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List of publications by members of the OntoGene project, in chronological order. All publications are peer-reviewed. Journal publications are highlighted.
  1. James Dowdall, Fabio Rinaldi, Andreas Persidis, Kaarel Kaljurand, Gerold Schneider, Michael Hess. Terminology expansion and relation identification between genes and pathways. Workshop on Terminology, Ontology and Knowledge Representation. Universite Jean Moulin (Lyon 3). 22-23 January 2004. Download as pdf
  2. Fabio Rinaldi, James Dowdall, Gerold Schneider, Andreas Persidis. Answering Questions in the Genomics Domain. ACL-2004 workshop on Question Answering in Restricted Domains, July 2004, Barcelona, Spain. Download as pdf
  3. Gerold Schneider, James Dowdall, Fabio Rinaldi. A Robust and Hybrid Deep-Linguistic Theory Applied to Large Scale Parsing. COLING-2004 workshop on Robust Methods in Analysis of Natural language Data, August 2004, Geneva, Switzerland. Download as pdf
  4. Gerold Schneider, Fabio Rinaldi, James Dowdall. Fast, Deep-Linguistic Statistical Minimalist Dependency Parsing. COLING-2004 workshop on Recent Advances in Dependency Grammars, August 2004, Geneva, Switzerland. Download as pdf
  5. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, James Dowdall and Andreas Persidis. Mining Relations in the GENIA corpus. Second European Workshop on Data Mining and Text Mining for Bioinformatics, at ECML/PKDD 2004, September 2004, Pisa, Italy. Download as pdf
  6. Gerold Schneider, Fabio Rinaldi, Kaarel Kaljurand, Michael Hess. Steps towards a GENIA Dependency Treebank. In Treebanks and Linguistic Theories (TLT) 2004, Tübingen, December 2004. Download as pdf
  7. Eric SanJuan, James Dowdall, Fidelia Ibekwe-SanJuan, Fabio Rinaldi. A symbolic approach to Automatic MultiWord Term Structuring. Computer Speech and Language, Special Issue on Multiword Expressions. Volume 19, Issue 4, October 2005, Pages 524–542. Elsevier Science.
  8. Fabio Rinaldi, Elia Yuste, Gerold Schneider, Michael Hess. Exploiting Technical Terminology for Knowledge Management. In Ontology Learning and Population, Paul Buitelaar, Philipp Cimiano, Bernardo Magnini (editors). IOS Press, 2005.
  9. Gerold Schneider, Fabio Rinaldi, Kaarel Kaljurand, Michael Hess, 2005. "Closing the Gap: Cognitively Adequate, Fast Broad-Coverage Grammatical Role Parsing". Proceedings of the 2nd International Workshop on Natural Language and Cognitive Science (NLUCS-2005). May 24-25, Miami.
  10. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Andreas Persidis, Ourania Konstanti. Relation Mining over a Corpus of Scientific Literature. In Proceedings of Artificial Intelligence in Medicine: AIME 2005, July 2005, Aberdeen, Scotland. Springer Verlag, LNAI 3581, pp. 550-559.
  11. Kaarel Kaljurand, Fabio Rinaldi, Gerold Schneider. Prolog-based query interface to syntactic dependencies extracted from biomedical literature. IFI Technical Report, ifi-2006.04.
  12. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA. SMBM 2006: 2nd International Symposium on Semantic Mining in Biomedicine. Jena, Germany, April 9th-12th 2006.
  13. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Tools for Text Mining over Biomedical Literature. Poster presented at ECAI2006.
  14. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Christos Andronis, Ourania Konstandi, Andreas Persidis. Mining of Functional Relations between Genes and Proteins over Biomedical Scientific Literature using a Deep-Linguistic Approach. Journal of Artificial Intelligence in Medicine . Volume 39, Issue 2, February 2007, Pages 127-136.
  15. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics 2006, 7(Suppl 3):S3. doi:10.1186/1471-2105-7-S3-S3 , PMC1764447, PMID: 17134476
  16. Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Michael Hess, Jean-Marc von Allmen, Martin Romacker, Therese Vachon. OntoGene in Biocreative II. Proceedings of the Second BioCreative Challenge Evaluation Workshop. Madrid, Spain, April 2007 (ISBN 84-933255-6-2).
