Fabio Rinaldi

Fabio Rinaldi, Dr.

Academic Associate

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Fabio Rinaldi was from 2005 to 2020 a lecturer and senior researcher at the University of Zurich, where he established and lead the biomedical text mining group.

Currently he is the leader of the NLP team at the Dalle Molle Institute for Artificial Intelligence (IDSIA) in Lugano.

He co-authored more than 100 scientific papers (including more than 20 journal papers), dealing with topics such as Ontologies, Entity Extraction, Answer Extraction, Text Classification, Document and Knowledge Management, Language Resources and Terminology.

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    Office: AND-2-30
    Department of Computational Linguistics
    University of Zurich
    Andreasstrasse 15
    CH-8050 Zurich
    Switzerland

List of publications (automatically imported from ZORA)

ZORA Publication List

Publications

Sedlakova, Jana; Daniore, Paola; Horn Wintsch, Andrea; Wolf, Markus; Stanikić, Mina; Haag, Christina; Sieber, Chloé; Schneider, Gerold; Staub, Kaspar; Ettlin, Dominik Alois; Grübner, Oliver; Rinaldi, Fabio; von Wyl, Viktor (2023). Challenges and best practices for digital unstructured data enrichment in health research: A systematic narrative review. PLOS Digital Health, 2(10):e0000347.
Shaitarova, Anastassia; Zaghir, Jamil; Lavelli, Alberto; Krauthammer, Michael; Rinaldi, Fabio (2023). Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey. Yearbook of medical informatics, 32(01):230-243.
Gaspar, Frederic; Lutters, Monika; Beeler, Patrick Emanuel; Lang, Pierre Olivier; Burnand, Bernard; Rinaldi, Fabio; Lovis, Christian; Csajka, Chantal; Le Pogam, Marie-Annick (2022). Automatic Detection of Adverse Drug Events in Geriatric Care: Study Proposal. JMIR research protocols, 11(11):e40456.
Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Horvath, Aron N; Nooralahzadeh, Farhad; Krauthammer, Michael (2022). Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 Juni 2022 - 17 Juni 2022, 322-329.
Cornelius, Joseph; Lithgow-Serrano, Oscar; Kanjirangat, Vani; Rinaldi, Fabio; Fujimoto, Koji; Nishio, Mizuho; Sugiyama, Osamu; Ichikawa, Kana; Nooralahzadeh, Farhad; Horvath, Aron N; Krauthammer, Michael (2022). Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task. In: NTCIR 16 Conference: Proceedings of the 16th NTCIR Conference on Evaluation of Information Access Technologies, Tokyo, Japan, 14 Juni 2022 - 17 Juni 2022, NTCIR.
Sedlakova, Jana; Daniore, Paola; Horn Wintsch, Andrea; Wolf, Markus; Stanikic, Mina; Haag, Christina; Sieber, Chloé; Schneider, Gerold; Staub, Kaspar; Ettlin, Dominik Alois; Grübner, Oliver; Rinaldi, Fabio; von Wyl, Viktor (2022). Challenges and best practices for digital unstructured data enrichment in health research: a systematic narrative review. medRxiv 22278137, Cold Spring Harbor Laboratory.
Edry, Tamar; Maani, Nason; Sykora, Martin; Elayan, Suzanne; Hswen, Yulin; Wolf, Markus; Rinaldi, Fabio; Galea, Sandro; Gruebner, Oliver (2021). Real-time geospatial surveillance of localized emotional stress responses to COVID-19: a proof of concept analysis. Health & Place, 70:102598.
Shaitarova, Anastassia; Rinaldi, Fabio (2021). Negation typology and general representation models for cross-lingual zero-shot negation scope resolution in Russian, French, and Spanish. In: Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Student Research Workshop, Online, 6 June 2021 - 11 June 2021, ACL Anthology.
Zühlke, Irene; Berezowski, John; Bodmer, Michèle; Küker, Susanne; Göhring, Anne; Rinaldi, Fabio; Faverjon, Céline; Gurtner, Corinne (2021). Factors associated with cattle necropsy submissions in Switzerland, and their importance for surveillance. Preventive veterinary medicine, 187:105235.
