Dr. Fabio Rinaldi Office: 5.E.10 Tel.: +41 44 635 7132Fax: +41 44 635 6809fabio.rinaldi AT uzh.ch
Fabio Rinaldi is a lecturer and senior researcher at the University of Zurich. He is author or co-author of 90+ scientific papers (including 17 journal papers), dealing with topics such as Ontologies, Entity Extraction, Answer Extraction, Text Classification, Document and Knowledge Management, Language Resources and Terminology. He has a solid computational background and considerable practical experience derived from participation in four European Projects (LRE-Gist, LE-FaCiLE, ESPRIT-Concerto, IST-Parmenides) and internal/departmental projects (ExtrAns, OntoGene). He has been involved in all the stages of project development, from initial draft to final report. He has direct work experience in major research centres of four European countries (ITC/IRST-Italy, UMIST-UK, GMD/IPSI-Germany and University of Zurich, Switzerland) and speaks four major European languages (Italian, English, German and Spanish). He is the initiator and team leader of the OntoGene project, which focuses on Text Mining for biomedical applications. Currently he is principal investigator of the SNF-funded SASEBio project (Semi-Automated Semantic Enrichment of the Biomedical Literature).
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Office: 5.E.10 Institute of Computational Linguistics University of Zurich Binzmühlestrasse 14 CH-8050 Zurich Switzerland
List of publications (automatically imported from ZORA)
Rinaldi, Fabio; Clematide, Simon; Hafner, Simon; Schneider, Gerold; Grigonyte, Gintare; Romacker, Martin; Vachon, Therese (2013). Using the OntoGene pipeline for the triage task of BioCreative 2012. Database, 2013:bas053.
Grigonyte, Gintare; Rinaldi, F; Volk, M (2012). Term evolution: use of biomedical terminologies. In: AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text, Arlington, 03 November 2012 - 05 November 2012, 79-80.
Rinaldi, Fabio; Schneider, Gerold; Clematide, Simon; Grigonyte, Gintare (2012). Notes about the OntoGene pipeline. In: AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text, Arlington, Virginia, USA., 02 November 2012 - 04 November 2012.
Grigonyte, Gintare; Rinaldi, Fabio; Volk, Martin (2012). Change of biomedical domain terminology over time. In: Human Language Technologies – The Baltic Perspective (Baltic HLT 2012), Tartu, 04 October 2012 - 05 October 2012, 74-81.
Rinaldi, Fabio (2012). Using biomedical databases as knowledge sources for large-scale text mining. In: 2nd International Workshop on Exploiting Large Knowledge Repositories, Castellon de la Plana, Spain, 07 September 2012 - 07 September 2012.
Schneider, Gerold; Clematide, Simon; Grigonyte, Gintare; Rinaldi, Fabio (2012). Using syntax features and document discourse for relation extraction on PharmGKB and CTD. In: SMBM 2012, Zurich, Switzerland, 03 September 2012 - 04 September 2012, 52-57.
Schneider, Gerold; Rinaldi, Fabio; Clematide, Simon (2012). Dependency parsing for interaction detection in pharmacogenomics. In: LREC 2012: The eighth international conference on Language Resources and Evaluation, Istanbul, 21 May 2012 - 25 May 2012.
Rinaldi, Fabio; Clematide, Simon; Hafner, Simon (2012). Ranking of CTD articles and interactions using the OntoGene pipeline. In: 2012 {BioCreative} workshop, Washington D.C., 04 April 2012 - 05 April 2012.
Clematide, Simon; Rinaldi, Fabio (2012). Ranking relations between diseases, drugs and genes for a curation task. Journal of Biomedical Semantics, 3(Suppl 3):S5.
Rinaldi, Fabio; Schneider, Gerold; Clematide, Simon (2012). Relation Mining Experiments in the Pharmacogenomics Domain. Journal of Biomedical Informatics, 45(5):851-861.
Rinaldi, Fabio (2012). The OntoGene system: an advanced information extraction application for biological literature. EMBnet Journal, 18(Suppl B):47-49.