  17. Gerold Schneider, Kaarel Kaljurand, Fabio Rinaldi, Tobias Kuhn. Pro3Gres Parser in the CoNLL Domain Adaptation Shared Task. Proceedings of the ACL Conference, Workshop on Computational Natural Language Learning (CoNLL-XI) Shared Task, Prague, June 2007.
  18. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand. Tools for detection of Protein Interactions in Biomedical Literature. Genome to Systems, Manchester, UK. 17-19 March 2008.
  19. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Dependency-Based Relation Mining for Biomedical Literature. LREC 2008, Marrakech, Morocco. May 2008.
  20. Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon. OntoGenein BioCreative II. Genome Biology, 2008, 9:S13, PMC2559984, PMID: 18834491
  21. Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, Gerold Schneider, Fabio Rinaldi. Towards Automatic Detection of Experimental Methods from Biomedical Literature. Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008).
  22. Kaarel Kaljurand, Thomas Kappeler, Gerold Schneider, Fabio Rinaldi.Detecting and grounding terms in biomedical literature. CICLING 2009.
  23. Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi.Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009.
  24. Thomas Kappeler, Kaarel Kaljurand, Fabio Rinaldi. TX Task: Automatic Detection of Focus Organisms in Biomedical Publications. BioNLP workshop, NAACL/HLT, Boulder, Colorado 2009.
  25. Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi. UZurich in the BioNLP 2009 Shared Task. BioNLP workshop, NAACL/HLT, Boulder, Colorado, 2009.
  26. Kaarel Kaljurand, Fabio Rinaldi, Thomas Kappeler, Gerold Schneider. Using existing biomedical resources to detect and ground terms in biomedical literature. Artificial Intelligence in Medicine, Verona, July 2009.
  27. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide. Effective Mining of Protein Interactions. LBM 2009: The 3rd International Symposium on Languages in Biology and Medicine. Jeju Island, South Korea, November 8-10, 2009.
  28. Fabio Rinaldi, Dietrich Rebholz-Schuhmann. Support tools for literature-based information access in the genomics domain. 3rd International Universal Communication Symposium. Tokyo, December 2009.
  29. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Simon Clematide, Thérèse Vachon, Martin Romacker, "OntoGene in BioCreative II.5," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3), pp. 472-480, 2010. http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.50, PMID: 20671319
  30. Fabio Rinaldi, Simon Clematide, Gerold Schneider. OntoGene in CALBC. Proceedings of the CALBC workshop. Hinxton, Cambridge, June, 2010.
  31. Fabio Rinaldi, Gerold Schneider, Simon Clematide, Silvan Jegen, Pierre Parisot, Martin Romacker and Therese Vachon. OntoGene (Team 65): preliminary analysis of participation in BioCreative III. BioCreative III workshop, Bethesda, Maryland, September 13-15, 2010.
  32. Fabio Rinaldi, Simon Clematide, Gerold Schneider, Martin Romacker, Thérèse Vachon. ODIN: An Advanced Interface for the Curation of Biomedical Literature. Biocuration 2010, the Conference of the International Society for Biocuration and the 4th International Biocuration Conference. Tokyo, Japan, 11-14 October 2010. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2010.5169.1>
  33. Dietrich Rebholz-Schuhmann, Antonio Jimeno, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekaterina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, Rene Witte, Jonas B. Laurila, Christopher JO Baker, Chen-Ju Kuo, Simon Clematide, Fabio Rinaldi, Richárd Farkas, György Móra, Kazuo Hara, Laura Furlong, Michael Rautschka, Mariana Lara Neves, Alberto Pascual-Montano, Qi Wei, Nigel Collier, Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga, Roser Morante, Vincent Van Asch, Walter Daelemans, José Luís Marina, Erik van Mulligen, Jan Kors and Udo Hahn. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Semantic Mining in Medicine, EBI, Cambridge, UK, 25-26 October 2010.
