text mining; molecular biology; syntactic parsing; semi-automated semantic annotation; information extraction; natural language processing; knowledge management; literature curation
Rinaldi Fabio, Gama-Castro Socorro, López-Fuentes Alejandra, Santos-Zavalet Alberto, Clematide Simon, Ellendorff Tilia, Collado-Vides Julio (2014), Assisted curation of experimental methods in RegulonDB, in
Proceedings of BioCuration 2014, Toronto, Canada..
Gama-Castro Socorro, Rinaldi Fabio, López-Fuentes Alejandra, Balderas-Martínez Yalbi Itzel, Clematide Simon, Ellendorff Tilia Renate, Santos-Zavaleta Alberto, Marques-Madeira Hernani, Collado-Vides Julio (2014), Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12, in
Database: The Journal of Biological Databases and Curation, bau049, bau049.
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, in
Database: The Journal of Biological Databases and Curation, bau059, 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, in
Database: The Journal of Biological Databases and Curation, bau049.
Furrer Lenz, Clematide Simon, Marques Hernani, Rodriguez-Esteban Raul, Romacker Martin, Rinaldi Fabio (2014), Collection-Wide Extraction of Protein-Protein Interactions, in
Proceedings of The Sixth International Symposium on Semantic Mining in Biomedicine (SMBM), Aveiro, Portugal.
Ellendorff Tilia, Rinaldi Fabio, Clematide Simon (2014), Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction, in
Proceedings of LREC 2014, Reykjavik, Iceland.
Gama-Castro Socorro, Rinaldi Fabio, López-Fuentes Alejandra, Balderas-Martínez Yalbi Itzel, Clematide Simon, Ellendorff Tilia Renate, Collado-Vides Julio (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, Maryland, 1, 1.
Rinaldi Fabio (2013), Assisted editing in the biomedical domain: motivation and challenges., in
Proceedings of DocEng 2013, Florence, Italy, September 10-12, 2013, ACM.
Comeau Donald C., Doğan Rezarta Islamaj, 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, in
The Journal of Biological Databases and Curation, bat064, bat064.
Rinaldi Fabio, Gama-Castro Socorro, López-Fuentes Alejandra, Balderas-Martínez Yalbi, Collado-Vides Julio (2013), Digital Curation Experiments for RegulonDB, in
Proceedings of the BioCuration conference, 2013, Cambridge, UK.
Gintare Grigonyte Fabio Rinaldi (2013), How preferred are preferred terms?, in
Proceedings of the eLex 2013 conference.
Rinaldi Fabio, Davis Allan Peter, Southan Christopher, Clematide Simon, Ellendorff Tilia Renate, Schneider Gerold (2013), ODIN: a customizable literature curation tool, in
Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, 1, 1.
Rinaldi Fabio, Clematide Simon, Ellendorff Tilia Renate, Marques Hernani (2013), OntoGene: CTD entity and action term recognition, in
Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, 1, 1.
Rinaldi Fabio, Marques Hernani (2013), PyBioC: a python implementation of the BioC core., in
Proceedings of the Fourth BioCreative Challenge Evaluation Workshop, Bethesda, Maryland, 1, 1.
Rinaldi Fabio (2013), The OntoGene literature mining web service, in
EMBnet.journal, 19(Suppl B), 32-35.
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, in
The Journal of Biological Databases and Curation, Oxford Journals, bas053.
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, in
The Journal of Biological Databases and Curation, Oxford Journals, bas053.ful.
Schneider Gerold, Clematide Simon, Ellendorff Tilia, Tuggener Don, Rinaldi Fabio, Grigonyte Gintare (2013), UZH in the BioNLP 2013 GENIA Shared Task, in
Proceedings of the BioNLP workshop, ACL 2013, Sofia, Bulgaria, Association for Computational Linguistics.
Grigonyte Gintare, Rinaldi Fabio, Volk Martin (2012), Change of Biomedical Domain Terminology Over Time, in
Proc. of 5th Baltic Conf. On Human Language Technologies, Tartu, Estonia.
