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Text mining and ontologies in biomedicine: Making sense of raw text

I. Spasic, S. Ananiadou, J. McNaught, A. Kumar
2005 Briefings in Bioinformatics  
This paper summarises different approaches in which ontologies have been used for text-mining applications in biomedicine.  ...  The volume of biomedical literature is increasing at such a rate that it is becoming difficult to locate, retrieve and manage the reported information without text mining, which aims to automatically distill  ...  Acknowledgments The National Centre for Text Mining (NaCTeM), UK is sponsored by the JISC. AK expresses his gratitude to Alexander von Humboldt Foundation.  ... 
doi:10.1093/bib/6.3.239 pmid:16212772 fatcat:ehw3jx2imze2xd2vfe4nuaqcgy

Challenges for Ontology Repositories and Applications to Biomedicine & Agronomy

Clément Jonquet
2017 Symposium on Information Management and Big Data  
The explosion of the number of ontologies and vocabularies available in the Semantic Web makes ontology libraries and repositories mandatory to find and use them.  ...  Then, we present some propositions to address these challenges and point to our previously published work and results obtained within applications -reusing NCBO technologyto biomedicine and agronomy in  ...  I also acknowledge the National Center for Biomedical Ontologies for their insights and thanks all my collaborators in Montpellier or Stanford interested like me on ontology repositories.  ... 
dblp:conf/simbig/Jonquet17 fatcat:v7xrirond5dkzjqy7u4nyra3yu

Approaches to verb subcategorization for biomedicine

Thomas Lippincott, Laura Rimell, Karin Verspoor, Anna Korhonen
2013 Journal of Biomedical Informatics  
We then describe the typical interpretation of subcategorization in biomedical text, and how subcategorization information can improve NLP and text mining applications in biomedicine.  ...  Information about verb subcategorization frames (SCFs) is important to many tasks in natural language processing (NLP) and, in turn, text mining.  ...  Introduction Text mining of the biomedical literature has an ever-increasing importance in biomedical informatics and systems biology due to the double-exponential growth in research publications in the  ... 
doi:10.1016/j.jbi.2012.12.001 pmid:23276747 fatcat:5x2cd375f5gf5hi6jjdk5hkiwa

Data Mining in Biomedicine: Current Applications and Further Directions for Research

S. L. TING, C. C. SHUM, S. K. KWOK, A. H. C. TSANG, W. B. LEE
2009 Journal of Software Engineering and Applications  
This paper introduces some basic data mining techniques, unsupervised learning and supervising learning and reviews the application of data mining in biomedicine.  ...  The advancement of the new medical deceives and the database management systems create a huge number of databases in the biomedicine world.  ...  The authors would like to express their sincere thanks to the Research Committee of The Hong Kong Polytechnic University for financial support of the research work presented in this paper.  ... 
doi:10.4236/jsea.2009.23022 fatcat:24qp2zpq2nbdhl22fzgtg7apwy

An ontology-based measure to compute semantic similarity in biomedicine

Montserrat Batet, David Sánchez, Aida Valls
2011 Journal of Biomedical Informatics  
The determination of semantic similarity between word pairs is an important component of text understanding that enables the processing, classification and structuring of textual resources.  ...  in clinical and translational research.  ...  Acknowledgments This work has been partially supported by the Universitat Rovira i Virgili (2009AIRE-04), the Spanish Ministry of Science and Innovation (DAMASK project, Data mining algorithms with semantic  ... 
doi:10.1016/j.jbi.2010.09.002 pmid:20837160 fatcat:fgkojwtk45fd7eaflkgbwtazem

A proposed draft protocol for the European Convention on Biomedicine relating to research on the human embryo and fetus

J C Byk
1997 Journal of Medical Ethics  
Foreword The nature of the human embryo and fetus is a longstanding issue in human history.  ...  , in Strasbourgfrom the 16th to the 18th of December 1996.  ...  I would reply that mine is a legal and international approach to embryo research and does not intendnor needto strive for ontological and theological consistency.  ... 
doi:10.1136/jme.23.1.32 pmid:9055160 pmcid:PMC1377182 fatcat:vgtka4jfu5ajjeb76abzx5tn24

Periodicity detection in lifelog data with missing and irregularly sampled data

Feiyan Hu, Alan F. Smeaton, Eamonn Newman
2014 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
management of data and in particular to search for and detect patterns of usage for individuals and across populations.  ...  In this paper, we present a framework that detects both lowlevel and high-level periodicity in lifelog data, detecting hidden patterns of which users would not otherwise be aware.  ...  In a sense lifelogging represents creating a "black box" of an individual human's life activities and may offer the potential to mine or infer knowledge about how we live our lives.  ... 
doi:10.1109/bibm.2014.6999284 dblp:conf/bibm/HuSN14 fatcat:oerpclr3qjcv5bymvo7dj5qmiu

Komenti: A semantic text mining framework [article]

Luke T Slater, William Bradlow, Robert Hoehndorf, Dino FA Motti, Simon Ball, Georgios V Gkoutos
2020 biorxiv/medrxiv   pre-print
full use of the semantic provision of biomedical ontologies in the text extraction and characterisation space.  ...  It also contains multiple novel components for vocabulary construction and context disambiguation, which can improve the power of text mining and ontology-based analysis tasks, with a view towards making  ...  , I., Ananiadou, S., McNaught, J., Kumar, A.: Text mining and ontologies in biomedicine: Making sense of raw text. Briefings in Bioinformatics 6(3), 239-251 (2005). doi:10.1093/bib/6.3.239 2.  ... 
doi:10.1101/2020.08.04.233049 fatcat:xumxio4m4fbhvllqaxt5232vny

