Collaborative Research: Core Database Technologies to Enable the Integration of AToL Information

AToL（组装生命之树）是由美国国家科学基金会赞助的一项大规模合作研究，旨在重建所有生物的进化起源。目前，涉及150多个PI的31个项目正在进行中，产生新的数据，包括细菌，微生物真核生物，脊椎动物，开花植物等的研究。这些项目产生的数据包括但不限于：（i）标本及其来源，包括采集信息、凭证存放等; (ii)表型描述及其来源;（iii）基因型描述及其来源;（iv）对主要测量结果的解释，包括同源性;（v）对遗传学的估计和采用的方法;和（vi）后树分析，如性状进化假设。虽然每个项目内的数据收集、储存和传播都得到了很好的协调，迫切需要开发基础设施，以整合所有ATOL数据源，使个人努力成为全球假设的倍增器。此外，随着项目的不断扩展和解决生命之树的各个角落，针对ATOL问题领域的工作流程和数据管理工具将大大有助于有效的项目管理。 该项目将为遗传学开发新的，紧凑的，抽象的数据模型，利用广泛的经验项目调查中的用例。该集成系统将开发不同系统发育数据域之间的新映射，并允许各个项目以增量方式加入集成数据库网络。数据来源系统允许跟踪每个数据对象是如何创建的，这将是系统数据管理的独特之处。起源系统不仅允许跟踪在产生特定树或数据矩阵的特定列时做出了什么样的决策，而且还允许跟踪替代数据谱系，例如，可以跟踪关于字符同源性的不同意见。研究结果将以强大的软件工具交付，可供整个进化生物学社区使用。 该研究将主要通过一系列持续的研讨会开发系统学中使用的基于社区的数据对象正式模型。这项活动不仅将开发新的数据管理工具，而且还将具有综合遗传学研究领域不同观点的效果。该系统的结果将可扩展到进化生物学的其他领域，从而有助于进化综合的更广泛的使命。 该项目还将为一般分类学界提供最新数据库技术方面的培训。最后，通过利用宾夕法尼亚大学生物信息学中心现有的外联工作，该项目将与基因组学和生物医学科学方面的其他生物数据库工作建立联系，向广泛的生物医学研究界传播系统发育信息。

The AToL (Assembling the Tree of Life ) is a large-scale collaborative research effort sponsoredby the National Science Foundation to reconstruct the evolutionary origins of all living things. Currently 31projects involving 150+ PIs are underway generating novel data including studies of bacteria, microbial eukaryotes, vertebrates, flowering plants and many more. The data being generated by these projects include and are not limited to: (i) Specimens and their provenance including collection information, voucher deposition, etc.; (ii) Phenotypic descriptions and their provenance; (iii) Genotypic descriptions and their provenance; (iv) Interpretation of the primary measurements including homology ; (v) Estimates of phylogenies and methods employed; and (vi) Post-tree analyses such as character evolution hypotheses.While the data collection, storage, and dissemination within each projects are well coordinated, there is a critical need to develop the infrastructure to integrate all ATOL data sources, allowing the individual efforts to become multipliers for global hypotheses. Furthermore, as the projects continue to expand and address diverse corners of the Tree of Life, efficient project management will be greatly aided by workflow and data management tools targeted towards the ATOL problem domain. The project will develop new, compact, abstract data models for phylogenetics, leveraging use cases from a broad survey of empirical projects. The integration system will develop novel mappings between different phylogenetic data domains, and allow individual projects to join a network of integrated databases in an incremental manner. The data provenance system, which allows tracking of how each data object was created, will be unique tosystematics data management. The provenance system will not only allow tracking of what kinds of decisions were made in producing a particular tree or a particular column of a data matrix, but will also allow tracking of alternative data lineages such that, for example, different opinions on character homology might be tracked. The results of the research will be delivered in robust software tools that can be used by the entire evolutionary biology community. The study will develop a community-based formal model of data objects used in systematics, primarily through a continuing set of workshops. This activity will not only develop new data management tools, but will also have the effect of synthesizing disparate views of the phylogenetics research domains. The results of the system will be extensible to other domains of evolutionary biology, thereby contributing to the broader mission of evolutionary synthesis. The project will also provide training for the general systematics community in latest database technologies. Finally, by leveraging existing outreach efforts at the Penn Center for Bioinformatics, the project will link to other biological database efforts in genomics and biomedical sciences, disseminating phylogenetic information to the broad biomedical research community.