Head-driven statistical models for natural language parsing
Head-driven statistical models for natural language parsing
Building a large annotated corpus of English: the penn treebank
Computational Linguistics - Special issue on using large corpora: II
Automatic rule induction for unknown-word guessing
Computational Linguistics
Applied morphological processing of English
Natural Language Engineering
A maximum entropy approach to identifying sentence boundaries
ANLC '97 Proceedings of the fifth conference on Applied natural language processing
Using grammatical relations to compare parsers
EACL '03 Proceedings of the tenth conference on European chapter of the Association for Computational Linguistics - Volume 1
IJCNLP'04 Proceedings of the First international joint conference on Natural Language Processing
Relation mining over a corpus of scientific literature
AIME'05 Proceedings of the 10th conference on Artificial Intelligence in Medicine
Guest editorial: Artificial Intelligence in Medicine AIME '05
Artificial Intelligence in Medicine
Methodological Review: Extracting interactions between proteins from the literature
Journal of Biomedical Informatics
Mining of Protein Subcellular Localizations based on a Syntactic Dependency Tree and WordNet
Proceedings of the 2008 conference on Knowledge-Based Software Engineering: Proceedings of the Eighth Joint Conference on Knowledge-Based Software Engineering
Tools for Text Mining over Biomedical Literature
Proceedings of the 2006 conference on ECAI 2006: 17th European Conference on Artificial Intelligence August 29 -- September 1, 2006, Riva del Garda, Italy
Syntactic dependency based heuristics for biological event extraction
BioNLP '09 Proceedings of the Workshop on Current Trends in Biomedical Natural Language Processing: Shared Task
Methodological Review: Text mining for traditional Chinese medical knowledge discovery: A survey
Journal of Biomedical Informatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Comparing and combining chunkers of biomedical text
Journal of Biomedical Informatics
Relation mining experiments in the pharmacogenomics domain
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
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Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. Materials and methods: This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. Results: We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. Conclusion: We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall.