Creation and evaluation of a dictionary-based tagger for virus species and proteins

BioNLP 2017 - SIGBioMed Workshop on Biomedical Natural Language Processing, Proceedings of the 16th BioNLP Workshop

Volumn , Issue , 2017, Pages 91-98

  Cook, Helen Victoria ^a   Bērziņš, Rūdolfs ^a   Rodríguez, Cristina Leal ^a   Cejuela, Juan Miguel ^b   Jensen, Lars Juhl ^a  

^a University of Copenhagen   (Denmark)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL LINGUISTICS; DATA MINING; NATURAL LANGUAGE PROCESSING SYSTEMS; PROTEINS;

AGRICULTURAL HEALTH; EXTRACT INFORMATIONS; HUMAN HEALTH; NAMED ENTITIES; TEXT-MINING; VIRAL PROTEINS;

VIRUSES;

EID: 85053829532     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (26)

1. Teresa Attwood, Bora Agit, and Lynda Ellis. 2015. Longevity of Biological Databases. EMBnet.journal 21(0).
2. Daniel C Cannon, Jeremy J Yang, Stephen L Mathias, Oleg Ursu, Subramani Mani, Anna Waller, Stephan C Schurer, Lars Juhl Jensen, Larry A Sklar, Cristian G Bologa, and Tudor I Oprea. 2017. TIN-X: Target Importance and Novelty Explorer. Bioinformatics pages 1–3.
3. Juan Miguel Cejuela, Peter McQuilton, Laura Ponting, S. J. Marygold, Raymund Stefancsik, Gillian H. Millburn, and Burkhard Rost. 2014. Tagtog: Interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. Database 2014:1–8. https://doi.org/10.1093/database/bau033.
4. Helen Cook, Evangelos Pafilis, and Lars Jensen. 2016. A dictionary- and rule-based system for identification of bacteria and habitats in text. In Proceedings of the 4th BioNLP Shared Task Workshop. pages 50–55. http://www.aclweb.org/anthology/W/W16/W1630.pdf#page=60.
5. Anthony S Fauci and David M Morens. 2016. Zika Virus in the Americas Yet Another Arbovirus Threat. The New England journal of medicine 374:601–604. https://doi.org/10.1056/NEJMp1600297.
6. Martin Gerner, Goran Nenadic, and Casey M Bergman. 2010. LINNAEUS: a species name identification system for biomedical literature. BMC bioinformatics 11(1):85. https://doi.org/10.1186/1471-2105-11-85.
7. Natali Gulbahce, Han Yan, Amélie Dricot, Megha Padi, Danielle Byrdsong, Rachel Franchi, Deok-Sun Lee, Orit Rozenblatt-Rosen, Jessica C. Mar, Michael A. Calderwood, Amy Baldwin, Bo Zhao, Balaji Santhanam, Pascal Braun, Nicolas Simonis, Kyung-Won Huh, Karin Hellner, Miranda Grace, Alyce Chen, Renee Rubio, Jarrod A. Marto, Nicholas A. Christakis, Elliott Kieff, Frederick P. Roth, Jennifer Roecklein-Canfield, James A. De-Caprio, Michael E. Cusick, John Quackenbush, David E. Hill, Karl Münger, Marc Vidal, and Albert-László Barabási. 2012. Viral Perturbations of Host Networks Reflect Disease Etiology. PLoS Computational Biology 8(6):e1002531. https://doi.org/10.1371/journal.pcbi.1002531.
8. Warren A. Kibbe, Cesar Arze, Victor Felix, Elvira Mitraka, Evan Bolton, Gang Fu, Christopher J. Mungall, Janos X. Binder, James Malone, Drashtti Vasant, Helen Parkinson, and Lynn M. Schriml. 2015. Disease Ontology 2015 update: An expanded and updated database of Human diseases for linking biomedical knowledge through disease data. Nucleic Acids Research 43(D1):D1071–D1078. https://doi.org/10.1093/nar/gku1011.
9. Andrew M.Q. King, Michael J. Adams, Eric B. Carstens, and Elliot J. Lefkowitz, editors. 2012. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press. https://doi.org/10.1016/B978-0-12-3846846.X0001-8.
10. T. J D Knight-Jones and J. Rushton. 2013. The economic impacts of foot and mouth disease - What are they, how big are they and where do they occur? Preventive Veterinary Medicine 112(3-4):162–173. https://doi.org/10.1016/j.prevetmed.2013.07.013.
11. Zhiyong Lu. 2011. PubMed and beyond: A survey of web tools for searching biomedical literature. Database 2011:1–13. https://doi.org/10.1093/database/baq036.
12. James N. Mills, Kenneth L. Gage, and Ali S. Khan. 2010. Potential influence of climate change on vector-borne and zoonotic diseases: A review and proposed research plan. Environmental Health Perspectives 118(11):1507–1514. https://doi.org/10.1289/ehp.0901389.
