Giraldo Olga, García Alexander, López Federico, Corcho Oscar
Ontology Engineering Group, Madrid, Universidad Politécnica de Madrid, Madrid, 28660, Spain.
Universidad Del Valle, Cali, Colombia.
J Biomed Semantics. 2017 Nov 13;8(1):52. doi: 10.1186/s13326-017-0160-y.
An experimental protocol is a sequence of tasks and operations executed to perform experimental research in biological and biomedical areas, e.g. biology, genetics, immunology, neurosciences, virology. Protocols often include references to equipment, reagents, descriptions of critical steps, troubleshooting and tips, as well as any other information that researchers deem important for facilitating the reusability of the protocol. Although experimental protocols are central to reproducibility, the descriptions are often cursory. There is the need for a unified framework with respect to the syntactic structure and the semantics for representing experimental protocols.
In this paper we present "SMART Protocols ontology", an ontology for representing experimental protocols. Our ontology represents the protocol as a workflow with domain specific knowledge embedded within a document. We also present the S ample I nstrument R eagent O bjective (SIRO) model, which represents the minimal common information shared across experimental protocols. SIRO was conceived in the same realm as the Patient Intervention Comparison Outcome (PICO) model that supports search, retrieval and classification purposes in evidence based medicine. We evaluate our approach against a set of competency questions modeled as SPARQL queries and processed against a set of published and unpublished protocols modeled with the SP Ontology and the SIRO model. Our approach makes it possible to answer queries such as Which protocols use tumor tissue as a sample.
Improving reporting structures for experimental protocols requires collective efforts from authors, peer reviewers, editors and funding bodies. The SP Ontology is a contribution towards this goal. We build upon previous experiences and bringing together the view of researchers managing protocols in their laboratory work. Website: https://smartprotocols.github.io/ .
实验方案是为在生物学和生物医学领域（如生物学、遗传学、免疫学、神经科学、病毒学）开展实验研究而执行的一系列任务和操作。方案通常包括对设备、试剂的引用，关键步骤的描述，故障排除及提示，以及研究人员认为对促进方案可重复使用很重要的任何其他信息。尽管实验方案对于可重复性至关重要，但其描述往往很简略。需要一个关于表示实验方案的句法结构和语义的统一框架。
在本文中，我们提出了“智能方案本体”，一种用于表示实验方案的本体。我们的本体将方案表示为一个嵌入文档内具有领域特定知识的工作流程。我们还提出了样本-仪器-试剂-目标（SIRO）模型，该模型表示跨实验方案共享的最小公共信息。SIRO与支持循证医学中搜索、检索和分类目的的患者-干预-对照-结局（PICO）模型处于同一领域。我们根据一组建模为SPARQL查询的能力问题来评估我们的方法，并针对一组使用SP本体和SIRO模型建模的已发表和未发表的方案进行处理。我们的方法使得能够回答诸如“哪些方案使用肿瘤组织作为样本”这样的查询。
改进实验方案的报告结构需要作者、同行评审人员、编辑和资助机构的共同努力。SP本体是朝着这个目标做出的一项贡献。我们借鉴以往经验，汇集了在实验室工作中管理方案的研究人员的观点。网站：https://smartprotocols.github.io/ 。
