Desiderata for ontologies to be used in semantic annotation of biomedical documents
Desiderata for ontologies to be used in semantic annotation of biomedical documents
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DOI：
10.1016/j.jbi.2010.10.002
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发表时间：
2011-02-01
影响因子：
4.5
通讯作者：
Hunter, Lawrence
中科院分区：
文献类型：
--
作者：
Bada, Michael;Hunter, Lawrence
大量的生物医学文献中包含着大量对翻译研究科学家有价值的知识，但这些知识通常是以自然语言的形式存在的。需要复杂的自然语言处理系统将文本翻译成基于高质量共识本体的明确的正式表示，而这些系统又依赖于黄金标准的注释文档语料库进行训练和测试。为此，我们正在构建科罗拉多丰富注释的全文（CRAFT）语料库，这是一个由97篇全文生物医学期刊文章组成的集合，这些文章正在使用来自精选词汇表的整套术语进行手动注释，主要来自开放生物医学本体（OBO）库。我们在建立这个语料库的努力已经阐明了这些本体论在生物医学文档的语义标注方面的不足之处，我们提出了必要条件，其实现可以大大提高它们在这项任务中的效用;这些包括跨OBO的重叠术语的集成、特定于OBO的歧义的解决、BFO与OBO的集成以及中级本体的使用，非规范实例的包含，以及关系和可实现实体的扩展。(C)2010年爱思唯尔公司All rights reserved.
A wealth of knowledge valuable to the translational research scientist is contained within the vast biomedical literature, but this knowledge is typically in the form of natural language. Sophisticated natural-language-processing systems are needed to translate text into unambiguous formal representations grounded in high-quality consensus ontologies, and these systems in turn rely on gold-standard corpora of annotated documents for training and testing. To this end, we are constructing the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-text biomedical journal articles that are being manually annotated with the entire sets of terms from select vocabularies, predominantly from the Open Biomedical Ontologies (OBO) library. Our efforts in building this corpus has illuminated infelicities of these ontologies with respect to the semantic annotation of biomedical documents, and we propose desiderata whose implementation could substantially improve their utility in this task; these include the integration of overlapping terms across OBOs, the resolution of OBO-specific ambiguities, the integration of the BFO with the OBOs and the use of mid-level ontologies, the inclusion of noncanonical instances, and the expansion of relations and realizable entities. (C) 2010 Elsevier Inc. All rights reserved.