Natural language processing and visualization in the molecular imaging domain Journal Article
| Authors: | Karina Tulipano, P.; Tao, Y.; Millar, W. S.; Zanzonico, P.; Kolbert, K.; Xu, H.; Yu, H.; Chen, L.; Lussier, Y. A.; Friedman, C. |
| Article Title: | Natural language processing and visualization in the molecular imaging domain |
| Abstract: | 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. © 2006 Elsevier Inc. All rights reserved. |
| Keywords: | phenotype; animals; computational biology; image analysis; cell line; user-computer interface; molecular imaging; diagnostic imaging; data base; genetic engineering; medical imaging; systems integration; databases, bibliographic; genomics; nomenclature; bioinformatics; computer program; software; image reconstruction; language processing; databases, genetic; natural language processing systems; programming languages; biomedicine; ontology; terminology; natural language processing; information storage and retrieval; biomedlee; geneways; information extraction; ontologies; pgviewer; java programming language; biomolecular substances; imaging information resources; molecular imaging domains; vocabulary, controlled |
| Journal Title: | Journal of Biomedical Informatics |
| Volume: | 40 |
| Issue: | 3 |
| ISSN: | 1532-0464 |
| Publisher: | Elsevier Inc. |
| Date Published: | 2007-06-01 |
| Start Page: | 270 |
| End Page: | 281 |
| Language: | English |
| DOI: | 10.1016/j.jbi.2006.08.002 |
| PUBMED: | 17084109 |
| PROVIDER: | scopus |
| DOI/URL: | |
| Notes: | --- - "Cited By (since 1996): 3" - "Export Date: 17 November 2011" - "CODEN: JBIOB" - "Source: Scopus" |
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