Schneider Gerold, Rinaldi Fabio, Clematide Simon (2012), Dependency parsing for interaction detection in pharmacogenomics, in
Proceedings of LREC 2012: The eighth international conference on Language Resources and Evaluation.
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.
Rinaldi Fabio, Clematide Simon, Schneider Gerold (2012), ODIN: Advanced Text Mining in Support of the Curation Process, in
Pacific Symposium on Biocomputing (PSB).
Rebholz-Schuhmann Dietrich, Pyysalo Sampo, Ananiadou Sophia, Rinaldi Fabio, Salakoski Tapio (ed.) (2012),
Proceedings of the Fifth International Symposium for Semantic Mining in Biomedicine (SMBM), University of Zurich, Zurich, Switzerland.
Rinaldi Fabio, Clematide Simon, Hafner Simon (2012), Ranking of CTD articles and interactions using the OntoGene pipeline, in
Proceedings of the 2012 {BioCreative} workshop.
Clematide Simon, Rinaldi Fabio (2012), Ranking relations between diseases, drugs and genes for a curation task, in
Journal of Biomedical Semantics, 3(Suppl 3), 5-5.
Rinaldi Fabio, Schneider Gerold, Clematide Simon (2012), Relation Mining Experiments in the Pharmacogenomics Domain, in
Journal of Biomedical Informatics, 45(5), 851-861.
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, Virginia, USA.
Rinaldi Fabio (2012), The OntoGene system: an advanced information extraction application for biological literature, in
EMBnet.journal, 18(Suppl B), 47-49.
Rinaldi Fabio (2012), Using biomedical databases as knowledge sources for large-scale text mining, in
E-LKR workshop, SEPLN 2012, Castellon de la Plana, Spain.
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, in
Database: The Journal of Biological Databases and Curation, bas021-bas021.
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.
Schneider Gerold, Rinaldi Fabio (2011), A data-driven approach to alternations based on protein-protein interactions, in
3rd Congreso Internacional de Lingüística de Corpus , Universitat Politècnica de València, València, Spain.
Tuggener D, Klenner M, Schneider G, Clematide S, Rinaldi F (2011), An incremental model for the coreference resolution task of BioNLP 2011, in
Proceedings of the BioNLP11 shared task. , Association for Computational Linguistics (ACL).
Rebholz-Schuhmann Dietrich, Yepes Antonio, Li Chen, Kafkas Senay, Lewin Ian, Kang Ning, Corbett Peter, Milward David, Buyko Ekaterina, Beisswanger Elena, Hornbostel Kerstin, Kouznetsov Alexandre, Witte Rene, Laurila Jonas, Baker Christopher, Kuo Cheng-Ju, Clematide Simon, Rinaldi Fabio, Farkas Richard, Mora Gyorgy, Hara Kazuo, Furlong Laura I, Rautschka Michael, Neves Mariana, Pascual-Montano Alberto (2011), Assessment of NER solutions against the first and second CALBC Silver Standard Corpus, in
Journal of Biomedical Semantics, 2(Suppl 5), 11-11.
Arighi Cecilia, Roberts Phoebe, Agarwal Shashank, Bhattacharya Sanmitra, Cesareni Gianni, Chatr rew -aryamontri, Clematide Simon, Gaudet Pascale, Giglio Michele Gwinn, Harrow Ian, Huala Eva, Krallinger Martin, Leser Ulf, Li Donghui, Liu Feifan, Lu Zhiyong, Maltais Lois, Okazaki Naoaki, Perfetto Livia, Rinaldi Fabio, Saetre Rune, Salgado David, Srinivasan Padmini, Thomas Philippe E., Toldo Luca (2011), BioCreative III Interactive Task: an Overview, in
BMC Bioinformatics, special issue on BioCreative III, -, S4.
Schneider Gerold, Clematide Simon, Rinaldi Fabio (2011), Detection of interaction articles and experimental methods in biomedical literature., in
BMC Bioinformatics, special issue on BioCreative III, -, S13.
Rinaldi Fabio, Schneider Gerold, Clematide Simon (2011), Mining complex Drug/Gene/Disease relations in PubMed, in
Pacific Symposium on Biocomputing, PSB2011, Kona, Hawaii.
