title: Advanced literature analysis in a Big Data world.
abstract: Comprehensive data mining of the scientific literature has become an increasing challenge. To address this challenge, Elsevier's Pathway Studio software uses the techniques of natural language processing to systematically extract specific biological information from journal articles and abstracts that is then used to create a very large, structured, and constantly expanding literature knowledgebase. Highly sophisticated visualization tools allow the user to interactively explore the vast number of connections created and stored in the Pathway Studio database. We demonstrate the value of this structured information approach by way of a biomarker use case example and describe a comprehensive collection of biomarkers and biomarker candidates, as reported in the literature. We use four major neuropsychiatric diseases to demonstrate common and unique biomarker elements, demonstrate specific enrichment patterns, and highlight strategies for identifying the most recent and novel reports for potential biomarker discovery. Finally, we introduce an innovative new taxonomy based on brain region identifications, which greatly increases the potential depth and complexity of information retrieval related to, and now accessible for, neuroscience research.
authors.affiliation: Department of Genomics Research, R&D Solutions, Rockville, Maryland.|Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
authors.forename: Chris
authors.initials: C
authors.lastname: Cheadle
authors.affiliation: Department of Genomics Research, R&D Solutions, Rockville, Maryland.
authors.forename: Hongbao
authors.initials: H
authors.lastname: Cao
authors.affiliation: Department of Genomics Research, R&D Solutions, Rockville, Maryland.
authors.forename: Andrey
authors.initials: A
authors.lastname: Kalinin
authors.affiliation: Department of Genomics Research, R&D Solutions, Rockville, Maryland.
authors.forename: Jaqui
authors.initials: J
authors.lastname: Hodgkinson
mesh_terms: D000043:Abstracting and Indexing; D000818:Animals; D001008:Anxiety Disorders / Q000145:classification / Q000175:diagnosis / Q000378:metabolism / Q000628:therapy; D015415:Biomarkers / Q000378:metabolism; D035843:Biomedical Research / Q000379:methods* / Q000639:trends; D001714:Bipolar Disorder / Q000145:classification / Q000175:diagnosis / Q000378:metabolism / Q000628:therapy; D019295:Computational Biology / Q000379:methods* / Q000639:trends; D057225:Data Mining / Q000379:methods* / Q000639:trends; D003628:Database Management Systems / Q000639:trends; D016206:Databases, Bibliographic; D003865:Major Depressive Disorder / Q000145:classification / Q000175:diagnosis / Q000378:metabolism / Q000628:therapy; D006801:Humans; D008403:Mass Screening / Q000379:methods* / Q000639:trends; D001523:Mental Disorders / Q000145:classification / Q000175:diagnosis* / Q000378:metabolism / Q000628:therapy; D009315:National Institute of Mental Health (U.S.); D009323:Natural Language Processing; D010506:Periodicals as Topic; D011379:Prognosis; D012559:Schizophrenia / Q000145:classification / Q000175:diagnosis / Q000378:metabolism / Q000628:therapy; D012984:Software; D057170:Translational Research, Biomedical / Q000379:methods / Q000639:trends; D014481:United States
chemical_list: D015415:Biomarkers
keywords: Pathway Studio; literature analysis; literature data mining; natural language processing