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Miao BY, Sushil M, Xu A, Wang M, Arneson D, Berkley E, Subash M, Vashisht R, Rudrapatna V, Butte AJ. Characterisation of digital therapeutic clinical trials: a systematic review with natural language processing. Lancet Digit Health 2024; 6:e222-e229. [PMID: 38395542 DOI: 10.1016/s2589-7500(23)00244-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 08/10/2023] [Accepted: 11/22/2023] [Indexed: 02/25/2024]
Abstract
Digital therapeutics (DTx) are a somewhat novel class of US Food and Drug Administration-regulated software that help patients prevent, manage, or treat disease. Here, we use natural language processing to characterise registered DTx clinical trials and provide insights into the clinical development landscape for these novel therapeutics. We identified 449 DTx clinical trials, initiated or expected to be initiated between 2010 and 2030, from ClinicalTrials.gov using 27 search terms, and available data were analysed, including trial durations, locations, MeSH categories, enrolment, and sponsor types. Topic modelling of eligibility criteria, done with BERTopic, showed that DTx trials frequently exclude patients on the basis of age, comorbidities, pregnancy, language barriers, and digital determinants of health, including smartphone or data plan access. Our comprehensive overview of the DTx development landscape highlights challenges in designing inclusive DTx clinical trials and presents opportunities for clinicians and researchers to address these challenges. Finally, we provide an interactive dashboard for readers to conduct their own analyses.
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Affiliation(s)
- Brenda Y Miao
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA.
| | - Madhumita Sushil
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Ava Xu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Michelle Wang
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Douglas Arneson
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Ellen Berkley
- Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, CA, USA; UC Davis Health, University of California, Sacramento, CA, USA
| | - Meera Subash
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA; School of Biomedical Informatics, UTHealth Houston, Houston, TX, USA
| | - Rohit Vashisht
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA
| | - Vivek Rudrapatna
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA, USA; University of California Health, Oakland, CA, USA
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Odufalu FD, Sewell JL, Rudrapatna V, Somsouk M, Mahadevan U. Assessing the Impact of COVID-19 on IBD Outcomes Among Vulnerable Patient Populations in a Large Metropolitan Center. Inflamm Bowel Dis 2024; 30:29-37. [PMID: 36943305 DOI: 10.1093/ibd/izad041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Indexed: 03/23/2023]
Abstract
BACKGROUND With the onset of COVID-19, there were rapid changes in healthcare delivery as remote access became the norm. The aim of this study was to determine the impact of changes in healthcare delivery during the COVID-19 pandemic on patients with inflammatory bowel disease (IBD), in both well-resourced and vulnerable populations. METHODS Using a mixed methods, observational study design, patients receiving IBD care at a university or a safety-net hospital were identified by the electronic health record. Patient demographics, IBD history, and disease activity were acquired from the electronic health record. IBD-related outcomes were compared from the onset of the pandemic in the United States until December 2020 (COVID-19 pandemic year 1) and compared with outcomes in the previous year. A subset of participants provided their perspective on how changes in healthcare delivery and financial stability impacted their IBD through a standardized questionnaire and semi-structured interview. RESULTS Data from a total of 1449 participants were captured, 1324 at the tertiary care university hospital and 125 at the safety-net hospital. During COVID-19, there was a decrease in healthcare utilization at both sites. Race/ethnicity and primary language were not associated with IBD-related hospitalizations or admissions. Patients that were employed and those with insurance had a higher number of IBD-related emergency department visits at both the university and safety-net hospitals (P = .03 and P = .01, respectively). Patients who did not speak English were more likely to report challenges using technology with telehealth and difficulty contacting IBD providers. CONCLUSIONS For IBD populations, during COVID-19, in both hospital settings, emergency department visits, hospitalizations, outpatient surgery, and clinic visits were reduced compared with the year prior. Patients with lower socioeconomic status and limited English proficiency reported facing more challenges with changes to healthcare delivery, healthcare access, and conveying changes in IBD activity. These results highlight the need for payors and providers to specifically attend to those populations most susceptible to these systemic and lasting changes in care delivery and promote greater equity in healthcare.