  34. Fabio Rinaldi, Gerold Schneider, Simon Clematide. Mining complex Drug/Gene/Disease relations in PubMed. Proceedings of the workshop "Mining the Pharmacogenomics Literature", Pacific Symposium on Biocomputing, Hawaii, January 2011. http://www.zora.uzh.ch/53013/
  35. Simon Clematide, Fabio Rinaldi, Gerold Schneider. OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization. Proceedings of the CALBC II workshop. EBI, Cambridge, UK, 16-18 March 2011.
  36. Gerold Schneider and Fabio Rinaldi. A data-driven approach to alternations based on protein-protein interactions. Proceedings of the 3rd Congreso Internacional de Lingüística de Corpus (CILC), Valencia, Spain, 7-9 April, 2011.
  37. Don Tuggener, Manfred Klenner, Gerold Schneider, Simon Clematide, Fabio Rinaldi. An Incremental Model for the Coreference Resolution Task of BioNLP 2011. Proceedings of the BioNLP11 shared task. Portland, Oregon, 24 June, 2011.
  38. Fabio Rinaldi, Kaarel Kaljurand, Rune Saetre. Terminological resources for Text Mining over Biomedical Scientific Literature. Journal of Artificial Intelligence in Medicine. Volume 52, Issue 2, June 2011, Pages 107-114. doi:10.1016/j.artmed.2011.04.011, PMID: 21652190
  39. Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu,, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova, Patrick Ruch, Martin Romacker, Fabio Rinaldi, Sanmitra Bhattacharya, Padmini Srinivasan, Hongfang Liu, Manabu Torii, Sergio Matos, David Campos, Karin Verspoor, Kevin M. Livingston, and W. John Wilbur. The Gene Normalization Task in BioCreative III. BMC Bioinformatics, special issue on BioCreative III, Volume 12 Suppl 8, October 2011.
  40. Cecilia Arighi, Phoebe Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michele Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu, Lois Maltais, Naoaki Okazaki, Livia Perfetto, Fabio Rinaldi, Rune Sætre, David Salgado, Padmini Srinivasan, Philippe E. Thomas, Luca Toldo, Lynette Hirschman and Cathy H Wu. BioCreative III Interactive Task: an Overview. BMC Bioinformatics, special issue on BioCreative III, Volume 12 Suppl 8, October 2011.
  41. Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman, Graciela Gonzalez, Sergio Matos, Sun Kim, W Wilbur, Luis Rocha, Hagit Shatkay, Ashish V Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu. The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics, special issue on BioCreative III, Volume 12 Suppl 8, October 2011.
  42. Gerold Schneider, Simon Clematide, Fabio Rinaldi. Detection of interaction articles and experimental methods in biomedical literature. BMC Bioinformatics, special issue on BioCreative III, Volume 12 Suppl 8, October 2011.
  43. Dietrich Rebholz-Schuhmann, Antonio Jimeno, Chen Li, Senay Kafkas, Ian Lewin, Ning Kang, Peter Corbett, David Milward, Ekatarina Buyko, Elena Beisswanger, Kerstin Hornbostel, Alexandre Kouznetsov, Rene Witte, Jonas B. Laurila, Christopher JO Baker, Chen-Ju Kuo, Simone Clematide, Fabio Rinaldi, Richard Farkas, György Móra, Kazuo Hara, Laura Furlong, Michael Rautschka, Mariana Lara Neves, Alberto Pascual-Morante, Qi Wei, Nigel Collier, Faisal Mahbub Chowdhury, Alberto Lavelli, Rafael Berlanga, Roser Morante, Vincent van Asch, Walter Daelemans, Erik van Mulligen, Jan Kors and Udo Hahn. Assessment of NER solutions against the first and second CALBC Silver Standard Corpus, Journal of Biomedical Semantics, Volume 2, Suppl 5, S11, October 2011.
  44. Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine (SMBM 2010), Cambridge, United Kingdom, October, 2010. Edited by Nigel Collier, Udo Hahn, Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo.
  45. Dietrich Rebholz-Schuhmann, Fabio Rinaldi, Sampo Pyysalo, Nigel Collier, Udo Hahn. Towards mature use of semantic resources for biomedical analyses. Journal of Biomedical Semantics, Volume 2, Suppl 5, S11, October 2011.
