title: Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.
abstract: BACKGROUND
  Biomedical studies need assistance from automated tools and easily accessible data to address the problem of the rapidly accumulating literature. Text-mining tools and curated databases have been developed to address such needs and they can be applied to improve the understanding of molecular pathogenesis of complex diseases like thyroid cancer.
  
  
  RESULTS
  We have developed a system, PWTEES, which extracts pathway interactions from the literature utilizing an existing event extraction tool (TEES) and pathway named entity recognition (PathNER). We then applied the system on a thyroid cancer corpus and systematically extracted molecular interactions involving either genes or pathways. With the extracted information, we constructed a molecular interaction network taking genes and pathways as nodes. Using curated pathway information and network topological analyses, we highlight key genes and pathways involved in thyroid carcinogenesis.
  
  
  CONCLUSIONS
  Mining events involving genes and pathways from the literature and integrating curated pathway knowledge can help improve the understanding of molecular interactions of complex diseases. The system developed for this study can be applied in studies other than thyroid cancer. The source code is freely available online at https://github.com/chengkun-wu/PWTEES.
authors.forename: Chengkun
authors.initials: C
authors.lastname: Wu
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Schwartz
authors.forename: Georg
authors.initials: G
authors.lastname: Brabant
authors.forename: Shao-Liang
authors.initials: SL
authors.lastname: Peng
authors.forename: Goran
authors.initials: G
authors.lastname: Nenadic
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining / Q000379:methods*; D006801:Humans; D060066:Protein Interaction Maps; D015398:Signal Transduction; D013964:Thyroid Neoplasms / Q000235:genetics* / Q000378:metabolism* / Q000473:pathology