Clinical Data and Informatics Core



The Clinical Data and Informatics (CDI) Core (formerly known as Human Subjects and Clinical Phenotyping - HSCP Core) provides researchers with access to a full range of services to facilitate successful identification and recruitment of patients for basic, translational, and clinical research studies in rheumatic disease.  The Core uses a patient-oriented approach to advance precision medicine in rheumatology by offering services relevant to conducting clinical research, such as consultation for study design, research ethics, patient recruitment, and disease expertise. Core faculty are national leaders in the use of electronic health record (EHR) data and provide consultation on a range of clinical informatics issues relevant to EHR data extraction, dataset construction and analyses. The Core is the national coordinating center for the American College of Rheumatology’s RISE registry and the COVID-19 Global Rheumatology Alliance registry.



Specifically, the CDI Core will:

  1. Provide consultation on human subjects study design, data collection, outcome measures, and research ethics for basic, translational, and clinical research studies of rheumatic diseases.
  2. Facilitate identification of patients with specific clinical phenotypes for basic, translational, and clinical research studies in rheumatology, leveraging collaborations between nationally recognized disease experts and clinical informaticists.
  3. Coordinate and provide resources for human subject recruitment and biospecimen collection.
  4. Offer state-of-the-art data retrieval and management resources, including construction of electronic health record-enabled registries.
  5. Assemble a panel of UCSF clinicians with expertise in particular rheumatic diseases, including RA, lupus, vasculitis, scleroderma, sjogren’s, spondyloarthropathies, as well as pediatric rheumatology and patient safety measures for Center rheumatic disease projects.


Recent Publications:

1. PMID: 33394601

Global research collaboration in a pandemic-challenges and opportunities: the COVID-19 Global Rheumatology Alliance.

Robinson PC, Yazdany J, Machado PM.Curr Opin Rheumatol. 2020 Dec 30;Publish Ahead of Print. doi: 10.1097/BOR.0000000000000783. Online ahead of print.PMID: 33394601

2. PMID: 33337580

High Disease Severity Among Asians in a US Multiethnic Cohort of Individuals with Systemic Lupus Erythematosus.

DeQuattro K, Trupin L, Murphy LB, Rush S, Criswell LA, Lanata CM, Dall'Era M, Katz P, Yazdany J.Arthritis Care Res (Hoboken). 2020 Dec 18. doi: 10.1002/acr.24544. Online ahead of print.PMID: 33337580

3. PMID: 33146001

Race/ethnicity association with COVID-19 outcomes in rheumatic disease: Data from the COVID-19 Global Rheumatology Alliance Physician Registry.

Gianfrancesco MA, Leykina LA, Izadi Z, Taylor T, Sparks JA, Harrison C, Trupin L, Rush S, Schmajuk G, Katz P, Jacobsohn L, Hsu TY, D'Silva KM, Serling-Boyd N, Wallwork R, Todd DJ, Bhana S, Costello W, Grainger R, Hausmann JS, Liew JW, Sirotich E, Sufka P, Wallace ZS, Machado PM, Robinson PC, Yazdany J; COVID-19 Global Rheumatology Alliance.Arthritis Rheumatol. 2020 Nov 3. doi: 10.1002/art.41567. Online ahead of print.PMID: 33146001

4. PMID: 33105057

Treatment of Sarcoidosis in U.S. Rheumatology Practices: Data from ACR's Rheumatology Informatics System for Effectiveness (RISE) Registry.

Hammam N, Evans M, Morgan E, Reimold A, Anastasiou C, Kay JL, Yazdany J, Schmajuk G.Arthritis Care Res (Hoboken). 2020 Oct 26. doi: 10.1002/acr.24496. Online ahead of print.PMID: 33105057

5. PMID: 32937026

Rheumatology Informatics System for Effectiveness (RISE) Practices See Significant Gains in Rheumatoid Arthritis Quality Measures.

Izadi Z, Schmajuk G, Gianfrancesco M, Subash M, Evans M, Trupin L, Yazdany J.Arthritis Care Res (Hoboken). 2020 Sep 16. doi: 10.1002/acr.24444. Online ahead of print.PMID: 32937026

6. PMID: 32937019

Quality of care for patients with SLE: data from the American College of Rheumatology's RISE registry.

Schmajuk G, Li J, Evans M, Anastasiou C, Kay JL, Yazdany J.Arthritis Care Res (Hoboken). 2020 Sep 16. doi: 10.1002/acr.24446. Online ahead of print.PMID: 32937019

7. PMID: 32807591

Reweighting to address nonparticipation and missing data bias in a longitudinal electronic health record study.

Gianfrancesco MA, McCulloch CE, Trupin L, Graf J, Schmajuk G, Yazdany J.Ann Epidemiol. 2020 Oct;50:48-51.e2. doi: 10.1016/j.annepidem.2020.06.008. Epub 2020 Jul 2.PMID: 32807591

8. PMID: 32789449

The COVID-19 Global Rheumatology Alliance: evaluating the rapid design and implementation of an international registry against best practice.