Shaitarova, Anastassia; Furrer, Lenz; Rinaldi, Fabio (2020). Cross-lingual transfer-learning approach to negation scope resolution. In: Swiss Text Analytics Conference & Conference on Natural Language Processing 2020, Zurich, 23 June 2020 - 25 June 2020, CEUR-WS.
Furrer, Lenz; Cornelius, Joseph; Rinaldi, Fabio (2019). UZH@CRAFT-ST: a Sequence-labeling Approach to Concept Recognition. In: Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, Hong Kong, China, 4 November 2019 - 5 November 2019. Association for Computational Linguistics, 185-195.
Vishnyakova, Dina; Rodriguez-Esteban, Raul; Rinaldi, Fabio (2019). A new approach and gold standard toward author disambiguation in MEDLINE. Journal of the American Medical Informatics Association (JAMIA), 26(10):1037-1045.
Hutmacher, Cornelia; Volta, Laura; Rinaldi, Francesco; Murer, Patrizia; Myburgh, Renier; Manz, Markus G; Neri, Dario (2019). Development of a novel fully-human anti-CD123 antibody to target acute myeloid leukemia. Leukemia Research, 84:106178.
Ellendorff, Tilia; Furrer, Lenz; Colic, Nicola; Aepli, Noëmi; Rinaldi, Fabio (2019). Approaching SMM4H with Merged Models and Multi-task Learning. In: ACL 2019 FOURTH CONFERENCE ON MACHINE TRANSLATION (WMT19), Florence, Italy, 1 August 2019 - 2 August 2019. ACL, 58-61.
Colic, Nicola; Rinaldi, Fabio (2019). Improving spaCy dependency annotation and PoS tagging web service using independent NER services. Genomics & Informatics, 17(2):e21.
Kim, J D; Cohen, K B; Collier, N; Lu, Z; Rinaldi, F (2019). Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining. Genomics & Informatics, 17(2):e12.
Sheikhalishahi, Seyedmostafa; Miotto, Riccardo; Dudley, Joel T; Lavelli, Alberto; Rinaldi, Fabio; Osmani, Venet (2019). Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review. JMIR Medical Informatics, 7(2):e12239.
Furrer, Lenz; Jancso, Anna; Colic, Nicola; Rinaldi, Fabio (2019). OGER++: hybrid multi-type entity recognition. Journal of Cheminformatics, 11(1):7.
Rodriguez-Esteban, Raul; Vishnyakova, Dina; Rinaldi, Fabio (2019). Revisiting the decay of scientific email addresses. bioRxiv 633255, Cold Spring Harbor Laboratory.
Holderness, Eben; Yepes, Antonio Jimeno; Lavelli, Alberto; Minard, Anne-Lyse; Pustejovsky, James; Rinaldi, Fabio (2019). Proceedings of the Tenth International Workshop on Health Text Mining and Information Analysis (LOUHI 2019). In: Association for Computational Linguistics, Hong Kong, November, Hong Kong, 2019 - 2019.
Ellendorff, Tilia; Cornelius, Joseph; Gordon, Heath; Colic, Nicola; Rinaldi, Fabio (2018). UZH@SMM4H: System Descriptions. In: SMM4H: The 3rd Social Media Mining for Health Applications Workshop and Shared Task, Brussels, 30 November 2018 - 30 November 2018, 56-60.
Lauriola, Ivano; Sella, Riccardo; Aiolli, Fabio; Lavelli, Alberto; Rinaldi, Fabio (2018). Learning Representations for Biomedical Named Entity Recognition. In: 2nd workshop on Natural Language for Artificial Intelligence, Trento, 22 November 2018 - 23 November 2018. AI2, 83-94.
Lauriola, Ivano; Polato, Mirko; Lavelli, Alberto; Rinaldi, Fabio; Aiolli, Fabio (2018). Learning Preferences for Large Scale Multi-label Problems. In: International Conference on Artificial Neural Networks, Rhodes, Greece, 4 October 2018 - 7 October 2018. Springer, 546-555.
