Artificial Intelligence in Medicine
Methodological Review: Extracting interactions between proteins from the literature
Journal of Biomedical Informatics
Extracting Protein-Protein Interactions from MEDLINE using the Hidden Vector State model
International Journal of Bioinformatics Research and Applications
Extraction of protein interaction data: a comparative analysis of methods in use
EURASIP Journal on Bioinformatics and Systems Biology
Building ontological relationships: A new approach
Journal of the American Society for Information Science and Technology
Training the Hidden Vector State Model from Un-annotated Corpus
ICCS '07 Proceedings of the 7th international conference on Computational Science, Part II
TSD '08 Proceedings of the 11th international conference on Text, Speech and Dialogue
Boosting Chinese Question Answering with Two Lightweight Methods: ABSPs and SCO-QAT
ACM Transactions on Asian Language Information Processing (TALIP)
Expert Systems with Applications: An International Journal
Finding optimal parameters for edit distance based sequence classification is NP-hard
Proceedings of the KDD-09 Workshop on Statistical and Relational Learning in Bioinformatics
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Extracting protein-protein interactions using simple contextual features
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Event extraction from trimmed dependency graphs
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
Identifying interaction sentences from biological literature using automatically extracted patterns
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing
Alignment-based surface patterns for factoid question answering systems
Integrated Computer-Aided Engineering - Selected papers from the IEEE Conference on Information Reuse and Integration (IRI), July 13-15, 2008
Collaborative text-annotation resource for disease-centered relation extraction from biomedical text
Journal of Biomedical Informatics
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Extracting protein-protein interactions using simple contextual features
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Predicting protein-protein interactions using numerical associational features
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
Journal of Biomedical Informatics
Measuring prediction capacity of individual verbs for the identification of protein interactions
Journal of Biomedical Informatics
ICIC'07 Proceedings of the intelligent computing 3rd international conference on Advanced intelligent computing theories and applications
Mining the relationship between gene and disease from literature
FSKD'09 Proceedings of the 6th international conference on Fuzzy systems and knowledge discovery - Volume 7
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Large scale relation detection
FAM-LbR '10 Proceedings of the NAACL HLT 2010 First International Workshop on Formalisms and Methodology for Learning by Reading
Canadian AI'11 Proceedings of the 24th Canadian conference on Advances in artificial intelligence
Biomedical events extraction using the hidden vector state model
Artificial Intelligence in Medicine
A tree kernel-based method for protein-protein interaction mining from biomedical literature
KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
Extracting protein-protein interactions in biomedical literature using an existing syntactic parser
KDLL'06 Proceedings of the 2006 international conference on Knowledge Discovery in Life Science Literature
ISWC'06 Proceedings of the 5th international conference on The Semantic Web
A new algorithm for pattern optimization in protein-protein interaction extraction system
IbPRIA'05 Proceedings of the Second Iberian conference on Pattern Recognition and Image Analysis - Volume Part II
Extraction of gene/protein interaction from text documents with relation kernel
KES'05 Proceedings of the 9th international conference on Knowledge-Based Intelligent Information and Engineering Systems - Volume Part II
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
Populating an allergens ontology using natural language processing and machine learning techniques
AIME'05 Proceedings of the 10th conference on Artificial Intelligence in Medicine
GeneTUC, GENIA and google: natural language understanding in molecular biology literature
Transactions on Computational Systems Biology V
Extracting protein-protein interactions from the literature using the hidden vector state model
ICCS'06 Proceedings of the 6th international conference on Computational Science - Volume Part II
International Journal of Data Mining and Bioinformatics
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
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Motivation: Although there are several databases storing protein--protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a robust and powerful methodology to mine protein--protein interactions from biomedical texts. Results: We present a novel and robust approach for extracting protein--protein interactions from literature. Our method uses a dynamic programming algorithm to compute distinguishing patterns by aligning relevant sentences and key verbs that describe protein interactions. A matching algorithm is designed to extract the interactions between proteins. Equipped only with a dictionary of protein names, our system achieves a recall rate of 80.0% and precision rate of 80.5%. Availability: The program is available on request from the authors.