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Here is another screenshot, where you can see the expansion for "Race" in the "Demographics" tree:
Where did the i2b2 ontology "concepts" come from?
Typically, the concepts that make up the various categories or "domains" are based on medical terminology standards published by various institutions. Concepts can also be created ad hoc for a specific i2b2 instance by the i2b2 administrator at that site. (For more information on custom metadata, please see Ontologies 201.)
The commonly used standards representing basic structured clinical patient data are represented by a number of different "coding schemes" — ICD-9, ICD-10, CPT-4, HCPCS, SNOMED CT, LOINC, RxNorm, UMLS, and VA Classes. See Appendix B for further information.
How does it work? How does the i2b2 ontology make the patient data queryable?
First, a little more terminology. The i2b2 "patient data" are stored in the i2b2 Clinical Research Chart database, or "CRC database." The concepts that describe those patient data are known as the "metadata." The metadata are stored in the i2b2 Metadata database, or "ONT database."
The i2b2 metadata in the ONT database work together with the patient data in the CRC database. Each patient "observation" in the CRC database must have a code associated with it, and that code must match a healthcare concept — diagnosis, procedure, medication, lab test, demographic descriptor, etc. — that exists in the metadata ONT database. So the CRC patient data will be queryable in i2b2 only if the patient facts in the CRC database are recorded utilizing standard codes that are referenced in the i2b2 metadata (ONT database) (or have been mapped to these standard codes as part of an ETL process).
For instance, if the patient's electronic health record indicates that the patient had the procedure "tonsillectomy with adenoidectomy," then that fact needs to be recorded in the CRC database using the standard code for that particular procedure. In the case of using the default i2b2 Procedures metadata tree, that code would be "ICD9:28.3". When a researcher makes a query in the user interface for "tonsillectomy with adenoidectomy," that query will be translated by i2b2 into a query for patients in the CRC database for patients who have the code ICD9:28.3 in their data records.
A) The ontology is made up of medical concepts. The ontology is visible to researchers through the webclient, and each medical concept in the ontology includes specific code(s) that match medical observation facts (such as diagnoses, medications, procedures, etc). A researcher can select concepts they are interested in to build a query, and medical data that matches those concepts' codes will be counted.
Where did the i2b2 ontology "concepts" come from?
Typically, the concepts that make up the various categories or "domains" are based on medical terminology standards published by various institutions. Concepts can also be created ad hoc for a specific i2b2 instance by the i2b2 administrator at that site. (For more information on custom metadata, please see Ontologies 201.)
The commonly used standards representing basic structured clinical patient data include ICD9, ICD10, CPT4, HCPCS, SNOMED CT, LOINC, RxNorm, UMLS, and VA Classes. See Appendix B for further information.
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| It's important to understand that each institution will have their own protocols for coding diagnoses, procedures, medications, etc., in the patient electronic health records (aka EHR) such as in Cerner or Epic databases, and that these protocols may use standard or non-standard codes. But when preparing the CRC database for i2b2, it's necessary for the ETL process (extract-translate-load) to map the codes from the patient EHR into the codes that are present in the i2b2 metadata. For instance, let's say a patient's EHR record includes a CPT-4 code for a surgery. And let's say that the i2b2 ontology tree your institution is using has codes for that same type of surgery as ICD-9, ICD-10, CPT-4, and HCPCS codes. Then the surgery record from the EHR would have to be mapped to 4 records in the i2b2 CRC database: one record that reflects the original CPT-4 code from the EHR, and 3 additional records where that CPT-4 code is mapped to the appropriate ICD-9, ICD-10, and HCPCS codes. |
There are many terms related to i2b2 ontologies that are new to me. Is there a Glossary?
Yes! Here is a Glossary that provides explainers for many of the key terms related to i2b2 ontologies and the i2b2 architecture.
Do all i2b2 instances share the same i2b2 ontology?
No. Several i2b2 ontologies have been developed and are openly available for use. Any organization may also modify an existing ontology for its own use, or develop a new ontology. (See Ontologies 201.)
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The i2b2 software includes i2b2 ontologies that you can use right away. There are additional ontology trees that can substitute, or can be added. (See Appendix E – Advanced Ontologies.)
Which ontologies can I use right away ('out of the box')?
The i2b2 database-loading modules come with at least 3 sets of "metadata" or ontology trees. These are the demo ontology, the ACT ontology, and the ACT-on-OMOP ontology.
| Name | Description | Target Data Model |
|---|---|---|
| i2b2 demo ontologyDemo Ontology | default metadata from i2b2 authors | i2b2 Common Data Model (star-schema); default CRC demo database has matching concepts |
| ACT ontologyOntology | ENACT project | i2b2 Common Data Model (star-schema); ACT CRC demo database has matching concepts |
| ACT-on-OMOP ontologyOntology | ENACT project | i2b2 Common Data Model (star-schema), but modified with views into the OMOP Common Data Model; the CRC database loaded with SYNPUF demo data has matching concepts |
The table below table outlines the domains and standards coding schemes included in each ontology. NOTE: if your local institution does not have data for a given domain that is included, such domains can easily be hidden or excluded.
| Domain / StandardCoding Scheme | i2b2 Demo Ontology | ACT Ontology | ACT-on-OMOP Ontology | ||
|---|---|---|---|---|---|
| Demographics | |||||
Diagnoses | |||||
| ICD-9- | ICD-9CMCM |  | | | |
| ICD-10- | ICD-10CMCM | Out of date | | ||
| SNOMED CT | | ||||
Medications | Homegrown? | Rx-Norm | |||
RxNorm | | ||||
NDC | | ||||
SNOMED CT | Rx-Norm | ||||
| Procedures-- | |||||
| ICD-9 | -CM | | | ||
| ICD-10 | -PCS | | |||
| CPT-4 | | --||||
| HCPCS | | ||||
| SNOMED CT | | ||||
| Lab Tests / Vital Signs | Homegrown? | ||||
| LOINC | LOINC | ||||
| SNOMED CT | |
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| If your local institution does not have data in the CRC database for a certain domain in your chosen i2b2 ontology, then user queries referencing that domain may come back empty. To avoid that, you can exclude that domain from the i2b2 user interface, so that the domain without matching data in the CRC database is never used in a query. |
How should I choose which ontology to use?
The ontology you choose to use depends on your local goals and local data. As long as your primary purpose is to understand and show how the i2b2 webclient works, the i2b2 demo ontology is sufficient. If your goal is to set up i2b2 for research use, one of the ACT ontologies will be more useful. In general, to set up an i2b2 instance to support research, start with the ACT Ontology. This Ontology includes a wide range of terminologies that should cover most code-sets you'll find in your EMR data. OMOP refers to a Common Data Model, so if you are using this model locally, then ACT on OMOP will be the most relevant.
There are many terms related to i2b2 ontologies that are new to me. Is there a Glossary?
Yes! Here is a Glossary that provides explainers for many of the key terms related to i2b2 ontologies and the i2b2 architecture.
What's the relationship between the metadata and the data?
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