Robust partial-parsing through incremental, multi-algorithm processing
Text-based intelligent systems
Foundations of statistical natural language processing
Foundations of statistical natural language processing
Light parsing as finite state filtering
Extended finite state models of language
Comparing noun phrasing techniques for use with medical digital library tools
Journal of the American Society for Information Science - Special topic issue on digital libraries: part 2
Speech and Language Processing: An Introduction to Natural Language Processing, Computational Linguistics, and Speech Recognition
Disambiguating ambiguous biomedical terms in biomedical narrative text: an unsupervised method
Computers and Biomedical Research
Selective automated indexing of findings and diagnoses in radiology reports
Computers and Biomedical Research
Medical informatics and bioinformatics: European efforts to facilitate synergy
Computers and Biomedical Research
ICTAI '02 Proceedings of the 14th IEEE International Conference on Tools with Artificial Intelligence
Coping with ambiguity and unknown words through probabilistic models
Computational Linguistics - Special issue on using large corpora: II
A stochastic parts program and noun phrase parser for unrestricted text
ANLC '88 Proceedings of the second conference on Applied natural language processing
ANLC '97 Proceedings of the fifth conference on Applied natural language processing
A cascaded finite-state parser for syntactic analysis of Swedish
EACL '99 Proceedings of the ninth conference on European chapter of the Association for Computational Linguistics
Statistical models for unsupervised prepositional phrase attachment
COLING '98 Proceedings of the 17th international conference on Computational linguistics - Volume 2
Deterministic parsing of syntactic non-fluencies
ACL '83 Proceedings of the 21st annual meeting on Association for Computational Linguistics
A rule-based approach to prepositional phrase attachment disambiguation
COLING '94 Proceedings of the 15th conference on Computational linguistics - Volume 2
A maximum entropy model for prepositional phrase attachment
HLT '94 Proceedings of the workshop on Human Language Technology
Tuning support vector machines for biomedical named entity recognition
BioMed '02 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain - Volume 3
Contrast and variability in gene names
BioMed '02 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain - Volume 3
The GENIA corpus: an annotated research abstract corpus in molecular biology domain
HLT '02 Proceedings of the second international conference on Human Language Technology Research
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
International Journal of Bioinformatics Research and Applications
Negation recognition in medical narrative reports
Information Retrieval
Postnominal prepositional phrase attachment in proteomics
BioNLP '06 Proceedings of the Workshop on Linking Natural Language Processing and Biology: Towards Deeper Biological Literature Analysis
Syntactic dependency based heuristics for biological event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Interpreting comparative constructions in biomedical text
BioNLP '07 Proceedings of the Workshop on BioNLP 2007: Biological, Translational, and Clinical Language Processing
Prepositions in applications: A survey and introduction to the special issue
Computational Linguistics
Towards Extraction of Conceptual Structures from Electronic Health Records
ICCS '09 Proceedings of the 17th International Conference on Conceptual Structures: Conceptual Structures: Leveraging Semantic Technologies
Postnominal prepositional phrase attachment in proteomics
LNLBioNLP '06 Proceedings of the HLT-NAACL BioNLP Workshop on Linking Natural Language and Biology
Journal of Biomedical Informatics
Measuring prediction capacity of individual verbs for the identification of protein interactions
Journal of Biomedical Informatics
Simplicity is better: revisiting single kernel PPI extraction
COLING '10 Proceedings of the 23rd International Conference on Computational Linguistics
Improving phenotype name recognition
Canadian AI'11 Proceedings of the 24th Canadian conference on Advances in artificial intelligence
CICLing'06 Proceedings of the 7th international conference on Computational Linguistics and Intelligent Text Processing
Journal of Biomedical Informatics
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
Development and evaluation of a biomedical search engine using a predicate-based vector space model
Journal of Biomedical Informatics
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Natural language processing for biomedical text currently focuses mostly on entity and relation extraction. These entities and relations are usually pre-specified entities, e.g., proteins, and pre-specified relations, e.g., inhibit relations. A shallow parser that captures the relations between noun phrases automatically from free text has been developed and evaluated. It uses heuristics and a noun phraser to capture entities of interest in the text. Cascaded finite state automata structure the relations between individual entities. The automata are based on closed-class English words and model generic relations not limited to specific words. The parser also recognizes coordinating conjunctions and captures negation in text, a feature usually ignored by others. Three cancer researchers evaluated 330 relations extracted from 26 abstracts of interest to them. There were 296 relations correctly extracted from the abstracts resulting in 90% precision of the relations and an average of 11 correct relations per abstract.