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 Admins Administrators. These pages may also be helpful for those persons who are performing the ETL (extract-translate-transform-load) of the patient electronic health records (EHR) into the i2b2 database. These These tutorials may also be helpful for SHRINE Admins.

These tutorials assume that the Admin 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.

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 A – Glossary

Appendix B – i2b2 Ontology Content (Categories and Coding Schemes)

Appendix C – Ontology Standards and Sources

Appendix D – i2b2 Ontology Tables

Appendix E – Test Queries

Appendix F – Advanced Ontologies

Appendix G – Diagrams