Article published in:Computational terminology and filtering of terminological information
Edited by Patrick Drouin, Natalia Grabar, Thierry Hamon, Kyo Kageura and Koichi Takeuchi
[Terminology 24:1] 2018
► pp. 91–121
A flexible, hybrid method to map phenotype concept mentions to terminological resources
Narrative clinical records and biomedical articles constitute rich sources of information about phenotypes, i.e., markers distinguishing individuals with specific medical conditions from the general population. Phenotypes help clinicians to provide personalised treatments. However, locating information about them within huge document repositories is difficult, since each phenotypic concept can be mentioned in many ways. Normalisation methods automatically map divergent phrases to unique concepts in domain-specific terminologies, to allow location and linking of all mentions of a concept of interest. We have developed a hybrid normalisation method (HYPHEN) to handle concept mentions with wide ranging characteristics, across different text types. HYPHEN integrates various normalisation techniques that handle surface-level variations (e.g., differences in word order, word forms or acronyms/abbreviations) and lexical-level variations (where terms have similar meanings, but potentially unrelated forms). HYPHEN achieves robust performance for both biomedical academic text and narrative clinical records, and has the ability to significantly outperform related methods.
Keywords: normalisation, term variation, phenotypic information, terminological resources
Published online: 31 May 2018
Alnazzawi, Noha, Paul Thompson, and Sophia Ananiadou
Aronson, Alan R., and François-Michel Lang
Bodenreider, O.[ p. 117 ]
Bodnari, Andreea, Louise Deleger, Thomas Lavergne, Aurelie Neveol, and Pierre Zweigenbaum
2013 “A Supervised Named-Entity Extraction System for Medical Text.” In Proceedings of the hARe/CLEF Evaluation Lab, Valencia, Spain (http://ceur-ws.org/Vol-1179/CLEF2013wn-CLEFeHealth-BodnariEt2013.pdf). Accessed 8 February 2018.
Carroll, John, Rob Koeling, and Shivani Puri
Cohen, William, Pradeep Ravikumar, and Stephen Fienberg
Collier, Nigel, Anika Oellrich, and Tudor Groza
Dai, Manhong, Nigam H. Shah, Wei Xuan, Mark A. Musen, Stanley J. Watson, Brian D. Athey, and Fan Meng
2008 “An Efficient Solution for Mapping Free Text to Ontology Terms.” In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, USA (https://knowledge.amia.org/amia-55142-tbi2008a-1.650887/t-002-1.985042/f-001-1.985043/a-041-1.985157/an-041-1.985158?qr=1). Accessed 8 February 2018.
Deléger, Louise, Fiammetta Namer, and Pierre Zweigenbaum
Doğan, Rezarta Islamaj, Robert Leaman, and Zhiyong Lu
Dogan, Rezarta Islamaj, and Zhiyong Lu
Duclos, C., A. Burgun, J. B. Lamy, P. Landais, J. M. Rodrigues, L. Soualmia, and P. Zweigenbaum
Elhadad, Noémie, Sameer Pradhan, W. W. Chapman, Suresh Manandhar, and G. K. Savova
Fan, Jung-wei, Navdeep Sood, and Yang Huang[ p. 118 ]
2013 “Disorder Concept Identification from Clinical Notes an Experience with the Share/Clef 2013 Challenge.” In Proceedings of the ShARe/CLEF Evaluation Lab., Valencia, Spain (http://ceur-ws.org/Vol-1179/CLEF2013wn-CLEFeHealth-FanEt2013.pdf). Accessed 8 February 2018.
Fu, Xiao, and Sophia Ananiadou
Fu, Xiao, Riza Batista-Navarro, Rafal Rak, and Sophia Ananiadou
Fu, Xiao, R. T. B. Batista-Navarro, Rafal Rak, and Sophia Ananiadou
Groza, Tudor, Sebastian Köhler, Dawid Moldenhauer, Nicole Vasilevsky, Gareth Baynam, Tomasz Zemojtel, Lynn Marie Schriml, Warren Alden Kibbe, Paul N. Schofield, and Tim Beck
Habash, Nizar, and Bonnie Dorr
Hamosh, Ada, Alan F. Scott, Joanna S. Amberger, Carol A. Bocchini, and Victor A. McKusick
Han, MeiLan K., Alvar Agusti, Peter M. Calverley, Bartolome R. Celli, Gerard Criner, Jeffrey L. Curtis, Leonardo M. Fabbri, Jonathan G. Goldin, Paul W. Jones, and William MacNee
Hersh, William R., and Robert A. Greenes
Jonquet, Clement, Nigam Shah, and Mark Musen
Kang, Ning, Rogier J. Barendse, Zubair Afzal, Bharat Singh, Martijn J. Schuemie, Erik M van Mulligen, and Jan A. Kors
2010 “Erasmus Mc Approaches to the I2b2 Challenge.” In Proceedings of the 2010 i2b2/VA Workshop on Challenges in Natural Language Processing for Clinical Data, Boston, MA, USA (http://biosemantics.org/downloads/i2b2_challenge.pdf). Accessed 15 February 2018.