Question Answering for Biomedicine

Yifeng Liu
2016
Over the past two decades the field of biomedical text mining has experienced significant advances, such as the development of high quality biomedical knowledge bases and ontologies, the construction of  ...  The field of biomedicine is reeling from "information overload".  ...  Ontology Matching In many text mining scenarios, extracted NEs need to be mapped to concepts in a target ontology.  ... 
doi:10.7939/r3wh2dk7t fatcat:ywhdngzimrcs7l5c36whglgk2u

Getting to the (c)ore of knowledge: mining biomedical literature

Berry de Bruijn, Joel Martin
2002 International Journal of Medical Informatics  
Literature mining offers powerful methods to support knowledge discovery and the construction of topic maps and ontologies. An overview is given of recent developments in medical language processing.  ...  The present article describes the range of text mining techniques that have been applied to scientific documents.  ...  On the other end of the see-saw sits the growing pressure on companies to make a profit on the web and therefore to regulate access to material. In biomedicine, the efforts of the U.S.  ... 
doi:10.1016/s1386-5056(02)00050-3 pmid:12460628 fatcat:ipgcakav7zhfnjy5leqp6tpnhe

Increasing Papers' Discoverability with Precise Semantic Labeling: the sci.AI Platform [article]

Roman Gurinovich, Alexander Pashuk, Yuriy Petrovskiy, Alex Dmitrievskij, Oleg Kuryan, Alexei Scerbacov, Antonia Tiggre, Elena Moroz, Yuri Nikolsky
2017 arXiv   pre-print
The number of published findings in biomedicine increases continually. At the same time, specifics of the domain's terminology complicates the task of relevant publications retrieval.  ...  In the current research, we investigate influence of terms' variability and ambiguity on a paper's likelihood of being retrieved.  ...  In many publications, plain unstructured text is supported by algorithms, code, and multiple files of processed and raw datasets with annotated metadata and graphs.  ... 
arXiv:1705.08321v1 fatcat:byfuvxtooravto5bm3ch2rccsq

Getting More Out of Biomedical Documents with GATE's Full Lifecycle Open Source Text Analytics

Hamish Cunningham, Valentin Tablan, Angus Roberts, Kalina Bontcheva, Andreas Prlic
2013 PLoS Computational Biology  
It forms a focal point for the integration and reuse of advances that have been made by many people (the majority outside of the authors' own group) who work in text processing for biomedicine and other  ...  We conclude that the deployment of text mining for document abstraction or rich search and navigation is best thought of as a process, and that with the right computational tools and data collection strategies  ...  Acknowledgments Several hundred people have contributed to the software and thousands have contributed bug reports, documentation fixes, etc. Thanks! Author Contributions  ... 
doi:10.1371/journal.pcbi.1002854 pmid:23408875 pmcid:PMC3567135 fatcat:34bk5dpu7bbefledifc6nnqlai

ICD10 Coding of Death Certificates with the NCBO and SIFR Annotator(s) at CLEF eHealth 2017 Task 1

Andon Tchechmedjiev, Amine Abdaoui, Vincent Emonet, Clément Jonquet
2017 Conference and Labs of the Evaluation Forum  
The portal facilitates the use and fostering of terminologies and ontologies by offering a set of services including semantic annotation.  ...  The web service relies on the ontology content (preferred labels and synonyms) as well as on the semantics of the ontologies (is-a hierarchies) and their mappings.  ...  Marie Curie actions (grant 701771), the University of Montpellier and the CNRS.  ... 
dblp:conf/clef/TchechmedjievAE17 fatcat:uendh37uxjapldstjglprkaije

Knowledge acquisition, semantic text mining, and security risks in health and biomedical informatics

Jingshan Huang
2012 World Journal of Biological Chemsitry  
traditional syntactic text mining, and how to handle security issues during the knowledge sharing and reuse.  ...  Challenges that have been encountered include: how to efficiently and effectively represent human knowledge in formal computing models, how to take advantage of semantic text mining techniques rather than  ...  Spasic et al [11] have summarized different approaches in applying ontologies to text-mining applications in biomedicine.  ... 
doi:10.4331/wjbc.v3.i2.27 pmid:22371823 pmcid:PMC3286791 fatcat:gr5azlohjffvrcqvd4mgv5k2yy

Introduction to the special issue on decision support in medicine

Gondy Leroy, Hsinchun Chen
2007 Decision Support Systems  
We provide an overview of the building blocks necessary for a medical decision support system and introduce seven research articles in this special issue that describe the development and evaluation of  ...  Information technology plays an important role in medicine because of the advanced decision support systems (DSS) it can provide.  ...  This special issue focuses on recent advances in DSS for medicine. We opted to use 'medicine' in its broadest sense and include fields such as genetics, biomedicine and consumer health informatics.  ... 
doi:10.1016/j.dss.2006.02.001 fatcat:o6mqpgbu5faipenuyj3b3wnzri
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