  46. Fabio Rinaldi, Simon Clematide, Gerold Schneider. SASEBio: Semi-Automated Semantic Enrichment of the Biomedical Literature. 1st International SystemsX.ch Conference on Systems Biology (poster presentation). Oct 24th-26th, Basel, Switzerland.
  47. Fabio Rinaldi, Simon Clematide, Gerold Schneider. ODIN: Advanced Text Mining in Support of the Curation Process. The Pacific Symposium on Biocomputing (PSB) 2012, Fairmont Orchid, Big Island of Hawaii, Jan 3rd-7th, 2012 (poster presentation).
  48. Simon Clematide, Fabio Rinaldi. Ranking interactions for a curation task. The Tenth International Conference on Machine Learning and Applications (special session on Machine Learning for Biomedical Literature Analysis and Text Retrieval). Honolulu, December 2011.
  49. Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman. Using ODIN for a PharmGKB revalidation experiment. The Journal of Biological Databases and Curation, Oxford Journals, 2012, bas021; doi:10.1093/database/bas021 [NOTE: presented at the Conference of the International Society for Biocuration, Washington D.C., April 2012], PMC3332569, PMID: 22529178
  50. Fabio Rinaldi, Gerold Schneider, Simon Clematide. Relation Mining Experiments in the Pharmacogenomics Domain. Journal of Biomedical Informatics, 2012. doi:10.1016/j.jbi.2012.04.014, PMID: 22580177
  51. Fabio Rinaldi, Simon Clematide and Simon Hafner. Ranking of CTD articles and interactions using the OntoGene pipeline. Proceedings of the BioCreative-2012 Workshop. Washington D.C., April 2012.
  52. Gerold Schneider, Fabio Rinaldi, Simon Clematide. Dependency parsing for interaction detection in pharmacogenomics. Proceedings of LREC 2012: The eighth international conference on Language Resources and Evaluation. Istanbul, 21-27 May 2012.
  53. Gerold Schneider, Simon Clematide, Gintarė Grigonytė, Fabio Rinaldi. Using syntax features and document discourse for relation extraction on PharmGKB and CTD. SMBM 2012, Zurich, September 3-4, 2012.
  54. Ananiadou, Sophia; Pyysalo, Sampo; Rebholz-Schuhmann, Dietrich; Rinaldi, Fabio; Salakoski, Tapio (eds.). Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine (SMBM 2012), Zurich, 2012. doi:10.5167/uzh-64476
  55. Fabio Rinaldi, Using biomedical databases as knowledge sources for large-scale text mining. E-LKR workshop, SEPLN 2012, Castellon de la Plana, Spain, September 7, 2012.
  56. Grigonytė, G., Rinaldi F., Volk, M. Change of Biomedical Domain Terminology Over Time. In Proc. of 5th Baltic Conf. On Human Language Technologies, Tartu, Estonia, October 4–5, 2012.
  57. Fabio Rinaldi, Gerold Schneider, Simon Clematide and Gintare Grigonyte, Notes about the OntoGene pipeline. AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text, November 2-4, 2012, Arlington, Virginia, USA.
  58. Gintare Grigonyte, Fabio Rinaldi and Martin Volk. Term evolution: use of biomedical terminologies. AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text, November 2-4, 2012, Arlington, Virginia, USA.
  59. Simon Clematide, Fabio Rinaldi. Ranking relations betweeen diseases, drugs, and genes for a curation task. Journal of Biomedical Semantics (BMC), 2012. doi:10.1186/2041-1480-3-S3-S5
  60. Fabio Rinaldi, Simon Clematide, Simon Hafner, Gerold Schneider, Gintare Grigonyte, Martin Romacker, Therese Vachon. Using the OntoGene pipeline for the triage task of BioCreative 2012, The Journal of Biological Databases and Curation, Oxford Journals, 2012. doi:10.1093/database/bas053, PMC3568389, PMID: 23396322
  61. Fabio Rinaldi. The OntoGene system: an advanced information extraction application for biological literature. NETTAB workshop on Integrated Bio-Search. November 14-16, 2012, Como, Italy. Also available in EMBnet.journal, Volume 18, Supplement B, pp 47-49.
