List of publications by members of the OntoGene project, in chronological order. Journal publications are marked in blue.

  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. Combining Shallow and Deep Processing for a Robust, Fast, Deep-Linguistic Dependency Parser. European Summer School in Logic, Language and Information ESSLLI 2004, Nancy, France. pdf
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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. Elsevier Science.
  9. Julie Weeds, James Dowdall, Gerold Schneider, Bill Keller, David Weir. Using Distributional Similarity to Organise BioMedical Terminology. Terminology: Special issue on Application-driven Terminology engineering. Ed. Maria-Teresa Cabré, Annes Condamines, Fidelia Ibekwe-SanJuan. John Benjamins, Amsterdam.
  10. 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.
  11. 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.
  12. 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.
  13. Kaarel Kaljurand, Fabio Rinaldi, Gerold Schneider. Prolog-based query interface to syntactic dependencies extracted from biomedical literature. IFI Technical Report, ifi-2006.04.
  14. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess, Martin Romacker. An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA. Accepted for publication at SMBM 2006: 2nd International Symposium on Semantic Mining in Biomedicine. Jena, Germany, April 9th-12th 2006.
  15. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Tools for Text Mining over Biomedical Literature. Poster to be presented at ECAI2006.
  16. 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.
  17. 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
  18. 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).  
  19. 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. 
  20. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand. Tools for detection of Protein Interactions in Biomedical Literature. Genome to Systems, Manchester, UK. 17-19 March 2008.  
  21. Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess. Dependency-Based Relation Mining for Biomedical Literature. LREC 2008, Marrakech, Morocco. May 2008. 
  22. Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, Gerold Schneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marc von Allmen, Pierre Parisot, Martin Romacker, Therese Vachon. OntoGene in BioCreative II. Genome Biology, 2008, 9:S13.
  23. 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). 
  24. Kaarel Kaljurand. ACE View — an ontology and rule editor based on Attempto Controlled English. 5th OWL Experiences and Directions Workshop (OWLED 2008).
  25. Kaarel Kaljurand. ACE View — an ontology and rule editor based on controlled English. Proceedings of the Poster and Demonstration Session at the 7th International Semantic Web Conference (ISWC2008), CEUR Workshop Proceedings, 2008.
  26. Kaarel Kaljurand, Thomas Kappeler, Gerold Schneider, Fabio Rinaldi.
    Detecting and grounding terms in biomedical literature. CICLING 2009. 
  27. Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi.Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009.
  28. Thomas Kappeler, Kaarel Kaljurand, Fabio Rinaldi. TX Task: Automatic Detection of Focus Organisms in Biomedical Publications. BioNLP workshop, NAACL/HLT, Boulder, Colorado 2009.
  29. Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi. UZurich in the BioNLP 2009 Shared Task. BioNLP workshop, NAACL/HLT, Boulder, Colorado, 2009.
  30. 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.
  31. 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.
  32. Fabio Rinaldi, Dietrich Rebholz-Schuhmann. Support tools for literature-based information access in the genomics domain. 3rd International Universal Communication Symposium. Tokyo, December 2009.
  33. 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>
  34. Fabio Rinaldi, Simon Clematide, Gerold Schneider. OntoGene in CALBC. Proceedings of the CALBC workshop. Hinxton, Cambridge, June, 2010.
  35. 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.
  36. 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>
  37. 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.
  38. 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.
  39. 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.
  40. Gerold Schneider and Fabio Rinaldi. A data-driven approach to alternations based on protein-protein interactions. To appear in Proceedings of the 3rd Congreso Internacional de Lingüística de Corpus (CILC), Valencia, Spain, 7-9 April, 2011.
  41. 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.
  42. 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
  43. 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.
  44. 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.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.
  50. 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.
  51. 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).
  52. 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.
  53. Fabio Rinaldi, Gerold Schneider, Simon Clematide. Relation Mining Experiments in the Pharmacogenomics Domain. Journal of Biomedical Informatics (accepted for publication, subject to revision).
  54. 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 re-validation experiment. Conference of the International Society for Biocuration, 2012. (accepted for publication) 
 

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