Journal of Biomedical Semantics最新文献

{"title":"Aspect and Thematic Roles","authors":"Toshiyuki Ogihara","doi":"10.1093/jos/ffz020","DOIUrl":"https://doi.org/10.1093/jos/ffz020","url":null,"abstract":"In this work, I propose a new semantic analysis of the Japanese progressive/resultative morpheme -te iru, which also leads to an improved account of the English progressive and contributes to cross-linguistic theory of aspect. The proposal is based on the modal analysis of the English progressive proposed by Portner (1998) and Ferreira (2016), but it is modified to accommodate the Japanese data. Crucially, the target state (resultative) reading of -te iru is available when the subject entity is a theme/undergoer; this is not controlled by the length of the event being described. To implement this idea, this work develops a formal system in which each thematic role predicate has its own temporal argument, and this time does not necessarily equal the temporal trace of the event in question. Specifically, a theme bears the target state role associated with an event e at a time that immediately follows the temporal trace of e. In addition, to describe and explain the behavior of -te iru, the traditional idea of “inertia worlds” according to which the relevant possible worlds are identical up to the utterance time is modified to allow them to differ in the past as well as in the future. It is noted that this modification is justified for the English progressive as well as for the Japanese -te iru form. This proposal allows us to predict that the behavior of achievements in English and Japanese is alike in simple past sentences and nominalized cases, but differs from each other in sentences containing the aspectual morphemes in question.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"3 1","pages":"83-115"},"PeriodicalIF":1.9,"publicationDate":"2020-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74248270","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":"Plural Marking and d-Linking in Spanish Interrogatives","authors":"Mora Maldonado","doi":"10.1093/jos/ffz024","DOIUrl":"https://doi.org/10.1093/jos/ffz024","url":null,"abstract":"\u0000 What is the semantic import of number morphology? This question has been traditionally addressed by focusing on singular and plural noun phrases. The present work brings interrogative phrases into the picture. We analyse Spanish bare interrogative ‘quién’ and its plural counterpart ‘quiénes’. Unlike which-questions in both English and Spanish, the behaviour of quién- and quiénes-interrogatives cannot be easily explained by most accounts of semantic number. In contrast, we argue that the distribution of these interrogatives in Spanish can be well accounted for by assuming that the plural ‘quiénes’ triggers a strong plurality presupposition, and can only be used in d-linking contexts, whereas ‘quién’ carries no specific requirement, as far as its semantics is concerned. As a result, our proposal shows that current approaches to number marking need to be refined in order to account for cross-linguistic and within-language variation.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"15 1","pages":"145-170"},"PeriodicalIF":1.9,"publicationDate":"2020-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91083854","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":"An Overt Even Operator over Covert-Based Focus Alternatives: The Case of Hebrew BIXLAL1","authors":"Y. Greenberg","doi":"10.1093/jos/ffz010","DOIUrl":"https://doi.org/10.1093/jos/ffz010","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"298 1","pages":"1-42"},"PeriodicalIF":1.9,"publicationDate":"2020-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76261062","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":"OHMI: the ontology of host-microbiome interactions.","authors":"Yongqun He, Haihe Wang, Jie Zheng, Daniel P Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L Curtis, Barry Smith, Alexander V Alekseyenko, Jihad S Obeid","doi":"10.1186/s13326-019-0217-1","DOIUrl":"10.1186/s13326-019-0217-1","url":null,"abstract":"<p><strong>Background: </strong>Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery.</p><p><strong>Methods: </strong>Through a multi-institutional collaboration, a community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the Open Biological/Biomedical Ontologies (OBO) Foundry principles. As an OBO library ontology, OHMI leverages established ontologies to create logically structured representations of (1) microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and (2) associated study protocols and types of data analysis and experimental results.</p><p><strong>Results: </strong>Aligned with the Basic Formal Ontology, OHMI comprises over 1000 terms, including terms imported from more than 10 existing ontologies together with some 500 OHMI-specific terms. A specific OHMI design pattern was generated to represent typical host-microbiome interaction studies. As one major OHMI use case, drawing on data from over 50 peer-reviewed publications, we identified over 100 bacteria and fungi from the gut, oral cavity, skin, and airway that are associated with six rheumatic diseases including rheumatoid arthritis. Our ontological study identified new high-level microbiota taxonomical structures. Two microbiome-related competency questions were also designed and addressed. We were also able to use OHMI to represent statistically significant results identified from a large existing microbiome database data analysis.</p><p><strong>Conclusion: </strong>OHMI represents entities and relations in the domain of HMIs. It supports shared knowledge representation, data and metadata standardization and integration, and can be used in formulation of advanced queries for purposes of data analysis.