Projekt

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Semi-automated semantic enrichment of biomedical literature

Gesuchsteller/in Rinaldi Fabio
Nummer 130558
Förderungsinstrument Projekte
Forschungseinrichtung Institut für Computerlinguistik Universität Zürich
Hochschule Universität Zürich - ZH
Hauptdisziplin Weitere Sprachen
Beginn/Ende 01.08.2010 - 31.07.2014
Bewilligter Betrag 279'484.00
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Alle Disziplinen (3)

Disziplin
Weitere Sprachen
Informatik
Molekularbiologie

Keywords (8)

text mining, molecular biology, syntactic parsing, semi-automated semantic annotation, information extraction, natural language processing, knowledge management, literature curation

Lay Summary (Englisch)

Lead
Lay summary
The understanding of the complex mechanism that support life, and are responsible for health or disease at the cellular level, promises to unveil new technologies that will benefit the health of every citizen, and support the growth of novel industries. The potential of Text Mining applications in the life sciences is widely acknowledged. Scientists and companies are looking for solutions that allow the automated processing of scientific literature. Text Mining tools aim at supporting the process of knowledge gaining from the literature, by supporting the search for relevant articles, the semi-automated extraction of relevant passages, and the transformation of the information from the textual format to a semantic representation. The SASEBio project focuses on the study and development of supporting tools for the semi-automated enrichment of biomedical literature and related documentation, in particular their potential role in the professional literature curation process. Curation is the activity performed by professionals who are paid to read the literature in search of particular items of information and store such information in public databases, which can be accessed later by the biologists. The project deals with entities and relationships that form complex Knowledge graphs, which are gaining relevance to initiate, guide and confirm research in the biosciences. The project leverages on the latest results in Natural Language Processing techniques (combining statistical approaches with human language expertise), in particular information extraction, including biomedical entity and relation detection. While fully unsupervised extraction of information of the literature is currently still unrealistic, text mining tools are already sufficiently reliable to be used to provide hints to the curators, in order to speed up their activities. The results of the project are of academic and industrial relevance for the knowledge management process. The pharmaceutical industry is facing an ever growing complexity of the knowledge space, e.g. genes, proteins and their relationships, as described in the literature. Various research groups maintain legacy systems containing valuable data which cannot be accessed because there is no shared semantic layer. The collaboration between the NITAS/TMS group at Novartis and the OntoGene group at the University of Zurich offers an interesting opportunity to successfully contribute to the solution of the data federation problem. Combining text mining and annotation tools, with the support of a novel web-based text mining application, will accelerate the generation or enrichment of the biomedical data.
Direktlink auf Lay Summary Letzte Aktualisierung: 21.02.2013

