OHDSI MEETINGS THIS WEEK
OHDSI Community Call - Tuesday at 12pm EThttps://meetings.webex.com/collabs/#/meetings/detail?uuid=M59X2V1U61WC9ASID2Z5N3UT95-D1JL&rnd=811649.986822
Patient-level prediction (Eastern hemisphere) workgroup meeting - Wednesday at 3pm Hong Kong/Taiwan timehttps://global.gotomeeting.com/join/9729176611
Population-Level Estimation (Western hemisphere) workgroup meeting - Thursday at 12pm EThttps://meetings.webex.com/collabs/#/meetings/detail?uuid=M3T9BZV9RSB6YNDM8WDDZMI19D-D1JL&occurrenceID=1501776000000
Hadoop WG meeting - Friday at 11am EThttp://cloudera.webex.com/meet/sdolley
GIS working group meeting - Monday (October 30th) at 10am EThttps://tufts.webex.com/mw3200/mywebex/default.do?service=1&siteurl=tufts&nomenu=true&main_url=%2Fmc3200%2Fe.do%3Fsiteurl%3Dtufts%26AT%3DMI%26EventID%3D562301137%26UID%3D528546812%26Host%3DQUhTSwAAAAT_EHuT3Ok-zHVhY1-kVGh78TH62dPsFk0x99qz1E9039sh_Eiepw8CoZeIF2SfnopQ8oAZaLN9PkzIZovRf2kV0%26FrameSet%3D2%26MTID%3Dm243d8e9a9c6c2d42d5182aeb5d30efdb1
ANNOUNCEMENTS
2017 OHDSI Symposium Materials - Presentation slides from this year’s symposium and tutorials have been uploaded here: https://www.ohdsi.org/past-events/
Symposium Videos - Recordings from the symposium and tutorial will be made available on November 1st here: https://www.ohdsi.org/past-events/
Computers make me totally blank out.
COMMUNITY PUBLICATIONS
Uncovering exposures responsible for birth season–disease effects: a global study
Personal Discovery in Diabetes Self-Management: Discovering Cause and Effect Using Self-Monitoring Data
L Mamykina, EM Heitkemper, AM Smaldone, R Kukafka, HJ Cole-Lewis, PG Davidson, ED Mynatt, A Cassells, JN Tobin and G Hripcsak,
Journal of biomedical informatics , Dec 2017
To outline new design directions for informatics solutions that facilitate personal discovery with self-monitoring data. We investigate this question in the context of chronic disease self-management with the focus on type 2 diabetes.We conducted an observational qualitative study of discovery with personal data among adults attending a diabetes self-management education (DSME) program that utilized a discovery-based curriculum. The study included observations of class sessions, and interviews and focus groups with the educator and attendees of the program (n = 14).The main discovery in diabetes self-management evolved around discovering patterns of association between characteristics of individuals' activities and changes in their blood glucose levels that the participants referred to as "cause and effect". This discovery empowered individuals to actively engage in self-management and provided a desired flexibility in selection of personalized self-management strategies. We show that discovery of cause and effect involves four essential phases: (1) feature selection, (2) hypothesis generation, (3) feature evaluation, and (4) goal specification. Further, we identify opportunities to support discovery at each stage with informatics and data visualization solutions by providing assistance with: (1) active manipulation of collected data (e.g., grouping, filtering and side-by-side inspection), (2) hypotheses formulation (e.g., using natural language statements or constructing visual queries), (3) inference evaluation (e.g., through aggregation and visual comparison, and statistical analysis of associations), and (4) translation of discoveries into actionable goals (e.g., tailored selection from computable knowledge sources of effective diabetes self-management behaviors).The study suggests that discovery of cause and effect in diabetes can be a powerful approach to helping individuals to improve their self-management strategies, and that self-monitoring data can serve as a driving engine for personal discovery that may lead to sustainable behavior changes.Enabling personal discovery is a promising new approach to enhancing chronic disease self-management with informatics interventions.
Extracting information from free-text electronic patient records to identify practice-based evidence of the performance of coronary stents.
