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Zoomorphologie auf eScience vorbereiten: 1) Datenstandards für die Zoomorphologie; 2) Basic Formal Ontology & Granularität; 3) Domain Referenz Ontologie für die Anatomie der Metazoa; 4) Modul für ontologiebasierte morphologischen Beschreibungen für Morph

为eScience准备动物形态学：1）动物形态学数据标准；

基本信息

批准号：
225236126
负责人：
Dr. Lars Vogt
金额：
--
依托单位：
Technische Informationsbibliothek (TIB)
依托单位国家：
德国
项目类别：
Research Grants
财政年份：
2013
资助国家：
德国
起止时间：
2012-12-31 至 2014-12-31
项目状态：
已结题

来源：
https://gepris.dfg.de/gepris/projekt/225236126?language=en
关键词：
Zoomorphologie auf eScience vorbereiten Datenstandards

项目摘要

Within the last decades, research practice in life sciences has changed significantly. The development of high-throughput techniques lead to the emergence of data-intensive science, with the consequence that more and more scientists use computers for data exploration. It is already common practice to compile new datasets from openly available data and analyze them under new premises. Because this new approach to science requires online data repositories and applications of the semantic web, it is commonly referred to as eScience. Unfortunately, because of two basic problems, zoomorphology did not take part in eScience so far: 1) its published data exist only in the literature and are thus not openly available and accessible via the internet and, ultimately, get lost (especially the corresponding unpublished raw data: images, serial sections, etc.); 2) to date, morphological descriptions cannot be deposited in general data repositories, because respective standards are not existing, i.e. taxon-independent, homology-free anatomy terminologies and a formalized method of documentation of data that makes morphological descriptions computer parsable. The solution to both problems involves the use of modern terminologies, i.e. ontologies (see OBO Foundry; http://www.obofoundry.org). The required anatomical ontologies still have to be developed. In order to be compatible with each other, they must use a Domain Reference Ontology for Metazoan Anatomy (DROMA) as template, which has to be developed as well. Moreover, to be compatible with the other OBO ontologies, DROMA must be based on OBO's top-level ontology, i.e. the Basic Formal Ontology (BFO). In order to accommodate biological reality, BFO must be extended by several categories. Therefore, this proposal is divided into four aspects: 1) continue developing the web pages of the recently started International Consortium of Zoomorphology Standards (http://iczs.org) and launch an internal Data Interest Group; 2) extending BFO and developing a general granularity framework that enables the organization and management of different perspectives on anatomical entities (purely anatomical, developmental, evolutionary, physiologically, etc.) in data repositories; 3) investigating the premises for the development of DROMA and developing DROMA; 4) developing a module for conducting ontology-based descriptions that will establish the already existing morphological database MorphDBase (http://www.morphdbase.de/) as a modern data repository for zoomorphological data and therewith providing an openly and freely accessible online web-portal for generating ontology-based descriptions. The resulting morphological data will be sustainably accessible to all biologists, and zoomorphology would be ready for eScience.

在过去的几十年里，生命科学的研究实践发生了重大变化。高通量技术的发展导致了数据密集型科学的出现，其结果是越来越多的科学家使用计算机进行数据探索。从公开的数据中汇编新的数据集并在新的前提下进行分析已经是常见的做法。由于这种新的科学方法需要在线数据存储库和语义网的应用程序，它通常被称为eScience。不幸的是，由于两个基本问题，动物形态学至今没有参与eScience：1）其已发表的数据仅存在于文献中，因此不能通过互联网公开获得和访问，最终丢失（特别是相应的未发表的原始数据：图像，连续切片等）; 2)迄今为止，形态学描述不能存放在一般的数据储存库中，因为不存在相应的标准，即独立于分类单元的、无同源性的解剖学术语和使形态学描述可计算机解析的数据的正式文件化方法。这两个问题的解决方案涉及使用现代术语，即本体论（参见OBO Foundry; http://www.obofoundry.org）。所需的解剖本体论仍有待开发。为了相互兼容，它们必须使用后生动物解剖学领域参考本体（DROMA）作为模板，这也必须开发。此外，为了与其他OBO本体兼容，DROMA必须基于OBO的顶级本体，即基本形式本体（BFO）。为了适应生物现实，BFO必须扩展几个类别。因此，该建议分为四个方面：1）继续开发最近启动的国际动物形态学标准联盟（http：//www.example.com）的网页，并启动内部数据兴趣小组; 2）扩展BFO，并开发一个通用的粒度框架，使组织和管理解剖实体的不同观点（纯解剖，发育，进化，生理等）成为可能。iczs.org数据存储库; 3）调查DROMA开发的前提并开发DROMA; 4）开发用于进行基于本体的描述的模块，该模块将建立已经存在的形态学数据库MorphDBase（http：//www.morphdbase.de/）作为动物形态学数据的现代数据储存库，并由此提供用于生成基于本体的描述的公开且免费访问的在线门户网站。由此产生的形态学数据将可持续地供所有生物学家使用，动物形态学将为eScience做好准备。