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Affiliation(s)
- Florence-Damilola Odufalu
- Division of Gastroenterology and Liver Diseases, Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Justin L Sewell
- Gastroenterology Division, Zuckerberg-Chan San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Rudrapatna
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ma Somsouk
- Gastroenterology Division, Zuckerberg-Chan San Francisco General Hospital and Trauma Center, University of California, San Francisco, San Francisco, CA, USA
- Center for Vulnerable Populations, University of California, San Francisco, San Francisco, CA, USA
| | - Uma Mahadevan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
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Singh S, Kim J, Luo J, Paul P, Rudrapatna V, Park S, Zheng K, Syal G, Ha C, Fleshner P, McGovern D, Sauk JS, Limketkai B, Dulai PS, Boland BS, Eisenstein S, Ramamoorthy S, Melmed G, Mahadevan U, Sandborn WJ, Ohno-Machado L. Comparative Safety and Effectiveness of Biologic Therapy for Crohn's Disease: A CA-IBD Cohort Study. Clin Gastroenterol Hepatol 2023; 21:2359-2369.e5. [PMID: 36343846 DOI: 10.1016/j.cgh.2022.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 10/05/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND & AIMS We compared the safety and effectiveness of tumor necrosis factor α (TNF-α) antagonists vs vedolizumab vs ustekinumab in patients with Crohn's disease (CD) in a multicenter cohort (CA-IBD). METHODS We created an electronic health record-based cohort of adult patients with CD who were initiating a new biologic agent (TNF-α antagonists, ustekinumab, vedolizumab) from 5 health systems in California between 2010 and 2017. We compared the risk of serious infections (safety) and all-cause hospitalization and inflammatory bowel disease-related surgery (effectiveness) between different biologic classes using propensity score (PS) matching. RESULTS As compared with TNF-α antagonists (n = 1030), 2:1 PS-matched, ustekinumab-treated patients with CD (n = 515) experienced a lower risk of serious infections (hazard ratio [HR], 0.36; 95% CI, 0.20-0.64), without any difference in the risk of hospitalization (HR, 0.99; 95% CI, 0.89-1.21) or surgery (HR, 1.08; 95% CI, 0.69-1.70). Compared with vedolizumab (n = 221), 1:1 PS-matched, ustekinumab-treated patients with CD (n = 221) experienced a lower risk of serious infections (HR, 0.20; 95% CI, 0.07-0.60), without significant differences in risk of hospitalization (HR, 0.76; 95% CI, 0.54-1.07) or surgery (HR, 1.42; 95% CI, 0.54-3.72). Compared with TNF-α antagonists (n = 442), 2:1 PS-matched, vedolizumab-treated patients with CD (n = 221) had a similar risk of serious infections (HR, 1.53; 95% CI, 0.84-2.78), hospitalization (HR, 1.32; 95% CI, 0.98-1.77), and surgery (HR, 0.63; 95% CI, 0.27-1.47). High comorbidity burden, concomitant opiate use, and prior hospitalization were associated with serious infections and hospitalization in biologic-treated patients with CD. CONCLUSION In a multicenter cohort of biologic-treated patients with CD, ustekinumab was associated with a lower risk of serious infections compared with TNF-α antagonists and vedolizumab, without any differences in risk of hospitalization or surgery. The risk of serious infections was similar for TNF-α antagonists vs vedolizumab.
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Affiliation(s)
- Siddharth Singh
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California.
