Pub Date : 2022-04-25DOI: 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.
{"title":"Applying the FAIR principles to data in a hospital: challenges and opportunities in a pandemic","authors":"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","doi":"10.1186/s13326-022-00263-7","DOIUrl":"https://doi.org/10.1186/s13326-022-00263-7","url":null,"abstract":"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.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"90 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138538450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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。
{"title":"Defining health data elements under the HL7 development framework for metadata management","authors":"Yang, Zhe, Jiang, Kun, Lou, Miaomiao, Gong, Yang, Zhang, Lili, Liu, Jing, Bao, Xinyu, Liu, Danhong, Yang, Peng","doi":"10.1186/s13326-022-00265-5","DOIUrl":"https://doi.org/10.1186/s13326-022-00265-5","url":null,"abstract":"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.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"24 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138538405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2022-03-15DOI: 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.
{"title":"Semantic modelling of common data elements for rare disease registries, and a prototype workflow for their deployment over registry data","authors":"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","doi":"10.1186/s13326-022-00264-6","DOIUrl":"https://doi.org/10.1186/s13326-022-00264-6","url":null,"abstract":"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.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"32 1","pages":""},"PeriodicalIF":1.9,"publicationDate":"2022-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138538468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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.
{"title":"Steps towards a Semantics of Dance","authors":"P. Patel-Grosz, P. Grosz, T. Kelkar, A. Jensenius","doi":"10.1093/jos/ffac009","DOIUrl":"https://doi.org/10.1093/jos/ffac009","url":null,"abstract":"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.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"34 1","pages":"693-748"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73098665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evidentiality in Abductive Reasoning: Experimental Support for a Modal Analysis of Evidentials","authors":"Anastasia Smirnova","doi":"10.1093/jos/ffab013","DOIUrl":"https://doi.org/10.1093/jos/ffab013","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"10 1","pages":"531-570"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85772677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Relative Tense without Existential Quantification and Before","authors":"Toshiyuki Ogihara","doi":"10.1093/jos/ffac013","DOIUrl":"https://doi.org/10.1093/jos/ffac013","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"23 1","pages":"657-691"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83077172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"All Focus is Contrastive: On Polarity (Verum) Focus, Answer Focus, Contrastive Focus and Givenness","authors":"Daniel Goodhue","doi":"10.1093/jos/ffab018","DOIUrl":"https://doi.org/10.1093/jos/ffab018","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"3 1","pages":"117-158"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75876273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"On the Role of Focus-Sensitivity for a Typology of Presupposition Triggers","authors":"Alexander Göbel","doi":"10.1093/jos/ffac011","DOIUrl":"https://doi.org/10.1093/jos/ffac011","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"26 1","pages":"617-656"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82412468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-28DOI: 10.1186/s13326-021-00250-4
Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He
Background: With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and comprehensive picture of host-coronavirus interaction (HCI) mechanisms. As of early April 2021, the ImmPort database has stored 7 studies (with 6 having details) that cover topics including molecular immune signatures, epitopes, and sex differences in terms of mortality in COVID-19 patients. The Coronavirus Infectious Disease Ontology (CIDO) represents basic HCI information. We hypothesize that the CIDO can be used as the platform to represent newly recorded information from ImmPort leading the reinforcement of CIDO.
Methods: The CIDO was used as the semantic platform for logically modeling and representing newly identified knowledge reported in the 6 ImmPort studies. A recursive eXtensible Ontology Development (XOD) strategy was established to support the CIDO representation and enhancement. Secondary data analysis was also performed to analyze different aspects of the HCI from these ImmPort studies and other related literature reports.
Results: The topics covered by the 6 ImmPort papers were identified to overlap with existing CIDO representation. SARS-CoV-2 viral S protein related HCI knowledge was emphasized for CIDO modeling, including its binding with ACE2, mutations causing different variants, and epitope homology by comparison with other coronavirus S proteins. Different types of cytokine signatures were also identified and added to CIDO. Our secondary analysis of two cohort COVID-19 studies with cytokine panel detection found that a total of 11 cytokines were up-regulated in female patients after infection and 8 cytokines in male patients. These sex-specific gene responses were newly modeled and represented in CIDO. A new DL query was generated to demonstrate the benefits of such integrative ontology representation. Furthermore, IL-10 signaling pathway was found to be statistically significant for both male patients and female patients.
Conclusion: Using the recursive XOD strategy, six new ImmPort COVID-19 studies were systematically reviewed, the results were modeled and represented in CIDO, leading to the enhancement of CIDO. The enhanced ontology and further seconary analysis supported more comprehensive understanding of the molecular mechanism of host responses to COVID-19 infection.
{"title":"CIDO ontology updates and secondary analysis of host responses to COVID-19 infection based on ImmPort reports and literature.","authors":"Anthony Huffman, Anna Maria Masci, Jie Zheng, Nasim Sanati, Timothy Brunson, Guanming Wu, Yongqun He","doi":"10.1186/s13326-021-00250-4","DOIUrl":"10.1186/s13326-021-00250-4","url":null,"abstract":"<p><strong>Background: </strong>With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span of time, we often lose an integrative and comprehensive picture of host-coronavirus interaction (HCI) mechanisms. As of early April 2021, the ImmPort database has stored 7 studies (with 6 having details) that cover topics including molecular immune signatures, epitopes, and sex differences in terms of mortality in COVID-19 patients. The Coronavirus Infectious Disease Ontology (CIDO) represents basic HCI information. We hypothesize that the CIDO can be used as the platform to represent newly recorded information from ImmPort leading the reinforcement of CIDO.</p><p><strong>Methods: </strong>The CIDO was used as the semantic platform for logically modeling and representing newly identified knowledge reported in the 6 ImmPort studies. A recursive eXtensible Ontology Development (XOD) strategy was established to support the CIDO representation and enhancement. Secondary data analysis was also performed to analyze different aspects of the HCI from these ImmPort studies and other related literature reports.</p><p><strong>Results: </strong>The topics covered by the 6 ImmPort papers were identified to overlap with existing CIDO representation. SARS-CoV-2 viral S protein related HCI knowledge was emphasized for CIDO modeling, including its binding with ACE2, mutations causing different variants, and epitope homology by comparison with other coronavirus S proteins. Different types of cytokine signatures were also identified and added to CIDO. Our secondary analysis of two cohort COVID-19 studies with cytokine panel detection found that a total of 11 cytokines were up-regulated in female patients after infection and 8 cytokines in male patients. These sex-specific gene responses were newly modeled and represented in CIDO. A new DL query was generated to demonstrate the benefits of such integrative ontology representation. Furthermore, IL-10 signaling pathway was found to be statistically significant for both male patients and female patients.</p><p><strong>Conclusion: </strong>Using the recursive XOD strategy, six new ImmPort COVID-19 studies were systematically reviewed, the results were modeled and represented in CIDO, leading to the enhancement of CIDO. The enhanced ontology and further seconary analysis supported more comprehensive understanding of the molecular mechanism of host responses to COVID-19 infection.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"12 1","pages":"18"},"PeriodicalIF":1.6,"publicationDate":"2021-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8400831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10217341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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