Measuring prediction capacity of individual verbs for the identification of protein interactions.
The identification of events such as protein-protein interactions (PPIs) from the scientific literature is a complex task. One of the reasons is that there is no formal syntax to denote such relations in the scientific literature. Nonetheless, it is important to understand such relational event representations to improve information extraction solutions (e.g., for gene regulatory events). In this study, we analyze publicly available protein interaction corpora (AIMed, BioInfer, BioCreAtIve II) to determine the scope of verbs used to denote protein interactions and to measure their predictive capacity for the identification of PPI events. Our analysis is based on syntactical language patterns. This restriction has the advantage that the verb mention is used as the independent variable in the experiments enabling comparability of results in the usage of the verbs. The initial selection of verbs has been generated from a systematic analysis of the scientific literature and existing corpora for PPIs. We distinguish modifying interactions (MIs) such as posttranslational modifications (PTMs) from non-modifying interactions (NMIs) and assumed that MIs have a higher predictive capacity due to stronger scientific evidence proving the interaction. We found that MIs are less frequent in the corpus but can be extracted at the same precision levels as PPIs. A significant portion of correct PPI reportings in the BioCreAtIve II corpus use the verb "associate", which semantically does not prove a relation. The performance of every monitored verb is listed and allows the selection of specific verbs to improve the performance of PPI extraction solutions. Programmatic access to the text processing modules is available online (www.ebi.ac.uk/webservices/whatizit/info.jsf) and the full analysis of Medline abstracts will be made through the Web pages of the Rebholz group.
Rebholz-Schuhmann
Dietrich
D
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB101SD, UK. rebholz@ebi.ac.uk
Jimeno-Yepes
Antonio
A
Arregui
Miguel
M
Kirsch
Harald
H
D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D053263:Gene Regulatory Networks; D009323:Natural Language Processing; D025941:Protein Interaction Mapping / Q000379:methods*; D011499:Protein Processing, Post-Translational; D011506:Proteins / Q000378:metabolism*; D015398:Signal Transduction; D018875:Vocabulary, Controlled
D011506:Proteins