Journal of Biomedical Semantics最新文献

{"title":"Text mining-based measurement of precision of polysomnographic reports as basis for intervention.","authors":"Florent Baty,&nbsp;Jemima Hegermann,&nbsp;Tiziana Locatelli,&nbsp;Claudio Rüegg,&nbsp;Christian Gysin,&nbsp;Frank Rassouli,&nbsp;Martin Brutsche","doi":"10.1186/s13326-022-00259-3","DOIUrl":"https://doi.org/10.1186/s13326-022-00259-3","url":null,"abstract":"<p><strong>Background: </strong>Text mining can be applied to automate knowledge extraction from unstructured data included in medical reports and generate quality indicators applicable for medical documentation. The primary objective of this study was to apply text mining methodology for the analysis of polysomnographic medical reports in order to quantify sources of variation - here the diagnostic precision vs. the inter-rater variability - in the work-up of sleep-disordered breathing. The secondary objective was to assess the impact of a text block standardization on the diagnostic precision of polysomnography reports in an independent test set.</p><p><strong>Results: </strong>Polysomnography reports of 243 laboratory-based overnight sleep investigations scored by 9 trained sleep specialists of the Sleep Center St. Gallen were analyzed using a text-mining methodology. Patterns in the usage of discriminating terms allowed for the characterization of type and severity of disease and inter-rater homogeneity. The variation introduced by the inter-rater (technician/physician) heterogeneity was found to be twice as high compared to the variation introduced by effective diagnostic information. A simple text block standardization could significantly reduce the inter-rater variability by 44%, enhance the predictive value and ultimately improve the diagnostic accuracy of polysomnography reports.</p><p><strong>Conclusions: </strong>Text mining was successfully used to assess and optimize the quality, as well as the precision and homogeneity of medical reporting of diagnostic procedures - here exemplified with sleep studies. Text mining methodology could lay the ground for objective and systematic qualitative assessment of medical reports.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":"5"},"PeriodicalIF":1.9,"publicationDate":"2022-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8805265/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39576218","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":"Ontology-based identification and prioritization of candidate drugs for epilepsy from literature.","authors":"Bernd Müller,&nbsp;Leyla Jael Castro,&nbsp;Dietrich Rebholz-Schuhmann","doi":"10.1186/s13326-021-00258-w","DOIUrl":"https://doi.org/10.1186/s13326-021-00258-w","url":null,"abstract":"<p><strong>Background: </strong>Drug repurposing can improve the return of investment as it finds new uses for existing drugs. Literature-based analyses exploit factual knowledge on drugs and diseases, e.g. from databases, and combine it with information from scholarly publications. Here we report the use of the Open Discovery Process on scientific literature to identify non-explicit ties between a disease, namely epilepsy, and known drugs, making full use of available epilepsy-specific ontologies.</p><p><strong>Results: </strong>We identified characteristics of epilepsy-specific ontologies to create subsets of documents from the literature; from these subsets we generated ranked lists of co-occurring neurological drug names with varying specificity. From these ranked lists, we observed a high intersection regarding reference lists of pharmaceutical compounds recommended for the treatment of epilepsy. Furthermore, we performed a drug set enrichment analysis, i.e. a novel scoring function using an adaptive tuning parameter and comparing top-k ranked lists taking into account the varying length and the current position in the list. We also provide an overview of the pharmaceutical space in the context of epilepsy, including a final combined ranked list of more than 70 drug names.</p><p><strong>Conclusions: </strong>Biomedical ontologies are a rich resource that can be combined with text mining for the identification of drug names for drug repurposing in the domain of epilepsy. The ranking of the drug names related to epilepsy provides benefits to patients and to researchers as it enables a quick evaluation of statistical evidence hidden in the scientific literature, useful to validate approaches in the drug discovery process.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":"3"},"PeriodicalIF":1.9,"publicationDate":"2022-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8785029/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39945193","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":"An annotated dataset for extracting gene-melanoma relations from scientific literature.","authors":"Roberto Zanoli,&nbsp;Alberto Lavelli,&nbsp;Theresa Löffler,&nbsp;Nicolas Andres Perez Gonzalez,&nbsp;Fabio Rinaldi","doi":"10.1186/s13326-021-00251-3","DOIUrl":"https://doi.org/10.1186/s13326-021-00251-3","url":null,"abstract":"<p><strong>Background: </strong>Melanoma is one of the least common but the deadliest of skin cancers. This cancer begins when the genes of a cell suffer damage or fail, and identifying the genes involved in melanoma is crucial for understanding the melanoma tumorigenesis. Thousands of publications about human melanoma appear every year. However, while biological curation of data is costly and time-consuming, to date the application of machine learning for gene-melanoma relation extraction from text has been severely limited by the lack of annotated resources.