Liew JW, Bhana S, Costello W, Hausmann JS, Machado PM, Robinson PC, Sirotich E, Sufka P, Wallace ZS, Yazdany J, Grainger R; COVID-19 Global Rheumatology Alliance.Rheumatology (Oxford). 2021 Jan 5;60(1):353-358. doi: 10.1093/rheumatology/keaa483.PMID: 32789449 Free PMC article.

9. PMID: 32741124

Major Depression and Adverse Patient-Reported Outcomes in Systemic Lupus Erythematosus: Results From a Prospective Longitudinal Cohort.

Dietz B, Katz P, Dall'Era M, Murphy LB, Lanata C, Trupin L, Criswell LA, Yazdany J.Arthritis Care Res (Hoboken). 2021 Jan;73(1):48-54. doi: 10.1002/acr.24398. Epub 2020 Dec 6.PMID: 32741124

10. PMID: 32741118

Impact of Limited Health Literacy on Patient-Reported Outcomes in Systemic Lupus Erythematosus.

Katz P, Dall'Era M, Trupin L, Rush S, Murphy LB, Lanata C, Criswell LA, Yazdany J.Arthritis Care Res (Hoboken). 2021 Jan;73(1):110-119. doi: 10.1002/acr.24361.PMID: 32741118

11. PMID: 32705748

COVID-19 in Rheumatic Diseases: A Research Agenda.

Yazdany J.Arthritis Rheumatol. 2020 Oct;72(10):1596-1599. doi: 10.1002/art.41447. Epub 2020 Sep 22.PMID: 32705748 Free PMC article.

12. PMID: 32675715

Epidemiology and outcomes of novel coronavirus 2019 in patients with immune-mediated inflammatory diseases.

Gianfrancesco M, Yazdany J, Robinson PC.Curr Opin Rheumatol. 2020 Sep;32(5):434-440. doi: 10.1097/BOR.0000000000000725.PMID: 32675715 Review.

13. PMID: 32558160

Mortality among Hospitalized Individuals with Systemic Lupus Erythematosus in the United States between 2006 and 2016.

Anastasiou C, Trupin L, Glidden DV, Li J, Gianfrancesco M, Shiboski S, Schmajuk G, Yazdany J.Arthritis Care Res (Hoboken). 2020 Jun 17:10.1002/acr.24356. doi: 10.1002/acr.24356. Online ahead of print.PMID: 32558160

14. PMID: 32471903

Characteristics associated with hospitalisation for COVID-19 in people with rheumatic disease: data from the COVID-19 Global Rheumatology Alliance physician-reported registry.

Gianfrancesco M, Hyrich KL, Al-Adely S, Carmona L, Danila MI, Gossec L, Izadi Z, Jacobsohn L, Katz P, Lawson-Tovey S, Mateus EF, Rush S, Schmajuk G, Simard J, Strangfeld A, Trupin L, Wysham KD, Bhana S, Costello W, Grainger R, Hausmann JS, Liew JW, Sirotich E, Sufka P, Wallace ZS, Yazdany J, Machado PM, Robinson PC; COVID-19 Global Rheumatology Alliance.Ann Rheum Dis. 2020 Jul;79(7):859-866. doi: 10.1136/annrheumdis-2020-217871. Epub 2020 May 29.PMID: 32471903 Free PMC article.

15. PMID: 32337372

Protected Health Information filter (Philter): accurately and securely de-identifying free-text clinical notes.

Norgeot B, Muenzen K, Peterson TA, Fan X, Glicksberg BS, Schenk G, Rutenberg E, Oskotsky B, Sirota M, Yazdany J, Schmajuk G, Ludwig D, Goldstein T, Butte AJ.NPJ Digit Med. 2020 Apr 14;3:57. doi: 10.1038/s41746-020-0258-y. eCollection 2020.PMID: 32337372 Free PMC article.

16. PMID: 32309814

Rheumatic disease and COVID-19: initial data from the COVID-19 Global Rheumatology Alliance provider registries.

Gianfrancesco MA, Hyrich KL, Gossec L, Strangfeld A, Carmona L, Mateus EF, Sufka P, Grainger R, Wallace Z, Bhana S, Sirotich E, Liew J, Hausmann JS, Costello W, Robinson P, Machado PM, Yazdany J; COVID-19 Global Rheumatology Alliance Steering Committee.Lancet Rheumatol. 2020 May;2(5):e250-e253. doi: 10.1016/S2665-9913(20)30095-3. Epub 2020 Apr 16.PMID: 32309814 Free PMC article. No abstract available.

17. PMID: 32270591

Patient and clinician perspectives on a patient-facing dashboard that visualizes patient reported outcomes in rheumatoid arthritis.

Liu LH, Garrett SB, Li J, Ragouzeos D, Berrean B, Dohan D, Katz PP, Barton JL, Yazdany J, Schmajuk G.Health Expect. 2020 Aug;23(4):846-859. doi: 10.1111/hex.13057. Epub 2020 Apr 9.PMID: 32270591 Free PMC article.

18. PMID: 32242121

The COVID-19 Global Rheumatology Alliance: collecting data in a pandemic.

