Natural language processing and visualization in the molecular imaging domain.
Molecular imaging is at the crossroads of genomic sciences and medical imaging. Information within the molecular imaging literature could be used to link to genomic and imaging information resources and to organize and index images in a way that is potentially useful to researchers. A number of natural language processing (NLP) systems are available to automatically extract information from genomic literature. One existing NLP system, known as BioMedLEE, automatically extracts biological information consisting of biomolecular substances and phenotypic data. This paper focuses on the adaptation, evaluation, and application of BioMedLEE to the molecular imaging domain. In order to adapt BioMedLEE for this domain, we extend an existing molecular imaging terminology and incorporate it into BioMedLEE. BioMedLEE's performance is assessed with a formal evaluation study. The system's performance, measured as recall and precision, is 0.74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information.
Tulipano
P Karina
PK
Department of Biomedical Informatics, Columbia University, 622 West 168th Street, Vanderbilt Clinic Floor 5, NY 10032, USA.
Tao
Ying
Y
Millar
William S
WS
Zanzonico
Pat
P
Kolbert
Katherine
K
Xu
Hua
H
Yu
Hong
H
Chen
Lifeng
L
Lussier
Yves A
YA
Friedman
Carol
C
D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods*; D016206:Databases, Bibliographic; D030541:Databases, Genetic; D003952:Diagnostic Imaging; D023281:Genomics; D006801:Humans; D016247:Information Storage and Retrieval; D009323:Natural Language Processing; D010641:Phenotype; D011381:Programming Languages; D012984:Software; D018511:Systems Integration; D009626:Terminology as Topic; D014584:User-Computer Interface; D018875:Vocabulary, Controlled