title: A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials.
abstract: Textual eligibility criteria in clinical trial protocols contain important information about potential clinically relevant pharmacogenomic events. Manual curation for harvesting this evidence is intractable as it is error prone and time consuming. In this paper, we develop and evaluate a Semantic Web-based system that captures and manages mutation evidences and related contextual information from cancer clinical trials. The system has 2 main components: an NLP-based annotator and a Semantic Web ontology-based annotation manager. We evaluated the performance of the annotator in terms of precision and recall. We demonstrated the usefulness of the system by conducting case studies in retrieving relevant clinical trials using a collection of mutations identified from TCGA Leukemia patients and Atlas of Genetics and Cytogenetics in Oncology and Haematology. In conclusion, our system using Semantic Web technologies provides an effective framework for extraction, annotation, standardization and management of genetic mutations in cancer clinical trials.
authors: Mayo Clinic, Rochester, MN ; Lehigh University, Bethlehem, PA.
authors: Sambhawa
authors: S
authors: Priya
authors: Mayo Clinic, Rochester, MN.
authors: Guoqian
authors: G
authors: Jiang
authors: Mayo Clinic, Rochester, MN.
authors: Surendra
authors: S
authors: Dasari
authors: Mayo Clinic, Rochester, MN.
authors: Michael T
authors: MT
authors: Zimmermann
authors: Mayo Clinic, Rochester, MN.
authors: Chen
authors: C
authors: Wang
authors: Lehigh University, Bethlehem, PA.
authors: Jeff
authors: J
authors: Heflin
authors: Mayo Clinic, Rochester, MN.
authors: Christopher G
authors: CG
authors: Chute