Event extraction for systems biology by text mining the literature, Trends in Biotechnology, vol.28, issue.7, pp.381-390, 2010. ,
Named entity recognition for bacterial type IV secretion systems, PLoS ONE, vol.6, issue.3, p.14780, 2011. ,
Gene ontology: tool for the unification of biology, Nature genetics, vol.25, pp.25-29, 2000. ,
Generalizing biomedical event extraction, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Coarseto-Fine n-Best Parsing and MaxEnt Discriminative Reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005. ,
Highthroughput identification of chemistry in life science texts, Computational Life Sciences II, pp.107-118, 2006. ,
Generating Typed Dependency Parses from Phrase Structure Parses, Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC'06), pp.449-454, 2006. ,
LINNAEUS: a species name identification system for biomedical literature, BMC bioinformatics, vol.11, issue.1, p.85, 2010. ,
Two-component signal transduction as potential drug targets in pathogenic bacteria, Cell regulation, vol.13, pp.232-239, 2010. ,
Adapting a general semantic interpretation approach to biological event extraction, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Introduction to the bio-entity recognition task at JNLPBA, 2004. ,
Corpus annotation for mining biomedical events from lterature, BMC Bioinformatics, vol.9, issue.1, p.10, 2008. ,
Overview of BioNLP'09 Shared Task on Event Extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge, Genome biology, vol.9, issue.2, p.1, 2008. ,
Bacterial sensor kinases: Diversity in the recognition of environmental signals. Annual Review of Microbiology, vol.64, pp.539-559, 2010. ,
Stimulus perception in bacterial signaltransducing histidine kinases. Microbiol, Mol. Biol. Rev, vol.70, issue.4, pp.910-938, 2006. ,
Event extraction as dependency parsing for bionlp 2011, Proceedings of the BioNLP, 2011. ,
, Workshop Companion Volume for Shared Task
Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2009. ,
Complex biological event extraction from full text using signatures of linguistic and semantic features, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Evaluating dependency representation for event extraction, Proceedings of COL-ING'10, pp.779-787, 2010. ,
Incorporating GENETAG-style annotation to GENIA corpus, Proceedings of BioNLP'09, pp.106-107, 2009. ,
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Towards event extraction from full texts on infectious diseases, Proceedings of BioNLP'10, pp.132-140, 2010. ,
Annotation guidelines for infectious diseases event corpus, 2011. ,
Robust biomedical event extraction with dual decomposition and minimal domain adaptation, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Model combination for event extraction in bionlp, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
How to make the most of NE dictionaries in statistical NER, BMC bioinformatics, issue.9, 2008. ,
BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Eukaryotic signal transduction via histidine-aspartate phosphorelay, J Cell Sci, vol.113, issue.18, pp.3141-3150, 2000. ,
Investigating heterogeneous protein annotations toward cross-corpora utilization, BMC Bioinformatics, issue.403, p.10, 2009. ,
Sinorhizobium meliloti 1021 loss-of-function deletion mutation in chvi and its phenotypic characteristics, Molecular Plant-Microbe Interactions, vol.23, issue.2, pp.153-160, 2010. ,
Exploring the Boundaries: Gene and Protein Identification in Biomedical Text, References References References Jenny Finkel, vol.6, p.5, 2005. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
, , 2007.
Identifying Gene and Protein Mentions in Text Using Conditional Random Fields, BMC Bioinformatics, vol.6, p.6, 2005. ,
Feature Forest Models for Probabilistic HPSG Parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008. ,
Exploring Domain Differences for the Design of Pronoun Resolution Systems for Biomedical Text, Proceedings of COLING, pp.625-632, 2008. ,
Challenges in Pronoun Resolution System for Biomedical Text, Proceedings of LREC, 2008. ,
Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
A general-purpose, off-the-shelf anaphora resolution module: implementation and preliminary evaluation, Proceedings of LREC, 2004. ,
A Public Reference Implementation of the Rap Anaphora Resolution Algorithm, Proceedings of LREC, 2004. ,
Reconcile: A Coreference Resolution Platform, 2010. ,
, Coreference Resolution with Reconcile. Proceedings of ACL, 2010.