  62. Fabio Rinaldi, Socorro Gama-Castro, Alejandra López-Fuentes, Yalbi Balderas-Martínez, Julio Collado-Vides. Digital Curation Experiments for RegulonDB, BioCuration 2013, April 10th, 2013, Cambridge, UK.
  63. Gerold Schneider, Simon Clematide, Tilia Ellendorff, Don Tuggener, Fabio Rinaldi. UZH in the BioNLP 2013 GENIA Shared Task. Proceedings of the BioNLP workshop, ACL 2013, Sofia, Bulgaria.
  64. Donald C. Comeau, Rezarta Islamaj Doğan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifang Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas Wiegers, Cathy Wu, and W. John Wilbur. BIoC: A Minimalist Approach to Interoperability for Biomedical Text Processing. The Journal of Biological Databases and Curation. Database 2013: bat064 doi:10.1093/database/bat064 published online September 18, 2013
  65. Fabio Rinaldi. Assisted Editing in the Biomedical Domain: Motivation and Challenges. Proceedings of DocEng 2013, Florence, Italy, September 10-12, 2013.
  66. Clematide, Simon; Martin, Davtyan; Rinaldi, Fabio; Rebholz-Schuhmann, Dietrich (2013). Exploiting BabelNet for multilingual biomedical synonym expansion. In: CLEF 2013: Evaluation Labs and Workshop: Online Working Notes, September 23-26, 2013, Valencia, Spain, 23 September 2013.
  67. Rebhoz-Schuhmann, Dietrich; Clematide, Simon; Rinaldi, Fabio; Kafkas, Senay; van Mulligen, Erik M; Bui, Chinh; Hellrich, Johannes; Lewin, Ian; Milward, David; Poprat, Michael; Jimeno-Yepes, Antonio; Hahn, Udo; Kors, Jan (2013). Entity recognition in parallel multi-lingual biomedical corpora: The CLEF-ER laboratory overview. In: Forner, Pamela; Mueller, Henning; Rosso, Paolo; Paredes, Roberto. Information Access Evaluation. Multilinguality, Multimodality, and Visualization. Valencia: Springer, 353-367. ISBN 978-3-642-40802-1.
  68. Hernani Marques, Fabio Rinaldi. PyBioC: a python implementation of the BioC core. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol. 1, pg. 2-4. Bethesda, Maryland, October 7-9, 2013.
  69. Fabio Rinaldi, Simon Clematide, Tilia Renate Ellendorff, Hernani Marques. OntoGene: CTD entity and action term recognition. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol. 1, pages 90-94. Bethesda, Maryland, October 7-9, 2013.
  70. Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Julio Collado-Vides. Assisted curation of growth conditions that affect gene expression in E. coli K-12. Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol. 1, pages 214-218. Bethesda, Maryland, October 7-9, 2013.
  71. Fabio Rinaldi, Allan Peter Davis, Christopher Southan, Simon Clematide, Tilia Renate Ellendorff, Gerold Schneider. ODIN: a customizable literature curation tool.   Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, vol. 1, pages 219-223. Bethesda, Maryland, October 7-9, 2013.
  72. Gintare Grigonyte, Simon Clematide, Fabio Rinaldi. How preferred are preferred terms? Kosem, I., Kallas, J., Gantar, P., Krek, S., Langemets, M., Tuulik, M. (eds.) 2013. Electronic lexicography in the 21st century: thinking outside the paper. Proceedings of the eLex 2013 conference, 17-19 October 2013, Tallinn, Estonia. Pages 452-459.
  73. Fabio Rinaldi. The OntoGene literature mining web service. NETTAB workshop on Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories.16-18 October 2013, Lido of Venice, Italy. Also available in EMBnet.journal, Volume 19, Supplement B, pp 32-35.