| | - Jihoon Kim
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Jiyu Luo
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California
| | - Paulina Paul
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Vivek Rudrapatna
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, California
| | - Sunhee Park
- Division of Gastroenterology, Department of Medicine, University of California Irvine, Orange, California
| | - Kai Zheng
- Department of Informatics, Donald Bren School of Information and Computer Sciences, University of California Irvine, Orange, California
| | - Gaurav Syal
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Christina Ha
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Phillip Fleshner
- Division of Colorectal Surgery, Department of Surgery, Cedars-Sinai Medical System, Los Angeles, California
| | - Dermot McGovern
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Jenny S Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Berkeley Limketkai
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, California
| | - Samuel Eisenstein
- Division of Colon and Rectal Surgery, Department of Surgery, University of California San Diego, La Jolla, California
| | - Sonia Ramamoorthy
- Division of Colon and Rectal Surgery, Department of Surgery, University of California San Diego, La Jolla, California
| | - Gil Melmed
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Uma Mahadevan
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, California
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, University of California San Diego, La Jolla, California
| | - Lucila Ohno-Machado
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, California
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Nguyen NH, Luo J, Paul P, Kim J, Syal G, Ha C, Rudrapatna V, Park S, Parekh N, Zheng K, Sauk JS, Limketkai B, Fleshner P, Eisenstein S, Ramamoorthy S, Melmed G, Dulai PS, Boland BS, Mahadevan U, Sandborn WJ, Ohno-Machado L, McGovern D, Singh S. Effectiveness and Safety of Biologic Therapy in Hispanic Vs Non-Hispanic Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Clin Gastroenterol Hepatol 2023; 21:173-181.e5. [PMID: 35644340 PMCID: PMC9701245 DOI: 10.1016/j.cgh.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS There are limited data on outcomes of biologic therapy in Hispanic patients with inflammatory bowel diseases (IBDs). We compared risk of hospitalization, surgery, and serious infections in Hispanic vs non-Hispanic patients with IBD in a multicenter, electronic health record-based cohort of biologic-treated patients. METHODS We identified adult patients with IBD who were new users of biologic agents (tumor necrosis factor α [TNF-α] antagonists, ustekinumab, vedolizumab) from 5 academic institutions in California between 2010 and 2017. We compared the risk of all-cause hospitalization, IBD-related surgery, and serious infections in Hispanic vs non-Hispanic patients using 1:4 propensity score matching and survival analysis. RESULTS We compared 240 Hispanic patients (53% male; 45% with ulcerative colitis; 73% TNF-α antagonist-treated; 20% with prior biologic exposure) with 960 non-Hispanic patients (51% male; 44% with ulcerative colitis; 67% TNF-α antagonist-treated; 27% with prior biologic exposure). After propensity score matching, Hispanic patients were younger (37 ± 15 vs 40 ± 16 y; P = .02) and had a higher burden of comorbidities (Elixhauser index, >0; 37% vs 26%; P < .01), without any differences in patterns of medication use, burden of inflammation, and hospitalizations. Within 1 year of biologic initiation, Hispanic patients had higher rates of hospitalizations (31% vs 23%; adjusted hazard ratio [aHR], 1.32; 95% CI, 1.01-1.74) and IBD-related surgery (7.1% vs 4.6%; aHR, 2.00; 95% CI, 1.07-3.72), with a trend toward higher risk of serious infections (8.8% vs 4.9%; aHR, 1.74; 95% CI, 0.99-3.05). CONCLUSIONS In a multicenter, propensity score-matched cohort of biologic-treated patients with IBD, Hispanic patients experienced higher rates of hospitalization, surgery, and serious infections. Future studies are needed to investigate the biological, social, and environmental drivers of these differences.
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Affiliation(s)
- Nghia H Nguyen
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California
| | - Jiyu Luo
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, UC San Diego, La Jolla, California
| | - Paulina Paul
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California
| | - Jihoon Kim
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California
| | - Gaurav Syal
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Christina Ha
- Division of Gastroenterology, Mayo Clinic, Scottsdale, Arizona
| | - Vivek Rudrapatna
- Division of Gastroenterology, Department of Medicine, UC San Francisco, California
| | - Sunhee Park
- Division of Gastroenterology, Department of Medicine, UC Irvine, Orange, California
| | - Nimisha Parekh
- Division of Gastroenterology, Department of Medicine, UC Irvine, Orange, California
| | - Kai Zheng
- Department of Informatics, Donald Bren School of Information and Computer Sciences, UC Irvine, Orange, California
| | - Jenny S Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UC Los Angeles, Los Angeles, California
| | - Berkeley Limketkai
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UC Los Angeles, Los Angeles, California
| | - Phillip Fleshner
- Division of Colorectal Surgery, Department of Surgery, Cedars-Sinai Medical System, Los Angeles, California
| | - Samuel Eisenstein
- Division of Colon and Rectal Surgery, Department of Surgery, UC San Diego, La Jolla, California
| | - Sonia Ramamoorthy
- Division of Colon and Rectal Surgery, Department of Surgery, UC San Diego, La Jolla, California
| | - Gil Melmed
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, Northwestern University, Chicago, Illinois
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California
| | - Uma Mahadevan
- Division of Gastroenterology, Department of Medicine, UC San Francisco, California
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California
| | - Lucila Ohno-Machado
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California
| | - Dermot McGovern
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California
| | - Siddharth Singh
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California; Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California.