Küker, Susanne; Faverjon, Céline; Furrer, Lenz; Berezowski, John; Posthaus, Horst; Rinaldi, Fabio; Vial, Flavie (2018). The value of necropsy reports for animal health surveillance. BMC Veterinary Research, 14:191.
Basaldella, Marco; Furrer, Lenz; Tasso, Carlo; Rinaldi, Fabio (2017). Entity recognition in the biomedical domain using a hybrid approach. Journal of Biomedical Semantics, 8(1):51.
Rinaldi, Fabio; Furrer, Lenz; Basaldella, Marco (2017). Efficient and Accurate Entity Recognition for Biomedical Text. In: BioCreative VI Workshop, Bethesda, MD, USA, 18 October 2017 - 20 October 2017, 195-197.
Faverjon, Céline; Küker, Susanne; Furrer, Lenz; Berezowski, John; Posthaus, Horst; Rinaldi, Fabio; Vial, Flavie (2017). Retrospective analysis of 11 years of livestock necropsy data : evaluation for animal health surveillance. In: 3rd International Conference on Animal Health Surveillance, Rotorua, New Zealand, 30 April 2017 - 4 May 2017, 228-230.
Furrer, Lenz; Rinaldi, Fabio (2017). OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task. In: BioCreative V.5 Challenge Evaluation Workshop, Barcelona, Spain, 26 April 2017 - 27 April 2017, 175-182.
Rinaldi, Fabio; Lithgow, Oscar; Gama-Castro, Socorro; Solano, Hilda; López-Fuentes, Alejandra; Muñiz Rascado, Luis José; Ishida-Gutiérrez, Cecilia; Méndez-Cruz, Carlos-Francisco; Collado-Vides, Julio (2017). Strategies towards digital and semi-automated curation in RegulonDB. Database, 2017(1):bax012.
Balderas-Martínez, Yalbi Itzel; Rinaldi, Fabio; Contreras, Gabriela; Solano-Lira, Hilda; Sánchez-Pérez, Mishael; Collado-Vides, Julio; Selman, Moisés; Pardo, Annie (2017). Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. Database, 2017(1):bax030.
Vishnyakova, Dina; Rodriguez-Esteban, Raul; Ozol, Khan; Rinaldi, Fabio (2016). Author Name Disambiguation in MEDLINE Based on Journal Descriptors and Semantic Types. In: Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining, Osaka, Japan, 12 December 2016 - 13 December 2016.
Basaldella, Marco; Furrer, Lenz; Colic, Nicola; Ellendorff, Tilia Renate; Tasso, Carlo; Rinaldi, Fabio (2016). Using a Hybrid Approach for Entity Recognition in the Biomedical Domain. In: 7th International Symposium on Semantic Mining in Biomedicine, Potsdam, Germany, 4 August 2016 - 5 August 2016. s.n., 11-19.
Ellendorff, Tilia Renate; Foster, Simon; Rinaldi, Fabio (2016). 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. European Language Resources Association (ELRA), 3723-3729.
Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane (2016). BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. Database, 2016:baw067.
Mazzocut, Mauro; Truccolo, Ivana; Antonini, Marialuisa; Rinaldi, Fabio; Omero, Paolo; Ferrarin, Emanuela; De Paoli, Paolo; Tasso, Carlo (2016). Web conversations about complementary and alternative medicines and cancer: content and sentiment analysis. Journal of Medical Internet Research, 18(6):e120.
Wang, Qinghua; Rinaldi, Fabio; Jimenez, Silvia; Rodriguez-Esteban, Raul; Arighi, Cecilia N; et al (2016). Overview of the interactive task in BioCreative V. Database, 2016:baw119.
Ellendorff, Tilia Renate; van der Lek, Adrian; Furrer, Lenz; Rinaldi, Fabio (2015). A Combined Resource of Biomedical Terminology and its Statistics. In: Proceedings of the 11th International Conference on Terminology and Artificial Intelligence, Granada, 4 November 2015 - 6 November 2015, 39-49.
