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Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature

Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadic, Julie Klein, John Keane, Robert Stevens
2018 Journal of Biomedical Semantics  
Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature.  ...  This study investigates: 1) if word embeddings from Deep Learning algorithms can provide a list of term variants for a given gene/protein of interest; and 2) if biological knowledge from the CVDO can improve  ...  Acknowledgements Thanks to Tim Furmston for help with software and e-infrastructure, and to the anonymous reviewers for their useful comments. Funding  ... 
doi:10.1186/s13326-018-0181-1 pmid:29650041 pmcid:PMC5896136 fatcat:rnyqpxihlralfcs7c5wxa5aaci

Matching biomedical ontologies based on formal concept analysis

Mengyi Zhao, Songmao Zhang, Weizhuo Li, Guowei Chen
2018 Journal of Biomedical Semantics  
Results: Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of  ...  Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings.  ...  Acknowledgements We would like to express sincere thanks to the anonymous reviewers whose comments and suggestions are invaluable, by taking advantage of which we have largely expanded the evaluation part  ... 
doi:10.1186/s13326-018-0178-9 pmid:29554977 pmcid:PMC5859804 fatcat:36daiwryozbwhk6sbaats4w54i

Best Paper Selection

2019 IMIA Yearbook of Medical Informatics  
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.  ...  Using OWL reasoning to support the generation of novel gene sets for enrichment analysis.  ...  This work combines semantic modelling (Cardiovascular Disease Ontology, CVDO) and learning algorithms (word embeddings).  ... 
doi:10.1055/s-0039-1677934 fatcat:ecmohlvwx5di5c3wiszlutzsbe

Contents IMIA Yearbook of Medical Informatics 2019

2019 IMIA Yearbook of Medical Informatics  
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature.  ...  An explainable deep-learning algorithm for the detection of acute intracranial hemorrhage from small datasets.  ... 
doi:10.1055/s-0039-1694828 fatcat:caeolubjnbdfhkdnwl2jodcmv4

Unsupervised Approaches for Textual Semantic Annotation, A Survey

Xiaofeng Liao, Zhiming Zhao
2019 ACM Computing Surveys  
Link to publication Creative Commons License (see CC BY Citation for published version (APA):  ...  ACKNOWLEDGMENTS The authors thank the anonymous reviewers for their helpful comments, in addition to Cees de Laat, Paul Martin, Jayachander Surbiryala, and ZeShun Shi for useful discussions.  ...  biomedical publications, with the support of knowledge formalized in Cardiovascular Disease Ontology (CVDO).  ... 
doi:10.1145/3324473 fatcat:fg5ucwtloze6ljdlh4hqjkqxfe

Domain-aware ontology matching [article]

Francisco José Quesada Real, University Of Edinburgh, Fiona McNeill, Alan Bundy
Nowadays, the way of tackling this heterogeneity is by applying ontology matching techniques with the aim of finding correspondences between the elements represented in different resources.  ...  The proposals have been evaluated by matching two of the most used classifications of diseases (ICD-10 and DSM-5), and the results show that matchers considerably improve their performance in terms of  ...  -Sheffield glossary: * CVD: Cardiovascular disease. * STH : Sheffield Children's Hospital.  ... 
doi:10.7488/era/1131 fatcat:pbxydm7bpvestpwlld63llywkm

A Community-Based Heart Health Intervention: Culture-Centered Study of Low-Income Malays and Heart Health Practices

Satveer Kaur-Gill, Mohan Jyoti Dutta, Munirah Binte Bashir
2020 Frontiers in Communication  
The community-based culture-centered intervention entailed working in the grassroots with community stakeholders to tailor a heart health campaign with and for low-income Malay Singaporeans.  ...  Community stakeholders designed and developed the heart health communicative infrastructures during six focus group sessions detailed in the results.  ...  AUTHOR CONTRIBUTIONS All authors have contributed to both the research process and writing of the paper. FUNDING This work was funded by the RG2013/1 Singapore Heart Foundation.  ... 
doi:10.3389/fcomm.2020.00016 fatcat:x2qwcsxl3vbn3jnqp7tq5mahq4

Effective Visualisations of Large Ontologies and Associations

Ontologies are structured vocabularies for organising domain knowledge, and are widely used in biological and biomedical research.  ...  It employs visual compression techniques and novel visual representations to facilitate effective ontology exploration and analysis. These techniques are implemented in the web-based system OntoPlot.  ...  Tasks As discussed in Chapter 2, a range of important use cases and user needs for biomedical ontologies were identified from the literature as well as from interviews with the domain expert.  ... 
doi:10.26180/13728733.v1 fatcat:mpppjviwqjehhetporuz6qd6lm

Opportunities and obstacles for deep learning in biology and medicine

Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M. Hoffman, Wei Xie, Gail L. Rosen (+24 others)
2018 Journal of the Royal Society Interface  
Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances  ...  We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be  ...  We thank Aaron Sheldon, who contributed text but did not formally approve the manuscript; Anna Greene for a careful proofreading of the manuscript in advance of the first submission; Sebastian Raschka  ... 
doi:10.1098/rsif.2017.0387 pmid:29618526 pmcid:PMC5938574 fatcat:65o4xmp53nc6zmj37srzuht6tq

Opportunities And Obstacles For Deep Learning In Biology And Medicine [article]

Travers Ching, Daniel S. Himmelstein, Brett K. Beaulieu-Jones, Alexandr A. Kalinin, Brian T. Do, Gregory P. Way, Enrico Ferrero, Paul-Michael Agapow, Michael Zietz, Michael M Hoffman, Wei Xie, Gail L. Rosen (+24 others)
2017 bioRxiv   pre-print
We examine applications of deep learning to a variety of biomedical problems - patient classification, fundamental biological processes, and treatment of patients - and discuss whether deep learning will  ...  We find that deep learning has yet to revolutionize or definitively resolve any of these problems, but promising advances have been made on the prior state of the art.  ...  We would like to thank Anna Greene for a careful proofreading of the manuscript in advance of the first submission.  ... 
doi:10.1101/142760 fatcat:l7zvbtbgxjamtd735vir2trw6q


Ch. Elsner, D. Häckl, H. van der Slikke, V. Della Mea, T.N. Arvanitis, H. Wiesmeth
2007 Technology and Health Care  
In addition to that, all data is geo-tagged, which enables users to find e.g. diabetics in the same region -this in turn empowers to connect and share experiences.  ...  subset of the GO and MeSH relevant to the keywords, and allows you to browse the ontologies and display only papers containing specific GO and MeSH terms.  ...  to the particularities of the biomedical sublanguage and an ontology of the Greek biomedical terminology.  ... 
doi:10.3233/thc-2007-15503 fatcat:bjb5zxdzwncrdkdufkdzathke4


The application of ontologies to scientific literature in order to create a standard in information retrieval has been recommended by various scholars (see Blake 2004, Seringhaus and in the biomedical  ...  In this case GO analysis is adopted to extract the information on function dispersed within the biomedical literature in order to enhance gene function prediction.  ... 
doi:10.13130/boem-federico_phd2016-03-18 fatcat:k3jef5p3t5fhtkbk56sfiortkq

Convergent Lines of Descent: Symptoms, Patterns, Constellations, and the Emergent Interface of Systems Biology and Chinese Medicine

V. Scheid
2014 East Asian Science, Technology and Society: an International Journal  
an imagined gulf between the modern West and ancient China in order to create a new type of personalized medicine.  ...  Finally, I insist that the medical humanities need to become actively involved in the construction of emergent articulations such as the ones I am exploring.  ...  Holding a Wellcome Trust Senior Research Fellowship in the medical humanities, Scheid is focusing his current research on a longue durée history of East Asian medicines from the Song to the present, which  ... 
doi:10.1215/18752160-2407180 pmid:25821530 pmcid:PMC4374107 fatcat:obrgr3qvsfgntp6mxgs3wsrxs4

Fox, Georgia L. The archaeology of smoking and tobacco. 169 pp., illus., bibliogr. Gainesville: Univ. Press of Florida, 2015. £64.95 (cloth)

Andrew Russell
2016 Journal of the Royal Anthropological Institute  
One of the ironies of universal health care, as we learn from this book, is that it depends upon the narrowing of the category of 'health' to biomedical terms.  ...  At the same time, members learn to reflect on the way they frequently fail to meet these demands as they answer to the norms they have internalized as highly educated professionals living at least part  ...  The experience of waiting 'persuades the destitute that they need to be patient' (p. 166). Burrell thus positions waiting and indeterminacy as instruments of state control.  ... 
doi:10.1111/1467-9655.12417 pmcid:PMC4946809 fatcat:5dhalqy7lnemnohums7r7xae4e

FACEing reality: productive tensions between our epidemiological questions, methods and mission

Nancy Krieger, George Davey Smith
2017 International Journal of Epidemiology  
General rights This document is made available in accordance with publisher policies. Please cite only the published version using the reference above.  ...  biology is invoked as an excuse for injustice, and to think expansively about the people's health in relation to history and social justice.  ...  Acknowledgement: NK dedicates this paper to the memory of Ruth Hubbard (1924-2016), her mentor since college, who taught her to think critically about science, to do science critically, to challenge whenever  ... 
doi:10.1093/ije/dyw330 pmid:28130315 fatcat:ebyqlx4jurathimni23fl3pwjy
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