑客活动，以添加服务或开发客户端。 该项目的结果可通过www.phylotastic.org查阅。

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.