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Realism-based versioning for biomedical ontologies

生物医学本体的基于现实主义的版本控制

基本信息

批准号：
7660638
负责人：
Werner M Ceusters
金额：
$ 28.53万
依托单位：
STATE UNIVERSITY OF NEW YORK AT BUFFALO
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-03-31 至 2011-03-30
项目状态：
已结题

项目摘要

DESCRIPTION (provided by applicant): Biomedical terminologies and ontologies are increasingly used to annotate patient data that are generated in the course of the clinical care process, for example in the context of an Electronic Health Record. The purpose is to make these data comparable and interoperable across caregivers, institutions and systems with the goal of providing better care on the one hand, and of advancing biomedical science on the other. Where data pertain to individuals and are thus specific, ontologies capture what is generic. For an ontology or terminology to maintain its usefulness, it must be updated at regular intervals. Updates occur because of changes in both the domain itself and in the understanding of scientists and clinicians. A serious drawback of current approaches to ontology versioning is that the changes made in new releases are either not documented, or information is limited as to which entries in the ontology appeared, disappeared, or became fused or split. Only in very rare cases is information provided about the reasons for the changes made. This makes backward compatibility of legacy annotations difficult, if not impossible at all. The long-term vision behind the work proposed is one in which biomedical ontologies do not just reflect the state of the art in biomedical science in terms of what entities exist in reality and of how they are related, but that they also keep track of whether the changes introduced in successive versions of ontologies reflect (1) changes in the underlying reality, (2) in the views of ontology authors - or in associated scientific theories, or (3) are corrections of editorial mistakes. The hypothesis is that such an approach to ontology versioning can serve as a means to measure quality improvements in successive versions of an ontology in an objective manner, which will also help to ensure an incremental improvement in terminologies and thus in clinical data. The project will test this hypothesis by applying this novel approach to ontology versioning to the Systematized Nomenclature of Medicine (SNOMED) according to the following plan: . a detailed analysis of SNOMED-CT's existing history mechanism, covering all versions that have been released since its inception, with the objective of detecting those ways in which this mechanism falls short with respect to ontology versioning principles (aim1), . development of a prototype in which these principles are implemented together with a metric for measuring quality improvements in successive versions and that can serve as a plug-in for ontology authoring systems such as Prot¿g¿, ODE or SWOOP (aim2) . use of this prototype to reorganize a representative sample of SNOMED-CT's history information in line with the principles of ontology versioning (aim3), and . computation of the quality improvement of SNOMED-CT over time in order to demonstrate the usefulness of the approach and foster its acceptance in other ontologies (aim 4).

描述(由申请人提供)：生物医学术语和本体论越来越多地用于注释在临床护理过程中生成的患者数据，例如在电子健康记录的背景下。其目的是使这些数据在护理人员、机构和系统之间具有可比性和互操作性，目标一方面是提供更好的护理，另一方面是促进生物医学科学。在数据与个人相关并因此是特定的情况下，本体论捕获了什么是通用的。为了使本体或术语保持其有用性，必须定期更新它。更新的发生是因为领域本身以及科学家和临床医生的理解发生了变化。当前本体版本化方法的一个严重缺陷是，新版本中所做的更改要么没有文档记录，要么关于本体中的哪些条目出现、消失、融合或拆分的信息有限。只有在极少数情况下，才会提供有关作出更改的原因的资料。这使得遗留批注的向后兼容性变得困难，如果不是根本不可能的话。拟议工作背后的长期愿景是，生物医学本体论不仅反映生物医学科学中现实中存在的实体及其如何相关的最新状态，而且还跟踪本体论的连续版本中引入的变化是否反映(1)基本现实的变化，(2)本体论作者的观点--或相关科学理论的观点，或(3)编辑错误的纠正。假设这样的本体版本化方法可以作为一种手段，以客观的方式衡量本体连续版本中的质量改进，这也将有助于确保术语和临床数据的增量改进。该项目将根据以下计划，将这一新的本体版本控制方法应用于医学系统化命名(SNOMED)，以检验这一假设：。详细分析SNOMED-CT的现有历史机制，涵盖自其成立以来发布的所有版本，目的是找出该机制在本体版本化原则(AIM1)方面的不足之处；。开发原型，在该原型中，这些原则与衡量连续版本中的质量改进的度量一起被实现，并且可以作为本体创作系统的插件，例如PROT、ODE或SWOOP(AIM2) 。使用该原型按照本体版本控制(AIM 3)的原则重新组织SNOMED-CT的历史信息的代表性样本，以及。计算SNOMED-CT随时间推移的质量改进，以证明该方法的有用性，并促进其在其他本体论中的接受(目标4)。