A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature

Anália Lourenço¹, Michael Conover^2,3, Andrew Wong⁴, Azadeh Nematzadeh^2,3, Fengxia Pan⁵, Hagit Shatkay^4,6,7*and Luis M. Rocha^2,3,*

¹IBB/CEB, University of Minho, Campus Gualtar, Braga, Portugal
²School of Informatics and Computing, Indiana University, 1900 East Tenth Street, Bloomington IN 47408, USA
³FLAD Computational Biology Collaboratorium, Instituto Gulbenkian de Ciencia, Portugal
⁴ School of Computing, Queen's University, Kingston, ON, Canada
⁵Microsoft Corp., Redmond, WA, USA
⁶ Dept. of Computer and Information Sciences, University of Delaware, Newark, DE, USA
⁷ Center for Bioinformatics and Computational Biology, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
^*To whom correspondence should be addressed: shatkay@cis.udel.edu (IMT) or rocha@indiana.edu (ACT)

Citation: A. Lourenço, M. Conover, A. Wong, A. Nematzadeh, F. Pan, H. Shatkay, and L.M. Rocha [2011]."A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature". BMC Bioinformatics, 12(Suppl 8):S12. DOI: 10.1186/1471-2105-12-S8-S12.

The full text and pdf re-print are available from the BMC Bioinformatics site. Due to mathematical notation and graphics, only the abstract is presented here. Our pdf pre-print is also available in the arxiv.org. Supplementary materials for this paper are also available as a zip file with instructions.

Background: We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of available Named Entity Recognition and dictionary tools, and used the most promising ones to extend our Variable Trigonometric Threshold linear classifier. Our main goal was to exploit the power of available named entity recognition and dictionary tools to aid in the classification of documents relevant to Protein-Protein Interaction (PPI). For the IMT, we focused on obtaining evidence in support of the interaction methods used, rather than on tagging the document with the method identifiers. We experimented with a primarily statistical approach, as opposed to employing a deeper natural language processing strategy. In a nutshell, we exploited classifiers, simple pattern matching for potential PPI methods within sentences, and ranking of candidate matches using statistical considerations. Finally, we also studied the benefits of integrating the method extraction approach that we have used for the IMT into the ACT pipeline.

Results: For the ACT, our linear article classifier leads to a ranking and classification performance significantly higher than all the reported submissions to the challenge in terms of Area Under the Interpolated Precision and Recall Curve, Mathew's Correlation Coefficient, and F-Score. We observe that the most useful Named Entity Recognition and Dictionary tools for classification of articles relevant to protein-protein interaction are: ABNER, NLPROT, OSCAR 3 and the PSI-MI ontology. For the IMT, our results are comparable to those of other systems, which took very different approaches. While the performance is not very high, we focus on providing evidence for potential interaction detection methods. A significant majority of the evidence sentences, as evaluated by independent annotators, are relevant to PPI detection methods.

Conclusions: For the ACT, we show that the use of named entity recognition tools leads to a substantial improvement in the ranking and classification of articles relevant to protein-protein interaction. Thus, we show that our substantially expanded linear classifier is a very competitive classifier in this domain. Moreover, this classifier produces interpretable surfaces that can be understood as "rules" for human understanding of the classification. We also provide evidence supporting certain named entity recognition tools as beneficial for protein-interaction article classification, or demonstrating that some of the tools are not beneficial for the task. In terms of the IMT task, in contrast to other participants, our approach focused on identifying sentences that are likely to bear evidence for the application of a PPI detection method, rather than on classifying a document as relevant to a method. As BioCreative III did not perform an evaluation of the evidence provided by the system, we have conducted a separate assessment, where multiple independent annotators manually evaluated the evidence produced by one of our runs. Preliminary results from this experiment are reported here and suggest that the majority of the evaluators agree that our tool is indeed effective in detecting relevant evidence for PPI detection methods. Regarding the integration of both tasks, we note that the time required for running each pipeline is realistic within a curation effort, and that we can, without compromising the quality of the output, reduce the time necessary to extract entities from text for the ACT pipeline by pre-selecting candidate relevant text using the IMT pipeline.

Keywords:Protein-protein interaction, text mining, bibliome informatics, Information Extraction, Literature Mining, Binary Classification.