Robinson PC, Yazdany J.Nat Rev Rheumatol. 2020 Jun;16(6):293-294. doi: 10.1038/s41584-020-0418-0.PMID: 32242121 Free PMC article. Review.

19. PMID: 32234243

RISE registry reveals potential gaps in medication safety for new users of biologics and targeted synthetic DMARDs.

Schmajuk G, Li J, Evans M, Anastasiou C, Izadi Z, Kay JL, Hammam N, Yazdany J.Semin Arthritis Rheum. 2020 Dec;50(6):1542-1548. doi: 10.1016/j.semarthrit.2020.03.003. Epub 2020 Mar 19.PMID: 32234243

20. PMID: 32062597

Using Process Improvement and Systems Redesign to Improve Rheumatology Care Quality in a Safety Net Clinic.

Aguirre A, Trupin L, Margaretten M, Goglin S, Noh JH, Yazdany J.J Rheumatol. 2020 Nov 1;47(11):1712-1720. doi: 10.3899/jrheum.190472. Epub 2020 Feb 15.PMID: 32062597

21. PMID: 31777787

Differences in Longitudinal Disease Activity Between Research Cohort and Noncohort Participants with Rheumatoid Arthritis Using Electronic Health Record Data.

Gianfrancesco MA, Trupin L, McCulloch CE, Shiboski S, Schmajuk G, Yazdany J.ACR Open Rheumatol. 2019 Apr 10;1(2):113-118. doi: 10.1002/acr2.1017. eCollection 2019 Apr.PMID: 31777787 Free PMC article.

22. PMID: 31722023

Demographic Characteristics of Participants in Rheumatoid Arthritis Randomized Clinical Trials: A Systematic Review.

Strait A, Castillo F, Choden S, Li J, Whitaker E, Falasinnu T, Schmajuk G, Yazdany J.JAMA Netw Open. 2019 Nov 1;2(11):e1914745. doi: 10.1001/jamanetworkopen.2019.14745.PMID: 31722023 Free PMC article.

23. PMID: 31651101

Reimagining Rheumatology: Big Data and the Future of Clinical Practice and Research.

Yazdany J, Hannan MT.Arthritis Care Res (Hoboken). 2020 Feb;72(2):163-165. doi: 10.1002/acr.24102. Epub 2020 Jan 13.PMID: 31651101 Free PMC article. No abstract available.

24. PMID: 31467281

A phenotypic and genomics approach in a multi-ethnic cohort to subtype systemic lupus erythematosus.

Lanata CM, Paranjpe I, Nititham J, Taylor KE, Gianfrancesco M, Paranjpe M, Andrews S, Chung SA, Rhead B, Barcellos LF, Trupin L, Katz P, Dall'Era M, Yazdany J, Sirota M, Criswell LA.Nat Commun. 2019 Aug 29;10(1):3902. doi: 10.1038/s41467-019-11845-y.PMID: 31467281 Free PMC article.

25. PMID: 31115180

Racial and Ethnic Differences in the Prevalence and Time to Onset of Manifestations of Systemic Lupus Erythematosus: The California Lupus Surveillance Project.

Maningding E, Dall'Era M, Trupin L, Murphy LB, Yazdany J.Arthritis Care Res (Hoboken). 2020 May;72(5):622-629. doi: 10.1002/acr.23887.PMID: 31115180

26. PMID: 30874779

Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.

Norgeot B, Glicksberg BS, Trupin L, Lituiev D, Gianfrancesco M, Oskotsky B, Schmajuk G, Yazdany J, Butte AJ.JAMA Netw Open. 2019 Mar 1;2(3):e190606. doi: 10.1001/jamanetworkopen.2019.0606.PMID: 30874779 Free PMC article.

27. PMID: 30740931

Three Quality Improvement Initiatives and Performance of Rheumatoid Arthritis Disease Activity Measures in Electronic Health Records: Results From an Interrupted Time Series Study.

Gandrup J, Li J, Izadi Z, Gianfrancesco M, Ellingsen T, Yazdany J, Schmajuk G.Arthritis Care Res (Hoboken). 2020 Feb;72(2):283-291. doi: 10.1002/acr.23848. Epub 2020 Jan 9.PMID: 30740931 Free PMC article.

28. PMID: 30686706

Gaps in Ambulatory Patient Safety for Immunosuppressive Specialty Medications.

Patterson S, Schmajuk G, Evans M, Aggarwal I, Izadi Z, Gianfrancesco M, Yazdany J.Jt Comm J Qual Patient Saf. 2019 May;45(5):348-357. doi: 10.1016/j.jcjq.2018.12.003. Epub 2019 Jan 25.PMID: 30686706 Free PMC article.

29. PMID: 30552172

Anticoagulation in patients with concomitant lupus nephritis and thrombotic microangiopathy: a multicentre cohort study.

Sciascia S, Yazdany J, Dall'Era M, Fenoglio R, Radin M, Aggarwal I, Cuadrado MJ, Schreiber K, Barreca A, Papotti M, Roccatello D.Ann Rheum Dis. 2019 Jul;78(7):1004-1006. doi: 10.1136/annrheumdis-2018-214559. Epub 2018 Dec 14.PMID: 30552172 Free PMC article. No abstract available.