Conundrums in Noun Phrase Coreference Resolution: Making Sense of the Stateof-the-Art, Proceedings of ACL-IJCNLP, 2009. ,
Bidirectional Inference with the Easiest-First Strategy for Tagging Sequence Data, Proceedings of HLT/EMNLP 2005, pp.467-474, 2005. ,
BART: A modular toolkit for coreference resolution, Proceedings of LREC, 2008. ,
A NP-Cluster Based Approach to Coreference Resolution, Proceedings of COLING, pp.226-232, 2004. ,
Improving Noun Phrase Coreference Resolution by Matching Strings, Proceedings of IJCNLP, pp.226-333, 2004. ,
Recognition of Protein/Gene Names from Text Using an Ensemble of Classifiers, BMC Bioinformatics, vol.6, p.7, 2005. ,
Guidelines for Annotation of Bacteria Biotopes, 2010. ,
BioNLP Shared Task 2011 -Bacteria Biotope, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task. Portland, Oregon, Association for Computational Linguistics, 2011. ,
A Large-scale Exploration of Effective Global Features for a Joint Entity Detection and Tracking Model, Proceedings of HLT-EMNLP 2005, pp.97-104, 2005. ,
Text and Knowlegde Mining for Coreference Resolution, Proceedings of NAACL 2001, pp.1-8, 2001. ,
A Maximum Entropy Tagger with Unsupervised Hidden Markov Models, Proceedings of NL-PRS, pp.333-340, 2001. ,
Simple Semi-supervised Dependency Parsing, Proceedings of ACL-08: HLT, pp.595-603, 2008. ,
Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data, Proceedings of ICML'01, pp.282-289, 2001. ,
Online EM for Unsupervised Models, Proceedings of NAACL 2009, pp.611-619, 2009. ,
A Mention-Synchronous Co-reference Resolution Algorithm based on the Bell Tree, Proceedings of ACL 2004, pp.135-142, 2004. ,
Comparing Knowledge Sources for Nominal Anaphora Resolution, Computational Linguistics, vol.31, pp.367-402, 2005. ,
A Graph Kernel for Protein-Protein Interaction Extraction, BioNLP2008: Current Trends in Biomedical Natural Language Processing, pp.1-9, 2008. ,
Effective mapping of biomedical text to the UMLS Metathesaurus: The MetaMap program, Proceedings of AMIA Symposium, pp.17-21, 2001. ,
Ontology enrichment and indexing process, 2003. ,
Ontology matching, p.333, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00817824
Towards a richer description of our complete collection of genomes and metagenomes: the Minimum Information about a Genome Sequence (MIGS) specification, Nature Biotechnology, vol.26, pp.541-547, 2008. ,
, GeoNames
Explorations in Automatic Thesaurus Discovery. Natural Language Processing and Machine Translation, 1994. ,
Centering: A Framework for Modelling the Local Coherence of Discourse. University of Pennsylvania Institute for Research in, Cognitive Science Technical Reports Series, 1995. ,
Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing, Proceedings of the 2007 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning, pp.228-237, 2007. ,
Improving term extraction with terminological resources, Advances in Natural Language Processing 5th International Conference on NLP (Fin-TAL'06), pp.380-387, 2006. ,
URL : https://hal.archives-ouvertes.fr/hal-00091444
Detection of synonymy links between terms: experiment and results, Recent Advances in Computational Terminology, 2001. ,
Automatic acquisition of hyponyms from large text corpora, Proceedings of the 14 th COLING, pp.539-545, 1992. ,
NLP for term variant extraction: A synergy of morphology, lexicon, and syntax, Natural language information retrieval, vol.7, pp.25-74, 1999. ,
Advances in record linkage methodology as applied to matching the 1985 census of, Journal of the American Statistical Association, vol.84, issue.406, pp.414-434, 1989. ,
Extracting bio-molecular events from literature -the Bi-oNLP'09 shared task, Special issue of the International Journal of Computational Intelligence ,
Binary codes capable of correcting deletions, insertions and reversals. Doklady akademii nauk SSSR, Russian. English translation in Soviet Physics Doklady, vol.163, pp.707-710, 1965. ,
Pronomial and Sortal Anaphora Resolution for Biomedical Literature, Proceedings of ROCLING XVI: Conference on Computational Linguistics and Speech Processing, 2004. ,
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata, 2009. ,
Information extraction as an ontology population task and its application to genic interactions, 20th IEEE Intl. Conf. Tools with Artificial Intelligence, ICTAI'08, vol.II, pp.74-81, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-02756569
, Building Large Lexicalized Ontologies from Text: a Use Case in Indexing Biotechnology Patents, International Conference on Knowledge Engineering and Knowledge Management, 2010.