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"10 1","pages":"25"},"PeriodicalIF":1.9,"publicationDate":"2019-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37500985","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":"A Note on Conservativity","authors":"R. Zuber, E. Keenan","doi":"10.1093/JOS/FFZ007","DOIUrl":"https://doi.org/10.1093/JOS/FFZ007","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"28 1","pages":"573-582"},"PeriodicalIF":1.9,"publicationDate":"2019-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75034738","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":"Decomposing Deontic Modality: Evidence from Korean","authors":"Woojin Chung","doi":"10.1093/jos/ffz016","DOIUrl":"https://doi.org/10.1093/jos/ffz016","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"94 1","pages":"665-700"},"PeriodicalIF":1.9,"publicationDate":"2019-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83908416","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":"Obligatory Irrelevance and the Computation of Ignorance Inferences","authors":"Brian Buccola, A. Haida","doi":"10.1093/JOS/FFZ013","DOIUrl":"https://doi.org/10.1093/JOS/FFZ013","url":null,"abstract":"\u0000 In recent work, Fox (2016) has argued, on the basis of both empirical and conceptual considerations, that relevance (the set of propositions relevant in an utterance context) is closed under speaker belief: if $phi $ is relevant, then it’s also relevant whether the speaker believes $phi $. We provide a formally explicit implementation of this idea and explore its theoretical consequences and empirical predictions. As Fox (2016) already observes, one consequence is that ignorance inferences (and scalar implicatures) can only be derived in grammar, via a covert belief operator of the sort proposed by Meyer (2013). We show, further, that the maxim of quantity no longer enriches the meaning of an utterance, per se, but rather acts as a filter on what can be relevant in an utterance context. In particular, certain alternatives (of certain utterances) are shown to be incapable of being relevant in any context where the maxim of quantity is active — a property we dub obligatory irrelevance. We show that the resulting system predicts a quite restricted range of interpretations for sentences with the scalar item some, as compared to both neo-Gricean (Geurts, 2010; Horn, 1972; Sauerland, 2004) and grammatical (Chierchia et al., 2012; Fox, 2007; Meyer, 2013) theories of scalar implicature, and we argue that these predictions seem largely on the right track.","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"6 1","pages":"583-616"},"PeriodicalIF":1.9,"publicationDate":"2019-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88807687","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":"Text mining brain imaging reports.","authors":"Beatrice Alex, Claire Grover, Richard Tobin, Cathie Sudlow, Grant Mair, William Whiteley","doi":"10.1186/s13326-019-0211-7","DOIUrl":"10.1186/s13326-019-0211-7","url":null,"abstract":"<p><strong>Background: </strong>With the improvements to text mining technology and the availability of large unstructured Electronic Healthcare Records (EHR) datasets, it is now possible to extract structured information from raw text contained within EHR at reasonably high accuracy. We describe a text mining system for classifying radiologists' reports of CT and MRI brain scans, assigning labels indicating occurrence and type of stroke, as well as other observations. Our system, the Edinburgh Information Extraction for Radiology reports (EdIE-R) system, which we describe here, was developed and tested on a collection of radiology reports.The work reported in this paper is based on 1168 radiology reports from the Edinburgh Stroke Study (ESS), a hospital-based register of stroke and transient ischaemic attack patients. We manually created annotations for this data in parallel with developing the rule-based EdIE-R system to identify phenotype information related to stroke in radiology reports. This process was iterative and domain expert feedback was considered at each iteration to adapt and tune the EdIE-R text mining system which identifies entities, negation and relations between entities in each report and determines report-level labels (phenotypes).</p><p><strong>Results: </strong>The inter-annotator agreement (IAA) for all types of annotations is high at 96.96 for entities, 96.46 for negation, 95.84 for relations and 94.02 for labels. The equivalent system scores on the blind test set are equally high at 95.49 for entities, 94.41 for negation, 98.27 for relations and 96.39 for labels for the first annotator and 96.86, 96.01, 96.53 and 92.61, respectively for the second annotator.</p><p><strong>Conclusion: </strong>Automated reading of such EHR data at such high levels of accuracies opens up avenues for population health monitoring and audit, and can provide a resource for epidemiological studies. We are in the process of validating EdIE-R in separate larger cohorts in NHS England and Scotland. The manually annotated ESS corpus will be available for research purposes on application.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":"10 Suppl 1","pages":"23"},"PeriodicalIF":1.9,"publicationDate":"2019-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13326-019-0211-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9147860","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":"Finding relevant free-text radiology reports at scale with IBM Watson Content Analytics: a feasibility study in the UK NHS","authors":"A. Piotrkowicz, O. Johnson, G. Hall","doi":"10.1186/s13326-019-0213-5","DOIUrl":"https://doi.org/10.1186/s13326-019-0213-5","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13326-019-0213-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44628039","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":"KLOSURE: Closing in on open–ended patient questionnaires with text mining","authors":"Irena Spasic, David Owen, Andrew P. Smith, K. Button","doi":"10.1186/s13326-019-0215-3","DOIUrl":"https://doi.org/10.1186/s13326-019-0215-3","url":null,"abstract":"","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2019-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s13326-019-0215-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46903324","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}