Clematide Simon, Rinaldi Fabio (2011), Ranking Interactions for a Curation Task, in
10th International Conference on Machine Learning and Applications and Workshops, 2, IEEE Computer Society, 2.
Rinaldi Fabio, Clematide Simon, Schneider Gerold (2011), SASEBio: Semi-Automated Semantic Enrichment of the Biomedical Literature, in
1st International SystemsX.ch Conference on Systems Biology.
Rinaldi Fabio, Kaljurand Kaarel, Saetre Rune (2011), Terminological resources for Text Mining over Biomedical Scientific Literature, in
Journal of Artificial Intelligence in Medicine, 52(2), 107-114.
Lu Zhiyong, Hung-Kao Yu, Chih-Wei Hsuan, Huang Minlie, Liu Jingchen, Cheng-Kuo Ju, Chun-Hsu Nan, Tzong Han, Hong-Dai Jie, Okazaki Naoaki, Han-Cho Cheol, Gerner Martin, Solt Illes, Agarwal Shashank, Liu Feifan, Vishnyakova Dina, Ruch Patrick, Clematide Simon, Rinaldi Fabio, Bhattacharya Sanmitra, Srinivasan Padmini, Liu Hongfang, Torii Manabu, Matos Sergio, Campos David (2011), The Gene Normalization Task in BioCreative III. BMC Bioinformatics, special issue on BioCreative III, in
BMC Bioinformatics, special issue on BioCreative III, -, S2.
Krallinger Martin, Vazquez Miguel, Leitner Florian, Salgado David, Chatr-Aryamontri Andrew, Winter Andrew, Perfetto Livia, Briganti Leonardo, Licata Luana, Iannuccelli Marta, Cesareni Gianni, Rinaldi Fabio, Leaman Robert, Gonzalez Graciela, Matos Sergio, Kim Sun, Wilbur John W., Rocha Luis, Tendulkar Ashish V, Agarwal Shashank, Liu Feifan, Wang Xinglong, Rak Rafal, Noto Keith, Elkan Charles (2011), The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text, in
BMC Bioinformatics, special issue on BioCreative III, -, S3.
Rebholz-Schuhmann D, Rinaldi F, Pyysalo S, Collier N, Hahn U (2011), Towards mature use of semantic resources for biomedical analyses, in
Journal of Biomedical Semantics, 2(Suppl 5), 1-1.
Dietrich Rebholz-Schuhmann Antonio Jimeno Chen Li Senay Kafkas Ian Lewin Ning Kang Peter Corbe (2010), Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Semantic Mining in Medicine, EBI, Cambridge,, in
Semantic Mining in Medicine, 2010, European Bioinformatics Institute, Cambridge, UK.
Rinaldi Fabio, Clematide Simon, Schneider Gerold, Romacker Martin, Vachon Thérèse (2010), ODIN: An Advanced Interface for the Curation of Biomedical Literature, in
The Conference of the International Society for Biocuration 2010, Nature Precedings, -.
Rinaldi. Fabio, Schneider Gerold, Clematide Simon, Jegen Silvan, Parisot Pierre, Romacker Martin, Vachon Thérèse (2010), OntoGene (Team 65): preliminary analysis of participation in BioCreative III, in
Proceedings of BioCreative III workshop, BioCreative III worksho, Bethesda, Maryland, US.
Rinaldi Fabio, Schneider Gerold, Kaljurand Kaarel, Vachon Thérèse, Romacker Martin (2010), OntoGene in BioCreative II.5, in
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 7(3), 472-480.
Pyysalo Sampo, Collier Nigel, Rinaldi Fabio, Hahn Udo, Rebholz-Schuhmann Dietrich (ed.) (2010),
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine (SMBM), European Bioinformatics Institute, Hinxton, Cambridge, UK.
Clematide Simon, Rinaldi Fabio, Schneider Gerold, OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization, in
Proceedings of the CALBC II workshop, EBI, Cambridge, UK.
