title: A method for automatically extracting infectious disease-related primers and probes from the literature.
abstract: 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 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Madrid, Spain. mgarcia@infomed.dia.fi.upm.es
authors.forename: Miguel
authors.initials: M
authors.lastname: García-Remesal
authors.forename: Alejandro
authors.initials: A
authors.lastname: Cuevas
authors.forename: Victoria
authors.initials: V
authors.lastname: López-Alonso
authors.forename: Guillermo
authors.initials: G
authors.lastname: López-Campos
authors.forename: Guillermo
authors.initials: G
authors.lastname: de la Calle
authors.forename: Diana
authors.initials: D
authors.lastname: de la Iglesia
authors.forename: David
authors.initials: D
authors.lastname: Pérez-Rey
authors.forename: José
authors.initials: J
authors.lastname: Crespo
authors.forename: Fernando
authors.initials: F
authors.lastname: Martín-Sánchez
authors.forename: Víctor
authors.initials: V
authors.lastname: Maojo
mesh_terms: D001483:Base Sequence; D017931:DNA Primers / Q000737:chemistry / Q000235:genetics*; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics*; D057225:Data Mining; D030541:Databases, Genetic; D010506:Periodicals as Topic
chemical_list: D017931:DNA Primers; D015342:DNA Probes