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An annotated corpus of clinical trial publications supporting schema-based relational information extraction 临床试验出版物的注释语料库,支持基于模式的关系信息提取
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-05-23 DOI: 10.1186/s13326-022-00271-7
Olivia Sanchez-Graillet, Christian Witte, Frank Grimm, P. Cimiano
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引用次数: 5
SemClinBr - a multi-institutional and multi-specialty semantically annotated corpus for Portuguese clinical NLP tasks. SemClinBr -一个多机构和多专业语义注释的语料库,用于葡萄牙临床NLP任务。
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-05-08 DOI: 10.1186/s13326-022-00269-1
Lucas Emanuel Silva E Oliveira, Ana Carolina Peters, Adalniza Moura Pucca da Silva, Caroline Pilatti Gebeluca, Yohan Bonescki Gumiel, Lilian Mie Mukai Cintho, Deborah Ribeiro Carvalho, Sadid Al Hasan, Claudia Maria Cabral Moro

Background: The high volume of research focusing on extracting patient information from electronic health records (EHRs) has led to an increase in the demand for annotated corpora, which are a precious resource for both the development and evaluation of natural language processing (NLP) algorithms. The absence of a multipurpose clinical corpus outside the scope of the English language, especially in Brazilian Portuguese, is glaring and severely impacts scientific progress in the biomedical NLP field.

Methods: In this study, a semantically annotated corpus was developed using clinical text from multiple medical specialties, document types, and institutions. In addition, we present, (1) a survey listing common aspects, differences, and lessons learned from previous research, (2) a fine-grained annotation schema that can be replicated to guide other annotation initiatives, (3) a web-based annotation tool focusing on an annotation suggestion feature, and (4) both intrinsic and extrinsic evaluation of the annotations.

Results: This study resulted in SemClinBr, a corpus that has 1000 clinical notes, labeled with 65,117 entities and 11,263 relations. In addition, both negation cues and medical abbreviation dictionaries were generated from the annotations. The average annotator agreement score varied from 0.71 (applying strict match) to 0.92 (considering a relaxed match) while accepting partial overlaps and hierarchically related semantic types. The extrinsic evaluation, when applying the corpus to two downstream NLP tasks, demonstrated the reliability and usefulness of annotations, with the systems achieving results that were consistent with the agreement scores.

Conclusion: The SemClinBr corpus and other resources produced in this work can support clinical NLP studies, providing a common development and evaluation resource for the research community, boosting the utilization of EHRs in both clinical practice and biomedical research. To the best of our knowledge, SemClinBr is the first available Portuguese clinical corpus.

背景:从电子健康记录(EHRs)中提取患者信息的大量研究导致对标注语料库的需求增加,这是开发和评估自然语言处理(NLP)算法的宝贵资源。在英语语言范围之外缺乏多用途临床语料库,特别是在巴西葡萄牙语中,这是显而易见的,并严重影响了生物医学NLP领域的科学进展。方法:在本研究中,使用来自多个医学专业、文献类型和机构的临床文本开发了一个语义注释的语料库。此外,我们提出了(1)一项调查,列出了共同的方面、差异和从以往研究中吸取的教训;(2)一个可以复制的细粒度注释模式,以指导其他注释计划;(3)一个基于web的注释工具,专注于注释建议功能;(4)对注释进行内在和外在评估。结果:该研究产生了SemClinBr,这是一个包含1000个临床记录的语料库,标记了65117个实体和11263个关系。此外,还生成了否定线索和医学缩写词典。在接受部分重叠和层次相关的语义类型时,注释器协议的平均得分从0.71(应用严格匹配)到0.92(考虑宽松匹配)不等。当将语料库应用于两个下游NLP任务时,外部评估证明了注释的可靠性和有用性,系统获得的结果与协议分数一致。结论:本工作生成的SemClinBr语料库和其他资源可以支持临床NLP研究,为研究界提供一个共同的开发和评估资源,促进电子病历在临床实践和生物医学研究中的应用。据我们所知,SemClinBr是第一个可用的葡萄牙临床语料库。
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引用次数: 14
Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic 将公平原则应用于医院数据:大流行中的挑战和机遇
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-04-25 DOI: 10.1186/s13326-022-00263-7
Queralt-Rosinach, Núria, Kaliyaperumal, Rajaram, Bernabé, César H., Long, Qinqin, Joosten, Simone A., van der Wijk, Henk Jan, Flikkenschild, Erik L.A., Burger, Kees, Jacobsen, Annika, Mons, Barend, Roos, Marco
