Collaborative Research: ABI Innovation: An Ontology-Based System for Querying Life in a Post-Taxonomic Age

提高我们对生命的理解，无论是像我们这样的个体物种的生物学，还是管理生物多样性的机制和过程，关键取决于整合，查询和汇总来自许多不同生物体的生物数据。直到今天，实现这一目标的最基本和最常见的方法依赖于生物体名称，使其成为查询和管理我们的生物知识和数据的支柱之一。然而，传统上使用的生物体和生物体群的名称，这是基于林奈命名法，遭受两个主要的限制，他们的有用性，当谈到整合和交流数据。首先，因为它们是简单的文本字符串，机器无法理解创造名称的人和应用名称的人所意图的含义。因此，一个名称到底是或不是要包括的生物体往往是模糊的，因此名称经常不一致。第二，有许多生物群还没有，也可能永远不会有一个林奈名字，但它们的分子或宏观特征已经被发现，构成了有价值的生物学知识。该项目旨在通过生成一种称为“遗传参考”的机制来解决这些问题，该机制允许通过机器可解释的独特血统模式定义来参考具有共同进化血统的任何生物群体，该独特血统模式将该群体与所有其他群体区分开来。这个项目建立在十多年的理论和应用研究的价值到系统发育分类学。随着最近的综合和不断更新的一个通用的系统发育树的生命，生命树参考将有直接和广泛的实际应用的通信，整合和查询生物数据的生命之树。与权威的命名法不同的是，用户可以立即为他们希望交流发现的任何共享进化后代群体构建参考文献。除了开发系统发育学参考标准和支持工具外，该项目还旨在创建课堂教学材料和课程，以培训生物学学生了解系统发育命名法的理论基础和实际应用。本项目将开发的Web引用机制使用为Web开发的标准和工具，特别是Web本体语言（OWL）、本体和机器推理。具体来说，这项工作的目的是开发OWL类表达式组成的充分和必要的条件，机器推理机可以使用它来识别子类和类实例的引用。本体论和推理技术已经显示出它们在生物学知识整合和发现方面的力量，并且越来越多地被用于进化研究。作为该项目的一部分，将研究、实现和测试一个在本体框架内构造和计算引用的规范。Phyloreference的设计目标是，生命之树上的任何元素，无论是节点、分支还是进化枝，都可以以一种明确的方式被引用，并且具有由进化相关性模式定义的完全可计算的语义。本研究的主要目标包括创建一个正式的规范，在OWL的参考和遗传编码和推理，确定使用领域专家验证的小规模测试规范的正确性，并最终扩展到一个大规模的生物多样性数据资源导航的概念验证应用程序的方法。具体来说，这些参考文献将被开发并整合到Open Tree of Life、磐仪和由Genealogy of Life项目新资助的项目中。该项目的结果将在http://www.phyloref.org上公布。

Improving our understanding of life, whether the biology of individual species such as our own, or the mechanisms and processes governing biodiversity at large, critically depends on integrating, querying, and aggregating biological data from many different organisms. To this day, the most fundamental and common way to accomplish this relies on organism names, making these one of the pillars of querying and managing our biological knowledge and data. However, the traditionally used names for organisms and groups of organisms, which are based in Linnaean nomenclature, suffer from two major limitations to their usefulness when it comes to integrating and communicating data. First, because they are simple text-strings, the meaning intended by those who coin a name and those who apply it is inaccessible to machines. As a result, exactly which organism a name is or is not meant to include is often ambiguous, and names are therefore often applied inconsistently. Second, there are many groups of organisms that do not yet and may never have a Linnaean name, but for which molecular or macroscopic characteristics have been discovered that constitute valuable biological knowledge. This project aims to address these issues by generating a mechanism, called phyloreferencing, that allows referring to any group of organisms of shared evolutionary descent by a machine-interpretable definition of the unique pattern of descent that distinguishes the group from all others. This project builds on more than a decade's worth of theoretical and applied research into phylogenetic taxonomy. With the recent synthesis and continuous update of a universal phylogenetic Tree of Life, phyloreferences will have immediate and broad practical applications for communicating, integrating, and querying biological data across the Tree of Life. In contrast to authoritative nomenclatural naming, the goal for phyloreferences is that users can construct them instantly for any group of shared evolutionary descent for which they wish to communicate discoveries. In addition to developing the phyloreferencing standard and supporting tools, this project also aims to create classroom-ready teaching materials and curricula for training biology students in the theoretical underpinnings and practical applications of phylogenetic nomenclature. The phyloreferencing mechanism that this project will develop uses standards and tools developed for the Web, specifically the Web Ontology Language (OWL), ontologies, and machine reasoning. Specifically, this work aims to develop phyloreferences as OWL class expressions consisting of sufficient and necessary conditions, which machine reasoners can use to identify subclasses and class instances. Ontology and reasoning technologies have already shown their power for biological knowledge integration and discovery and are increasingly being adopted for evolutionary research as well. As part of this project, a specification for constructing and computing with phyloreferences within an ontological framework will be researched, implemented, and tested. Phyloreferences will be designed with the goal that any element, whether node, branch, or clades, on the Tree of Life can be referenced in a way that is unambiguous and has fully computable semantics defined by patterns of evolutionary relatedness. The main objectives of this research include creating a formal specification for phyloreference and phylogeny encoding and reasoning in OWL; ascertaining correctness of the specification using small-scale tests verifiable by domain experts; and finally scaling the approach to a large-scale biodiversity data resource navigation proof-of-concept application. Specifically phyloreferences will be developed and integrated into Open Tree of Life, ARBOR and projects newly funded by the Genealogy of Life program. Results of the project will be available at http://www.phyloref.org.