VBO - A Tool for Bridging Vertebrate Anatomy Ontologies

解剖学是生物医学的核心概念。对于多细胞动物来说，细胞分化成不同的结构和细胞类型，它们在空间上的排列——它们的解剖结构——定义了有机体。生物学家需要正式的、明确的方法来描述解剖学，虽然我们熟悉的拉丁术语描述我们的手臂、腿、手指和血管等几个世纪以来一直为我们提供了很好的帮助，但我们现在所处的位置是，收集的大量数据，例如，基因表达的位置，需要以计算机可以理解的方式进行注释。目前广泛使用的一种方法是建立一个“本体论”，这是一种常识性层次结构中解剖学术语的树形排列。“大脚趾”是“脚”的一部分，而“脚”又是“腿”的一部分。这样的本体已经被用于一些物种，如人类和老鼠。然而，由于物种之间的解剖结构存在差异，即使在密切相关的物种之间，这种单一物种的解剖本体也不能重复使用。这个项目通过开发一个系统来解决这个问题，在这个系统中，我们可以通过结构的共同进化祖先将人类、小鼠、鱼类和鸟类的结构的解剖描述联系起来。因此，我们可以把鸟的翅膀、老鼠的爪子和鱼的鳍通过它们共同的进化祖先结构联系起来。分子生物学告诉我们，这是一个真正的联系，负责所有这些结构发展的基因有很多共同之处，在许多情况下是同源的。通过开发这种详细的跨物种解剖的可计算描述，我们将使目前收集大量关于不同组织中基因表达、异常形态和生物过程数据的科学家能够将他们的数据与其他研究不同脊椎动物物种的科学家收集的数据进行计算比较。这将有助于发现有关基因功能和生物体内基因产物相互作用的新信息，并最终使我们了解人类和其他物种的相似或不同之处。计算比较是必要的，因为现代技术允许科学家对基因表达进行比较——一个基因在何时何地活跃，一次可以对数千个基因进行比较。

Anatomy is a central concept to the biomedical sciences. For multicellular animals the differentiation of cells into different structures and cell types, their arrangement in space - their Anatomy - defines the organism. Biologists need formal, unambiguous ways to describe Anatomy, and whilst the familiar Latin terms to describe our arms, legs, fingers and blood vessels for example have stood us in good stead for centuries, we are now in a position where the amount of data being collected on, for example, where genes are expressed, needs to be annotated in ways that a computer can understand. An approach to this, now widely used, is to make an 'ontology' which is a tree-like arrangement of anatomical terms in a common-sense hierarchy. The 'big toe' is a part of the 'foot' which is a part of the 'leg' etc. Such ontologies have been made for several species such as human and mouse. However, as there are differences in anatomy between species such single species anatomy ontologies are not re-usable, even between closely related species. This project addresses this problem by developing a system whereby we can link the anatomical descriptions of structures in humans, mice, fish and birds through the common evolutionary ancestor of the structure. Thus we can link the bird's wing, the mouse's paw and the fish's fin through their common evolutionary ancestral structure. Molecular biology tells us that this is a true linkage and that genes responsible for the development of all of these structures have a great deal in common and in many cases are orthologs. By developing this computable description of detailed cross-species anatomy we will enable scientists currently collecting large amounts of data on gene expression, abnormal morphology and biological processes in different tissues to compare their data computationally with that being collected by other scientists working in different vertebrate species. This will allow the discovery of new information about the function of genes and the interaction of gene products in the organism and ultimately inform us about the way that humans and other species are similar, or different. Computational comparison is needed as modern technologies allow scientists to compare gene expression - where and when a gene is active, for thousands of genes at a time.