The COVID-19 pandemic has challenged healthcare systems and research worldwide. Data is collected all over the world and needs to be integrated and made available to other researchers quickly. However, the various heterogeneous information systems that are used in hospitals can result in fragmentation of health data over multiple data ‘silos’ that are not interoperable for analysis. Consequently, clinical observations in hospitalised patients are not prepared to be reused efficiently and timely. There is a need to adapt the research data management in hospitals to make COVID-19 observational patient data machine actionable, i.e. more Findable, Accessible, Interoperable and Reusable (FAIR) for humans and machines. We therefore applied the FAIR principles in the hospital to make patient data more FAIR. In this paper, we present our FAIR approach to transform COVID-19 observational patient data collected in the hospital into machine actionable digital objects to answer medical doctors’ research questions. With this objective, we conducted a coordinated FAIRification among stakeholders based on ontological models for data and metadata, and a FAIR based architecture that complements the existing data management. We applied FAIR Data Points for metadata exposure, turning investigational parameters into a FAIR dataset. We demonstrated that this dataset is machine actionable by means of three different computational activities: federated query of patient data along open existing knowledge sources across the world through the Semantic Web, implementing Web APIs for data query interoperability, and building applications on top of these FAIR patient data for FAIR data analytics in the hospital. Our work demonstrates that a FAIR research data management plan based on ontological models for data and metadata, open Science, Semantic Web technologies, and FAIR Data Points is providing data infrastructure in the hospital for machine actionable FAIR Digital Objects. This FAIR data is prepared to be reused for federated analysis, linkable to other FAIR data such as Linked Open Data, and reusable to develop software applications on top of them for hypothesis generation and knowledge discovery.
COVID-19大流行给世界各地的医疗保健系统和研究带来了挑战。数据是在世界各地收集的,需要进行整合,并迅速提供给其他研究人员。然而,医院中使用的各种异构信息系统可能会导致卫生数据分散在多个数据“孤岛”上,这些“孤岛”无法互操作以进行分析。因此,住院患者的临床观察没有准备好有效和及时地重复使用。有必要调整医院的研究数据管理,使COVID-19观察患者数据机器可操作,即人类和机器更易于查找、可访问、可互操作和可重复使用(FAIR)。因此,我们在医院应用了公平原则,使患者数据更加公平。在本文中,我们提出了我们的FAIR方法,将医院收集的COVID-19观察患者数据转换为机器可操作的数字对象,以回答医生的研究问题。为了实现这一目标,我们基于数据和元数据的本体论模型在利益相关者之间进行了协调的公平化,并基于公平的体系结构来补充现有的数据管理。我们将FAIR数据点用于元数据暴露,将研究参数转换为FAIR数据集。我们通过三种不同的计算活动证明了该数据集是机器可操作的:通过语义网沿着世界各地开放的现有知识来源对患者数据进行联合查询,实现数据查询互操作性的Web api,以及在这些FAIR患者数据之上构建应用程序,用于医院中的FAIR数据分析。我们的工作表明,FAIR研究数据管理计划基于数据和元数据的本体论模型、开放科学、语义网技术和FAIR数据点,为医院中机器可操作的FAIR数字对象提供了数据基础设施。这些FAIR数据可用于联邦分析,可与其他FAIR数据(如链接开放数据)链接,并可用于在其基础上开发用于假设生成和知识发现的软件应用程序。
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引用次数: 11
Defining health data elements under the HL7 development framework for metadata management 在用于元数据管理的HL7开发框架下定义运行状况数据元素
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-03-18 DOI: 10.1186/s13326-022-00265-5
Yang, Zhe, Jiang, Kun, Lou, Miaomiao, Gong, Yang, Zhang, Lili, Liu, Jing, Bao, Xinyu, Liu, Danhong, Yang, Peng
Health data from different specialties or domains generallly have diverse formats and meanings, which can cause semantic communication barriers when these data are exchanged among heterogeneous systems. As such, this study is intended to develop a national health concept data model (HCDM) and develop a corresponding system to facilitate healthcare data standardization and centralized metadata management. Based on 55 data sets (4640 data items) from 7 health business domains in China, a bottom-up approach was employed to build the structure and metadata for HCDM by referencing HL7 RIM. According to ISO/IEC 11179, a top-down approach was used to develop and standardize the data elements. HCDM adopted three-level architecture of class, attribute and data type, and consisted of 6 classes and 15 sub-classes. Each class had a set of descriptive attributes and every attribute was assigned a data type. 100 initial data elements (DEs) were extracted from HCDM and 144 general DEs were derived from corresponding initial DEs. Domain DEs were transformed by specializing general DEs using 12 controlled vocabularies which developed from HL7 vocabularies and actual health demands. A model-based system was successfully established to evaluate and manage the NHDD. HCDM provided a unified metadata reference for multi-source data standardization and management. This approach of defining health data elements was a feasible solution in healthcare information standardization to enable healthcare interoperability in China.
