Presentation is loading. Please wait.

Presentation is loading. Please wait.

Informatics for Integrating Biology and the Bedside Presented by: Terri Shkuda i2b2 Administrator Research Informatics Efforts are supported by: Clinical.

Similar presentations

Presentation on theme: "Informatics for Integrating Biology and the Bedside Presented by: Terri Shkuda i2b2 Administrator Research Informatics Efforts are supported by: Clinical."— Presentation transcript:

1 Informatics for Integrating Biology and the Bedside Presented by: Terri Shkuda i2b2 Administrator Research Informatics Efforts are supported by: Clinical and Translational Science Award Grant # UL1TR000127

2 What is i2b2? i2b2 = informatics for integrating biology and the bedside Developed at Harvard Partners Healthcare through a CTSA grant. Simple user interface to query selected clinical and billing data from Penn State Hershey care delivery from January 2011 to present. 3/30/15i2b2 Introductory Training V3.32

3 i2b2’s fundamental purpose Cohort identification - Users search a de-identified database, without IRB approval, to determine the existence of a set of patients meeting specified criteria. The data are presented as unique patient counts. This means a patient is counted exactly once if he/she ever met the criteria specified by the query. 3/30/15i2b2 Introductory Training V3.33

4 Research tool continuum Hypothesis Collaboration Data capture Analysis Publication i2b2 Cohort Discovery Tool Research Networking Electronic Data Capture Statistics 3/30/15i2b2 Introductory Training V3.34

5 What is the source of the data? Operational Data Store i2b2 - PSU 3/30/15i2b2 Introductory Training V3.3 Cerner Millennium Eclipsys & Signature Billing Systems Cancer Registry Personalized Medicine 5

6 What does the data contain? De-identified data for over 630,000 unique patients Basic demographics (age, ethnicity, gender, language, marital status, race, religion, vital status) Diagnoses and procedures (inpatient) coded with ICD-9 for HMC billing Procedures coded with CPT (outpatient) Lab tests performed by HMC Medications (administered during inpatient, med list reported at outpatient) Personalized Medicine (sample availability, consent for research, tobacco) Visit types (inpatient, outpatient, emergency, same day care, etc.) Cancer Registry Key dates associated with each event above 3/30/15i2b2 Introductory Training V3.36

7 What will we accomplish today? You’ll receive an overview of i2b2, including:  Intended uses  Strengths and limitations You’ll see a few i2b2 queries, supplemented by materials to facilitate your subsequent hands-on learning.  This PowerPoint presentation  Listing of the Standard Data Set These materials can be found in the i2b2 website ( services-core/training-resources/). services-core/training-resources/ 3/30/15i2b2 Introductory Training V3.37

8 Setting expectations… i2b2 is a vast collection of data, but it does not contain all data types that you might need. Not included are: Summaries and clinic notes (free-form text) Narrative reports (e.g., radiology, surgical pathology, operative reports) Images (e.g., digital x-rays, EKGs, scanned documents) Microbiology data (not yet recorded discreetly in the EMR) Family History and Medical History (unless coded for billing purposes) Genomic data Problem Lists Height, weight, vital signs, allergies, and other data from nursing forms Primary/Attending physician Department location 3/30/15i2b2 Introductory Training V3.38

9 From hypothesis to data collection 3/30/15i2b2 Introductory Training V3.3 Develop criteria for queries and refine to establish the cohort Re-query and request a Patient Set Review aggregate data and refine IRB approval Request standard data set from Decision Support based on query Export data for preliminary exploration and analysis – OR – Request a de-identified data set from Decision Support based on query 9

10 A quick cohort example Patients with the diagnosis of alcohol withdrawal Find the ICD diagnosis for Streptococcal Sore Throat and Scarlet Fever using Find Terms, Search by Names Query for all patients with the ICD diagnosis ~4423 patients Date restrict the search to 1/1/2013 to 03/01/2013 ~268 patients Find the CPT for Strep test searching for the “CPT rapid strep test” on Google, then search using Find Terms, Search by Codes, CPT (87880) Drag the Rapid Strep CPT code (87880) to Group 2 query~35 patients Apply a temporal constraint of same financial encounter for both the Dx and Procedure~30 patients 3/30/15i2b2 Introductory Training V3.310

11 i2b2 query assistance i2b2’s Navigate Terms and Find Terms functions allow you to select your query terms. The tips below might help you. Sometimes, it’s easier to:  Perform an Internet search on the concept + the coding system: for example: heart failure ICD code  Use the resulting code(s) in i2b2’s Find Terms, Search by Codes 3/30/15i2b2 Introductory Training V3.311