Verantw. Gesuchsteller/in und weitere Gesuchstellende

Mitarbeitende

Publikationen

Publikation
Mining complex Drug/Gene/Disease relations in PubMed
Rinaldi Fabio, Schneider Gerold, Clematide Simon (2011), Mining complex Drug/Gene/Disease relations in PubMed, in Pacific Symposium on Biocomputing, PSB2011, Kona, Hawaii.
Using the OntoGene pipeline for the triage task of BioCreative 2012
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.
Ranking Interactions for a Curation Task
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.
Relation Mining Experiments in the Pharmacogenomics Domain
Rinaldi Fabio, Schneider Gerold, Clematide Simon (2012), Relation Mining Experiments in the Pharmacogenomics Domain, in Journal of Biomedical Informatics, 45(5), 851-861.
Using ODIN for a PharmGKB re-validation experiment
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.
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus
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.
Towards mature use of semantic resources for biomedical analyses
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.
An incremental model for the coreference resolution task of BioNLP 2011
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).
Ranking of CTD articles and interactions using the OntoGene pipeline
Rinaldi Fabio, Clematide Simon, Hafner Simon (2012), Ranking of CTD articles and interactions using the OntoGene pipeline, in Proceedings of the 2012 {BioCreative} workshop.
SASEBio: Semi-Automated Semantic Enrichment of the Biomedical Literature
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.
ODIN: Advanced Text Mining in Support of the Curation Process
Rinaldi Fabio, Clematide Simon, Schneider Gerold (2012), ODIN: Advanced Text Mining in Support of the Curation Process, in Pacific Symposium on Biocomputing (PSB).
Dependency parsing for interaction detection in pharmacogenomics
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.
Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine (SMBM)
Collier Nigel, Hahn Udo, Rebholz-Schuhmann Dietrich, Rinaldi Fabio, Pyysalo Sampo (ed.) (2010), Proceedings of the Fourth International Symposium for Semantic Mining in Biomedicine (SMBM), European Bioinformatics Institute, Hinxton, Cambridge, UK.
Proceedings of the Fifth International Symposium for Semantic Mining in Biomedicine (SMBM)
Ananiadou Sophia, Pyysalo Sampo, Rebholz-Schuhmann Dietrich, Rinaldi Fabio, Salakoski Tapio (ed.) (2012), Proceedings of the Fifth International Symposium for Semantic Mining in Biomedicine (SMBM), University of Zurich, Zurich, Switzerland.
Using syntax features and document discourse for relation extraction on PharmGKB and CTD
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.
Using biomedical databases as knowledge sources for large-scale text mining
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.
Change of Biomedical Domain Terminology Over Time
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.
Notes about the OntoGene pipeline
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.
Term evolution: use of biomedical terminologies
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.
Ranking relations between diseases, drugs and genes for a curation task
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.
Using the OntoGene pipeline for the triage task of BioCreative 2012
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.
The OntoGene system: an advanced information extraction application for biological literature
Rinaldi Fabio (2012), The OntoGene system: an advanced information extraction application for biological literature, in EMBnet.journal, 18(Suppl B), 47-49.
Digital Curation Experiments for RegulonDB
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.
UZH in the BioNLP 2013 GENIA Shared Task
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.
BIoC: a minimalist approach to interoperability for biomedical text processing
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.
Assisted editing in the biomedical domain: motivation and challenges.
Rinaldi Fabio (2013), Assisted editing in the biomedical domain: motivation and challenges., in Proceedings of DocEng 2013, Florence, Italy, September 10-12, 2013, ACM.
PyBioC: a python implementation of the BioC core.
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.
OntoGene: CTD entity and action term recognition
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.
Assisted curation of growth conditions that affect gene expression in E. coli K-12
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.
ODIN: a customizable literature curation tool
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.
The OntoGene literature mining web service
Rinaldi Fabio (2013), The OntoGene literature mining web service, in EMBnet.journal, 19(Suppl B), 32-35.
How preferred are preferred terms?
Gintare Grigonyte Fabio Rinaldi (2013), How preferred are preferred terms?, in Proceedings of the eLex 2013 conference.
Assisted curation of experimental methods in RegulonDB
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..
Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction
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.
OntoGene in BioCreative II.5
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.
OntoGene (Team 65): preliminary analysis of participation in BioCreative III
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.
ODIN: An Advanced Interface for the Curation of Biomedical Literature
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, -.
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. Semantic Mining in Medicine, EBI, Cambridge,
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.
Terminological resources for Text Mining over Biomedical Scientific Literature
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.
The Gene Normalization Task in BioCreative III. BMC Bioinformatics, special issue on BioCreative III
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.
BioCreative III Interactive Task: an Overview
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.
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text
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.
Detection of interaction articles and experimental methods in biomedical literature.
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.
A data-driven approach to alternations based on protein-protein interactions
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.
BioC Interoperability Track Overview
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.
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12
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.
BioC Implementations in Go, Perl, Python and Ruby
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.
Collection-Wide Extraction of Protein-Protein Interactions
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.
The OntoGene literature mining web service
Rinaldi Fabio, Clematide Simon, Marques Hernani, Ellendorff Tilia, Romacker Martin, Rodriguez-Esteban Raul (accepted), The OntoGene literature mining web service, in BMC Bioinformatics.
OntoRest: Text Mining Web Services in BioC Format
Marques Hernani, Rinaldi Fabio (accepted), OntoRest: Text Mining Web Services in BioC Format, in Proceedings of The Sixth International Symposium on Semantic Mining in Biomedicine (SMBM), Aveiro, Portugal.
OntoPDF: using a text mining pipeline to generate enriched pdf versions of scientific papers
Yi Zhu, Rinaldi Fabio (accepted), 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.
OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization
Clematide Simon, Rinaldi Fabio, Schneider Gerold (accepted), OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization, in Proceedings of the CALBC II workshop, EBI, Cambridge, UK.
Proceedings of the 5th International Symposium on Languages in Biology and Medicine (LBM 2013)
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.