Furrer, Lenz; Küker, Susanne; Berezowski, John; Posthaus, Horst; Vial, Flavie; Rinaldi, Fabio (2015). Constructing a Syndromic Terminology Resource for Veterinary Text Mining. In: Proceedings of the 11th International Conference on Terminology and Artificial Intelligence, Granada, 4 November 2015 - 6 November 2015. s.n., 61-70.
Wang, Qinghua; Rinaldi, Fabio; et al (2015). Overview of the Interactive Task in BioCreative V. In: BioCreative V, Sevilla, 9 September 2015 - 11 September 2015. BioCreative, 364-383.
Balderas Martinez, Yalbi I; Rinaldi, Fabio; Contreras, Gabriela (2015). Biocuration of microRNAs in idiopathic pulmonary fibrosis. In: BioCreative V, Sevilla, 9 September 2015 - 11 September 2015, 435-441.
Fluck, Juliane; Madan, Sumit; Ellendorff, Tilia Renate; Mevissen, Theo; Clematide, Simon; van der Lek, Adrian; Rinaldi, Fabio (2015). Track 4 Overview: Extraction of Causal Network Information in Biological Expression Language (BEL). In: BioCreative V, Sevilla, 9 September 2015 - 11 September 2015, 333-346.
Ellendorff, Tilia Renate; Clematide, Simon; van der Lek, Adrian; Furrer, Lenz; Rinaldi, Fabio (2015). Ontogene Term and Relation Recognition for CDR. In: BioCreative V, Sevilla, 9 September 2015 - 11 September 2015, 305-310.
Marques, Hernani; Rinaldi, Fabio (2014). OntoRest: Text Mining Web Services in BioC Format. In: 6th International Symposium on Semantic Mining in Biomedicine, Aveiro, Portugal, 6 October 2014 - 7 October 2014. s.n., 91-95.
Zhu, Yi; Rinaldi, Fabio (2014). OntoPDF: using a text mining pipeline to generate enriched PDF versions of scientific papers. In: 6th International Symposium on Semantic Mining in Biomedicine, Aveiro, Portugal, 6 October 2014 - 7 October 2014, 85-89.
Furrer, Lenz; Clematide, Simon; Marques, Hernani; Rodriguez‐Esteban, Raul; Romacker, Martin; Rinaldi, Fabio (2014). Collection‐Wide Extraction of Protein‐Protein Interactions. In: 6th International Symposium on Semantic Mining in Biomedicine, Aveiro, Portugal, 6 October 2014 - 7 October 2014. s.n., 61-66.
Edited by: Bodenreider, Olivier; Oliveira, José Luis; Rinaldi, Fabio (2014). Aveiro: University of Aveiro. Proceedings of the 6th International Symposium on Semantic Mining in Biomedicine (SMBM 2014).
Rinaldi, Fabio; Clematide, Simon; Marques, Hernani; Ellendorff, Tilia; Rodriguez-Esteban, Raul; Romacker, Martin (2014). OntoGene web services for biomedical text mining. BMC Bioinformatics, 15(Suppl 14):S6.
Liu, Wanli; Doğan, Rezarta Islamaj; Kwon, Dongseop; Marques, Hernani; Rinaldi, Fabio; Wilbur, W John; Comeau, Donald C (2014). BioC Implementations in Go, Perl, Python and Ruby. Database, 2014:bau059.
Comeau, Donald C; Batista-Navarro, Riza Theresa; Dai, Hong-Jie; Doğan, Rezarta Islamaj; Jimeno, Antonio; Khare, Ritu; Lu, Zhiyong; Marques, Hernani; Mattingly, Carolyn J; Neves, Mariana; Peng, Yifan; Rak, Rafal; Rinaldi, Fabio; Tsai, Richard Tzong-Han; Verspoor, Karin; Wiegers, Thomas C; Wu, Cathy H; Wilbur, W John (2014). BioC interoperability track overview. Database, 2014:bau053.
Ellendorff, Tilia; Rinaldi, Fabio; Clematide, Simon (2014). Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14), Reykjavik, Iceland, 2014. European Language Resources Association (ELRA), 3736-3741.