12 Refining i2b2 queries i2b2 provides different ways to refine your queries. For example: You can specify whether the concept ever occurs or occurs at least a certain number of times in a defined time period.  If you specified occurs > 4 times, then the only patients counted would those who had 5 or more occurrences in that time period. In all cases, however, i2b2 counts reflect unique patients. 3/30/15i2b2 Introductory Training V3.312

13 Now that I have enough patients in the cohort, what is next? Rerun the same query requesting patient set, by checking Patient List Use visualization tools: Demographic composition shows the distribution of age, sex, race, and vital status Timeline plug-in depicting temporal relationships among its “concepts” (diagnoses, meds, lab tests) timing of their occurrence. Export data Request data set from Decision Support Turnaround time will be approximately 5-7 business days for the Standard Data Set. The dataset you receive will be a standard data set, either de- identified or with HIPAA identifiers depending on what you have rights to see (IRB-determined or non-research) 3/30/15i2b2 Introductory Training V3.313

14 i2b2 Analysis Tools Demographics Switch from Find Patients to Analysis Tools (make this selection at the very top right section of the Web page) From the Plugins tab at the bottom:  Select the plug-in called Demographics (1 Patient Set)  For Patient Set, use the last query, Strep with Scarlet Fever patient set and choose the Patient Set in the Previous Queries tab.  Drag the Patient Set to the Patient Set field in the Analysis Tool window.  Select the View Results tab 3/30/15i2b2 Introductory Training V3.314

15 i2b2 data export From the Specify Data tab: 1. At the bottom pane of the screen, under Plugins, select ExportXLS 2. Drag the Strep with Scarlet Fever patient set into the Patient Set box 3. Locate Strep Test in your Workplace, then drag this to the Concept(s) box 4. Navigate the Ontology (Medications) pane to locate Amoxicillin, then drag this parent folder to the Concept(s) box 5. Under Output Options: For Formatting, select 1 row per observation (detailed, 1 column per obs…) For Demographic data, select a few (e.g., Sex, Age) 6. Under Options (may cause long running time): Select Resolve Concept/Modifier Codes Select the View Results tab, then wait until the export is displayed. 3/30/15i2b2 Introductory Training V3.315

16 Important caveat about coded terms The i2b2 Ontology lists >450,000 individual terms, but only a small subset of these terms are populated in Penn State’s i2b2.  For example, hundreds of acetaminophen products are sold in the U.S. Fewer than 20 are part of HMC’s drug formulary and thus populated in Penn State’s i2b2. Since not all available i2b2 terms are populated with HMC data, you must construct your queries carefully. At the far right of several terms in the Ontology pane (diagnoses, procedures, medications, lab tests), you can see which terms are populated.  If you choose a term with zero patients, then your i2b2 query will return no patients for that query. 3/30/15i2b2 Introductory Training V3.316

17 Requesting Standard Data Set Once you are satisfied with your patient set, you may request a Standard Data Set from Decision Support which will encompass all dates for the patient. Locate your query in the Previous Queries or Workplace window and copy the entire name to clipboard. Submit a Report Request to IT: Infonet > Departments > Support > Information Technology > Our Teams > Decision Support > Request a Decision Support Service > Report and Service Request Form Log into BMC Remedy with your EPASS, select the Request Now button and complete the form as follows: Type of Request: New Report Source: Connected EMR Provide a detailed description of your request including data fields: Identify this as an i2b2 query and including the query name (paste from clipboard) Date Report Needed: for Standard Data Set, allow for at least 5-7 business days, for custom report, allow for 4 weeks. Reason for Request: Research Complete the remaining subfields with type of research and IRB # (if requesting PHI). The report (spreadsheets) will appear in your LaunchPad inbox and a representative from Decision Support will contact you: Internet browser > URL = myapps > login > folders (Business Objects) > LaunchPad > Documents > Inbox Please note that the standard data set may be large. PHS can also assist with the data reduction. 3/30/15i2b2 Introductory Training V3.317

18 Support Training, patience, and experience are the keys Need assistance? We can provide individual help. Contact call the Help Desk at 717-531-6281 requesting help with i2b2-PSU. A ticket will be sent to i2b2 Support. Drop in on i2b2/REDCap Open Office Hours every Thursday, 3:00 pm – 4:00 in HMC, Room H4510J. Visit the i2b2 website at programs/clinical-services-core/i2b2-home programs/clinical-services-core/i2b2-home 3/30/15i2b2 Introductory Training V3.318

19 3/30/15i2b2 Introductory Training V3.319

Download ppt "Informatics for Integrating Biology and the Bedside Presented by: Terri Shkuda i2b2 Administrator Research Informatics Efforts are supported by: Clinical."

Similar presentations

Ads by Google