Intended Audience
These tutorial pages are intended to educate those persons responsible for setting up the i2b2 server instance at an institution. We call them the i2b2 Administrators. These pages may also be helpful for those persons who are performing the ETL (extract-transform-load) of the patient electronic health records (EHR) into the i2b2 database. These tutorials may also be helpful for SHRINE Admins.
These tutorials assume that the i2b2 Admin has familiarity with the setup of Java Application Servers such as Wildfly and Tomcat, and configuration of web servers such as Apache and IIS. They should have familiarity with SQL queries, database setup and administration, principles of software security and network security, and principles of software testing and validation.
Familiarity with medical terminology and healthcare informatics is a huge advantage, but is not required.
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Acknowledgement
These tutorials build on a previous Ontologies 101 tutorial page authored by Matvey Palchuk and Jay Pedersen. Their insights and contributions guided the development of this course.
Course
Lesson titles in blue are existing pages. Lesson titles in gray or red are planned pages.
Introductory Topics
Most i2b2 Admins will want to know these topics.
Ontologies 101 – Introduction – Your First i2b2 Ontology
Ontologies 102 – Patient Counts ("totalnum
")
Ontologies 103 – Ontology Table Structure and Query Mechanism (DRAFT)
Ontologies 104 – Comments – Your First Customization
Ontologies 105 – New Query Breakdowns
Advanced Topics
Ontologies 201 – Custom Metadata – Additions and Modifications
Ontologies 202 – Role-Based Permissions
Ontologies 203 – Concept Modifiers
Appendices
Appendix B – i2b2 Ontology Content (Categories and Coding Schemes)
Appendix C – Ontology Standards and Sources
Appendix D – i2b2 Ontology Tables
Appendix F – Advanced Ontologies
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