Rinaldi, Fabio; Davis, Allan Peter; Southan, Christopher; Clematide, Simon; Ellendorff, Tilia Renate; Schneider, Gerold (2013). ODIN: a customizable literature curation tool. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, MD, US, 7 October 2013 - 9 October 2013, 219-223.
Gama, Socorro -Castro; Rinaldi, Fabio; et al (2013). Assisted curation of growth conditions that affect gene expression in E. coli K-12. In: Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, MD, US, 7 October 2013 - 9 October 2013, 214-218.
Marques, Hernani; Rinaldi, Fabio (2013). PyBioC: a python implementation of the BioC core. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, MD, US, 7 October 2013 - 9 October 2013, 2-4.
Rinaldi, Fabio; Clematide, Simon; Ellendorff, Tilia Renate; Marques, Hernani (2013). OntoGene: CTD entity and action term recognition. In: Fourth BioCreative Challenge Evaluation Workshop, Bethesda, MD, US, 7 October 2013 - 9 October 2013, 90-94.
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, Valencia, Spain, 23 September 2013, 156.
Rinaldi, Fabio (2013). Assisted editing in the biomedical domain: motivation and challenges. In: ACM Symposium on Document Engineering, Florence, Italy, 10 September 2013 - 12 September 2013. ACM, 197-200.
Schneider, Gerold; Clematide, Simon; Ellendorff, Tilia; Tuggener, Don; Rinaldi, Fabio; Grigonyte, Gintare (2013). UZH in BioNLP 2013. In: Proceedings of the BioNLP Shared Task 2013 Workshop, Sophia, Bulgaria, 9 August 2013 - 9 August 2013, 116-120.
Edited by: Rinaldi, Fabio; Kim, Jin-Dong (2013). Tokyo: Database Center for Life Science. Proceedings of the 5th International Symposium on Languages in Biology and Medicine, Tokyo, 12-13 December.
Rinaldi, Fabio (2013). The OntoGene literature mining web service. EMBnet Journal, 19(Suppl B):32-35.
Comeau, Donald C; Ciccarese, Paolo; Cohen, Kevin Bretonnel; Krallinger, Martin; Leitner, Florian; Lu, Zhiyong; Peng, Yifang; Rinaldi, Fabio; Torii, Manabu; Valencia, Alfonso; Verspoor, Karin; Wiegers, Thomas C; Wu, Cathy H; Wilbur, W John (2013). BIoC: a minimalist approach to interoperability for biomedical text processing. Database, 2013:bat064.
Grigonyte, Gintare; Clematide, Simon; Rinaldi, Fabio (2013). How preferred are preferred terms?. In: Kosem, I; Kallas, J; Gantar, P; Krek, S; Langemets, M; Tuulik, M. Electronic lexicography in the 21st century: thinking outside the paper. Proceedings of the eLex 2013 conference, 17-19 October 2013, Tallinn, Estonia. Ljubljana/Tallinn: eLex, 452-459.
Rebholz-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.
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, Fabio; Volk, Martin (2012). Term evolution: use of biomedical terminologies. In: AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text, Arlington, 3 November 2012 - 5 November 2012. AAAI, 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., 2 November 2012 - 4 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, 4 October 2012 - 5 October 2012. I O S Press, 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, 7 September 2012, CEUR-WS.
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, 3 September 2012 - 4 September 2012, 52-57.
Edited by: Ananiadou, Sophia; Pyysalo, Sampo; Rebholz-Schuhmann, Dietrich; Rinaldi, Fabio; Salakoski, Tapio (2012). Zurich: Institute of Computational Linguistics, University of Zurich. Proceedings of the 5th International Symposium on Semantic Mining in Biomedicine (SMBM 2012).
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., 4 April 2012 - 5 April 2012.
Rinaldi, Fabio (2012). The OntoGene system: an advanced information extraction application for biological literature. EMBnet Journal, 18(Suppl B):47-49.
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; 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.
