Data Warehousing & Informatics Resources

DBMI faculty support secondary research use of clinical data, and manage data for biological and clinical research, and participate in local, regional and national efforts for reuse of EHR data. DBMI has contributed to the formation and ongoing success of national clinical data research networks. Other clinical research informatics efforts include the development of tools for extracting patient summaries

from clinical notes and building interactive tools to use those summaries for cancer research, development of NLP tools for use by state cancer registries, and analysis of OHDSI retrospective data for pharmacovigilance.

DBMI faculty lead the implementation of a research data warehouse that provides data from UPMC’s electronic health records and additional related sources to researchers across campus. COVID-related efforts include developing a COVID ontology for the national Accrual of patients to Clinical Trials network, aiding in COVID-19 EHR data acquisition and harmonization for N3C, collaborating in EHR data analyses in 4CE, and provisioning EHR data for COVID-19 surveillance to Allegheny County, PA and to the CDC.

Sample Publications:

Bernstam EV, Shireman PK, Meric-Bernstam F, N Zozus M, Jiang X, Brimhall BB, Windham AK, Schmidt S, Visweswaran S, Ye Y, Goodrum H, Ling Y, Barapatre S, Becich MJ. Artificial intelligence in clinical and translational science: Successes, challenges and opportunities. Clin Transl Sci. 2022 Feb;15(2):309-321. doi: 10.1111/cts.13175. Epub 2021 Oct 30. PMID: 34706145; PMCID: PMC8841416.

Visweswaran S, McLay B, Cappella N, Morris M, Milnes JT, Reis SE, Silverstein JC, Becich MJ. An atomic approach to the design and implementation of a research data warehouse. J Am Med Inform Assoc. 2021 Oct 6:ocab204. doi: 10.1093/jamia/ocab204. Epub ahead of print. PMID: 34613409.

Haendel MA, Chute CG, Bennett TD, Eichmann DA, Guinney J, Kibbe WA, Payne PRO, Pfaff ER, Robinson PN, Saltz JH, Spratt H, Suver C, Wilbanks J, Wilcox AB, Williams AE, Wu C, Blacketer C, Bradford RL, Cimino JJ, Clark M, Colmenares EW, Francis PA, Gabriel D, Graves A, Hemadri R, Hong SS, Hripscak G, Jiao D, Klann JG, Kostka K, Lee AM, Lehmann HP, Lingrey L, Miller RT, Morris M, Murphy SN, Natarajan K, Palchuk MB, Sheikh U, Solbrig H, Visweswaran S, Walden A, Walters KM, Weber GM, Zhang XT, Zhu RL, Amor B, Girvin AT, Manna A, Qureshi N, Kurilla MG, Michael SG, Portilla LM, Rutter JL, Austin CP, Gersing KR, N3C Consortium. The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment. Journal of the American Medical Informatics Association. 2021 Mar 1; 28(3):427-443. PMID: 32805036 PMCID: PMC7454687

Visweswaran S, Becich MJ, D’Itri VS, Sendro ER, MacFadden D, Anderson NR, Allen KA, Ranganathan D, Murphy SN, Morrato EH, Pincus HA, Toto R, Firestein GS, Nadler LM, Reis SE. Accrual to Clinical Trials (ACT): A Clinical and Translational Science Award Consortium network. JAMIA Open. 2018 Oct; 1(2):147-152. PMID: 30474072 PMCID: PMC6241502

Amin W, Tsui FR, Borromeo C, Chuang CH, Espino JU, Ford D, Hwang W, Kapoor W, Lehmann H, Martich GD, Morton S, Paranjape A, Shirey W, Sorensen A, Becich MJ, Hess R; PaTH network team. PaTH: towards a learning health system in the Mid-Atlantic region. J Am Med Inform Assoc. 2014 Jul-Aug;21(4):633-6. doi: 10.1136/amiajnl-2014-002759. Epub 2014 May 12. PMID: 24821745; PMCID: PMC4078296.