Rinaldi, Fabio; Clematide, Simon; Garten, Yael; Whirl-Carrillo, Michelle; Gong, Li; Hebert, Joan M.; Sangkuhl, Katrin; Thorn, Caroline F; Klein, Teri E; Altman, Russ B (2012). Using ODIN for a PharmGKB re-validation experiment. Database: The Journal Of Biological Databases And Curation, 2012:bas021.
Clematide, S; Rinaldi, F (2011). Ranking Interactions for a Curation Task. In: 10th International Conference on Machine Learning and Applications and Workshops, Honolulu, Hawaii USA , 18 December 2011 - 21 December 2011, 100-105.
Schneider, G; Clematide, S; Rinaldi, F (2011). Detection of interaction articles and experimental methods in biomedical literature. BMC Bioinformatics, 12(Suppl 8):S13.
Tuggener, D; Klenner, M; Schneider, G; Clematide, S; Rinaldi, F (2011). An incremental model for the coreference resolution task of BioNLP 2011. In: BioNLP 2011, Portland, Oregon, USA, 23 June 2011 - 24 June 2011, 151-152.
Schneider, Gerold; Rinaldi, Fabio (2011). A data-driven approach to alternations based on protein-protein interactions. In: III Congreso Internacional de Lingüística de Corpus, Valencia, Spain, 07 April 2011 - 09 April 2011, 597-607.
Clematide, S; Rinaldi, F; Schneider, G (2011). OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization. In: Second CALBC Workshop, Hinxton, Cambridgeshire, UK, 16 March 2011 - 18 March 2011, 48-51.
Rinaldi, F; Schneider, G; Clematide, S (2011). Mining complex Drug/Gene/Disease relations. In: Pacific Symposium on Biocomputing Workshop "Mining the Pharmacogenomics Literature", Hawaii, 03 January 2011 - 07 January 2011.
Rebholz-Schuhmann, D; Jimeno, A; Li, C; Kafkas, S; Lewin, I; Kang, N; Corbett, P; Milward, D; Buyko, E; Beisswanger, E; Hornbostel, K; Kouznetsov, A; Witte, R; Laurila, J; Baker, C; Kuo, C; Clematide, S; Rinaldi, F; Farkas, R; Móra, G; Hara, K; Furlong, L; Rautschka, M; Neves, M; Pascual-Montan, A; Wei, Q; Collier, N; Chowdhury, F; Lavelli, A; Berlanga, R; Morante, R; Van Asch, V; Daelemans, W; Marina, J; van Mulligen, E; Kors, J; Hahn, U (2011). Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Journal of Biomedical Semantics, 2(Suppl 5):S11.
Arighi, C; Roberts, P; Agarwal, S; Bhattacharya, S; Cesareni, G; Chatr-aryamontri, A; Clematide, S; Gaudet, P; Giglio, M; Harrow, I; Huala, E; Krallinger, M; Leser, U; Li, D; Liu, F; Lu, Z; Maltais, L; Okazaki, N; Perfetto, L; Rinaldi, F; Saetre, R; Salgado, D; Srinivasan, P; Thomas, P; Toldo, L; Hirschman, L; Wu, C (2011). BioCreative III interactive task: an overview. BMC Bioinformatics, 12(Suppl 8):S4.
Rinaldi, F; Kaljurand, K; Saetre, R (2011). Terminological resources for text mining over biomedical scientific literature. Artificial Intelligence in Medicine, 52(2):107 - 114.
Krallinger, M; Vazquez, M; Leitner, F; Salgado, D; Chatr-aryamontri, A; Winter, A; Perfetto, L; Briganti, L; Licata, L; Iannuccelli, M; Castagnoli, L; Cesareni, G; Tyers, M; Schneider, G; Rinaldi, F; Leaman, R; Gonzalez, G; Matos, S; Kim, S; Wilbur, W; Rocha, L; Shatkay, H; Tendulkar, A; Agarwal, S; Liu, F; Wang, X; Rak, R; Noto, K; Elkan, C; Lu, Z (2011). The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. BMC Bioinformatics, 12(Suppl 8):S3.