</p><p><strong>Results: </strong>To overcome this lack of resources for melanoma, we have exploited the information of the Melanoma Gene Database (MGDB, a manually curated database of genes involved in human melanoma) to automatically build an annotated dataset of binary relations between gene and melanoma entities occurring in PubMed abstracts. The entities were automatically annotated by state-of-the-art text-mining tools. Their annotation includes both the mention text spans and normalized concept identifiers. The relations among the entities were annotated at concept- and mention-level. The concept-level annotation was produced using the information of the genes in MGDB to decide if a relation holds between a gene and melanoma concept in the whole abstract. The exploitability of this dataset was tested with both traditional machine learning, and neural network-based models like BERT. The models were then used to automatically extract gene-melanoma relations from the biomedical literature. Most of the current models use context-aware representations of the target entities to establish relations between them. To facilitate researchers in their experiments we generated a mention-level annotation in support to the concept-level annotation. The mention-level annotation was generated by automatically linking gene and melanoma mentions co-occurring within the sentences that in MGDB establish the association of the gene with melanoma.</p><p><strong>Conclusions: </strong>This paper presents a corpus containing gene-melanoma annotated relations. Additionally, it discusses experiments which show the usefulness of such a corpus for training a system capable of mining gene-melanoma relationships from the literature. Researchers can use the corpus to develop and compare their own models, and produce results which might be integrated with existing structured knowledge databases, which in turn might facilitate medical research.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":"2"},"PeriodicalIF":1.9,"publicationDate":"2022-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8772125/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39832970","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":"End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach.","authors":"Sheeba Samuel,&nbsp;Birgitta König-Ries","doi":"10.1186/s13326-021-00253-1","DOIUrl":"https://doi.org/10.1186/s13326-021-00253-1","url":null,"abstract":"<p><strong>Background: </strong>The advancement of science and technologies play an immense role in the way scientific experiments are being conducted. Understanding how experiments are performed and how results are derived has become significantly more complex with the recent explosive growth of heterogeneous research data and methods. Therefore, it is important that the provenance of results is tracked, described, and managed throughout the research lifecycle starting from the beginning of an experiment to its end to ensure reproducibility of results described in publications. However, there is a lack of interoperable representation of end-to-end provenance of scientific experiments that interlinks data, processing steps, and results from an experiment's computational and non-computational processes.</p><p><strong>Results: </strong>We present the \"REPRODUCE-ME\" data model and ontology to describe the end-to-end provenance of scientific experiments by extending existing standards in the semantic web. The ontology brings together different aspects of the provenance of scientific studies by interlinking non-computational data and steps with computational data and steps to achieve understandability and reproducibility. We explain the important classes and properties of the ontology and how they are mapped to existing ontologies like PROV-O and P-Plan. The ontology is evaluated by answering competency questions over the knowledge base of scientific experiments consisting of computational and non-computational data and steps.</p><p><strong>Conclusion: </strong>We have designed and developed an interoperable way to represent the complete path of a scientific experiment consisting of computational and non-computational steps. We have applied and evaluated our approach to a set of scientific experiments in different subject domains like computational science, biological imaging, and microscopy.</p>","PeriodicalId":15055,"journal":{"name":"Journal of Biomedical Semantics","volume":" ","pages":"1"},"PeriodicalIF":1.9,"publicationDate":"2022-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8734275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39903869","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":"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}