Zusammenarbeit

Gruppe / Person Land
Felder der Zusammenarbeit
RegulonDB group, Center for Genomic Sciences, UNAM, Mexico (Nordamerika)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Forschungsinfrastrukturen
- Austausch von Mitarbeitern
Data Science Group (Pharma Research and Early Development Informatics) at Hoffmann-La Roche (Europa)
- vertiefter/weiterführender Austausch von Ansätzen, Methoden oder Resultaten
- Publikation
- Industrie/Wirtschaft/weitere anwendungs-orientierte Zusammenarbeit

Wissenschaftliche Veranstaltungen

Aktiver Beitrag

Titel Art des Beitrags Titel des Artikels oder Beitrages Datum Ort Beteiligte Personen
LREC 2014 Vortrag im Rahmen einer Tagung Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction 26.05.2014 Reykjavik, Island Ellendorff Tilia
BioCuration 2014 Vortrag im Rahmen einer Tagung Assisted curation of experimental methods in RegulonDB 07.04.2014 Toronto, Kanada Rinaldi Fabio
NETTAB workshop on Semantic, Social, and Mobile Applications for Bioinformatics and Biomedical Laboratories Vortrag im Rahmen einer Tagung The OntoGene literature mining web service 16.10.2013 Venice, Italien Rinaldi Fabio
Fourth BioCreative Challenge Evaluation Vortrag im Rahmen einer Tagung PyBioC: a python implementation of the BioC core 07.10.2013 Bethesda, Maryland, Vereinigte Staaten von Amerika Rinaldi Fabio
Fourth BioCreative Challenge Evaluation Vortrag im Rahmen einer Tagung OntoGene: CTD entity and action term recognition 07.10.2013 Washington, Vereinigte Staaten von Amerika Rinaldi Fabio
Fourth BioCreative Challenge Evaluation Vortrag im Rahmen einer Tagung Assisted curation of growth conditions that affect gene expression in E. coli K-12 07.10.2013 Bethesda, Maryland, Vereinigte Staaten von Amerika Rinaldi Fabio
DocEng 2013 Vortrag im Rahmen einer Tagung Assisted Editing in the Biomedical Domain: Motivation and Challenges 10.09.2013 Florence, Italien Rinaldi Fabio
BioCuration 2013 Vortrag im Rahmen einer Tagung Digital Curation Experiments for RegulonDB 10.04.2013 Cambridge, Grossbritannien und Nordirland Rinaldi Fabio
NETTAB workshop on Integrated Bio-Search Vortrag im Rahmen einer Tagung The OntoGene system: an advanced information extraction application for biological literature 14.11.2012 Como, Italien Rinaldi Fabio
AAAI-2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text Vortrag im Rahmen einer Tagung Notes about the OntoGene pipeline. 02.11.2012 Arlington, Virginia, Vereinigte Staaten von Amerika Rinaldi Fabio
E-LKR workshop, SEPLN 2012 Vortrag im Rahmen einer Tagung Using biomedical databases as knowledge sources for large-scale text mining 07.09.2012 Castellon de la plana, Spanien Rinaldi Fabio
SMBM 2012 Vortrag im Rahmen einer Tagung Using syntax features and document discourse for relation extraction on PharmGKB and CTD 03.09.2012 Zurich, Schweiz Schneider Gerold
The eighth international conference on Language Resources and Evaluation Vortrag im Rahmen einer Tagung Dependency parsing for interaction detection in pharmacogenomics 21.05.2012 Istanbul, Türkei Rinaldi Fabio
BioCreative-2012 Workshop Vortrag im Rahmen einer Tagung Ranking of CTD articles and interactions using the OntoGene pipeline 16.04.2012 Washington, D.C., Vereinigte Staaten von Amerika Rinaldi Fabio
The Pacific Symposium on Biocomputing (PSB) 2012 Poster ODIN: Advanced Text Mining in Support of the Curation Process 03.01.2012 Hawaii, Vereinigte Staaten von Amerika Rinaldi Fabio
The Tenth International Conference on Machine Learning and Applications Vortrag im Rahmen einer Tagung Ranking interactions for a curation task 21.12.2011 Hawaii, Vereinigte Staaten von Amerika Rinaldi Fabio
1st International SystemsX.ch Conference on Systems Biology Poster SASEBio: Semi-Automated Semantic Enrichment of the Biomedical Literature 24.10.2011 Basel, Schweiz Rinaldi Fabio
3rd Congreso Internacional de Lingüística de Corpus Vortrag im Rahmen einer Tagung A data-driven approach to alternations based on protein-protein interactions 07.04.2011 Valencia, Spanien Schneider Gerold
CALBC II workshop Vortrag im Rahmen einer Tagung OntoGene at CALBC II and Some Thoughts on the Need of Document-Wide Harmonization 16.03.2011 EBI, Cambridge, UK, Grossbritannien und Nordirland Clematide Simon; Rinaldi Fabio
Mining the Pharmacogenomics Literature, Pacific Symposium on Biocomputing Vortrag im Rahmen einer Tagung Mining complex Drug/Gene/Disease relations in PubMed. 03.01.2011 Hawaii , Vereinigte Staaten von Amerika Rinaldi Fabio
Biocuration 2010 Poster ODIN: An Advanced Interface for the Curation of Biomedical Literature 11.10.2010 Tokyo, Japan Rinaldi Fabio
BioCreative III workshop Vortrag im Rahmen einer Tagung OntoGene (Team 65): preliminary analysis of participation in BioCreative III 13.09.2010 Bethesda, Maryland, Vereinigte Staaten von Amerika Rinaldi Fabio


