Kernel-based learning for biomedical relation extraction
Journal of the American Society for Information Science and Technology
Methodological Review: Extracting interactions between proteins from the literature
Journal of Biomedical Informatics
The role of syntactic features in protein interaction extraction
Proceedings of the 2nd international workshop on Data and text mining in bioinformatics
Detecting Protein-Protein Interactions in Biomedical Texts Using a Parser and Linguistic Resources
CICLing '09 Proceedings of the 10th International Conference on Computational Linguistics and Intelligent Text Processing
A graph kernel for protein-protein interaction extraction
BioNLP '08 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Event extraction from trimmed dependency graphs
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Molecular event extraction from link grammar parse trees
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Syntactic dependency based heuristics for biological event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Analyzing text in search of bio-molecular events: a high-precision machine learning framework
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Static relations: a piece in the biomedical information extraction puzzle
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
A local alignment kernel in the context of NLP
COLING '08 Proceedings of the 22nd International Conference on Computational Linguistics - Volume 1
The Stanford typed dependencies representation
CrossParser '08 Coling 2008: Proceedings of the workshop on Cross-Framework and Cross-Domain Parser Evaluation
Modeling Common Real-Word Relations Using Triples Extracted from n-Grams
ASWC '09 Proceedings of the 4th Asian Conference on The Semantic Web
A rich feature vector for protein-protein interaction extraction from multiple corpora
EMNLP '09 Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1 - Volume 1
Journal of Biomedical Informatics
Journal of Biomedical Informatics
DEEPER: a full parsing based approach to protein relation extraction
EvoBIO'08 Proceedings of the 6th European conference on Evolutionary computation, machine learning and data mining in bioinformatics
Extracting Protein Interactions from Text with the Unified AkaneRE Event Extraction System
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Efficient Extraction of Protein-Protein Interactions from Full-Text Articles
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
CALC '10 Proceedings of the NAACL HLT 2010 Second Workshop on Computational Approaches to Linguistic Creativity
Semantic relations for problem-oriented medical records
Artificial Intelligence in Medicine
Simplicity is better: revisiting single kernel PPI extraction
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Entity-focused sentence simplification for relation extraction
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Using text to build semantic networks for pharmacogenomics
Journal of Biomedical Informatics
Journal of Biomedical Informatics
Using local alignments for relation recognition
Journal of Artificial Intelligence Research
Bootstrapping location relations from text
Proceedings of the 73rd ASIS&T Annual Meeting on Navigating Streams in an Information Ecosystem - Volume 47
Towards semantic annotation supported by dependency linguistics and ILP
ISWC'10 Proceedings of the 9th international semantic web conference on The semantic web - Volume Part II
Multiple kernel learning in protein-protein interaction extraction from biomedical literature
Artificial Intelligence in Medicine
Exploiting syntactico-semantic structures for relation extraction
HLT '11 Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies - Volume 1
BioNLP '11 Proceedings of BioNLP 2011 Workshop
Improving phenotype name recognition
Canadian AI'11 Proceedings of the 24th Canadian conference on Advances in artificial intelligence
Identifying relations between medical concepts by parsing UMLS® definitions
ICCS'11 Proceedings of the 19th international conference on Conceptual structures for discovering knowledge
A practice-driven systematic review of dependency analysis solutions
Empirical Software Engineering
Neighborhood hash graph kernel for protein-protein interaction extraction
Journal of Biomedical Informatics
Dependency parsing schemata and mildly non-projective dependency parsing
Computational Linguistics
Mixture of logistic models and an ensemble approach for protein-protein interaction extraction
Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine
Recursive sequence mining to discover named entity relations
IDA'10 Proceedings of the 9th international conference on Advances in Intelligent Data Analysis
Score-Based approach for anaphora resolution in drug-drug interactions documents
NLDB'09 Proceedings of the 14th international conference on Applications of Natural Language to Information Systems
Sequential patterns to discover and characterise biological relations
CICLing'10 Proceedings of the 11th international conference on Computational Linguistics and Intelligent Text Processing
Extraction of genic interactions with the recursive logical theory of an ontology
CICLing'10 Proceedings of the 11th international conference on Computational Linguistics and Intelligent Text Processing
Hash Subgraph Pairwise Kernel for Protein-Protein Interaction Extraction
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Discovering linguistic patterns using sequence mining
CICLing'12 Proceedings of the 13th international conference on Computational Linguistics and Intelligent Text Processing - Volume Part I
A framework for biological event extraction from text
Proceedings of the 2nd International Conference on Web Intelligence, Mining and Semantics
Tree kernel-based protein-protein interaction extraction from biomedical literature
Journal of Biomedical Informatics
Using a shallow linguistic kernel for drug-drug interaction extraction
Journal of Biomedical Informatics
Journal of Biomedical Informatics
Relation mining experiments in the pharmacogenomics domain
Journal of Biomedical Informatics
International Journal of Data Mining and Bioinformatics
Combining tree structures, flat features and patterns for biomedical relation extraction
EACL '12 Proceedings of the 13th Conference of the European Chapter of the Association for Computational Linguistics
Improving distantly supervised extraction of drug-drug and protein-protein interactions
ROBUS-UNSUP '12 Proceedings of the Joint Workshop on Unsupervised and Semi-Supervised Learning in NLP
High precision rule based PPI extraction and per-pair basis performance evaluation
Proceedings of the ACM sixth international workshop on Data and text mining in biomedical informatics
PIMiner: a web tool for extraction of protein interactions from biomedical literature
International Journal of Data Mining and Bioinformatics
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Motivation: The discovery of regulatory pathways, signal cascades, metabolic processes or disease models requires knowledge on individual relations like e.g. physical or regulatory interactions between genes and proteins. Most interactions mentioned in the free text of biomedical publications are not yet contained in structured databases. Results: We developed RelEx, an approach for relation extraction from free text. It is based on natural language preprocessing producing dependency parse trees and applying a small number of simple rules to these trees. We applied RelEx on a comprehensive set of one million MEDLINE abstracts dealing with gene and protein relations and extracted ~150 000 relations with an estimated perfomance of both 80% precision and 80% recall. Availability: The used natural language preprocessing tools are free for use for academic research. Test sets and relation term lists are available from our website (http://www.bio.ifi.lmu.de/publications/RelEx/). Contact: katrin.fundel@bio.ifi.lmu.de