Lu, Z; Kao, H Y; Wei, C H; Huang, M; Liu, J; Kuo, C J; Hsu, C N; Tsai, R; Dai, H J; Okazaki, N; Cho, H C; Gerner, M; Solt, I; Agarwal, S; Liu, F; Vishnyakova, D; Ruch, P; Romacker, M; Rinaldi, F; Bhattacharya, S; Srinivasan, P; Liu, H; Torii, M; Matos, S; Campos, D; Verspoor, K; Livingston, K; Wilbur, W (2011). The gene normalization task in BioCreative III. BMC Bioinformatics, 12(Suppl 8):S2.
Rebholz-Schuhmann, D; Rinaldi, F; Pyysalo, S; Collier, N; Hahn, U (2011). Towards mature use of semantic resources for biomedical analyses. Journal of Biomedical Semantics, 2(Suppl 5):1-4.
Rinaldi, F; Clematide, S; Schneider, G; Romacker, M; Vachon, Th (2010). ODIN: an advanced interface for the curation of biomedical literature. In: Biocuration 2010, Tokyo, Japan, 11 October 2010 - 14 October 2010.
Rinaldi, F; Schneider, G; Clematide, S; Romacker, M; Vachon, T (2010). OntoGene (Team 65): preliminary analysis of participation in BioCreative III. In: BioCreative III workshop, Bethesda, Maryland, 13 September 2010 - 15 September 2010.
Rinaldi, F; Schneider, G; Kaljurand, K; Clematide, S; Vachon, T; Romacker, M (2010). OntoGene in BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3):472-480.
Rinaldi, F; Schneider, G; Kaljurand, K; Clematide, S (2009). Effective Mining of Protein Interactions. In: Third international symposium on languages in biology and medecine (LBM 2009), Jeju Island, South Korea, 08 November 2009 - 10 November 2009, 115-118.
Kaljurand, K; Rinaldi, F; Kappeler, T; Schneider, G (2009). Using existing biomedical resources to detect and ground terms in biomedical literature. In: Combi, C; Shahar, Y; Abu-Hanna, A. Artificial Intelligence in Medicine: 12th Conference on Artificial Intelligence in Medicine, AIME 2009, Verona, Italy, July 18-22, 2009. Proceedings. Berlin, 225-234. ISBN 978-3-642-02975-2.
Kaljurand, K; Schneider, G; Rinaldi, F (2009). UZurich in the BioNLP 2009 Shared Task. In: BioNLP 2009 Companion Volume: Shared Task on Event Extraction, NAACL/HLT, Boulder, Colorado, 04 June 2009 - 05 June 2009, 28-36.
Kappeler, T; Kaljurand, K; Rinaldi, F (2009). TX Task: Automatic detection of focus organisms in biomedical publications. In: Workshop on BioNLP, Boulder, June 2009 - June 2009, 80-88.
Schneider, G; Kaljurand, K; Rinaldi, F (2009). Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. In: Gelbukh, A. Computational Linguistics and Intelligent Text Processing. Berlin, 406-417. ISBN 978-3-642-00381-3.
Kaljurand, K; Rinaldi, F; Kappeler, T; Schneider, G (2009). Detecting and grounding terms in biomedical literature. Advances in Computational Linguistics, 41:15-26.
Rinaldi, F; Rebholz-Schuhmann, D (2009). Support tools for literature-based information access in molecular biology. In: Enami, K. Proceedings of the 3rd International Universal Communication Symposium. New York, NY, USA, 273-277. ISBN 978-1-60558-641-0.
Kappeler, T; Clematide, S; Kaljurand, K; Schneider, G; Rinaldi, F (2008). Towards automatic detection of experimental methods from biomedical literature. In: Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, 01 September 2008 - 03 September 2008, 61-68.
Rinaldi, F; Kappeler, T; Kaljurand, K; Schneider, G; Klenner, M; Clematide, S; Hess, M; von Allmen, J M; Parisot, P; Romacker, M; Vachon, T (2008). OntoGene in BioCreative II. Genome Biology, 9 (Sup:1-12.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M (2008). Dependency-based relation mining for biomedical literature. In: The 6th edition of the Language Resources and Evaluation Conference (LREC 2008), Marrakech, Morocco , 28 May 2008 - 30 May 2008, 1-6.