Rinaldi, Fabio; Schneider, Gerold; Clematide, Simon (2012). Relation Mining Experiments in the Pharmacogenomics Domain. Journal of Biomedical Informatics, 45(5):851-861.
Clematide, S; Rinaldi, Fabio (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. IEEE Computer Society, 100-105.
Schneider, Gerold; Clematide, Simon; Rinaldi, Fabio (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, Fabio (2011). An incremental model for the coreference resolution task of BioNLP 2011. In: BioNLP 2011, Portland, Oregon, USA, 23 June 2011 - 24 June 2011. Association for Computational Linguistics (ACL), 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, 7 April 2011 - 9 April 2011, 597-607.
Clematide, S; Rinaldi, Fabio; 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, Fabio; Schneider, G; Clematide, S (2011). Mining complex Drug/Gene/Disease relations. In: Pacific Symposium on Biocomputing Workshop "Mining the Pharmacogenomics Literature", Hawaii, 3 January 2011 - 7 January 2011.
Rebholz-Schuhmann, D; Rinaldi, Fabio; Pyysalo, S; Collier, N; Hahn, U (2011). Towards mature use of semantic resources for biomedical analyses. Journal of Biomedical Semantics, 2(Suppl 5):I1.
Rinaldi, Fabio; 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, Fabio; Leaman, R; Gonzalez, G; Matos, S; Kim, S; Wilbur, W J; Rocha, L; Shatkay, H; Tendulkar, A V; 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.
Arighi, Cecilia N; Roberts, Phoebe M; Agarwal, S; Bhattacharya, S; Cesareni, G; Chatr-aryamontri, A; Clematide, S; Gaudet, P; Giglio, M G; Harrow, I; Huala, E; Krallinger, M; Leser, U; Li, D; Liu, F; Lu, Z; Maltais, Lois J; Okazaki, N; Perfetto, L; Rinaldi, Fabio; Saetre, R; Salgado, D; Srinivasan, P; Thomas, Philippe E; Toldo, L; Hirschman, L; Wu, Cathy H (2011). BioCreative III interactive task: an overview. BMC Bioinformatics, 12(Suppl 8):S4.
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, Fabio; 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; 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, Fabio; 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.
Rinaldi, Fabio; Clematide, S; Schneider, G; Romacker, M; Vachon, Th (2010). ODIN: an advanced interface for the curation of biomedical literature. Nature Precedings:online.
Rinaldi, Fabio; Schneider, Gerold; Clematide, Simon; Jegen, Silvan; et al (2010). OntoGene (Team 65): preliminary analysis of participation in BioCreative III. In: BioCreative III workshop, Bethesda, Maryland, 13 September 2010 - 15 September 2010.
Rinaldi, Fabio; Schneider, Gerold; Kaljurand, Kaarel; Clematide, Simon; Vachon, Thérèse; Romacker, Martin (2010). OntoGene in BioCreative II.5. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3):472-480.
Clematide, S; Rinaldi, Fabio; Schneider, G (2010). OntoGene in CALBC. In: First CALBC Workshop, Hinxton, Cambridgeshire, UK, 17 June 2010 - 18 June 2010, 30-31.
Rinaldi, Fabio; 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, 8 November 2009 - 10 November 2009, 115-118.
Kaljurand, K; Rinaldi, Fabio; 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: Springer, 225-234.
Kaljurand, Kaarel; Schneider, Gerold; Rinaldi, Fabio (2009). UZurich in the BioNLP 2009 Shared Task. In: BioNLP 2009 Companion Volume: Shared Task on Event Extraction, NAACL/HLT, Boulder, Colorado, 4 June 2009 - 5 June 2009, 28-36.
Kappeler, T; Kaljurand, K; Rinaldi, Fabio (2009). TX Task: Automatic detection of focus organisms in biomedical publications. In: Workshop on BioNLP, Boulder, June 2009, 80-88.
Schneider, Gerold; Kaljurand, Kaarel; Rinaldi, Fabio (2009). Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. In: Gelbukh, Alexander. Computational Linguistics and Intelligent Text Processing. Berlin: Springer, 406-417.
