A method for automatically extracting infectious disease-related primers and probes from the literature

Background: Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1) convert each document into a tree of paper sections, (2) detect the candidate sequences using a set of finite state machine-based recognizers, (3) refine problem sequences using a rule-based expert system, and (4) annotate the extracted sequences with their related organism/gene information. Results: We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organi...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Miguel García-Remesal, Alejandro Cuevas, Victoria López-Alonso, Guillermo López-Campos, Guillermo de la Calle, Diana de la Iglesia, David Pérez-Rey, José Crespo, Fernando Martín-Sánchez, Victor Maojo
• Keywords: BMCBI 2010, Extracted Sequences, Infectious Diseases, Sequences