Rinaldi, F; Schneider, G; Kaljurand, K (2008). Tools for detection of protein interactions in biomedical literature. In: Genomes to Systems Conference 2008, Manchester, UK, 17 March 2008 - 19 March 2008.
Schneider, G; Kaljurand, K; Rinaldi, F; Kuhn, T (2007). Pro3Gres parser in the CoNLL domain adaptation shared task. In: ACL Conference, Workshop on Computational Natural Language Learning (CoNLL-XI) Shared Task, Prague, June 2007 - June 2007, 1161-1165.
Rinaldi, F; Kappeler, T; Kaljurand, K; Schneider, G; Klenner, M; Hess, M; von Allmen, J M; Romacker, M; Vachon, T (2007). OntoGene in Biocreative II. In: Second BioCreative Challenge Evaluation Workshop, Madrid, Spain, 23 April 2007 - 25 April 2007.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M; Andronis, C; Konstanti, O; Persidis, A (2007). Mining of functional relations between genes and proteins over biomedical scientific literature using a deep-linguistic approach. Artificial Intelligence in Medicine, 39(2):127-136.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M; Romacker, M (2006). An environment for relation mining over richly annotated corpora: the case of GENIA. BMC Bioinformatics, 7(Sup. 3):S3.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M; Romacker, M (2006). An environment for relation mining over richly annotated corpora: the case of GENIA. In: Second International Symposium on Semantic Mining in Biomedicine (SMBM 2006), Jena, Germany, 09 April 2006 - 12 April 2006, 68-75.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M (2006). Tools for text mining over biomedical literature. In: ECAI2006, Riva del Garda, Italy, 2006 - 2006, 825-826.
SanJuan, E; Dowdall, J; Imbekwe-SanJuan, F; Rinaldi, F (2005). A symbolic approach to automatic multiword term structuring. Computer Speech and Language, 19(4):524-542.
Rinaldi, F; Schneider, G; Kaljurand, K; Hess, M; Andronis, C; Persidis, A (2005). Relation mining over a corpus of scientific literature. In: 10th Conference on Artificial Intelligence in Medicine, AIME 2005, Aberdeen, Scotland, 23 July 2005 - 27 July 2005, 535-544.
Fuchs, N E; Hoefler, S; Kaljurand, K; Rinaldi, F; Schneider, G (2005). Attempto controlled English: a knowledge representation language readable by humans and machines. In: Reasoning Web, First International Summer School 2005, Msida, Malta, July 2005 - July 2005, 213-250.
Schneider, G; Rinaldi, F; Kaljurand, K; Hess, M (2005). Closing the gap: cognitively adequate, fast broad-coverage grammatical role parsing. In: 2nd International Workshop on Natural Language and Cognitive Science (NLUCS-2005), Miami, USA, May 2005 - May 2005, 178-184.
Rinaldi, F; Yuste, E; Schneider, G; Hess, M; Roussel, D (2005). Exploiting technical terminology for knowledge management. In: Ontology Learning from Text: Methods, Evaluation and Applications, Amsterdam: IOS Press (Frontiers in artificial intelligence and applications, edited by J. Breuker et al., volume 123), 2005 - 2005, 140-154.
Rinaldi, F; Schneider, G; Kaljurand, K; Dowdall, J; Andronis, C; Persidis, A; Konstanti, O (2004). Mining relations in the GENIA corpus. In: Second European Workshop on Data Mining and Text Mining for Bioinformatics, Pisa, Italy, September 2004 - September 2004, 61-68.
Schneider, G; Rinaldi, F; Dowdall, J (2004). A robust and hybrid deep-linguistic theory applied to large scale parsing. In: COLING-2004 Robust Methods in Analysis of Natural language Data, Geneva, Switzerland, August 2004 - August 2004, 14-23.