来自不同专业或领域的健康数据通常具有不同的格式和含义,当这些数据在异构系统之间交换时,可能会造成语义通信障碍。因此,本研究旨在建立国家健康概念数据模型(HCDM)并开发相应的系统,以促进医疗数据标准化和元数据的集中管理。基于来自中国7个健康业务领域的55个数据集(4640个数据项),采用自底向上的方法,参照HL7 RIM构建HCDM的结构和元数据。根据ISO/IEC 11179,采用了自顶向下的方法来开发和标准化数据元素。HCDM采用类、属性、数据类型三级架构,由6个类和15个子类组成。每个类都有一组描述性属性,每个属性都被分配了一个数据类型。从HCDM中提取了100个初始数据元素(initial data elements, DEs),并由相应的初始数据元素衍生出144个通用数据元素(general data elements),利用HL7词汇表和实际健康需求发展而来的12个受控词汇表,对通用数据元素进行专门化转换。成功建立了一个基于模型的NHDD评估与管理系统。HCDM为多源数据的标准化和管理提供了统一的元数据参考。这种定义健康数据元素的方法是实现中国医疗保健互操作性的医疗保健信息标准化的可行解决方案。
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引用次数: 2
Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data 罕见病注册表常用数据元素的语义建模,以及在注册表数据上部署这些元素的原型工作流
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-03-15 DOI: 10.1186/s13326-022-00264-6
Kaliyaperumal, Rajaram, Wilkinson, Mark D., Moreno, Pablo Alarcón, Benis, Nirupama, Cornet, Ronald, dos Santos Vieira, Bruna, Dumontier, Michel, Bernabé, César Henrique, Jacobsen, Annika, Le Cornec, Clémence M. A., Godoy, Mario Prieto, Queralt-Rosinach, Núria, Schultze Kool, Leo J., Swertz, Morris A., van Damme, Philip, van der Velde, K. Joeri, Lalout, Nawel, Zhang, Shuxin, Roos, Marco
The European Platform on Rare Disease Registration (EU RD Platform) aims to address the fragmentation of European rare disease (RD) patient data, scattered among hundreds of independent and non-coordinating registries, by establishing standards for integration and interoperability. The first practical output of this effort was a set of 16 Common Data Elements (CDEs) that should be implemented by all RD registries. Interoperability, however, requires decisions beyond data elements - including data models, formats, and semantics. Within the European Joint Programme on Rare Diseases (EJP RD), we aim to further the goals of the EU RD Platform by generating reusable RD semantic model templates that follow the FAIR Data Principles. Through a team-based iterative approach, we created semantically grounded models to represent each of the CDEs, using the SemanticScience Integrated Ontology as the core framework for representing the entities and their relationships. Within that framework, we mapped the concepts represented in the CDEs, and their possible values, into domain ontologies such as the Orphanet Rare Disease Ontology, Human Phenotype Ontology and National Cancer Institute Thesaurus. Finally, we created an exemplar, reusable ETL pipeline that we will be deploying over these non-coordinating data repositories to assist them in creating model-compliant FAIR data without requiring site-specific coding nor expertise in Linked Data or FAIR. Within the EJP RD project, we determined that creating reusable, expert-designed templates reduced or eliminated the requirement for our participating biomedical domain experts and rare disease data hosts to understand OWL semantics. This enabled them to publish highly expressive FAIR data using tools and approaches that were already familiar to them.
