Journal of Biomedical Semantics最新文献

{"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}

{"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":"Notes on Iterated Rationality Models of Scalar Implicatures","authors":"D. Fox, Roni Katzir","doi":"10.1093/jos/ffab015","DOIUrl":"https://doi.org/10.1093/jos/ffab015","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"26 1","pages":"571-600"},"PeriodicalIF":1.9,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88721250","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}

{"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}

{"title":"The Origin of Cross-Cultural Differences in Referential Intuitions: Perspective Taking in the Gödel Case","authors":"Jincai Li","doi":"10.1093/jos/ffab010","DOIUrl":"https://doi.org/10.1093/jos/ffab010","url":null,"abstract":"How do proper names refer? This question about reference is critical for philosophers studying language, linguists investigating meaning and reference, and psycholinguists interested in how children acquire names. Over the past century, philosophers have put forward two classical theories to explain the link between a name and the entity it refers to, i.e., the descriptivist theory proposed by Frege (1892/1948), Russell (1905) and Searle (1958) among others, and the causal-historical view most notably advocated by Kripke (1980). On the former account, a name gets its referent through associated definite descriptions. Thus, when a speaker uses a name, they typically refer to whoever best fits the descriptive content attached to that name. For instance, the name “Kamala Harris” refers to the lady Kamala Harris because she is the sole individual who could uniquely satisfy the descriptive content “the first female vice president of the United States” that is commonly associated with the name nowadays. In contrast, according to the Kripkean causal-historical view, a name refers to a person via a link that is originated in the initial naming ceremony and then gets passed down through a community of speakers. Kripke contends that proper names are rigid designators and they continue to refer to the individuals who were initially given the name, even when they turn out to have none of the properties that speakers associate with this name (1980). That means, on the causal-historical picture, the name “Kamala Harris” would still refer to the person Kamala Harris even if she had not been elected the vice president of the United States. In the philosophical literature, the received wisdom is that Kripke supported his causalhistorical view of reference with the famous “Gödel” thought experiment. Suppose the only thing most people have heard about the mathematician Kurt Gödel is that he is the person who proved the incompleteness of arithmetic, which thus is the only possible definite description these people could associate with Gödel. And now imagine that the person who bears this name (Kurt Gödel) didn’t actually prove the theorem, but instead stole it from a fellow named Schmidt who did all the work. In this case, the descriptivist theory predicts that the name “Gödel” would refer to Schmidt, because Schmidt is the person best fitting","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"64 1","pages":"415-440"},"PeriodicalIF":1.9,"publicationDate":"2021-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74534964","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":"A Note on the Cardinalities of Sets of Scalar Alternatives","authors":"S. Mascarenhas","doi":"10.1093/jos/ffab011","DOIUrl":"https://doi.org/10.1093/jos/ffab011","url":null,"abstract":"\u0000 Formal theories of scalar implicature appeal crucially to a set of alternatives. These are the alternative statements that a speaker could have made but chose not to in pragmatic accounts, and the alternative statements that figure in the computation of exhaustivity operators in grammatical approaches. I show that the three sufficiently explicit theories of alternatives in the literature generate sets of alternatives that grow at least exponentially as a function of the input, and that these theories generate very large sets even for relatively small inputs. For pragmatic accounts of scalar implicature, I argue these results are hard or impossible to square with what we know independently about manipulating alternatives from the psychology of human reasoning. I propose that they pose a weaker but more general challenge for grammatical approaches, since alternatives as required by exhaustivity operators occur elsewhere in grammar, for example as part of the semantics of operators like “only” and “even.”","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"73 1","pages":"473-482"},"PeriodicalIF":1.9,"publicationDate":"2021-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86077672","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}