Kate, Rohit J.[ p. 119 ]
Leaman, Robert, Rezarta Islamaj Doğan, and Zhiyong Lu
Leaman, Robert, Ritu Khare, and Zhiyong Lu
Leaman, Robert, Christopher Miller, and G. Gonzalez
Lee, Hsin-Chun, Yi-Yu Hsu, and Hung-Yu Kao
Li, Jiao, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, and Zhiyong Lu
Maglott, Donna, Jim Ostell, Kim D. Pruitt, and Tatiana Tatusova
Markó, Kornél, Stefan Schulz, Olena Medelyan, and Udo Hahn
Miyao, Yusuke, and Jun’ichi Tsujii
Namer, Fiammetta, and Robert Baud
Névéol, A., and P. Zweigenbaum
Nunes, Tiago, David Campos, Sérgio Matos, and José Luís Oliveira
Oellrich, Anika, Nigel Collier, Damian Smedley, and Tudor Groza
Okazaki, N., S. Ananiadou, and J. Tsujii
Patrick, Jon, Yefeng Wang, and Peter Budd
Pradhan, Sameer, Noémie Elhadad, Wendy Chapman, Suresh Manandhar, and Guergana Savova[ p. 120 ]
Pradhan, Sameer, Noémie Elhadad, Brett R. South, David Martinez, Lee Christensen, Amy Vogel, Hanna Suominen, Wendy W. Chapman, and Guergana Savova
Rais, Meriem, and Natalia Grabar
Ramanan, S. V., Shereen Broido, and P Senthil Nathan
2013 “Performance of a Multi-Class Biomedical Tagger on Clinical Records.” In Proceedings of the ShARe/CLEF Evaluation Lab., Valencia, Spain (http://ceur-ws.org/Vol-1179/CLEF2013wn-CLEFeHealth-RamananEt2013.pdf). Accessed 8 February 2018.
Ruch, Patrick, Julien Gobeill, Christian Lovis, and Antoine Geissbühler
Savova, Guergana K., James J. Masanz, Philip V. Ogren, Jiaping Zheng, Sunghwan Sohn, Karin C. Kipper-Schuler, and Christopher G. Chute
Schriml, Lynn Marie, Cesar Arze, Suvarna Nadendla, Yu-Wei Wayne Chang, Mark Mazaitis, Victor Felix, Gang Feng, and Warren Alden Kibbe
Suominen, Hanna, Sanna Salanterä, Sumithra Velupillai, Wendy W. Chapman, Guergana Savova, Noemie Elhadad, Sameer Pradhan, Brett R. South, Danielle L. Mowery, and Gareth J. F. Jones
Tanenblatt, Michael A., Anni Coden, and Igor L. Sominsky
Thompson, Paul, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo Del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, and Valeria Quochi
Uzuner, Özlem, Brett R. South, Shuying Shen, and Scott L. DuVall
Wang, Chunye, and Ramakrishna Akella
2013 “Ucsc’s System for Clef Ehealth 2013 Task 1.” In Proceedings of the ShARe/CLEF Evaluation Lab., Valencia, Spain (http://ceur-ws.org/Vol-1179/CLEF2013wn-CLEFeHealth-WangEt2013.pdf). Accessed 8 February 2018.
Wang, Liqin, Bruce E. Bray, Jianlin Shi, Guilherme Del Fiol, and Peter J. Haug[ p. 121 ]
Wulff, Henrik R.
Cited by 3 other publications
Henry, Sam, Yanshan Wang, Feichen Shen & Ozlem Uzuner
Ju, Meizhi, Andrea D Short, Paul Thompson, Nawar Diar Bakerly, Georgios V Gkoutos, Loukia Tsaprouni & Sophia Ananiadou
Thompson, Paul, Sophia Daikou, Kenju Ueno, Riza Batista-Navarro, Jun’ichi Tsujii & Sophia Ananiadou
This list is based on CrossRef data as of 24 april 2021. Please note that it may not be complete. Sources presented here have been supplied by the respective publishers. Any errors therein should be reported to them.