IEEE EMBS presents

Simona Carini

I have substantial experience in clinical trials as an oncology nurse and as a clinical trials data analyst at Bracco SpA and Chiron Corporation.

Since 2002, working in Dr. Ida Sim’s research lab at UCSF, I have been a principal contributor to the Trial Bank Project, the design and evaluation of the Ontology of Clinical Research (OCRe), our work with the National Center for Biomedical Ontology on clinical trial annotation and visualization, and to the Human Studies Database (HSDB), our data federation project for the Clinical and Translational Science Awards.

Through OCRe, I have acquired experience in ontology design and data representation formalisms (XML, RDF/OWL) and have been a key member of the OCRe team to develop an end-to-end data sharing architecture for semantically standardized exchange of human studies data based on OCRe.

Since Q4 of 2013, I have been involved in the definition of data schemas for mobile health applications for the non-profit organization Open mHealth and then for the IEEE P1752 Open Mobile Health Working Group, within which I also serve as Secretary.

I have experience with standardizing clinical data elements to standard clinical vocabularies (SNOMED, RxNORM, etc.) through both manual and automated methods (e.g., natural language processing). I have been been lead author on a number of publications about OCRe, the Trial Bank, HSDB and other projects pertaining metadata abstraction, mapping and visualization.


1984               Nursing Diploma, “R. Donatelli” School of Nursing (Perugia, Italy)

1991              B.A. English and German, Università Cattolica del Sacro Cuore (Milan, Italy)

2001               M.A. Interdisciplinary computer Science, Mills College (Oakland, CA)

Positions and Honors

Positions and Employment

1984 – 91       Registered Nurse, Various employers (in Italy)

1991 – 93       Clinical Data Coordinator, Bracco SpA (Milan, Italy)

1994 – 96       Clinical Data Coordinator II, Chiron Corporation, Emeryville, CA (now Novartis)

1996 – 97       Clinical Data Coordinator III, Chiron Corporation, Emeryville, CA (now Novartis)

1997 – 98       Data Quality Analyst, Chiron Corporation, Emeryville, CA (now Novartis)

2001 – 02       Lecturer in Computer Science, Mills College (Oakland, CA)

2004 – 05       Lecturer in Computer Science, Mills College (Oakland, CA)

2004 – 05       Research Associate, Environmental Working Group (Oakland, CA)

2006 –            Programmer / Analyst III, University of California, San Francisco, San Francisco, CA

2017 – 18       Technical Consultant, Vivli Center for Global Clinical Research Data, Cambridge, MA

Selected Awards and Honors

2000               Diane McEntyre Award for Excellence in Computer Science (2000)

Professional Development

2016               SNOMED CT Foundation Course, IHTSDO (online)

2017               SNOMED CT Implementation Course, IHTSDO (online)

2019               SNOMED CT Authoring I, IHTSDO (online)


Peer-Reviewed Publications

Note: In biomedical informatics, as in computer science, publications in conference proceedings are equivalent to journal publications in traditional medical fields.

  1. Chia, a large annotated corpus of clinical trial eligibility criteria. Sci Data. 2020 08 27; 7(1):281.Kury F, Butler A, Yuan C, Fu LH, Sun Y, Liu H, Sim I, Carini S, Weng C. PMID: 32855408.
  2. A randomized trial provided new evidence on the accuracy and efficiency of traditional vs. electronically annotated abstraction approaches in systematic reviews. J Clin Epidemiol. 2019 11; 115:77-89.Li T, Saldanha IJ, Jap J, Smith BT, Canner J, Hutfless SM, Branch V, Carini S, Chan W, de Bruijn B, Wallace BC, Walsh SA, Whamond EJ, Murad MH, Sim I, Berlin JA, Lau J, Dickersin K, Schmid CH. PMID: 31302205.
  3. Saldanha IJ, Schmid CH, Lau J, Dickersin K, Berlin JA, Jap J, Smith BT, Carini S, Chan W, De Bruijn B, Wallace BC, Hutfless SM, Sim I, Murad MH, Walsh SA, Whamond EJ, Li T. Evaluating Data Abstraction Assistant, a novel software application for data abstraction during systematic reviews: protocol for a randomized controlled trial. Syst Rev. 2016 Nov 22; 5(1):196. PMID: 27876082.
  4. He Z, Ryan P, Hoxha J, Wang S, Carini S, Sim I, Weng C. Multivariate analysis of the population representativeness of related clinical studies. J Biomed Inform. 2016 Apr; 60:66-76. PMID: 26820188.
  5. He Z, Carini S, Sim I, Weng C. Visual aggregate analysis of eligibility features of clinical trials. J Biomed Inform. 2015 Apr; 54:241-55. PMID: 25615940; PMCID: PMC4408222 [Available on 04/01/16].
  6. He Z, Carini S, Hao T, Sim I, Weng C. A method for analyzing commonalities in clinical trial target populations. AMIA Annu Symp Proc. 2014; 2014:1777-86. PMID: 25954450; PMCID: PMC4419878.
  7. Sim I, Tu SW, Carini S, Lehmann HP, Pollock BH, Peleg M, Wittkowski KM. The Ontology of Clinical Research (OCRe): An Informatics Foundation for the Science of Clinical Research. J Biomed Inform. 2013 Nov 13.