Rinaldi, Fabio. Knowledge mining over scientific literature and technical documentation. 2009, University of Zurich, Faculty of Arts.
Rinaldi, Fabio; 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: ACM, 273-277.
Kaljurand, K; Rinaldi, Fabio; Kappeler, T; Schneider, G (2009). Detecting and grounding terms in biomedical literature. Advances in Computational Linguistics, 41:15-26.
Kappeler, T; Clematide, S; Kaljurand, K; Schneider, G; Rinaldi, Fabio (2008). Towards automatic detection of experimental methods from biomedical literature. In: Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), Turku, Finland, 1 September 2008 - 3 September 2008, 61-68.
Rinaldi, Fabio; 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(Suppl 2):S13.
Rinaldi, Fabio; 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, Fabio; 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, Fabio; 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, 1161-1165.
Rinaldi, Fabio; 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, Fabio; Schneider, G; Kaljurand, K; Hess, M; Andronis, C; Konstandi, 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, Fabio; 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(Suppl 3):S3.
Rinaldi, Fabio; Schneider, G; Kaljurand, K; Hess, M (2006). Tools for text mining over biomedical literature. In: ECAI2006, Riva del Garda, Italy, 2006, 825-826.
SanJuan, E; Dowdall, J; Imbekwe-SanJuan, F; Rinaldi, Fabio (2005). A symbolic approach to automatic multiword term structuring. Computer Speech and Language, 19(4):524-542.
Rinaldi, Fabio; 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, Fabio; 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, 213-250.
Schneider, G; Rinaldi, Fabio; 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, 178-184.
Rinaldi, Fabio; 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, Fabio; 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, Fabio; 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, Fabio; 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.
Schwitter, R; Rinaldi, Fabio; 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.
Spiliopoulou, M; Rinaldi, Fabio; 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.
Dowdall, J; Rinaldi, Fabio; 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.
Dowdall, J; Lowe, W; Elleman, J; Rinaldi, Fabio; Hess, M (2004). The role of MultiWord Terminology in Knowledge Management. In: LREC-2004, Lisbon, Portugal, 2004, 915-918.
Kaljurand, K; Rinaldi, Fabio; Dowdall, J; Hess, M (2004). Exploiting language resources for semantic web annotations. In: LREC-2004, Lisbon, Portugal, 2004, 815-818.
Klenner, M; Rinaldi, Fabio; Hess, M (2004). Steps towards Semantically Annotated Language Resources. In: LREC-2004, Lisbon, Portugal, 2004, 1161-1164.
Rinaldi, Fabio; 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: AAAI Press, 133-140.
Schneider, G; Rinaldi, Fabio; Dowdall, J (2004). Fast, deep-linguistic statistical minimalist dependency parsing. In: COLING-2004 Recent Advances in Dependency Grammars, Geneva, Switzerland, 2004 - 2004, 33-40.
Schneider, G; Rinaldi, Fabio; 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.
Rinaldi, Fabio; 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, Fabio; 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.
Dowdall, J; Rinaldi, Fabio; 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, Fabio; 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.
Rinaldi, Fabio; 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.
Mollà Aliod, D; Schwitter, R; Rinaldi, Fabio; 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, Fabio; 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, Fabio; Schwitter, R; Dowdall, J; Hess, M (2003). Answer Extraction from Technical Texts. IEEE Intelligent Systems, 18(4):12-17.
Mollà Aliod, D; Rinaldi, Fabio; 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, Fabio; 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, 876-888.
Yuste, E; Rinaldi, Fabio (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.
Rinaldi, Fabio; 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, Fabio; Vider, K (2002). Technical terminology as a critical resource. In: LREC-2002, Las Palmas, Spain, May 2002.
Hess, M; Dowdall, J; Rinaldi, Fabio (2002). The challenge of technical text. In: LREC-2002, Workshop on Question Answering: Strategy and Resources, Las Palmas, Spain, May 2002 - May 2002.
Rinaldi, Fabio; Hess, M; Mollà, Diego; 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, 165-177.
Rinaldi, Fabio; 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.

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