RelEx---Relation extraction using dependency parse trees
Bioinformatics
Text processing through Web services
Bioinformatics
International Journal of Data Mining and Bioinformatics
Extraction of protein interaction data: a comparative analysis of methods in use
EURASIP Journal on Bioinformatics and Systems Biology
Large-scale Protein-Protein Interaction prediction using novel kernel methods
International Journal of Data Mining and Bioinformatics
International Journal of Intelligent Systems - Granular Computing: Models and Applications
Prediction of protein protein interactions from primary sequences
International Journal of Data Mining and Bioinformatics
Developing a robust part-of-speech tagger for biomedical text
PCI'05 Proceedings of the 10th Panhellenic conference on Advances in Informatics
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Information on Protein Interactions PIs is valuable for biomedical research, but often lies buried in the scientific literature and cannot be readily retrieved. While much progress has been made over the years in extracting PIs from the literature using computational methods, there is a lack of free, public, user-friendly tools for the discovery of PIs. We developed an online tool for the extraction of PI relationships from PubMed-abstracts, which we name PIMiner. Protein pairs and the words that describe their interactions are reported by PIMiner so that new interactions can be easily detected within text. The interaction likelihood levels are reported too. The option to extract only specific types of interactions is also provided. The PIMiner server can be accessed through a web browser or remotely through a client's command line. PIMiner can process 50,000 PubMed abstracts in approximately 7 min and thus appears suitable for large-scale processing of biological/biomedical literature.