  74. Fabio Rinaldi, Socorro Gama-Castro, Alejandra López-Fuentes, Alberto Santos-Zavaleta, Simon Clematide, Tilia Renate Ellendorff, Julio Collado-Vides. Assisted curation of experimental methods in RegulonDB. BioCuration 2014, April 7th, 2014, Toronto, Canada.
  75. Tilia Ellendorff, Fabio Rinaldi, Simon Clematide. Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction. Proceedings of LREC 2014: The ninth international conference on Language Resources and Evaluation. Reykjavik, Iceland, 26-31 May 2014.
  76. Socorro Gama-Castro, Fabio Rinaldi, Alejandra Lopez-Fuentes, Yalbi Itzel Balderas-Martinez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, Julio Collado-Vides. Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12.Database 2014: bau049, Oxford Journals, 2014. doi:10.1093/database/bau049
  77. Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Doğan, Antonio Jimeno, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, and W. John Wilbur. BioC Interoperability Track Overview. The Journal of Biological Databases and Curation, Database 2014, doi: 10.1093/database/bau053
  78. Wanli Liu, Rezarta Islamaj Doğan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau. BioC implementations in Go, Perl, Python and Ruby. Database 2014:  bau059, Oxford Journals. doi:10.1093/database/bau059
  79. Fabio Rinaldi. Text Mining technologies for database curation. European Conference on Computational Biology (ECCB), Strasbourg, France, 7-10 September 2014 (highlight presentation).
  80. Zhu Yi and Fabio Rinaldi. OntoPDF: using a text mining pipeline to generate enriched pdf versions of scientific papers. Sixth International Symposium on Semantic Mining in Biomedicine (SMBM). University of Aveiro, Portugal, 6-7 October 2014.
  81. Hernani Marques and Fabio Rinaldi. OntoRest: Text Mining Web Services in BioC Format. Sixth International Symposium on Semantic Mining in Biomedicine (SMBM). University of Aveiro, Portugal, 6-7 October 2014.
  82. Lenz Furrer, Simon Clematide, Hernani Marques, Raul Rodriguez-Esteban, Martin Romacker, and Fabio Rinaldi. Collection-Wide Extraction of Protein-Protein Interactions. Sixth International Symposium on Semantic Mining in Biomedicine (SMBM). University of Aveiro, Portugal, 6-7 October 2014.
  83. Fabio Rinaldi. Semi-Automated Semantic Annotation of the Biomedical Literature. The 13th International Semantic Web Conference. Riva del Garda, Italy, 19-23 October 2014.
  84. Fabio Rinaldi. Text mining technologies for database curation. Sixth International Conference on Knowledge Discovery and Information Retrieval (KDIR), special session on Text Mining (SSTM). Rome, Italy, 24 October 2014.
  85. Fabio Rinaldi, Simon Clematide,  Hernani Marques, Tilia Ellendorff, Martin Romacker, and Raul Rodriguez-Esteban. OntoGene web services for biomedical text mining. BMC Bioinformatics 2014, 15(Suppl 14):S6  doi:10.1186/1471-2105-15-S14-S6
  86. Tilia Renate Ellendorff, Adrian van der Lek, Lenz Furrer, Fabio Rinaldi. A Combined Resource of Biomedical Terminology and its Statistics. Proceedings of the conference Terminology and Artificial Intelligence 2015 (Granada, Spain), pg. 39--50.
  87. Lenz Furrer, Susanne Kuker, John Berezowski, Horst Posthaus, Flavie Vial, Fabio Rinaldi. Constructing a Syndromic Terminology Resource for Veterinary Text Mining. Proceedings of the conference Terminology and Artificial Intelligence 2015 (Granada, Spain), pg. 61--70.
  88. Socorro Gama-Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira-Hernández, Irma Martínez-Flores, Lucia Pannier, Jaime Abraham Castro-Mondragón, Alejandra Medina-Rivera, Hilda Solano-Lira, César Bonavides-Martínez, Ernesto Pérez-Rueda, Shirley Alquicira-Hernández, Liliana Porrón-Sotelo, Alejandra López-Fuentes, Anastasia Hernández-Koutoucheva, Víctor Del Moral-Chávez, Fabio Rinaldi and Julio Collado-Vides. RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond. Nucleic Acids Research, 2015, D133-D143. doi:10.1093/nar/gkv1156
  89. Fabio Rinaldi,Tilia Renate Ellendorff, Sumit Madan, Simon Clematide, Adrian van der Lek, Theo Mevissen, Juliane Fluck. BioCreative V Track 4: A Shared Task for the Extraction of Causal Network Information in Biological Expression Language.