Intricacies of Collins' Parsing Model, Computational Linguistics, vol.30, issue.4, pp.479-511, 2004. ,
Complex event extraction at PubMed scale, Bioinformatics, vol.26, issue.12, p.382, 2010. ,
BioNLP Shared Task 2011 -Bacteria Biotope, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
CoNLL-X shared task on multilingual dependency parsing, Proceedings of the Tenth Conference on Computational Natural Language Learning, pp.149-164, 2006. ,
Evaluating the impact of alternative dependency graph encodings on solving event extraction tasks, Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, pp.982-992, 2010. ,
Coarseto-Fine n-Best Parsing and MaxEnt Discriminative Reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005. ,
MSR-NLP entry in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Parsing the WSJ using CCG and log-linear models, Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, page 103. Association for Computational Linguistics, 2004. ,
A new statistical parser based on bigram lexical dependencies, Proceedings of the 34th Annual Meeting of the Association for Computational Linguistics, pp.184-191, 1996. ,
Generating Typed Dependency Parses from Phrase Structure Parses, Proceedings of the Fifth International Conference on Language Resources and Evaluation (LREC'06), pp.449-454, 2006. ,
Interferons inhibit activation of STAT6 by interleukin 4 in human monocytes by inducing SOCS-1 gene expression, Proceedings of the National Academy of Sciences of the United States of America, vol.96, p.10800, 1999. ,
A generalizable and efficient machine learning approach for biological event extraction from text, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Frame semantics and the nature of language, Annals of the New York Academy of Sciences, vol.280, issue.1, pp.20-32, 1976. ,
Extended constituent-to-dependency conversion for English, Proc. of the 16th Nordic Conference on Computational Linguistics (NODALIDA), 2007. ,
BioNLP Shared Task 2011 -Bacteria Gene Interactions and Renaming, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00641586
U-Compare: share and compare text mining tools with UIMA, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, vol.25, pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Fast exact inference with a factored model for natural language parsing, Advances in neural information processing systems, pp.3-10, 2003. ,
Building a large annotated corpus of English: The Penn Tree Bank, Computational Linguistics, pp.313-318, 1993. ,
Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2009. ,
Evaluating Dependency Representation for Event Extraction, the 23rd International Conference on Computational Linguistics (COLING 2010), pp.779-787, 2010. ,
Feature forest models for probabilistic HPSG parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008. ,
Task-oriented evaluation of syntactic parsers and their representations, Takuya Matsuzaki, and Jun'ichi Tsujii, pp.46-54, 2008. ,
Memory-based resolution of in-sentence scopes of hedge cues, CoNLL-2010: Shared Task, p.40, 2010. ,
Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Learning accurate, compact, and interpretable tree annotation, Proceedings of the 21st International Conference on Computational Linguistics and the 44th annual meeting of the Association for Computational Linguistics, pp.433-440, 2006. ,
Joint inference for knowledge extraction from biomedical literature, Human Language Technologies: The 2010 Annual Conference of the North American Chapter of the Association for Computational Linguistics, pp.813-821, 2010. ,
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Porting a lexicalized-grammar parser to the biomedical domain, Journal of Biomedical Informatics, vol.42, issue.5, pp.852-865, 2009. ,
, Biomedical Natural Language Processing
AKANE system: proteinprotein interaction pairs in BioCreAtIvE2 challenge, PPI-IPS subtask, Proceedings of the Second BioCreative Challenge Workshop, pp.209-212, 2007. ,
Dependency parsing and domain adaptation with LR models and parser ensembles, Proceedings of the CoNLL, 2007. ,
Hybrid long-distance functional dependency parsing, 2007. ,
The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing, pp.38-45, 2008. ,
Syntax Annotation for the GENIA corpus, Proceedings of the IJCNLP, pp.222-227, 2005. ,
The SWISS-PROT protein sequence data bank and its new supplement TREMBL, Nucleic Acids Research, vol.24, issue.1, p.21, 1996. ,
The universal protein resource (UniProt), vol.33, p.154, 2005. ,
, GenBank. Nucleic acids research, vol.36, p.25, 2008.