YS Kim, D Yoon, J Byun, H Park, A Lee, IH Kim, S Lee, HS Lim and RW Park,
PloS one , 2017
Percutaneous coronary intervention (PCI) using drug-eluting stents (DES) is an indispensable treatment for coronary artery disease. However, to evaluate the performance of various types of stents for PCI, numerous resources are required. We extracted clinical information from free-text records and, using practice-based evidence, compared the efficacy of various DES.We developed a text mining tool based on regular expression and applied it to PCI reports stored in the electronic health records (EHRs) of Ajou University Hospital from 2010-2014. The PCI data were extracted from EHRs with a sensitivity of 0.996, a specificity of 1.000, and an F-measure of 0.995 when compared with a sample of 200 reports. Using these data, we compared the performance of stents by Kaplan-Meier analysis and the Cox hazard proportional regression.In the self-validation analysis comparing the first-generation to the second-generation DES, the second-generation DES was superior to the first-generation DES (hazard ratio [HR]: 0.423, 95% confidence interval [CI]: 0.284-0.630) in terms of target vessel revascularization (TVR), showing similar findings to the established results of previous studies. Among the second-generation DES, the biodegradable-polymer DES tended to be superior, with a risk of TVR (HR: 0.568, 95% CI: 0.281-1.147) falling below than that for the durable-polymer DES approximately 1 year after the index procedure. The Endeavor stent had the highest TVR risk among the newer generation DES (HR: 2.576, 95% CI: 1.273-5.210).In this study, we demonstrated how to construct a PCI data warehouse of PCI-related parameters obtained from free-text electronic records with high accuracy for use in the post surveillance of coronary stents in a time- and cost effective manner. Post surveillance of the practice based evidence in the PCI data warehouse indicated that the biodegradable-polymer DES might have a lower risk of TVR than the durable-polymer DES.
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.
JA McMurry, N Juty, N Blomberg, T Burdett, T Conlin, N Conte, M Courtot, J Deck, M Dumontier, DK Fellows, A Gonzalez-Beltran, P Gormanns, J Grethe, J Hastings, JK Hériché, H Hermjakob, JC Ison, RC Jimenez, S Jupp, J Kunze, C Laibe, N Le Novère, J Malone, MJ Martin, JR McEntyre, C Morris, J Muilu, W Müller, P Rocca-Serra, SA Sansone, M Sariyar, JL Snoep, S Soiland-Reyes, NJ Stanford, N Swainston, N Washington, AR Williams, SM Wimalaratne, LM Winfree, K Wolstencroft, C Goble, CJ Mungall, MA Haendel and H Parkinson,
PLoS biology , Jun 2017
In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure. Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers. We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability. We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.
Calcium Channel Blockers in Secondary Cardiovascular Prevention and Risk of Acute Events: Real-World Evidence from Nested Case-Control Studies on Italian Hypertensive Elderly.
A Bettiol, E Lucenteforte, A Vannacci, N Lombardi, G Onder, N Agabiti, C Vitale, G Trifirò, G Corrao, G Roberto, A Mugelli, A Chinellato, N Agabiti, C Bartolini, R Bernabei, A Bettiol, S Bonassi, AP Caputi, S Cascini, A Chinellato, G Corrao, M Davoli, M Fini, R Gini, F Giorgianni, U Kirchmayer, F Lapi, N Lombardi, E Lucenteforte, A Mugelli, G Onder, F Rea, G Roberto, C Sorge, M Tari, G Trifirò, A Vannacci, DL Vetrano and C Vitale,
Clinical drug investigation , Dec 2017
Antihypertensive treatment with calcium channel blockers (CCBs) is consolidated in clinical practice; however, different studies observed increased risks of acute events for short-acting CCBs. This study aimed to provide real-world evidence on risks of acute cardiovascular (CV) events, hospitalizations and mortality among users of different CCB classes in secondary CV prevention.Three case-control studies were nested in a cohort of Italian elderly hypertensive CV-compromised CCBs users. Cases were subjects with CV events (n = 25,204), all-cause hospitalizations (n = 19,237), or all-cause mortality (n = 17,996) during the follow-up. Up to four controls were matched for each case. Current or past exposition to CCBs at index date was defined based on molecule, formulation and daily doses of the last CCB delivery. The odds ratio (OR) and 95% confidence intervals (CI) were estimated using conditional logistic regression models.Compared to past users, current CCB users had significant reductions in risks of CV events [OR 0.88 (95% CI: 0.84-0.91)], hospitalization [0.90 (0.88-0.93)] and mortality [0.48 (0.47-0.49)]. Current users of long-acting dihydropyridines (DHPs) had the lowest risk [OR 0.87 (0.84-0.90), 0.86 (0.83-0.90), 0.55 (0.54-0.56) for acute CV events, hospitalizations and mortality], whereas current users of short-acting CCBs had an increased risk of acute CV events [OR 1.77 (1.13-2.78) for short-acting DHPs; 1.19 (1.07-1.31) for short-acting non-DHPs] and hospitalizations [OR 1.84 (0.96-3.51) and 1.23 (1.08-1.42)].The already-existing warning on short-acting CCBs should be potentiated, addressing clinicians towards the choice of long-acting formulations.