13. Noelle Angelique M. Molinari, Ismael R. Ortega-Sanchez, Mark L. Messonnier, William W. Thompson, Pascale M. Wortley, Eric Weintraub, and Carolyn B. Bridges. 2007. The annual impact of seasonal influenza in the US: Measuring disease burden and costs. Vaccine 25(27):5086–5096. https://doi.org/10.1016/j.vaccine.2007.03.046.
14. Ettore Mosca, Roberta Alfieri, and Luciano Milanesi. 2014. Diffusion of Information throughout the Host Interactome Reveals Gene Expression Variations in Network Proximity to Target Proteins of Hepatitis C Virus. PLoS ONE 9(12):e113660. https://doi.org/10.1371/journal.pone.0113660.
15. Arvind Neelakantan and Michael Collins. 2014. Learning Dictionaries for Named Entity Recognition using Minimal Supervision. Proceedings of the 14th Conference of the European Chapter of the Association for Computational Linguistics pages 452–461. http://www.aclweb.org/anthology/E14-1048.
16. Evangelos Pafilis, Sune P. Frankild, Lucia Fanini, Sarah Faulwetter, Christina Pavloudi, Aikaterini Vasileiadou, Christos Arvanitidis, and Lars Juhl Jensen. 2013. The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. PLoS ONE 8(6):2–7. https://doi.org/10.1371/journal.pone.0065390.
17. David J Paton and Geraldine Taylor. 2011. Developing vaccines against foot-and-mouth disease and some other exotic viral diseases of livestock. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 366(1579):2774–81. https://doi.org/10.1098/rstb.2011.0107.
18. William E Paul, Michael Mcheyzer-williams, and David Barthold, Stephen. Bowen, R. Hedrick, Ronald. Knowles, Donald. Lair-more, Michael. Parrish, Colin. Saif, Linda. Swayne. 2010. Fenner’S Veterinary Virology. Elsevier 5th editio(August):43–51. https://doi.org/10.1016/B978-0-12-3751584.X0001-6.
19. Olga V. Saik, Timofey V. Ivanisenko, Pavel S. Demenkov, and Vladimir A. Ivanisenko. 2015. Interactome of the hepatitis C virus: Literature mining with ANDSystem. Virus Research 218:40–48. https://doi.org/10.1016/j.virusres.2015.12.003.
20. Eric W Sayers, Tanya Barrett, Dennis A Benson, Stephen H Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M Church, Michael DiCuccio, Ron Edgar, Scott Federhen, Michael Feolo, Lewis Y Geer, Wolfgang Helmberg, Yuri Kapustin, David Landsman, David J Lipman, Thomas L Madden, Donna R Maglott, Vadim Miller, Ilene Mizrachi, James Ostell, Kim D Pruitt, Gregory D Schuler, Edwin Sequeira, Stephen T Sherry, Martin Shumway, Karl Sirotkin, Alexandre Souvorov, Grigory Starchenko, Tatiana A Tatusova, Lukas Wagner, Eugene Yaschenko, and Jian Ye. 2009. Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 37:D5–15. https://doi.org/10.1093/nar/gkn741.
21. Priya S. Shah, Jason A. Wojcechowskyj, Manon Eckhardt, and Nevan J. Krogan. 2015. Comparative mapping of host-pathogen protein-protein interactions. Current Opinion in Microbiology 27:62–68. https://doi.org/10.1016/j.mib.2015.07.008.
22. Damian Szklarczyk, Andrea Franceschini, Stefan Wyder, Kristoffer Forslund, Davide Heller, Jaime Huerta-Cepas, Milan Simonovic, Alexander Roth, Alberto Santos, Kalliopi P. Tsafou, Michael Kuhn, Peer Bork, Lars J. Jensen, and Christian Von Mering. 2015. STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Research 43(D1):D447–D452. https://doi.org/10.1093/nar/gku1003.
23. Buzhou Tang, Yonghui Wu, Min Jiang, Joshua C. Denny, and Hua Xu. 2013. Recognizing and Encoding Discorder Concepts in Clinical Text using Machine Learning and Vector Space. Proceedings of the ShARe/CLEF Evaluation Lab http://www.clefinitiative.eu/documents/71612/d596ae25-c4b3-4a9a-be4a-648a77712aaf.
24. The UniProt Consortium. 2014. UniProt: a hub for protein information. Nucleic Acids Research 43(D1):D204–212. https://doi.org/10.1093/nar/gku989.
25. WHO. 2014. WHO Fact Sheets: Influenza, HCV, HPV. http://www.who.int/mediacentre/factsheets/.
26. Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller. 2000. A Greedy Algorithm for Aligning DNA Sequences. Journal of Computational Biology 7(12):203–214. https://doi.org/10.1089/10665270050081478.