    The Journal of Biological Databases and Curation, 2016, baw067. doi:10.1093/database/baw067
  90. 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 M. 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. The Journal of Biological Databases and Curation, 2016, baw119. doi:10.1093/database/baw119
  91. Mauro Mazzocut, Ivana Truccolo, Marialuisa Antonini, Fabio Rinaldi, Paolo Omero, Emanuela Ferrarin, Paolo De Paoli, Carlo Tasso. Insight of Italian Web conversations in Complementary and Alternative Medicines and Cancer, Journal of Medical Internet Research, 2016, 18(6):e120. doi:10.2196/jmir.5521
  92. Tilia Renate Ellendorff, Simon Foster, Fabio Rinaldi. The PsyMine Corpus - A Corpus annotated with Psychiatric Disorders and their Etiological Factors. In: 10th edition of the Language Resources and Evaluation Conference, Portorož (Slovenia), 23 May 2016 - 28 May 2016.
  93. Marco Basaldella, Lenz Furrer, Nicola Colic, Tilia Renate Ellendorff, Carlo Tasso, Fabio Rinaldi. Using a Hybrid Approach for Entity Recognition in the Biomedical Domain. 7th International Symposium on Semantic Mining in Biomedicine. Potsdam, Germany, 4–5 August 2016, pg. 11–19.
  94. Dina Vishnyakova, Raul Rodriguez-Esteban, Khan Ozol and Fabio Rinaldi. Author Name Disambiguation in MEDLINE Based on Journal Descriptors and Semantic Types. Fifth workshop on building and evaluating resources for biomedical text mining. COLING 2016, Osaka, Japan.
  95. Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman, Annie Pardo; Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. Database (Oxford) 2017; 2017 (1): bax030. doi:10.1093/database/bax030
  96. Fabio Rinaldi, Oscar Lithgow, Socorro Gama-Castro, Hilda Solano, Alejandra López-Fuentes Luis José Muñiz Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides; Strategies towards digital and semi-automated curation in RegulonDB. Database (Oxford) 2017; 2017 (1): bax012. doi:10.1093/database/bax012
  97. Lenz Furrer, Fabio Rinaldi. OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task. Proceedings of the BioCreative V.5 Challenge Evaluation Workshop. Barcelona, Spain, 26–27 April 2017, pg. 175–182.
  98. Marco Basaldella, Lenz Furrer, Carlo Tasso,  Fabio Rinaldi. Entity Recognition in the Biomedical domain using a hybrid approach. Journal of Biomedical Semantics (2017), 8:51. doi:10.1186/s13326-017-0157-6
  99. Susanne Küker, Céline Faverjon, Lenz Furrer, John Berezowski, Horst Posthaus, Fabio Rinaldi, Flavie Vial. The value of necropsy reports for animal health surveillance. BMC Veterinary Research (2018) 14:191. doi:10.1186/s12917-018-1505-1
  100. Ivano Lauriola, Mirko Polato, Alberto Lavelli, Fabio Rinaldi, Fabio Aiolli. Learning Preferences for Large Scale Multi-label problems. Proceedings of International Conference of Artificial Neural Networks (ICANN), 2018.
  101. Ivano Lauriola, Riccardo Sella, Fabio Aiolli, Alberto Lavelli, Fabio Rinaldi. Learning Representations for Biomedical Named Entity Recognition. Proceedings of the 2nd Workshop on Natural Language for Artificial Intelligence (NL4AI), 2018.
  102. Lenz Furrer, Anna Jancso, Nicola Colic, Fabio Rinaldi. OGER++: Hybrid multi-type entity recognition.  Journal of Cheminformatics (2019) 11:1. doi:10.1186/s13321-018-0326-3