Beyond the Bag of Words: A Text Representation for Sentence Selection, Advances in Artificial Intelligence, pp.324-335, 2006. ,
Experiments in automatic phrase indexing for document retrieval: a comparison of syntactic and non-syntactic methods, 1987. ,
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database: The Journal of Biological Databases and Curation, BMC systems biology, vol.2, issue.1, p.20, 2008. ,
The WEKA data mining software: an update, ACM SIGKDD Explorations Newsletter, vol.11, issue.1, pp.10-18, 2009. ,
Overview of BioCre-AtIvE: critical assessment of information extraction for biology, BMC bioinformatics, vol.6, 2005. ,
GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Research, vol.36, p.469, 2008. ,
URL : https://hal.archives-ouvertes.fr/pasteur-02634892
Sentence filtering for information extraction in genomics, a classification problem. Principles of Data Mining and Knowledge Discovery, pp.326-337, 2001. ,
URL : https://hal.archives-ouvertes.fr/hal-02764043
Information Extraction. Handbook on Ontologies, pp.663-685, 2009. ,
Status of genome projects for nonpathogenic bacteria and archaea, Nature biotechnology, vol.18, issue.10, pp.1049-54, 2000. ,
Construction of the Bacillus subtilis ORF database (BSORF DB), Genome Informatics, pp.228-229, 1996. ,
Probabilistic part-of-speech tagging using decision trees, 1994. ,
Genome reviews: standardizing content and representation of information about complete genomes, Omics: a journal of integrative biology, vol.10, issue.2, pp.114-118, 2006. ,
La relation de synonymie en Génomique, 2004. ,
Feature selection for SVMs, Advances in neural information processing systems, pp.668-674, 2001. ,
Automatic extraction of gene and protein synonyms from MED-LINE and journal articles, Proceedings of the AMIA Symposium, p.919, 2002. ,
An overview of metamap: historical perspective and recent advances, J Am Med Inform Assoc, vol.17, issue.3, pp.229-265, 2010. ,
Complex event extraction at pubmed scale, Bioinformatics, vol.26, issue.12, pp.382-390, 2010. ,
The unified medical language system (UMLS): integrating biomedical terminology, Nucleic acids research, vol.32, issue.1, p.267, 2004. ,
Generating typed dependency parses from phrase structure parses, Proceedings of LREC, 2006. ,
Automatic labeling of semantic roles, Computational Linguistics, vol.28, issue.3, pp.245-288, 2002. ,
Making large scale SVM learning practical, Advances in Kernel Methods -Support Vector Learning, 1999. ,
Overview of bionlp'09 shared task on event extraction, Proceedings of the Workshop on BioNLP: Shared Task, vol.6, pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
Accurate unlexicalized parsing, Proceedings of the 41st Annual Meeting on Association for Computational Linguistics, vol.1, pp.423-430, 2003. ,
Biomedical event annotation with crfs and precision grammars, Proceedings of the Workshop on BioNLP: Shared Task, pp.77-85, 2009. ,
Simple tricks for improving pattern-based information extraction from the biomedical literature, J. Bioinform. Comput. Biol, vol.8, issue.1, p.9, 2010. ,
Towards event extraction from full texts on infectious diseases, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.132-140, 2010. ,
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
