An open annotation ontology for science on web 3.0.
An open annotation ontology for science on web 3.0.
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DOI：
10.1186/2041-1480-2-s2-s4
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发表时间：
2011-05-17
影响因子：
1.9
通讯作者：
Clark T
中科院分区：
文献类型：
--
作者：
Ciccarese P;Ocana M;Garcia Castro LJ;Das S;Clark T
目前，在丰富和富有表现力的已发表生物医学本体集合与科学研究人员每天消耗的生物医学论文的自然语言表达之间存在差距。本文的目的是提供一个开放的，可共享的结构，动态集成的生物医学领域本体的科学文件，在注释本体论（AO）的形式，从而缩小这一差距，使正式的生物医学本体直接应用到文献中，因为它出现。AO的最初要求是通过分析生物医学网络社区之间的集成需求，以及代表和集成生物医学文本挖掘结果的需求得出的。还对这一领域以往工作的优缺点进行了分析。随后沿着OWL中的元数据模型开发了一系列日益完善的注释工具，并将本体部署给一家大型制药公司和一家大型学术中心的用户，以满足反馈和其他需求。通过与许多同事的讨论，还提出了对模型的进一步要求和批评，并将其纳入工作。本文提出了一种基于OWL-DL的开放式本体，即标注本体（AO），用于标注Web上的科学文献。AO支持人工和算法内容注释。它可以通过几种方法中的任何一种将“独立”或独立的元数据锚定到Web文档中的特定位置。在AO中，文档可以被注释，但不需要在注释者的更新控制下。AO包含一个支持版本控制的起源模型，以及一个用于指定注释组和容器的集合模型。AO可以在http：//purl.org/ao/的开源许可下免费获得，并且可以在AO的Google代码页面http://code.google.com/p/annotation-ontology/上获得包括屏幕播放在内的大量文档。注释本体满足OWL中开放、可自由共享的注释元数据模型的关键需求，该模型是针对Web上的科学文档创建的。我们相信，AO可以成为一个非常有用的通用模型的注释元数据的Web文档，并将使生物医学领域本体被广泛用于注释科学文献。潜在的合作者和那些有新的相关用例的人被邀请与作者联系。
There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ . The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors.