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Constructing a Syndromic Terminology Resource for Veterinary Text Mining

Lenz Furrer, Susanne Küker, John Berezowski, Horst Posthaus, Flavie Vial, Fabio Rinaldi
2015
While building a text mining system for veterinary syndromic surveillance, we exploit automatic and semi-automatic methods for terminology construction at different stages.  ...  While building a text mining system for veterinary syndromic surveillance, we exploit automatic and semi-automatic methods for terminology construction at different stages.  ...  Acknowledgements This work was funded by the Swiss Federal Food Safety and Veterinary Office (Bundesamt für Lebensmittelsicherheit und Veterinärwesen).  ... 
doi:10.5167/uzh-114496 fatcat:f5s5h4tzn5fk3akununekv2zh4

The value of necropsy reports for animal health surveillance

Susanne Küker, Celine Faverjon, Lenz Furrer, John Berezowski, Horst Posthaus, Fabio Rinaldi, Flavie Vial
2018 BMC Veterinary Research  
This data has potential value for monitoring endemic disease syndromes in different age and production groups, or for early detection of emerging or re-emerging diseases.  ...  This data has potential value for monitoring endemic disease syndromes in different age and production groups, or for early detection of emerging or re-emerging diseases.  ...  Acknowledgments We would like to thank Corinne Gurtner of the ITPA for helping to develop the terminology, Sara Schaerrer (FSVO) for extracting data from the TVD and Michael Binggeli (FSVO) for extracting  ... 
doi:10.1186/s12917-018-1505-1 pmid:29914502 pmcid:PMC6006731 fatcat:3om52mstije3zg6nvxtzy7gd3i

Machine learning for syndromic surveillance using veterinary necropsy reports

Nathan Bollig, Lorelei Clarke, Elizabeth Elsmo, Mark Craven, Paweł Pławiak
2020 PLoS ONE  
In this study, we evaluate machine learning methods for conducting syndromic surveillance using free-text veterinary necropsy reports.  ...  We train a system to detect if a necropsy report from the Wisconsin Veterinary Diagnostic Laboratory contains evidence of gastrointestinal, respiratory, or urinary pathology.  ...  Marie Pinkerton at the University of Wisconsin School of Veterinary Medicine for their mentorship and advice. We would like to thank Dr.  ... 
doi:10.1371/journal.pone.0228105 pmid:32023271 pmcid:PMC7001958 fatcat:hlyhqicyura5hffvgekte4qhmu

Prevalence, survival analysis and multimorbidity of chronic diseases in the general veterinarian-attended horse population of the UK

Claire E. Welsh, Marco Duz, Timothy D.H. Parkin, John F. Marshall
2016 Preventive Veterinary Medicine  
Using text mining of first-opinion electronic medical records from seven veterinary practices around the UK, Kaplan-Meier and Cox proportional hazard modelling, we were able to estimate the apparent prevalence  ...  However, evidence for this trend in ageing is very limited, and the current prevalence of many chronic diseases, and of multimorbidity, is unknown.  ...  through text mining of electronic medical records.  ... 
doi:10.1016/j.prevetmed.2016.07.011 pmid:27544263 fatcat:apjjjej5tbaf3oytn5c4qrbgcq

Disease and pharmacologic risk factors for first and subsequent episodes of equine laminitis: A cohort study of free-text electronic medical records

Claire E. Welsh, Marco Duz, Timothy D.H. Parkin, John F. Marshall
2017 Preventive Veterinary Medicine  
practice may represent a unique resource for epidemiologic research.  ...  2017) Disease and pharmacologic risk factors for first and subsequent episodes of equine laminitis: a cohort study of free-text electronic medical records.  ...  CW is funded by the British Veterinary Association -Animal Welfare Foundation (grant number: Norman Hayward Fund_2014_1_JM).  ... 
doi:10.1016/j.prevetmed.2016.11.012 pmid:28010903 fatcat:vcb4medurfhb7j2e3nh6bdi4oi

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J.P. Gourdine (+14 others)
2016 Nucleic Acids Research  
diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations.  ...  Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary  ...  ACKNOWLEDGEMENTS We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1093/nar/gkw1128 pmid:27899636 pmcid:PMC5210586 fatcat:tbsgmbgu4vfmpiwwsenemxj2cm

Translating Big Data into Smart Data for Veterinary Epidemiology

Kimberly VanderWaal, Robert B. Morrison, Claudia Neuhauser, Carles Vilalta, Andres M. Perez
2017 Frontiers in Veterinary Science  
The advent of big data requires the incorporation of new skills into veterinary epidemiology training, including, for example, machine learning and coding, to prepare a new generation of scientists and  ...  meaningful insights for animal health.  ...  While it is possible to use text-mining techniques to extract information from unstructured text fields in clinical or diagnostic records (52, 53) , homogenizing and naturalizing data into uniform and  ... 
doi:10.3389/fvets.2017.00110 pmid:28770216 pmcid:PMC5511962 fatcat:zvm66ua3ojbjlfkeez6lk6rkii

Drivers for the development of an Animal Health Surveillance Ontology (AHSO)

Fernanda C. Dórea, Flavie Vial, Karl Hammar, Ann Lindberg, Patrick Lambrix, Eva Blomqvist, Crawford W. Revie
2019 Preventive Veterinary Medicine  
Discussions with syndromic surveillance experts in the fields of animal and public health, as well as computer scientists from the field of information management, have led to the conclusion that a major  ...  The AHSO framework is modelled in OWL, the W3C standard Semantic Web language for representing rich and complex knowledge.  ...  Appendix A. Supplementary data Supplementary material related to this article can be found, in the online version, at doi:https://doi.org/10.1016/j.prevetmed.2019.03. 002.  ... 
doi:10.1016/j.prevetmed.2019.03.002 fatcat:p2nkqo24pzhsfbmijppydmhqri

The Monarch Initiative: Insights across species reveal human disease mechanisms [article]

Christopher Mungall, Julie McMurry, Sebastian Koehler, James Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, TOM CONLIN, Nathan Dunn, Mark Engelstad, Erin Foster, Jean-Philippe Gourdine (+14 others)
2016 bioRxiv   pre-print
The Monarch Initiative (https://monarchinitiative.org) is an international consortium dedicated to providing computational tools that leverage a computational representation of phenotypic data for genotype-phenotype  ...  We can exploit this common ancestry at the level of sequences, but also in terms of observable outcomes (phenotypes), to learn more about health and disease for humans and all other species.  ...  Acknowledgments We thank members of the Undiagnosed Disease Program, the International Mouse Phenotyping Consortium, the NCI Semantic Infrastructure team, and NIF/SciCrunch for their contributions.  ... 
doi:10.1101/055756 fatcat:26ov5gydkvgmxekc5z7yvcqzly

Animal health syndromic surveillance: a systematic literature review of the progress in the last 5 years (2011–2016)

Fernanda C Dórea, Flavie Vial
2016 Veterinary Medicine : Research and Reports  
This review presents the current initiatives and potential for development in the field of animal health surveillance (AHSyS), 5 years on from its advent to the front of the veterinary public health scene  ...  Thus, Bayesian methodologies, which are much more apt to discover the interplay among multiple syndromic data sources, are foreseen to play a big part in the future of AHSyS.  ...  Acknowledgment The authors thank their affiliated institutions for the support to undertake this work.  ... 
doi:10.2147/vmrr.s90182 pmid:30050848 pmcid:PMC6044799 fatcat:3ligi7atnfcgjjpndh4rcijrie

A Mouse by Any Other Name …

John P. Sundberg, Paul N. Schofield
2009 Journal of Investigative Dermatology  
An appropriate exhortation for the biomedical sciences would be "Standardization, Standardization, Standardization."  ...  A recurring motto from the Tony Blair government in the UK was "Education, Education, Education."  ...  ACKNOWLEDGMENTS We thank Beverly Richards-Smith for her constructive comments and verification of nomenclature issues raised in the manuscript.  ... 
doi:10.1038/jid.2009.81 pmid:19521404 pmcid:PMC3804061 fatcat:5hltjzjuivfp3npf2utxkzu4t4

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

2019 Nucleic Acids Research  
in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources  ...  Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research.  ...  In this example, a user has entered text from a publication entitled 'A specific mutation in TBL1XR1 causes Pierpont syndrome' (51).  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

Different Data Mining Approaches Based Medical Text Data

Wenke Xiao, Lijia Jing, Yaxin Xu, Shichao Zheng, Yanxiong Gan, Chuanbiao Wen, Óscar Belmonte Fernández
2021 Journal of Healthcare Engineering  
We also explored the applications of algorithms for providing insights to the users and enabling them to use the resources for the specific challenges in medical text data.  ...  Findings of this paper are benefit for helping the researchers to choose the reasonable techniques for mining medical text data and presenting the main challenges to them in medical text data mining.  ...  It can be used as a good method for data classification in medical text data mining.  ... 
doi:10.1155/2021/1285167 pmid:34912530 pmcid:PMC8668297 fatcat:sr6zc5lfpvabdfgcd57uif76m4

Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance

Kristen J. Margevicius, Nicholas Generous, Kirsten J. Taylor-McCabe, Mac Brown, W. Brent Daniel, Lauren Castro, Andrea Hengartner, Alina Deshpande, Vittoria Colizza
2014 PLoS ONE  
To demonstrate utility, the framework and definitions were used as the basis for a schema of a relational database for biosurveillance resources and in the development and use of a decision support tool  ...  that can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities.  ...  Sales Drugs Ambulance dispatch records Human Syndromic Ambulance Records ED/Nurse triage notes Human Syndromic ED/Hospital Records EMR -narrative text Human Syndromic ED/Hospital Records  ... 
doi:10.1371/journal.pone.0083730 pmid:24392093 pmcid:PMC3879288 fatcat:fripg5jrzvftxarg7riddxm43a

Infectious Disease Informatics and Syndromic Surveillance [chapter]

Daniel Zeng, Hsinchun Chen, Ping Yan
2008 Digital Government  
Syndromic surveillance is used to illustrate these components of IDI research, as it is a widely-adopted approach to detecting and responding to public health and bioterrorism events.  ...  We would like to thank the members of the BioPortal project for insightful discussions.  ...  The first author is an affiliated professor at the Institute of Automation, the Chinese Academy of Sciences, and wishes to acknowledge support from a research grant (60573078) from the National Natural  ... 
doi:10.1007/978-0-387-71611-4_26 fatcat:zvvonnnrcjaqlhhb4hqvitfuoy
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