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

We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name.We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.Molecular technologies are used in routine clinical practice to identify microorganisms, and evaluate the presence of virulence factors, antibiotic resistance determinants and host-microbe interactions [1]. For instance, numerous nucleic acid assays have been developed [2] using hybridization or DNA extension techniques that include a wide range of technologies, such as polymerase chain reaction (PCR) methods [3], gene and whole genome sequencing [4,5], Luminex [6] and microarray analysis [7].There is a wide range of technologies that provide specific short base sequences of DNA as probes — used to detect the complementary base sequence of interest—or as primers—that guide the DNA amplification process—used for different purposes. Primers and probes are the main components of nucleic acid-based detection systems and have been the subject of multiple studies. Therefore, different software programs have been developed to design these specific sequences of primers and probes mini