An exploratory study of a text classification framework for internet-based surveillance of emerging epidemics, International Journal of Medical Informatics, vol.80, issue.1, pp.56-66, 2011. ,
New models in probabilistic information retrieval, 1980. ,
The Nature of Statistical Learning Theory, 1995. ,
KAF: a generic semantic annotation format Proceedings of the 5th International Conference on Generative Approaches to the Lexicon GL, 2009. ,
High-precision biological event extraction: Effects of system and data, Computational Intelligence, pp.89-96, 2009. ,
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task. Association for Computational Linguistics, 2011. ,
Two Strong Baselines for the BioNLP 2009 Event Extraction Task, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.1-9, 2010. ,
BioEve: Bio-Molecular Event Extraction from Text Using Semantic Classification and Dependency Parsing, A System for Mining, Structuring, and Distributing Knowledge Across Languages and Cultures. Proceedings of LREC, pp.99-102, 2008. ,
Exploring ways beyond the simple supervised learning approach for biological event extraction, Proceedings of the Workshop on Bi-oNLP'09 Shared Task, pp.137-140, 2009. ,
Overview of BioNLP?09 shared task on event extraction, Proceedings of the Workshop on BioNLP'09 Shared Task, pp.1-9, 2009. ,
UZurich in the BioNLP 2009 shared task, Proceedings of the Workshop on Bi-oNLP'09 Shared Task, pp.28-36, 2009. ,
Syntactic dependency based heuristics for biological event extraction, Proceedings of the Workshop on BioNLP'09 Shared Task, pp.119-127, 2009. ,
A hybrid approach to extract protein-protein interactions, Bioinformatics, vol.27, issue.2, pp.259-265, 2011. ,
Event Extraction with Complex Event Classification Using Rich Features, Journal of Bioinformatics and Computational Biology, vol.8, pp.131-146, 2010. ,
Complex event extraction at PubMed scale, Bioinformatics, vol.26, pp.382-390, 2010. ,
, Event Class Recall Precision Fscore Gene_expression References David Jurgens and Keith Stevens. 2010. The S-Space package: an open source package for word space models, Proceedings of the ACL 2010 System Demonstrations, ACLDemos '10, pp.30-35
Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, vol.9, issue.1, p.10, 2008. ,
Overview of the Entity Relations (REL) supporting task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2000. ,
Integration of static relations to enhance event extraction from text, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.144-152, 2010. ,
Event Extraction from Trimmed Dependency Graphs, Proceedings of the Workshop on BioNLP: Shared Task, pp.19-27, 2009. ,
Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Proceedings of the Workshop on BioNLP: Shared Task, pp.10-18, 2009. ,
Inkrementelle koreferenzanalyse für das deutsche, Proceedings der 10. Konferenz zur Verarbeitung Natürlicher Sprache, 2010. ,
An algorithm for pronominal anaphora resolution, Computational Linguistics, vol.20, pp.535-561, 1994. ,
A mention-synchronous coreference resolution algorithm based on the bell tree, Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics, 2004. ,
Supervised models for coreference resolution, Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing, vol.2, pp.968-977, 2009. ,
An Environment for Relation Mining over Richly Annotated Corpora: the case of GENIA, BMC Bioinformatics, vol.7, p.3, 2006. ,
, OntoGene in BioCreative II, vol.9, p.13, 2008.
