title: Sophia: A Expedient UMLS Concept Extraction Annotator.
abstract: An opportunity exists for meaningful concept extraction and indexing from large corpora of clinical notes in the Veterans Affairs (VA) electronic medical record. Currently available tools such as MetaMap, cTAKES and HITex do not scale up to address this big data need. Sophia, a rapid UMLS concept extraction annotator was developed to fulfill a mandate and address extraction where high throughput is needed while preserving performance. We report on the development, testing and benchmarking of Sophia against MetaMap and cTAKEs. Sophia demonstrated improved performance on recall as compared to cTAKES and MetaMap (0.71 vs 0.66 and 0.38). The overall f-score was similar to cTAKES and an improvement over MetaMap (0.53 vs 0.57 and 0.43). With regard to speed of processing records, we noted Sophia to be several fold faster than cTAKES and the scaled-out MetaMap service. Sophia offers a viable alternative for high-throughput information extraction tasks.
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Guy
authors.initials: G
authors.lastname: Divita
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Qing T
authors.initials: QT
authors.lastname: Zeng
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Adi V
authors.initials: AV
authors.lastname: Gundlapalli
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Scott
authors.initials: S
authors.lastname: Duvall
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Nebeker
authors.affiliation: VA Salt Lake City Health Care System and University of Utah School of Medicine, Salt Lake City, UT.
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Samore
mesh_terms: D000465:Algorithms; D057286:Electronic Health Records; D016247:Information Storage and Retrieval / Q000379:methods*; D009323:Natural Language Processing; D017432:Unified Medical Language System; D014481:United States; D014493:United States Department of Veterans Affairs