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Scripps Health Clinical Data Resources for Research

imageMedical records of patients, such as this cancer survivor, shown with her family, help investigators to assemble data on demographics and other factors.

Identifying the best sources of clinical data can be confusing for any investigator because data are collected and stored across assorted electronic systems as well as in paper form (e.g. patient charts). 

Determining the best data sources for specific research needs depends on several factors including: data types required, specific data elements, ability to pull data from a given system, and length of time available to obtain data. 

This document provides an overview of categories (or types of data), brief descriptions of key Scripps Health hospital and ambulatory clinic systems, and a cross reference chart (systems and types of data they hold).

Categories (or types) of patient data:

  • Patient Demographics (such as age, sex, race, ethnicity, and home zip code)
  • Encounter detail (e.g. physician, facility, length of inpatient stay, inpatient admit/discharge dates,  outpatient visit dates, for a specific inpatient stay or outpatient visit)
  • Medical diagnoses / symptoms
  • Medical procedures
  • Lab tests performed/results
  • Medications
  • Vital signs (e.g. height, weight, blood pressure, and temperature at time of visit)
  • Allergies
  • Individual medical history
  • Family medical history
  • Lifestyle (smoking/drinking/exercise/etc)

Data most commonly requested by researchers:


  • Patient demographics (such as age, sex, race, ethnicity, and home zip code)
  • Encounter detail (e.g. physician, facility, length of inpatient stay, inpatient admit/discharge dates, outpatient visit dates, for a specific inpatient stay or outpatient visit)
  • Medical diagnoses
  • Medical procedures
  • Lab tests performed/results
  • Medications
  • Vital signs (e.g. height, weight, blood pressure, and temperature at time of visit)

Due to the complexity of our medical environment, data are collected and stored across various paper (e.g. patient charts) and electronic systems. As a result, obtaining clinical data may require time.

Clinical data resources at Scripps Health

Hospital systems – Electronic systems for directly collecting and/or reporting patient data on inpatient stays, visits for outpatient hospital services, and emergency room visits

  • GE Centricity – Scripps Hospitals Electronic Medical Record (EMR) System (covering CV, EN, GR, LJ, MH)

    Hospital electronic medical record (EMR) system for patient charting and assessments (use of modules varies slightly by hospital).  Contains orders labs, imaging, pharmacy and lab results.  Can display various categories of transcribed notes.  Display of patient demographics and admit/ discharge/ transfer (ADT) data, bed tracking, emergency room short registration.  Can view census info for hospital site/dept/patients assigned to nurses.  It can be difficult to get reports developed to pull data from the inpatient EMR, since day-to-day patient care priorities are numerous, and supporting related data needs must take precedence. 

  • Eclipsys Multi-Entity – Patient registration (covering all sites – both hospitals & clinic) and the hospitals’ patient accounting/billing system (covering CV, EN, GR, LJ, MH)

    Registration front end system for GE Centricity hospital EMR system.  Holds basic, minimum demographics for all Scripps patients (controls assignment of central medical record number to patients).  Also used to assign central medical record number to ambulatory/clinic patients).

    Plus holds and processes patient accounting / billing data for hospital patients. Eclipsys is updated with hospital patients’ ICD9 Diagnoses and Procedure coding post discharge.  Reports can be requested for Eclipsys data. 

  • ORMIS – Surgery scheduling and tracking system

    Schedules patients / rooms / equipment for Scripps hospital operating rooms and ambulatory surgery centers.  Holds data on surgeries scheduled and actual start/stop times, surgeon, other surgery team members, anesthesiologist, anesthesia type, procedures performed, meds given during surgery, and on implants.  Requests for ORMIS would provide only ORMIS data.  For a combination of surgery data with diagnoses and/or procedures info, the Enterprise Data Warehouse (EDW) has selected data available for reporting.

  • Misys – Lab System

    Processes and stores lab orders and results for hospitals.  Reports can be requested but will only cover lab tests and results data.  Lab results data recently was brought into the Enterprise Data Warehouse (EDW).  This would support incorporating additional diagnoses and/or procedure data with lab results (see Electronic Data Warehouse below).

  • Trendstar - Decision Support System (DSS)

    It holds selected patient demographics, ICD9 diagnoses, ICD9 procedures, service charges, and applied overhead costs.  Has been used for approximately 20 years, and can be very cumbersome to pull data from.  Reporting from Trendstar can be requested, but its’ reporting capabilities are limited.  Generally, the same data can be reported on through the Electronic Data Warehouse (EDW).

  • Enterprise Data Warehouse (incorporates a core database and a number of downstream data marts)

    Data loaded weekly/monthly depending on the particular clinical system it is being extracted from (Trendstar, Midas, Ormis).  For inpatient and outpatient hospital visits, it holds selected patient demographics, ICD9 diagnoses, ICD9 procedures, service charges, applied overhead costs, physicians associated to the encounter, and lab results.  Additionally, the EDW team hopes to incorporate data on ordered and dispensed inpatient medications into the EDW by early 2011.