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Gu P, Luo J, Kim J, Paul P, Limketkai B, Sauk JS, Park S, Parekh N, Zheng K, Rudrapatna V, Syal G, Ha C, McGovern DP, Melmed GY, Fleshner P, Eisenstein S, Ramamoorthy S, Dulai PS, Boland BS, Grunvald E, Mahadevan U, Ohno-Machado L, Sandborn WJ, Singh S. Effect of Obesity on Risk of Hospitalization, Surgery, and Serious Infection in Biologic-Treated Patients With Inflammatory Bowel Diseases: A CA-IBD Cohort Study. Am J Gastroenterol 2022; 117:1639-1647. [PMID: 35973139 DOI: 10.14309/ajg.0000000000001855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/22/2022] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Obesity is variably associated with treatment response in biologic-treated patients with inflammatory bowel diseases (IBD). We evaluated the association between obesity and risk of hospitalization, surgery, or serious infections in patients with IBD in new users of biologic agents in a large, multicenter, electronic health record (EHR)-based cohort (CA-IBD). METHODS We created an EHR-based cohort of adult patients with IBD who were new users of biologic agents (tumor necrosis factor [TNF-α] antagonists, ustekinumab, and vedolizumab) between January 1, 2010, and June 30, 2017, from 5 health systems in California. Patients were classified as those with normal body mass index (BMI), overweight, or obese based on the World Health Organization classification. We compared the risk of all-cause hospitalization, IBD-related surgery, or serious infections among patients with obesity vs those overweight vs those with normal BMI, using Cox proportional hazard analyses, adjusting for baseline demographic, disease, and treatment characteristics. RESULTS Of 3,038 biologic-treated patients with IBD (69% with Crohn's disease and 76% on TNF-α antagonists), 28.2% (n = 858) were overweight, and 13.7% (n = 416) were obese. On a follow-up after biologic initiation, obesity was not associated with an increased risk of hospitalization (adjusted hazard ratio [aHR] vs normal BMI, 0.90; [95% confidence interval, 0.72-1.13]); IBD-related surgery (aHR, 0.62 [0.31-1.22]); or serious infection (aHR, 1.11 [0.73-1.71]). Similar results were observed on stratified analysis by disease phenotype (Crohn's disease vs ulcerative colitis) and index biologic therapy (TNF-α antagonists vs non-TNF-α antagonists). DISCUSSION In a multicenter, EHR-based cohort of biologic-treated patients with IBD, obesity was not associated with hospitalization, surgery, or serious infections. Further studies examining the effect of visceral obesity on patient-reported and endoscopic outcomes are needed.
