Dataset Information

Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization.

ABSTRACT: Surgical pathology reports (SPR) contain rich clinical diagnosis information. The text information extraction system (TIES) is an end-to-end application leveraging natural language processing technologies and focused on the processing of pathology and/or radiology reports.We deployed the TIES system and integrated SPRs into the TIES system on a daily basis at Kaiser Permanente Southern California. The breast cancer cases diagnosed in December 2013 from the Cancer Registry (CANREG) were used to validate the performance of the TIES system. The National Cancer Institute Metathesaurus (NCIM) concept terms and codes to describe breast cancer were identified through the Unified Medical Language System Terminology Service (UTS) application. The identified NCIM codes were used to search for the coded SPRs in the back-end datastore directly. The identified cases were then compared with the breast cancer patients pulled from CANREG.A total of 437 breast cancer concept terms and 14 combinations of "breast"and "cancer" terms were identified from the UTS application. A total of 249 breast cancer cases diagnosed in December 2013 was pulled from CANREG. Out of these 249 cases, 241 were successfully identified by the TIES system from a total of 457 reports. The TIES system also identified an additional 277 cases that were not part of the validation sample. Out of the 277 cases, 11% were determined as highly likely to be cases after manual examinations, and 86% were in CANREG but were diagnosed in months other than December of 2013.The study demonstrated that the TIES system can effectively identify potential breast cancer cases in our care setting. Identified potential cases can be easily confirmed by reviewing the corresponding annotated reports through the front-end visualization interface. The TIES system is a great tool for identifying potential various cancer cases in a timely manner and on a regular basis in support of clinical research studies.

SUBMITTER: Xie F

PROVIDER: S-EPMC5760847 | biostudies-other | 2017

REPOSITORIES: biostudies-other

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Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization.

Xie Fagen F Lee Janet J Munoz-Plaza Corrine E CE Hahn Erin E EE Chen Wansu W

Journal of pathology informatics 20171214

<h4>Background</h4>Surgical pathology reports (SPR) contain rich clinical diagnosis information. The text information extraction system (TIES) is an end-to-end application leveraging natural language processing technologies and focused on the processing of pathology and/or radiology reports.<h4>Methods</h4>We deployed the TIES system and integrated SPRs into the TIES system on a daily basis at Kaiser Permanente Southern California. The breast cancer cases diagnosed in December 2013 from the Canc ...[more]

PMID: 29416911

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Project description:BackgroundFor ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.ResultsEnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.ConclusionEnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.

Project description:This study highlights an unmet need in osteoporosis management, suggesting that beyond bone mineral density and fracture history, gender, fracture type, and age should be considered for fracture risk assessment. Following fragility fracture, men, patients with a spine or hip fracture, and those aged ≥ 65 have a higher disease burden.IntroductionThe objective of this study was to characterize osteoporosis-related fracture incidence and identify predictors of subsequent fractures and mortality.MethodsThis retrospective cohort study, conducted within Kaiser Permanente Southern California, included patients aged ≥ 50 years with qualifying fractures from 1/1/2007 to 12/31/2016, identified from diagnosis/procedure codes. Rates for fracture incidence, mortality, and resource utilization in the year post-fracture are reported. Associations between index fracture types and demographic/clinical characteristics, and mortality, subsequent fracture, and rehospitalization outcomes were estimated.ResultsOf 63,755 eligible patients, 66.7% were ≥ 65 years and 69.1% female. Index fractures included nonhip/nonspine (64.4%), hip (25.3%), and spine (10.3%). Age-adjusted subsequent fracture rate/100 person-years was higher for those with an index spine (14.5) versus hip fracture (6.3). Hospitalization rate/100 person-years was highest for patients ≥ 65 (31.8) and for spine fractures (43.5). Men (vs women) had higher age-adjusted rates of hospitalization (19.4; 17.7), emergency room visits (73.8; 66.3), and use of rehabilitation services (31.7; 27.2). The 30-day age-adjusted mortality rate/100 person-years was 46.7, 32.4, and 15.5 for spine, hip, and nonspine/nonhip fractures. The 1-year age-adjusted mortality rate/100 person-years was 14.7 for spine and 15.6 for hip fractures. In multivariable analyses, spine and hip fractures (vs nonhip/nonspine fractures) were significant predictors of 1-year mortality, all-cause and osteoporosis-related hospitalization, and nursing home use (all P-values < 0.0001).ConclusionMorbidity is high in the year following a fragility fracture and men, patients with a spine or hip fracture, and those aged ≥ 65 have a greater disease burden.

Dataset Information

Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization.

Publications

Application of Text Information Extraction System for Real-Time Cancer Case Identification in an Integrated Healthcare Organization.

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