Selber organisiert

Titel Datum Ort
Fifth International Symposium on Semantic Mining in Biomedicine (SMBM 2012) 03.09.2012 Zurich, Schweiz
Fourth International Symposium on Semantic Mining in Biomedicine (SMBM 2010) 11.10.2010 European Bioinformatics Institute, Hinxton, Cambridgeshire, UK, Grossbritannien und Nordirland

Verbundene Projekte

Nummer Titel Start Förderungsinstrument
118396 Detection of biological interactions from biomedical literature 01.04.2008 Projektförderung (Abt. I-III)
125509 A comparative study of syntactic parsers and their applications in biomedical text mining 01.07.2009 Stipendien für angehende Forschende
162758 MelanoBase 01.03.2016 Interdisziplinäre Projekte

Abstract

SASEBio: Semi-Automated Semantic Enrichment of Biomedical Literature The OntoGene group at the University of Zurich has developed efficient techniques for text mining in the molecular biology domain. One of their core interests in recent years has been the detection of mentions of protein-protein interactions. Using the IntAct database as a gold standard, they have developed techniques for the identification of information relevant to the process of curation, such as the experimental methods used by the authors [1], the organism which are hosts 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 by participation 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 at Novartis, they have developed an interesting prototype of an environment supporting the process of semi-automated semantic enrichment of the literature. The environment allows an expert user to efficiently revise annotations suggested by the system, or to add new annotations where the system missed an entity or an interaction. The system is also capable of reusing the annotations added by the expert in subsequent applications, using a process of incremental learning. The SASEBio project aims at consolidating the existing text mining activities of the OntoGene group, by further improving their relation extraction techniques, and applying them to new areas, within the context of the literature curation process. New types of interactions, such as drug/diseases (of particular interest to their industrial partner) will be considered, along with incremental improvements to their 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 through participation in shared text mining challenges. Additionally, the project offers an opportunity to turn the existing semi-automated annotation prototype into a fully fledged system which can then be employed by the target user groups. Intensive collaborations with both NITAS and EBI will be sought at all stages of development, in particular to guarantee a continuous feedback on the effective usability of the proposed tools. References [1] 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). [2] Thomas Kappeler, Kaarel Kaljurand, Fabio Rinaldi. TX Task: Automatic Detection of Focus Organisms in Biomedical Publications. BioNLP workshop, NAACL/HLT, Boulder, Colorado 2009. [3] 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. [4] Gerold Schneider, Kaarel Kaljurand, Thomas Kappeler, Fabio Rinaldi. Detecting protein-protein interactions in biomedical texts using a parser and linguistic resources. CICLING 2009. [5] 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. [6] Kaarel Kaljurand, Gerold Schneider and Fabio Rinaldi. A dependency based approach to the BioNLP 2009 Shared Task. BioNLP workshop, NAACL/HLT, Boulder, Colorado, 2009