Clinic Systems – Electronic systems for directly collecting &/or reporting data on Scripps’ clinic visits (ambulatory, non-hospital visits)

imageSamir Damani, Ph.D., PharmD., Scripps Clinic cardiologist and STSI clinical scholar, depends on electronic medical records for both patient care and research.
  • IDX Flowcast / PMA System – Partial EMR functions for Scripps’ clinics (covering approximately 1/3rd of Scripps’ 19 clinics, this system is in process of being replaced by Allscripts ambulatory EHR during 2010.

    Patient demographics, Billing& Accounts Receivable, Managed Care (case management), Scheduling / visits tracking, and Chart Tracking.  It is a complete, integrated EMR system (like Allscripts).  This system is not generally available for direct reporting.  Instead the system’s patient registration, billing, accounts receivable and managed care / visit data is fed into the Oracle Data Warehouse twice a week.

  • Allscripts Enterprise – Electronic Health Record (EHR) system (covering two-thirds of the 19 clinics, system in process of being implemented across all 19 Scripps clinics, with completion by end of 2010)

    Allscripts Enterprise EHR core suite includes base capabilities with full integration with e-Prescribing, charges/billing, transcription/documentation, orders and results, and document scanning.  Selected Allscripts patient data (related to billing & AR, encounter detail, and up to four diagnoses and procedures per visit) is fed from Allscripts into the Oracle Data Warehouse weekly to ensure availability of selected data across all clinics.  See Oracle Data Warehouse below.

    Note:  The Allscripts E-Prescribing module has been implemented across all clinics.  Usage across the clinics is still being improved.  Eventually this system will provide the means of tracking clinic patients’ prescribed medications.  The IS Enterprise Data Warehouse (EDW) team has been working on integrating key Allscripts patient visit data (including prescribed medications) into a supporting data mart (utilizing Cognos BI as the front end tool for querying and reporting). The new Allscripts’ data mart extends research access to a much broader range of clinic patient data.

  • Misys – Lab System

    Lab orders and results for patients utilizing Scripps Green Hospital and Scripps Clinic labs.  Data for Scripps Green feed into GE Centricity for display on patient level.  Data for clinics on lab results and normal values feed into the Oracle Data Warehouse (and is available for reporting) and Allscripts.

  • Oracle Data Warehouse (ODW)

    Data from the Flowcast/PMA system, Allscripts, and Misys lab systems loads into the Oracle Data Warehouse loads either once or twice weekly (depending on specific data types).  It holds clinic patients’ demographics, service charges, ICD-9 diagnoses per visit, CPT procedure codes per visit, and names of primary care physician and the attending physician per visit.  Plus lab results if patients utilized Scripps Clinic labs. It sometimes takes a few weeks from the time a report is requested until it is received.  Reporting is done utilizing the Hummingbird BiQuery front-end to the ODW.

  • Enterprise Data Warehouse (EDW) – The data warehouse incorporates multiple databases and downstream data marts. 

    The EDW was initially developed to integrate a variety of hospital patient data that is held across multiple systems (see Enterprise Data Warehouse above under Hospital Systems).  But in conjunction with the Allscripts implementation, the EDW team has also developed a separate data mart with a Cognos reporting front-end to better support groups reporting needs.  Reporting access to Allscripts patient data will improve with the development of the data mart in 2010.

Systems can overlap in terms of specific data elements.  They also differ in how data can be accessed. 

For assistance in identifying the systems that best fit the research needs, investigators may contact:
Sandy MacKenzie
Manager, Research Medical Informatics
Scripps Translational Science Institute
(858) 554-5744  

Requesting data for research purposes

How data are requested varies according to the investigator’s departmental affiliation. To make a request through Scripps CRS (Clinical Research Services), please contact Pam Pulido at .(JavaScript must be enabled to view this email address) or call (858) 632-5409.

To make a request through Scripps Genomic Medicine or Scripps Translational Science Institute, please contact Sandy MacKenzie at .(JavaScript must be enabled to view this email address) or call (858)554-5744. 

“Aggregated” versus “Patient Identifiable” data:

imageRequests for aggregated (summary data) are based on very specific criteria.  For example, an investigator needs to know the number and gender of inpatients at Scripps Green Hospital, who underwent a specific surgical procedure during a one year period. If the data are not reporting based on patient identifiable data fields (as defined under HIPAA), the data request form is fairly brief and, generally the data are readily accessible.  Such requests are usually “preparatory to research” (e.g. made to support hypothesis development or testing) or to determine feasibility of a given trial (e.g. ability to recruit a sufficient number of trial participants).

If a trial does not yet exist, or hasn’t yet received IRB approval, aggregated, non-patient identifiable data can be requested by researchers.  Regardless of the level of detail in requested data, an investigator must obtain IRB approval prior to publishing the research findings.

If an investigator is requesting data that can specifically identify patients as individuals (as defined under HIPAA), specific requirements must be met.  Under the preparatory to research exclusion, a Scripps Health employee can request individual patient data; however the employee is not allowed to contact the patient without IRB approval.  Also, a Confidential Data Request form must be submitted through the Scripps IS Help Desk.  The form will be examined and approved by the Privacy Officer prior to being sent to the appropriate report developer.  Please consider time restraints in obtaining patient identifiable data to ensure these steps can be completed prior to the time the data are needed.

Types of Data Held in these Systems