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Affiliation(s)
- Phillip Gu
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Jiyu Luo
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, UC San Diego, La Jolla, California, USA
| | - Jihoon Kim
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Paulina Paul
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Berkeley Limketkai
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UC Los Angeles, Los Angeles, California, USA
| | - Jenny S Sauk
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UC Los Angeles, Los Angeles, California, USA
| | - Sunhee Park
- Division of Gastroenterology, Department of Medicine, UC Irvine, Orange, California, USA
| | - Nimisha Parekh
- Division of Gastroenterology, Department of Medicine, UC Irvine, Orange, California, USA
| | - Kai Zheng
- Department of Informatics, Donald Bren School of Information and Computer Sciences, UC Irvine, Orange, California, USA
| | - Vivek Rudrapatna
- Division of Gastroenterology, Department of Medicine, UC San Francisco, California, USA
| | - Gaurav Syal
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Christina Ha
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Dermot P McGovern
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Gil Y Melmed
- Karsh Division of Gastroenterology and Hepatology, Department of Medicine, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Phillip Fleshner
- Division of Colorectal Surgery, Department of Surgery, Cedars-Sinai Medical System, Los Angeles, California, USA
| | - Samuel Eisenstein
- Division of Colon and Rectal Surgery, Department of Surgery, UC San Diego, La Jolla, California, USA
| | - Sonia Ramamoorthy
- Division of Colon and Rectal Surgery, Department of Surgery, UC San Diego, La Jolla, California, USA
| | - Parambir S Dulai
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Brigid S Boland
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Eduardo Grunvald
- Division of General Internal Medicine, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Uma Mahadevan
- Division of Gastroenterology, Department of Medicine, UC San Francisco, California, USA
| | - Lucila Ohno-Machado
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - William J Sandborn
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California, USA
| | - Siddharth Singh
- Division of Biomedical Informatics, Department of Medicine, UC San Diego, La Jolla, California, USA
- Division of Gastroenterology, Department of Medicine, UC San Diego, La Jolla, California, USA
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Glicksberg BS, Oskotsky B, Giangreco N, Thangaraj PM, Rudrapatna V, Datta D, Frazier R, Lee N, Larsen R, Tatonetti NP, Butte AJ. ROMOP: a light-weight R package for interfacing with OMOP-formatted electronic health record data. JAMIA Open 2019; 2:10-14. [PMID: 31633087 PMCID: PMC6800657 DOI: 10.1093/jamiaopen/ooy059] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/26/2018] [Accepted: 12/02/2018] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVES Electronic health record (EHR) data are increasingly used for biomedical discoveries. The nature of the data, however, requires expertise in both data science and EHR structure. The Observational Medical Out-comes Partnership (OMOP) common data model (CDM) standardizes the language and structure of EHR data to promote interoperability of EHR data for research. While the OMOP CDM is valuable and more attuned to research purposes, it still requires extensive domain knowledge to utilize effectively, potentially limiting more widespread adoption of EHR data for research and quality improvement. MATERIALS AND METHODS We have created ROMOP: an R package for direct interfacing with EHR data in the OMOP CDM format. RESULTS ROMOP streamlines typical EHR-related data processes. Its functions include exploration of data types, extraction and summarization of patient clinical and demographic data, and patient searches using any CDM vocabulary concept. CONCLUSION ROMOP is freely available under the Massachusetts Institute of Technology (MIT) license and can be obtained from GitHub (http://github.com/BenGlicksberg/ROMOP). We detail instructions for setup and use in the Supplementary Materials. Additionally, we provide a public sandbox server containing synthesized clinical data for users to explore OMOP data and ROMOP (http://romop.ucsf.edu).
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Affiliation(s)
- Benjamin S Glicksberg
- Department of Pediatrics Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
| | - Boris Oskotsky
- Department of Pediatrics Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
| | - Nicholas Giangreco
- Departments of Biomedical Informatics, Systems Biology, and Medicine, Columbia University, New York, New York, USA
| | - Phyllis M Thangaraj
- Departments of Biomedical Informatics, Systems Biology, and Medicine, Columbia University, New York, New York, USA
| | - Vivek Rudrapatna
- Department of Pediatrics Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
| | - Debajyoti Datta
- Department of Pediatrics Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
| | - Remi Frazier
- Academic Research Systems, Department of Enterprise Data Warehouse University of California San Francisco, San Francisco, California, USA
| | - Nelson Lee
- Academic Research Systems, Department of Enterprise Data Warehouse University of California San Francisco, San Francisco, California, USA
| | - Rick Larsen
- Academic Research Systems, Department of Enterprise Data Warehouse University of California San Francisco, San Francisco, California, USA
| | - Nicholas P Tatonetti
- Departments of Biomedical Informatics, Systems Biology, and Medicine, Columbia University, New York, New York, USA
| | - Atul J Butte
- Department of Pediatrics Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, USA
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