David Campos

Subject	Term expansion methodologies in biomedical information retrieval
Advisor	José Luís Oliveira, Sérgio Matos
Group
Status	Other
Starts	2009/10/01
Ends	2013/09/30
Country	Portugal
Projects
Past projects
Events
Proposals
Personal page	www.davidcampos.org

Publications

Articles in international journals listed in the ISI

• Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, and Donald C. Comeau. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database, vol. 2016, no. baw121, September 2016 [IF 2016: 3.290 (Q1, 8/57)]
• Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez, Riza Batista-Navarro, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck, Socorro Gama-Castro, Nancy George, Georgios Gkoutos, Afroza K. Irin, Lars J. Jensen, Silvia Jimenez, Toni R. Jue, Ingrid Keseler, Sumit Madan, Sérgio Matos, Peter McQuilton, Marija Milacic, Matthew Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira, Shruti Rao, Fabio Rinaldi, Karen Rothfels, David Salgado, Raquel Silva, Onkar Singh, Raymund Stefancsik, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole Vasilevsky, Xiaodong Wang, Andrew Chatr-Aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna McEntyre, Sandra Orchard, Sangya Pundir, Raul Rodriguez-Esteban, Kimberly Van Auken, Zhiyong Lu, Mary Schaeffer, Cathy H. Wu, Lynette Hirschman, and Cecilia N. Arighi. Overview of the interactive task in BioCreative V. Database, vol. 2016, p. baw119, September 2016 [IF 2016: 3.290 (Q1, 8/57)]
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Mining clinical attributes of genomic variants through assisted literature curation in Egas. Database, vol. 2016, June 2016 [IF 2016: 3.290 (Q1, 8/57)]
• David Campos, Sérgio Matos, José Luís Oliveira. A document processing pipeline for annotating chemical entities in scientific documents. Journal of Cheminformatics, vol. 7, no. Suppl. 1, p. S7, January 2015 [IF 2015: 3.949 (Q1, 36/163)] [IF 2017: 3.893 (Q1, 16/148)]
• Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M Lowe, Roger A Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, SV Ramanan, Senthil Nathan, Slavko Žitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A Akhondi, Jan A Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C Lee Giles, Hongfang Liu, Komandur Elayavilli Ravikumar, Andre Lamurias, Francisco M Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usié, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, Alfonso Valencia. The CHEMDNER corpus of chemicals and drugs and its annotation principles. Journal of Cheminformatics, vol. 7, no. Suppl 1, p. S2, January 2015 [IF 2015: 3.949 (Q1, 36/163)] [IF 2017: 3.893 (Q1, 16/148)]
• David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira. Egas: a collaborative and interactive document curation platform. Database, vol. 2014, no. 10.1093, p. 1-12, June 2014 [IF 2014: 3.372 (Q1, 7/57)]
• Pedro Lopes, Tiago Nunes, David Campos, Laura Ines Furlong, Anna Bauer-Mehren, Ferran Sanz, Maria Carmen Carrascosa, Jordi Mestres, Jan Kors, Bharat Singh, Erik van Mulligen, Johan Van der Lei, Gayo Diallo, Paul Avillach, Ernst Ahlberg, Scott Boyer, Carlos Diaz, José Luís Oliveira. Gathering and Exploring Scientific Knowledge in Pharmacovigilance. PLoS ONE, vol. 8, no. 12, p. e83016, December 2013 [IF 2013: 3.534 (Q1, 8/55)] [IF 2017: 2.766 (Q1, 15/64)]
• David Campos, Sérgio Matos, José Luís Oliveira. A modular framework for biomedical concept recognition. BMC Bioinformatics, vol. 14, no. 281, September 2013 [IF 2013: 2.672 (Q1, 8/52)]
• Tiago Nunes, David Campos, Sérgio Matos, José Luís Oliveira. BeCAS: biomedical concept recognition services and visualization. Bioinformatics, vol. 29, no. 15, p. 1915-1916, June 2013 [IF 2013: 4.621 (Q1, 4/52)] [IF 2017: 5.481 (Q1, 3/59)]
• José Luís Oliveira, Pedro Lopes, Tiago Nunes, David Campos, E. Ahlberg, E. van Mullingen, J. Kors, B. Singh, L. I. Furlong, F. Sanz, A. Bauer-Mehren, M. D. C. Carrascosa, J. Mestres, P. Avillach, C. Díaz Acedo, J. van der Lei. The EU-ADR Web Platform: delivering advanced pharmacovigilance tools. Pharmacoepidemiology and Drug Safety, vol. 22, no. 5, p. 459-467, May 2013 [IF 2013: 3.172, 3.172, 3.172 (Q2, Q2, 66/256, 66/256)]
• David Campos, Sérgio Matos, José Luís Oliveira. Gimli: open source and high-performance biomedical name recognition (Highly accessed). BMC Bioinformatics, vol. 14, no. 1, p. 54, February 2013 [IF 2013: 2.672 (Q1, 8/52)]
• David Campos, Sérgio Matos, Ian Lewin, José Luís Oliveira, Dietrich Rebholz-Schuhmann. Harmonisation of gene/protein annotations: towards a gold standard MEDLINE. Bioinformatics, vol. 28, no. 9, p. 1253-1261, March 2012 [IF 2012: 5.323 (Q1, 2/47)] [IF 2017: 5.481 (Q1, 3/59)]
• Z. Lu, H.-Y. Kao, C.-H. Wei, M. Huang, J. Liu, C.-J. Kuo, C.-N. Hsu, R.T.-H. Tsai, H.-J. Dai, N. Okazaki, H.-C. Cho, M. Gerner, I. Solt, S. Agarwal, F. Liu, D. Vishnyakova, P. Ruch, M. Romacker, F. Rinaldi, S. Bhattacharya, P. Srinivasan, H. Liu, M. Torii, Sérgio Matos, David Campos, K. Verspoor, K.M. Livingston, W.J. Wilbur. The Gene Normalization Task in BioCreative III. BMC Bioinformatics, vol. 12, no. Suppl 8, p. S2, September 2011 [IF 2011: 2.751 (Q1, 7/47)]

Other articles in journals

• David Campos, Quoc-Chinh Bui, Sérgio Matos, José Luís Oliveira. TrigNER: automatically optimized biomedical event trigger recognition on scientific documents. Source Code for Biology and Medicine, vol. 9, no. 1, January 2014

Chapters in books

• David Campos, Sérgio Matos, José Luís Oliveira. Current methodologies for biomedical Named Entity Recognition. Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Ed.), Wiley, p. 1390, January 2014
• David Campos, Sérgio Matos, José Luís Oliveira. Biomedical Named Entity Recognition: A Survey of Machine-Learning Tools. Theory and Applications for Advanced Text Mining, Shigeaki Sakurai (Ed.), InTech, p. 175-195, November 2012

Articles in conference proceedings

• André Santos, Sérgio Matos, David Campos, José Luís Oliveira. A Curation Pipeline and Web-Services for PDF Documents. Proceedings of the 7th International Symposium on Semantic Mining in Biomedicine, Potsdam, Germany, August 2016
• Sérgio Matos, David Campos, Renato Pinho, Raquel Silva, Matthew Mort, David N. Cooper, José Luís Oliveira. Assisted Mining and Curation of Genomic Variants using Egas. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 396-402, September 2015
• Sérgio Matos, José Sequeira, David Campos, José Luís Oliveira. Identification of chemical and gene mentions in patent texts using feature-rich conditional random fields. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 76-81, September 2015
• Sérgio Matos, André Santos, David Campos, José Luís Oliveira. Neji: a BioC compatible framework for biomedical concept recognition. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, Sevilla, Spain, p. 17-21, September 2015
• Pedro Sernadela, Pedro Lopes, David Campos, Sérgio Matos, José Luís Oliveira. A Semantic Layer for Unifying and Exploring Biomedical Document Curation Results. Bioinformatics and Biomedical Engineering, Proceeedings of the Third International Conference, IWBBIO, Part I, Granada, Spain, vol. Part I, p. 8-17, April 2015
• David Campos, Sérgio Matos, José Luís Oliveira. Chemical name recognition with harmonized feature-rich conditional random fields. Fourth BioCreative Challenge Evaluation Workshop, vol. 2, p. 82-87, October 2013
• David Campos, Jóni Lourenço, Tiago Nunes, Rui Vitorino, Pedro Domingues, Sérgio Matos, José Luís Oliveira. Egas - Collaborative Biomedical Annotation as a Service. Fourth BioCreative Challenge Evaluation Workshop, vol. 1, p. 254-259, October 2013
• Quoc-Chinh Bui, David Campos, Erik van Mulligen, Jan Kors. A fast rule-based approach for biomedical event extraction. Proceedings of BioNLP Shared Task 2013 Workshop, Association for Computational Linguistics, Sofia, Bulgaria, August 2013
• David Campos, Sérgio Matos, José Luís Oliveira. Neji: a tool for heterogeneous biomedical concept identification. Proceedings of the BioLINK SIG, ISMB/ECCB, Berlin, Germany, p. 28-31, July 2013
• David Campos, D. Rebholz-Schuhman, Sérgio Matos, José Luís Oliveira. A CRF-based approach to harmonize heterogeneous gene/protein annotations. Proceedings of the Second CALBC workshop, p. 17-18, March 2011
• David Campos, Sérgio Matos, José Luís Oliveira. Annotating the CALBC corpus with a machine learning harmonization approach. Proceedings of the Second CALBC workshop, p. 43-45, March 2011
• Pedro Lopes, David Campos, José Luís Oliveira. A tagging system for bioinformatics resources. 10th IEEE International Conference on Information Technology and Applications in Biomedicine (ITAB 2010), Corfu, Greece, November 2010
• David Campos, Sérgio Matos, José Luís Oliveira. Recognition of Gene/Protein names using Conditional Random Fields. Proceedings of the International Conference on Knowledge Discovery and Information Retrieval 2010 (KDIR2010), Valencia, Spain, October 2010
• Sérgio Matos, David Campos, José Luís Oliveira. Vector-space models and terminologies in gene normalization and document classification. Proceedings of BioCreative III Workshop, Bethesda, Maryland, USA, p. 119-124, September 2010
• Pedro Lopes, David Pinto, David Campos, José Luís Oliveira. Arabella: A Directed Web Crawler. International Conference on Knowledge Discovery and Information Retrieval (KDIR 2009), Madeira, Portugal, 2009

PhD thesis

• David Campos. Term expansion methodologies in biomedical information retrieval. PhD Thesis, Universidade de Aveiro, February 2014