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BioInfer: a corpus for information extraction in the biomedical domain
TLDR
We present BioInfer (Bio Information Extraction Resource), a new public resource providing an annotated corpus of biomedical English sentences annotated for relationships, named entities, and syntactic dependencies. Expand
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All-paths graph kernel for protein-protein interaction extraction with evaluation of cross-corpus learning
TLDR
We show that the graph kernel approach performs on state-of-the-art level in PPI extraction, and note the possible extension to the task of extracting complex interactions. Expand
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Extracting Complex Biological Events with Rich Graph-Based Feature Sets
TLDR
We describe a system for extracting complex events among genes and proteins from biomedical literature, developed in context of the BioNLP'09 Shared Task on Event Extraction. Expand
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A large-scale evaluation of computational protein function prediction
Automated annotation of protein function is challenging. As the number of sequenced genomes rapidly grows, the overwhelming majority of protein products can only be annotated computationally. IfExpand
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Distributional Semantics Resources for Biomedical Text Processing
TLDR
We introduce the first set of such language resources created from analysis of the entire available biomedical literature, including a dataset of all 1to 5-grams and their probabilities in these texts and new models of word semantics. Expand
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Generalizing Biomedical Event Extraction
TLDR
We present a system for extracting biomedical events (detailed descriptions of biomolecular interactions) from research articles. Expand
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Comparative analysis of five protein-protein interaction corpora
TLDR
We present the first comparative evaluation of the diverse PPI corpora, performing quantitative evaluation using two separate information extraction methods as well as detailed statistical and qualitative analyses of their properties. Expand
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TEES 2.1: Automated Annotation Scheme Learning in the BioNLP 2013 Shared Task
TLDR
We participate in the BioNLP 2013 Shared Task with Turku Event Extraction System (TEES) version 2.1, a support vector machine based text mining system for the extraction of events and relations from natural language texts. Expand
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An expanded evaluation of protein function prediction methods shows an improvement in accuracy
TLDR
We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology. Expand
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A Graph Kernel for Protein-Protein Interaction Extraction
TLDR
In this paper, we propose a graph kernel based approach for the automated extraction of protein-protein interactions (PPI) from scientific literature. Expand
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