欧洲罕见病注册平台(EU RD Platform)旨在通过建立整合和互操作性标准,解决欧洲罕见病(RD)患者数据分散在数百个独立和非协调注册中心的问题。这项工作的第一个实际输出是一组16个公共数据元素(cde),应该由所有RD注册中心实现。然而,互操作性需要超越数据元素的决策——包括数据模型、格式和语义。在欧洲罕见病联合计划(EJP RD)中,我们的目标是通过生成遵循FAIR数据原则的可重用RD语义模型模板来进一步实现欧盟研发平台的目标。通过基于团队的迭代方法,我们创建了基于语义的模型来表示每个cde,使用SemanticScience集成本体作为表示实体及其关系的核心框架。在该框架内,我们将cde中表示的概念及其可能的值映射到领域本体中,例如孤儿罕见疾病本体、人类表型本体和国家癌症研究所同义词库。最后,我们创建了一个范例,可重用的ETL管道,我们将在这些非协调数据存储库上部署它,以帮助他们创建模型兼容的FAIR数据,而不需要特定于站点的编码,也不需要关联数据或FAIR方面的专业知识。在EJP RD项目中,我们确定创建可重用的、专家设计的模板减少或消除了我们参与的生物医学领域专家和罕见疾病数据主机理解OWL语义的需求。这使他们能够使用他们已经熟悉的工具和方法发布具有高度表现力的FAIR数据。
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引用次数: 16
Steps towards a Semantics of Dance 走向舞蹈的语义学
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffac009
P. Patel-Grosz, P. Grosz, T. Kelkar, A. Jensenius
As formal theoretical linguistic methodology has matured, recent years have seen the advent of applying it to objects of study that transcend language, e.g., to the syntax and semantics of music (Lerdahl & Jackendoff 1983, Schlenker 2017a; see also Rebuschat et al. 2011). One of the aims of such extensions is to shed new light on how meaning is construed in a range of communicative systems. In this paper, we approach this goal by looking at narrative dance in the form of Bharatanatyam. We argue that a semantic approach to dance can be modeled closely after the formal semantics of visual narrative proposed by Abusch (2013, 2014, 2021). A central conclusion is that dance not only shares properties of other fundamentally human means of expression, such as visual narrative and music, but that it also exhibits similarities to sign languages and the gestures of non-signers (see, e.g., Schlenker 2020) in that it uses space to track individuals in a narrative and performatively portray the actions of those individuals. From the perspective of general human cognition, these conclusions corroborate the idea that linguistic investigations beyond language (see Patel-Grosz et al. forthcoming) can yield insights into the very nature of the human mind and of the communicative devices that it avails.
随着正式理论语言学方法论的成熟,近年来出现了将其应用于超越语言的研究对象的出现,例如,音乐的语法和语义(Lerdahl & Jackendoff 1983, Schlenker 2017a;另见Rebuschat et al. 2011)。这种扩展的目的之一是揭示在一系列交际系统中如何解释意义。在本文中,我们通过观察巴拉塔那塔姆形式的叙事舞蹈来实现这一目标。我们认为,舞蹈的语义方法可以在Abusch(2013, 2014, 2021)提出的视觉叙事的形式语义之后紧密建模。一个核心结论是,舞蹈不仅具有视觉叙事和音乐等其他基本人类表达方式的特性,而且与手语和非手语的手势也有相似之处(例如,参见Schlenker 2020),因为它利用空间来跟踪叙事中的个体,并表演地描绘这些个体的动作。从一般人类认知的角度来看,这些结论证实了一种观点,即超越语言的语言研究(见Patel-Grosz等人即将出版)可以深入了解人类思维的本质及其所利用的交际手段。
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引用次数: 5
Evidentiality in Abductive Reasoning: Experimental Support for a Modal Analysis of Evidentials 溯因推理中的证据性:证据模态分析的实验支持
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffab013
Anastasia Smirnova
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引用次数: 3
Relative Tense without Existential Quantification and Before 没有存在量化的相对时态和之前
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffac013
Toshiyuki Ogihara
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引用次数: 0
Notes on Iterated Rationality Models of Scalar Implicatures 关于标量蕴涵的迭代合理性模型的注解
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffab015
D. Fox, Roni Katzir
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引用次数: 7
All Focus is Contrastive: On Polarity (Verum) Focus, Answer Focus, Contrastive Focus and Givenness 所有的焦点都是对比的:关于极性(Verum)焦点,回答焦点,对比焦点和给予性
IF 1.9 3区 工程技术 Q3 MATHEMATICAL & COMPUTATIONAL BIOLOGY Pub Date : 2022-01-01 DOI: 10.1093/jos/ffab018
Daniel Goodhue
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引用次数: 7
期刊
Journal of Biomedical Semantics
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