Druzinsky Robert E, Balhoff James P, Crompton Alfred W, Done James, German Rebecca Z, Haendel Melissa A, Herrel Anthony, Herring Susan W, Lapp Hilmar, Mabee Paula M, Muller Hans-Michael, Mungall Christopher J, Sternberg Paul W, Van Auken Kimberly, Vinyard Christopher J, Williams Susan H, Wall Christine E
Department of Oral Biology, University of Illinois at Chicago, Chicago, Illinois, United States of America.
RTI International, Research Triangle Park, North Carolina, United States of America.
PLoS One. 2016 Feb 12;11(2):e0149102. doi: 10.1371/journal.pone.0149102. eCollection 2016.
In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required.
Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar.
Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.
近年来,大型文献数据库提供了大量已发表的生物学文献以供检索。然而,这些数据库中集成的基于文本的文献检索引擎的功能有限。为了实现能够提供比较解剖学家期望的结果的检索,需要一种称为本体的底层逻辑结构。
在此,我们展示了哺乳动物摄食肌肉本体(MFMO),这是一个多物种本体,专注于参与摄食和其他口腔/咽部行为的解剖结构。MFMO的一个独特特征是,每个肌肉的简单、可计算的定义,包括其附着点和神经支配,在所有哺乳动物中都是适用的。这种构建反映了比较解剖学的逻辑基础,并允许使用生物学家熟悉的语言进行检索。此外,它为肌肉提供了一个模板,这对于扩展任何解剖学本体都将是有用的。MFMO的开发是为了支持摄食实验最终用户数据库项目(FEED,https://feedexp.org/),这是一个公开可用的在线存储库,用于存储从哺乳动物摄食(如咀嚼、咬、吞咽)的体内研究中收集的生理数据。目前,MFMO已集成到FEED中,也集成到Textpresso的两个特定于文献的实现中,Textpresso是一个文本挖掘系统,便于对科学出版物语料库进行强大的检索。我们通过提出测试本体返回适当答案能力的问题(能力问题)来评估MFMO。我们将MFMO的查询结果与PubMed和谷歌学术中类似搜索的结果进行比较。
我们的测试表明,MFMO能够回答以比较解剖学通用语言形成的查询,但PubMed和谷歌学术则不能。总体而言,我们的结果表明,通过将解剖学本体纳入检索,可以获得一组扩展且在解剖学上全面的结果。更广泛的科学和出版界应考虑迎接语义启用搜索功能的挑战。