OntoGene in BioCreative II.5, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.3, pp.472-480, 2010. ,
Hybrid Long-Distance Functional Dependency Parsing, 2008. ,
An np-cluster based approach to coreference resolution, Proceedings of the 20th international conference on Computational Linguistics, 2004. ,
Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Computational Linguistics, pp.10-18, 2009. ,
The WEKA data mining software: an update, ACM SIGKDD Explorations Newsletter, vol.11, issue.1, pp.10-18, 2009. ,
Making large scale SVM learning practical, Advances in Kernel Methods -Support Vector Learnin, 1999. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
BioNLP Shared Task 2011: Supporting Resources, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Extracting Complex Biological Events with Rich Graph-Based Feature Sets, Proceedings of the Workshop on BioNLP: Shared Task, 2009. ,
Introduction to Algorithms, 2002. ,
Accurate methods for the statistics of surprise and coincidence, Computational Linguistics, vol.19, issue.1, pp.61-74, 1993. ,
Intelligent Writing Assistance, Handbook of Natural Language Processing, 2000. ,
PEGASUS: Deriving Argument Structures after Syntax, Natural Language Processing: the PLNLP approach, 1993. ,
Generating Typed Dependency Parses from Phrase Structure Parses, LREC, 2006. ,
Feature forest models for probabilistic HPSG parsing, Computational Linguistics, vol.34, issue.1, pp.35-80, 2008. ,
Self-Training for Biomedical Parsing, Proceedings of the Association for Computational Linguistics, 2008. ,
Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2010. ,
Discriminative training and spanning tree algorithms for dependency parsing, 2006. ,
Forestbased Translation, Proceedings of ACL, 2008. ,
Web-Scale Distributional Similarity and Entity Set Expansion, Proceedings of EMNLP, 2009. ,
Joint inference for knowledge extraction from biomedical literature, Proceedings of NAACL-HLT 2010, 2010. ,
An algorithm for suffix stripping, vol.14, pp.130-137, 1980. ,
Support vector machine learning for interdependent and structured output spaces, 2004. ,
Biological relation extraction and query answering from medline abstracts using ontology-based text mining, Data & Knowledge Engineering, vol.61, issue.2, pp.228-262, 2007. ,
Text Mining for Biology And Biomedicine, 2005. ,
Event extraction for systems biology by text mining the literature, Trends in Biotechnology, vol.28, issue.7, pp.381-390, 2010. ,
Event extraction from trimmed dependency graphs, BioNLP '09: Proceedings of the Workshop on BioNLP, pp.19-27, 2009. ,
A (sub)graph isomorphism algorithm for matching large graphs, IEEE Trans. Pattern Anal. Mach. Intell, vol.26, issue.10, pp.1367-1372, 2004. ,
Introduction to Algorithms, 2001. ,
WordNet: An Electronic Lexical Database, 1998. ,
Statistical anaphora resolution in biomedical texts, COLING '08: Proceedings of the 22nd International Conference on Computational Linguistics, pp.257-264, 2008. ,
A unification algorithm for typed lambda-calculus, Theor. Comput. Sci, vol.1, issue.1, pp.27-57, 1975. ,
The Processes of Life: An Introduction to Molecular Biology, 2009. ,
Syntactic dependency based heuristics for biological event extraction, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, BioNLP '09, pp.119-127, 2009. ,
Overview of bionlp'09 shared task on event extraction, Proceedings of the NAACL-HLT 2009 Workshop on Natural Language Processing in Biomedicine (BioNLP'09), pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
, Workshop Companion Volume for Shared Task
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Evaluating contributions of natural language parsers to protein-protein interaction extraction, Proceedings of the 4th International Symposium on Semantic Mining in Biomedicine (SMBM-2010), October. Yusuke Miyao, Kenji Sagae, Rune Saetre, Takuya Matsuzaki, and Jun'ichi Tsujii, vol.25, pp.394-400, 2009. ,
Syntax annotation for the genia corpus, Proceedings of the IJCNLP 2005, pp.222-227, 2005. ,
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Pubmeth: a cancer methylation database combining text-mining and expert annotation. Nucleic Acids Research, pp.1-5, 2007. ,
Matching hierarchical structures using association graphs, IEEE Trans. Pattern Anal. Mach. Intell, vol.21, issue.11, pp.1105-1120, 1999. ,
An algorithm for suffix stripping, pp.313-316, 1997. ,
Saga: a subgraph matching tool for biological graphs, Bioinformatics, vol.23, issue.2, pp.232-239, 2007. ,
An algorithm for subgraph isomorphism, J. ACM, vol.23, issue.1, pp.31-42, 1976. ,
Searching substructures with superimposed distance, Association for Computational Linguistics References Robert Bossy, Julien Jourde, Philippe Bessières, Marteen van de Guchte, and Claire Nédellec, vol.88, pp.173-182, 2006. ,
Coarse-tofine n-best parsing and maxent discriminative reranking, Proceedings of the 43rd Meeting of the Association for Computational Linguistics, pp.173-180, 2005. ,