  8. Roumiantseva D, Carini S, Sim I, Wagner TH. Sponsorship and design characteristics of trials registered in Contemp Clin Trials. 2013 Mar; 34(2):348-55. PMID: 23380028.
  1. Ochs C, Agrawal A, Perl Y, Halper M, Tu SW, Carini S, Sim I, Noy N, Musen M, Geller J. Deriving an abstraction network to support quality assurance in OCRe. AMIA Annu Symp Proc. 2012; 2012:681-9. PMID: 23304341; PMCID: PMC3540580.
  1. Sim I, Carini S, Tu SW, Detwiler LT, Brinkley J, Mollah SA, Burke K, Lehmann HP, Chakraborty S, Wittkowski KM, Pollock BH, Johnson TM, Huser V. Ontology-based federated data access to human studies information. AMIA Annu Symp Proc. 2012; 2012:856-65. PMID: 23304360; PMCID: PMC3540523. [AMIA Distinguished Paper Award]
  1. Boland MR, Tu SW, Carini S, Sim I, Weng C. EliXR-TIME: A Temporal Knowledge Representation for Clinical Research Eligibility Criteria. AMIA Jt Summits Transl Sci Proc. 2012; 2012:71-80. PMID: 22779055; PMCID: PMC3392056.
  1. Bhavnani SK, Carini S, Ross J, Sim I. Network analysis of clinical trials on depression: implications for comparative effectiveness research. AMIA Annu Symp Proc. 2010; 2010:51-5. PMID: 21346939; PMCID: PMC3041357.
  1. Kiritchenko S, de Bruijn B, Carini S, Martin J, Sim I. ExaCT: automatic extraction of clinical trial characteristics from journal publications. BMC Med Inform Decis Mak. 2010; 10:56. PMID: 20920176; PMCID: PMC2954855.
  1. Tu SW, Peleg M, Carini S, Bobak M, Ross J, Rubin D, Sim I. A practical method for transforming free-text eligibility criteria into computable criteria. J Biomed Inform. 2011 Apr; 44(2):239-50. PMID: 20851207; PMCID: PMC3129371.
  1. Wynden R, Weiner MG, Sim I, Gabriel D, Casale M, Carini S, Hastings S, Ervin D, Tu S, Gennari JH, Anderson N, Mobed K, Lakshminarayanan P, Massary M, Cucina RJ. Ontology mapping and data discovery for the translational investigator. AMIA Jt Summits Transl Sci Proc. 2010; 2010:66-70. PMID: 21347152; PMCID: PMC3041530. [AMIA Distinguished Paper Award]
  1. Ross J, Tu S, Carini S, Sim I. Analysis of eligibility criteria complexity in clinical trials. AMIA Jt Summits Transl Sci Proc. 2010; 2010:46-50. PMID: 21347148; PMCID: PMC3041539.
  1. Sim I, Carini S, Tu S, Wynden R, Pollock BH, Mollah SA, Gabriel D, Hagler HK, Scheuermann RH, Lehmann HP, Wittkowski KM, Nahm M, Bakken S. The human studies database project: federating human studies design data using the ontology of clinical research. AMIA Jt Summits Transl Sci Proc. 2010; 2010:51-5. PMID: 21347149; PMCID: PMC3041546.
  1. Carini S, Pollock BH, Lehmann HP, Bakken S, Barbour EM, Gabriel D, Hagler HK, Harper CR, Mollah SA, Nahm M, Nguyen HH, Scheuermann RH, Sim I. Development and Evaluation of a Study Design Typology for Human Subjects Research. AMIA Annu Symp Proc., 2009:81-85. PMID: 20351827; PMCID: PMC2815479. [AMIA Distinguished Paper Award]
  1. Hernandez M, Carini S, Storey M, Sim I. An Interactive Tool for Visualizing Design Heterogeneity in Clinical Trials. AMIA Annu Symp Proc. 2008 Nov 6:298-302. PMID: 18998925
  1. de Bruijn B, Carini S, Kiritchenko S, Martin J, Sim I. Automated information extraction of key trial design elements from clinical trial publications. AMIA Annu Symp Proc. 2008; 141-5. PMID: 18999067; PMCID: PMC2655966.
  1. Sim I, Olasov B, Carini S. An Ontology of Randomized Trials for Evidence-Based Medicine: Content Specification and Evaluation Using the Competency Decomposition Method. Journal of Biomedical Informatics, 2004; 37(2):108-119.
  1. Sim I, Carini S, Olasov B, Jeng S. Trial bank publishing: phase I results. Stud Health Technol Inform. 2004; 107(Pt 2):1476-80. PMID: 15361060.
  1. Carini S, Sim I. SysBank: a knowledge base for systematic reviews of randomized clinical trials. AMIA Annu Symp Proc. 2003; 804. PMID: 14728309; PMCID: PMC1479927.
  1. Sim I, Olasov B, Carini S. The Trial Bank system: capturing randomized trials for evidence-based medicine. AMIA Annu Symp Proc. 2003; 1076. PMID: 14728579; PMCID: PMC1479965.