Rinaldi, F; Dowdall, J; Schneider, G (2004). Answering questions in the genomics domain. In: ACL-2004 workshop on Question Answering in Restricted Domains, Barcelona, Spain., July 2004 - July 2004, 46-53.
Spiliopoulou, M; Rinaldi, F; Black, B; Zarri, G P; Mueller, R M; Brunzel, M; Theodoulidis, B; Orphanos, G; Hess, M; Dowdall, J; McNaught, J; King, M; Persidis, A; Bernard, L (2004). Coupling information extraction and data mining for ontology learning in PARMENIDES. In: RIAO'2004, Avignon, France, April 2004 - April 2004, 156-169.
Schwitter, R; Rinaldi, F; Clematide, S (2004). The importance of how-questions in technical domains. In: Proc of the Question-Answering workshop of TALN 04, Fez, Morocco, April 2004 - April 2004, 451-460.
Dowdall, J; Rinaldi, F; Persidis, A; Kaljurand, K; Schneider, G; Hess, M (2004). Terminology expansion and relation identification between genes and pathways. In: Workshop on Terminology, Ontology and Knowledge Representation, Universit Jean Moulin (Lyon 3), January 2004 - January 2004, 61-68.
Kaljurand, K; Rinaldi, F; Dowdall, J; Hess, M (2004). Exploiting language resources for semantic web annotations. In: LREC-2004, Lisbon, Portugal, 2004 - 2004, 815-818.
Schneider, G; Rinaldi, F; Dowdall, J (2004). Fast, deep-linguistic statistical minimalist dependency parsing. In: COLING-2004 Recent Advances in Dependency Grammars, Geneva, Switzerland, 2004 - 2004, 33-40.
Rinaldi, F; Hess, M; Dowdall, J; Aliod Moll, D; Schwitter, R (2004). Question answering in terminology-rich technical domains. In: Maybury, M T. New directions in question answering. Menlo Park, 133-140. ISBN 978-0-262-63304-8.
Klenner, M; Rinaldi, F; Hess, M (2004). Steps towards Semantically Annotated Language Resources. In: LREC-2004, Lisbon, Portugal, 2004 - 2004, 1161-1164.
Schneider, G; Rinaldi, F; Kaljurand, K; Hess, M (2004). Steps towards a GENIA dependency treebank. In: Third Workshop on Treebanks and Linguistic Theories (TLT) 2004, Tübingen, Germany, 2004 - 2004, 137-149.
Dowdall, J; Lowe, W; Elleman, J; Rinaldi, F; Hess, M (2004). The role of MultiWord Terminology in Knowledge Management. In: LREC-2004, Lisbon, Portugal, 2004 - 2004, 915-918.
Rinaldi, F; Dowdall, J; Hess, M; Elleman, J; Zarri, G P; Persidis, A; Bernard, L; Karanikas, H (2003). Multilayer annotations in Parmenides. In: K-CAP2003 workshop on, Sanibel, Florida, USA, October 2003 - October 2003.
Rinaldi, F; Dowdall, J; Hess, M; Mollà Aliod, D; Schwitter, R; Kaljurand, K (2003). Knowledge-based Question Answering. In: Knowledge-Based Intelligent Information & Engineering Systems, KES-2003, Oxford, UK, September 2003 - September 2003.
Dowdall, J; Rinaldi, F; Imbekwe-SanJuan, F; SanJuan, E (2003). Complex structuring of term variants for Question Answering. In: MultiWord Expressions: Analysis, Acquisition and Treratment. Workshop at the 41st Annual Meeting of the Association for Computational Linguistics ACL-03, Sapporo, Japan, July 2003 - July 2003, 1-8.
Rinaldi, F; Dowdall, J; Kaljurand, K; Hess, M; Mollà Aliod, D (2003). Exploiting paraphrases in a question answering system. In: ACL-2003, Second International Workshop on Paraphrasing: Paraphrase Acquisition and Applications, Sapporo, Japan, July 2003 - July 2003, 25-32.
