PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

The Impact of Automatic Pre-annotation in Clinical Note Data Element Extraction - the CLEAN Tool

Objective. Annotation is expensive but essential for clinical note review and clinical natural language processing (cNLP). However, the extent to which computer-generated pre-annotation is beneficial to human annotation is still an open question. Our study introduces CLEAN (CLinical note rEview and ANnotation), a pre-annotation-based cNLP annotation system to improve clinical note annotation of data elements, and comprehensively compares CLEAN with the widely-used annotation system Brat Rapid Annotation Tool (BRAT). Materials and Methods. CLEAN includes an ensemble pipeline (CLEAN-EP) with a newly developed annotation tool (CLEAN-AT). A domain expert and a novice user/annotator participated in a comparative usability test by tagging 87 data elements related to Congestive Heart Failure (CHF) and Kawasaki Disease (KD) cohorts in 84 public notes. Results. CLEAN achieved higher note-level F1-score (0.896) over BRAT (0.820), with significant difference in correctness (P-value < 0.001), and the mostly related factor being system/software (P-value < 0.001). No significant difference (P-value 0.188) in annotation time was observed between CLEAN (7.262 minutes/note) and BRAT (8.286 minutes/note). The difference was mostly associated with note length (P-value < 0.001) and system/software (P-value 0.013). The expert reported CLEAN to be useful/satisfactory, while the novice reported slight improvements. Discussion. CLEAN improves the correctness of annotation and increases usefulness/satisfaction with the same level of efficiency. Limitations include untested impact of pre-annotation correctness rate, small sample size, small user size, and restrictedly validated gold standard. Conclusion. CLEAN with pre-annotation can be beneficial for an expert to deal with complex annotation tasks involving numerous and diverse target data elements

Nocturnal Continuous Glucose and Sleep Stage Data in Adults with Type 1 Diabetes in Real-World Conditions

BackgroundSleep plays an important role in health, and poor sleep is associated with negative impacts on diabetes management, but few studies have objectively evaluated sleep in adults with type 1 diabetes mellitus (T1DM). Nocturnal glycemia and sleep characteristics in T1DM were evaluated using body-worn sensors in real-world conditions.MethodsAnalyses were performed on data collected by the Diabetes Management Integrated Technology Research Initiative pilot study of 17 T1DM subjects: 10 male, 7 female; age 19-61 years; T1DM duration 14.9 ± 11.0 years; hemoglobin A1c (HbA1c) 7.3% ± 1.3% (mean ± standard deviation). Each subject was equipped with a continuous glucose monitor and a wireless sleep monitor (WSM) for four nights. Sleep stages [rapid eye movement (REM), light, and deep sleep] were continuously recorded by the WSM. Nocturnal glycemia (mg/dl) was evaluated as hypoglycemia (&lt;50 mg/dl), low (50-69 mg/dl), euglycemia (70-120 mg/dl), high (121-250 mg/dl), and hyperglycemia (&gt;250 mg/dl) and by several indices of glycemic variability. Glycemia was analyzed within each sleep stage.ResultsSubjects slept 358 ± 48 min per night, with 85 ± 27 min in REM sleep, 207 ± 42 min in light sleep, and 66 ± 30 min in deep sleep (mean ± standard deviation). Increased time in deep sleep was associated with lower HbA1c (R2 = 0.42; F = 9.37; p &lt; .01). Nocturnal glycemia varied widely between and within subjects. Glycemia during REM sleep was hypoglycemia 5.5% ± 18.1%, low 6.6% ± 18.5%, euglycemia 44.6% ± 39.5%, high 37.9% ± 39.7%, and hyperglycemia 5.5% ± 21.2%; glycemia during light sleep was hypoglycemia 4.8% ± 12.4%, low 7.3% ± 12.9%, euglycemia 42.1% ± 33.7%, high 39.2% ± 34.6%, and hyperglycemia 6.5% ± 20.5%; and glycemia during deep sleep was hypoglycemia 0.5% ± 2.2%, low 5.8% ± 14.3%, euglycemia 48.0% ± 37.5%, high 39.5% ± 37.6%, and hyperglycemia 6.2% ± 19.5%. Significantly less time was spent in the hypoglycemic range during deep sleep compared with light sleep (p = .02).ConclusionsIncreased time in deep sleep was associated with lower HbA1c, and less hypoglycemia occurred in deep sleep in T1DM, though this must be further evaluated in larger subsequent studies. Furthermore, the consumer-grade WSM device was useful for objectively studying sleep in a real-world setting

PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net