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BMCBI
2011

Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles

8 years 1 months ago
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles
Background: Experimentally verified protein-protein interactions (PPIs) cannot be easily retrieved by researchers unless they are stored in PPI databases. The curation of such databases can be facilitated by employing textmining systems to identify genes which play the interactor role in PPIs and to map these genes to unique database identifiers (interactor normalization task or INT) and then to return a list of interaction pairs for each article (interaction pair task or IPT). These two tasks are evaluated in terms of the area under curve of the interpolated precision/recall (AUC iP/R) score because the order of identifiers in the output list is important for ease of curation. Results: Our INT system developed for the BioCreAtIvE II.5 INT challenge achieved a promising AUC iP/R of 43.5% by using a support vector machine (SVM)-based ranking procedure. Using our new re-ranking algorithm, we have
Richard Tzong-Han Tsai, Po-Ting Lai
Added 12 May 2011
Updated 12 May 2011
Type Journal
Year 2011
Where BMCBI
Authors Richard Tzong-Han Tsai, Po-Ting Lai
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