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AMIA20-i2b2workshop_slides.pdf
Jeffrey Klann, PhD Harvard Medical School / Mass General Brigham Twitter: @JeffKlann #AMIA2020 Introduction to querying electronic health records for patient cohorts using the i2b2 data platform I2b2 and the Query Tool W16, Session 1: Introduction to i2b2 What is i2b2? • A Clinical Data Warehousing and AnalyticsExportXLS v3.3 User's Manual.pdf
smaller queries of patient subgroups (from the large patient set) iteratively, in place of one single large query of that huge patient set, to reduce risk … the server. • Provides feedbacks on current progress, elapsed time, and estimated remaining run time. • Provides notification & suggestion in cases of paging (queryAMIA20-i2b2workshop_qt_excercises.pdf
Exercise Set 1: Query 1a) Using the ontology browser and find terms, find how many females had circulatory system disease and create a bar chart by age. 1b) How many patients had circulatory system disease and a CPK test >=400 u/l. (Answer: 5 patients.) 1c) Using the query from 1a, find the number of patientsData Mart Request Plug-in Doc.pdf
the appropriate access to run a SCILHS network query in the SHRINE client. • The Site Administrator has the appropriate level of access to do the following in their local i2b2 Web Client and Admin Module. o View SHRINE queries run by the Principal Investigator. o Generate a patient set in the i2b2 by running a local queryData Exporter (v 1.8.1)
Overview The Data Exporter functionality enables an i2b2 user to request patient data for the patients found by a desired query. In the configured workflow, data is requested and generated through new breakdown types that can be selected in the Run Query dialog. Users will see "data request" breakdowns, which sendAUG2016_Murphy-Mendis.pdf
Developing Specialized Hives to Contribute to the i2b2 Ecosystem Shawn Murphy Michael Mendis 1 Distributed Query System links together Specialized i2b2 Hives … that Exist and are in Development 5 L a rg e r Greater Specialization I2b2/RPDR Text-based Queries 130 Million Notes Available alongside 2.4 Billion FactsMapping Systems.xls
generation x x Will eventually provide a GUI for instance map definition x Runs in batch before query x x (with Ontomapper) Examples: Source Target Type of Mapping … for exposure (does not allow query by value) Med Ctr Specific LOINC Instance Mapping Normalization of all lab data into LOINC (allows query by value) Instance MapOntology basics.ppt
I2b2 Metadata Defining concepts Defining values Defining modifiers Building queries with i2b2 metadata Star Schema One fact table surrounded radially … of a model across systems. Ease of use by end-users. Dimensional Modeling 1. FACTS - the quantitative or factual data being queried. 2. DIMENSIONS – groupsAUG2016_Cimino.pdf
agreed that i2b2 summary queries are not human subjects data • Data without identifiers (but with dates and zip codes) are limited data sets • One acknowledgment of data use agreement is sufficient for all data sets (renewable annually) • Download (but not query) requires title, description, other data users (mustViewCreator-Installation-Document.doc
queries by creating views on the impacted i2b2 tables. Download View Creator executable (ViewCreator-1.1.jar) from Released Builds section (available under … pertaining to unique visits from i2b2 query. The significance of this view is that it not only returns diagnostic (OBSERVATION_FACT) records pertaining