Rinaldi, F; Dowdall, J; Hess, M; Kaljurand, K; Persidis, A; Theodoulidis, B; Black, B; McNaught, J; Karanikas, H; Vasilakopoulos, A; Zervanou, K; Bernard, L; Zarri, G P; Bruins Slot, H; van der Touw, C; Daniel-King, M; Underwood, N; Lisowska, A; van der Plas, L; Sauron, V; Spiliopoulou, M; Brunzel, M; Elleman, J; Orphanos, G; Mavroudakis, T; Taraviras, S (2003). Parmenides: an opportunity for ISO TC37 SC4? In: ACL-2003: Workshop on Linguistic Annotation: Getting the Model Right, Sapporo, Japan, July 2003 - July 2003, 38-45.
Mollà Aliod, D; Schwitter, R; Rinaldi, F; Dowdall, J; Hess, M (2003). Anaphora resolution in ExtrAns. In: International Symposium on Reference Resolution and Its Applications to Question Answering and Summarization, Venice, Italy, June 2003 - June 2003, 67-74.
Rinaldi, F; Dowdall, J; Hess, M; Kaljurand, K; Karlsson, M (2003). The role of technical Terminology in Question Answering. In: Terminologie et Intelligence Artificielle, TIA-2003, Strasbourg, France, March 2003 - March 2003, 156-165.
Aliod Moll, D; Rinaldi, F; Schwitter, R; Dowdall, J; Hess, M (2003). Answer Extraction from Technical Texts. IEEE Intelligent Systems, 18(4):12-17.
Rinaldi, F; Kaljurand, K; Dowdall, J; Hess, M (2003). Breaking the deadlock. In: ODBASE, 2003 (International Conference on Ontologies, Databases and Applications of SEmantics), Catania, Italy, 2003 - 2003, 876-888.
Yuste, E; Rinaldi, F (2003). Extracción automática de respuestas para documentación técnica. In: SEPLN 2003 (XIX Congreso de la Sociedad Espaola para el Procesamiento del Lenguaje Natural), Alcal de Henares (Madrid), Spain, 2003 - 2003.
Mollà Aliod, D; Rinaldi, F; Schwitter, R; Dowdall, J; Hess, M (2003). NLP for answer extraction in technical domains. In: 10th Conference of The European Chapter of the Association for Conputational Linguistics. Workshop: Natural Language Processing for Question Answering EACL-2003, Budapest, Hungary, 2003 - 2003, 5-11.
Rinaldi, F; Dowdall, J; Hess, M; Kaljurand, K; Koitand, M; Kahusk, N; Vider, K (2002). Terminology as knowledge in answer extraction. In: TKE-2002: 6th International Conference on Terminology and Knowledge Engineering, Nancy, France, August 2002 - August 2002.
Dowdall, J; Hess, M; Kahusk, N; Kaljurand, K; Koit, M; Rinaldi, F; Vider, K (2002). Technical terminology as a critical resource. In: LREC-2002, Las Palmas, Spain, May 2002 - May 2002.
Hess, M; Dowdall, J; Rinaldi, F (2002). The challenge of technical text. In: LREC-2002, Workshop on Question Answering: Strategy and Resources, Las Palmas, Spain, May 2002 - May 2002.
Rinaldi, F; Hess, M; Mollà Aliod, D; Schwitter, R; Dowdall, J; Schneider, G; Fournier, R (2002). Answer extraction in technical domains. In: Computational Linguistics and Intelligent Text Processing. Lecture Notes in Computer Science. VOL. 2276, Mexico City, Mexico, February 2002 - February 2002, 165-177.
Rinaldi, F; Dowdall, J; Hess, M; Mollà Aliod, D; Schwitter, R (2002). Towards answer extraction: an application to technical domains. In: ECAI 2002. Proceedings of the 15th European Conference on Artificial Intelligence, Amsterdam, Netherlands, 2002 - 2002.
Clematide, S; Rinaldi, F; Schneider, G (2010). OntoGene in CALBC. In: First CALBC Workshop, Hinxton, Cambridgeshire, UK, 17 June 2010 - 18 June 2010, 30-31.
Forschungsteam und Doktoranden