Yi Zhu, Rinaldi Fabio, OntoPDF: using a text mining pipeline to generate enriched pdf versions of scientific papers, in
Proceedings of The Sixth International Symposium on Semantic Mining in Biomedicine (SMBM), Aveiro, Portugal.
Marques Hernani, Rinaldi Fabio, OntoRest: Text Mining Web Services in BioC Format, in
Proceedings of The Sixth International Symposium on Semantic Mining in Biomedicine (SMBM), Aveiro, Portugal.
Rinaldi Fabio, Kim Jin-Dong (ed.),
Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM 2013), Database Center for Life Sciences, Tokyo, Japan.
Rinaldi Fabio, Clematide Simon, Marques Hernani, Ellendorff Tilia, Romacker Martin, Rodriguez-Esteban Raul, The OntoGene literature mining web service, in
BMC Bioinformatics.
SASEBio: Semi-Automated Semantic Enrichment of Biomedical LiteratureThe OntoGene group at the University of Zurich has developed efficienttechniques for text mining in the molecular biology domain. One oftheir core interests in recent years has been the detection of mentionsof protein-protein interactions. Using the IntAct database as a goldstandard, they have developed techniques for the identification ofinformation relevant to the process of curation, such as theexperimental methods used by the authors [1], the organism which arehosts of the experiment and which contribute the interacting proteins[2], the protein themselves [3], and their interactions [4].The effectiveness of their approach has been validated byparticipation to numerous shared evaluations, such as BioCreative II[5], BioNLP event extraction task [6], and BioCreative II.5[forthcoming]. Recently, in collaboration with the NITAS group atNovartis, they have developed an interesting prototype of anenvironment supporting the process of semi-automated semanticenrichment of the literature. The environment allows an expert user toefficiently revise annotations suggested by the system, or to add newannotations where the system missed an entity or an interaction. Thesystem is also capable of reusing the annotations added by the expertin subsequent applications, using a process of incremental learning.The SASEBio project aims at consolidating the existing text miningactivities of the OntoGene group, by further improving their relationextraction techniques, and applying them to new areas, within thecontext of the literature curation process. New types of interactions,such as drug/diseases (of particular interest to their industrialpartner) will be considered, along with incremental improvements totheir existing techniques for protein-protein interaction detection(of potential interest to the IntAct group at EBI). As in the past,their techniques will be subject to community-based evaluation throughparticipation in shared text mining challenges.Additionally, the project offers an opportunity to turn the existingsemi-automated annotation prototype into a fully fledged system whichcan then be employed by the target user groups. Intensivecollaborations with both NITAS and EBI will be sought at all stagesof development, in particular to guarantee a continuous feedback onthe effective usability of the proposed tools.References[1] Thomas Kappeler, Simon Clematide, Kaarel Kaljurand, GeroldSchneider, Fabio Rinaldi. Towards Automatic Detection of ExperimentalMethods from Biomedical Literature. Third International Symposium onSemantic Mining in Biomedicine (SMBM 2008).[2] Thomas Kappeler, Kaarel Kaljurand, Fabio Rinaldi. TX Task:Automatic Detection of Focus Organisms in BiomedicalPublications. BioNLP workshop, NAACL/HLT, Boulder, Colorado 2009.[3] Kaarel Kaljurand, Fabio Rinaldi, Thomas Kappeler, GeroldSchneider. Using existing biomedical resources to detect and groundterms in biomedical literature. Artificial Intelligence in Medicine,Verona, July 2009.[4] Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, FabioRinaldi. Detecting protein-protein interactions in biomedical textsusing a parser and linguistic resources. CICLING 2009.[5] Fabio Rinaldi, Thomas Kappeler, Kaarel Kaljurand, GeroldSchneider, Manfred Klenner, Simon Clematide, Michael Hess, Jean-Marcvon Allmen, Pierre Parisot, Martin Romacker, Therese Vachon. OntoGenein BioCreative II. Genome Biology, 2008, 9:S13.[6] Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi. A dependencybased approach to the BioNLP 2009 Shared Task. BioNLP workshop,NAACL/HLT, Boulder, Colorado, 2009