The structural and content aspects of abstracts versus bodies of full text journal articles are different, BMC Bioinformatics, vol.11, p.492, 2010. ,
Discourse verbs" and discourse periphrastic links, Second Workshop on Constraints in Discourse (CID06), pp.59-65, 2006. ,
Generating typed dependency parses from phrase structure parses, Proceedings of the 5th International Conference on Language Resources and Evaluation, pp.449-454, 2006. ,
BioNLP Shared Task 2011 -Bacteria Gene Interactions and Renaming, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00641586
Recognizing speculative language in biomedical research articles: a linguistically motivated perspective, BMC Bioinformatics, vol.9, issue.11, p.10, 2008. ,
Syntactic dependency based heuristics for biological event extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.119-127, 2009. ,
Corpus annotation for mining biomedical events from literature, BMC Bioinformatics, vol.9, p.10, 2008. ,
Overview of BioNLP'09 Shared Task on Event Extraction, Proceedings of Natural Language Processing in Biomedicine (BioNLP) NAACL 2009 Workshop, pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
Overview of the Genia Event task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Rhetorical structure theory: Toward a functional theory of text organization, Text, vol.8, issue.3, pp.243-281, 1988. ,
Selftraining for biomedical parsing, Proceedings of the 46th Meeting of the Association for Computational Linguistics, pp.101-104, 2008. ,
Overview of the Protein Coreference task in BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Overview of the Epigenetics and Post-translational Modifications (EPI) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
Overview of the Infectious Diseases (ID) task of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 1986. ,
ABNER: An open source tool for automatically tagging genes, proteins, and other entity names in text, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, vol.21, pp.3191-3192, 2005. ,
Extracting complex biological events with rich graph-based feature sets, Association for Computational Linguistics References Jari Björne, Juho Heimonen, Filip Ginter, Antti Airola, Tapio Pahikkala, and Tapio Salakoski, pp.10-18, 2005. ,
Scaling up biomedical event extraction to the entire PubMed, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.28-36, 2010. ,
Extracting contextualized complex biological events with rich graph-based feature sets, Computational Intelligence, Special issue on Extracting Bio, 2009. ,
Event extraction from trimmed dependency graphs, Proceedings of the BioNLP, 2009. ,
, Workshop Companion Volume for Shared Task, pp.19-27
Coarse-tofine n-best parsing and maxent discriminative reranking, Proceedings of the 43rd Annual Meeting of the Association for Computational Linguistics (ACL'05), pp.173-180, 2005. ,
Generating typed dependency parses from phrase structure parses, Proceedings of LREC-06, pp.449-454, 2006. ,
List of bacterial names with standing in nomenclature: a folder available on the internet, Int J Syst Bacteriol, vol.47, issue.2, pp.590-592, 1997. ,
, WordNet: an electronic lexical database, 1998.
Reconstruction of semantic relationships from their projections in biomolecular domain, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, pp.108-116, 2010. ,
Syntactic dependency based heuristics for biological event extraction, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.119-127, 2009. ,
Overview of BioNLP'09 Shared Task on Event Extraction, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.1-9, 2009. ,
Overview of BioNLP Shared Task, Proceedings of the BioNLP 2011 Workshop Companion Volume for Shared Task, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-02745923
The Stanford typed dependencies representation, COLING Workshop on Cross-framework and Cross-domain Parser Evaluation, 2008. ,
Any Domain Parsing: Automatic Domain Adaptation for Natural Language Parsing, 2010. ,
A comparative study of syntactic parsers for event extraction, Proceedings of the 2010 Workshop on Biomedical Natural Language Processing, BioNLP '10, pp.37-45, 2010. ,
Event extraction with complex event classification using rich features, J Bioinform Comput Biol, vol.8, pp.131-146, 2010. ,
An algorithm for suffix stripping, vol.14, pp.130-137, 1980. ,
A markov logic approach to bio-molecular event extraction, Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task, BioNLP '09, pp.41-49, 2009. ,
Large margin methods for structured and interdependent output variables, Journal of Machine Learning Research, vol.6, pp.1453-1484, 2005. ,
Analyzing text in search of bio-molecular events: a high-precision machine learning framework, Proceedings of the BioNLP 2009 Workshop Companion Volume for Shared Task, pp.128-136, 2009. ,
, Author Index