Semi-automated ontology generation within OBO-Edit.
Semi-automated ontology generation within OBO-Edit.
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DOI：
10.1093/bioinformatics/btq188
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发表时间：
2010-06-15
期刊：
影响因子：
--
通讯作者：
Schroeder M
中科院分区：
文献类型：
--
作者：
Wächter T;Schroeder M
动机：本体论和分类学已被证明对生物修复非常有益。仅开放生物医学本体论(OBO)Foundry就列出了90多个本体论，主要是使用OBO-编辑构建的。创建和维护这样的本体是一个劳动密集型的、困难的、手工的过程。它的部分自动化对于本体论的进一步发展和生物定位具有重要意义。结果：我们开发了Dresden Ontology Generator for Directed ACYCLICS GRAPH(DOG4DAG)，该系统通过半自动地从PubMed、Web和PDF资源库中的文本生成术语、定义和父子关系，支持OBO本体的创建和扩展。DOG4DAG无缝集成到OBO-编辑中。它通过识别文本中具有统计意义的名词短语来生成术语。对于定义和亲子关系，它采用了基于模式的网络搜索。我们使用手动验证的基准来系统地评估每个生成步骤。术语生成导致了高质量的术语，这些术语也可以在手动创建的本体中找到。高达78%的定义是有效的，高达54%的子孙-祖先关系可以检索。没有其他经过验证的系统可以取得类似的结果。通过将对高质量术语、定义和亲子关系的预测与本体编辑器OBO-Edit相结合，我们为所有OBO本体工程师提供了一个经过彻底验证的工具。供货情况：DOG4DAG可在OBO-Edit2.1中获得，网址为：http://www.oboedit.org联系方式：thomas.waechter@Biotec.tu-resden.de；补充信息：补充数据可在生物信息学在线上获得。
Motivation: Ontologies and taxonomies have proven highly beneficial for biocuration. The Open Biomedical Ontology (OBO) Foundry alone lists over 90 ontologies mainly built with OBO-Edit. Creating and maintaining such ontologies is a labour-intensive, difficult, manual process. Automating parts of it is of great importance for the further development of ontologies and for biocuration. Results: We have developed the Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG), a system which supports the creation and extension of OBO ontologies by semi-automatically generating terms, definitions and parent–child relations from text in PubMed, the web and PDF repositories. DOG4DAG is seamlessly integrated into OBO-Edit. It generates terms by identifying statistically significant noun phrases in text. For definitions and parent–child relations it employs pattern-based web searches. We systematically evaluate each generation step using manually validated benchmarks. The term generation leads to high-quality terms also found in manually created ontologies. Up to 78% of definitions are valid and up to 54% of child–ancestor relations can be retrieved. There is no other validated system that achieves comparable results. By combining the prediction of high-quality terms, definitions and parent–child relations with the ontology editor OBO-Edit we contribute a thoroughly validated tool for all OBO ontology engineers. Availability: DOG4DAG is available within OBO-Edit 2.1 at http://www.oboedit.org Contact: thomas.waechter@biotec.tu-dresden.de; Supplementary Information: Supplementary data are available at Bioinformatics online.
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