Page History
...
In i2b2's domain of Clinical Research Informatics, an ontology is a collection of healthcare-related "concepts," that define a set of terms representing the various categories of clinical and translational science. Categories such as demographics, diagnoses, procedures, laboratory tests, and medications are described as using hierarchical lists of "concepts" in an i2b2 ontology.
...
- diabetes mellitus is an endocrine disorder, which is a type of diagnosis; it will be found in both the "Diagnoses" tree and in the "Diagnoses (ICD10)" tree;
- aspirin is a non-steroidal anti-inflammatory drug, which is an analgesic, which is a type of medication; it will be found in the "Medications" tree;
- tonsillectomy is a type of surgery, which is a procedure; it will be found in the "Procedures" tree;
- hemoglobin A1c is a blood test, which is a type of laboratory test; it will be found in the "Laboratory Tests" tree; and
- race is a patient-demographic descriptor; it will be found in the "Demographics" tree.
Here is another screenshot, where you can see the hierarchy expansion for "Race" in the "Demographics" tree:
...
First, a little more terminology. The i2b2 "patient data" are stored in the Clinical Research Chart database, or "CRC database." The ontology of concepts that describe those patient data is are known as the "metadata." The metadata or ontology is stored in the Metadata database, or "ONT database."
...
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 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". A query in the user interface for "tonsillectomy with adenoidectomy" will be translated by i2b2 into a query in the database for patients who have the code ICD9:28.3 in their CRC data records.
...
The commonly used standards representing basic structured clinical patient data include:
| Source | Standard | Relevant i2b2 Domains or Categories |
|---|
| American Medical Association (AMA) | Current Procedural Terminology (CPT; Level 1 of HCPCS) | Procedures |
| American Medical Association (AMA) | Healthcare Common Procedure Coding System (HCPCS) | Procedures |
| Health Level 7 International | HL7 Administrative | Demographics |
| International Health Terminology Standards Development Organisation (IHTSDO), aka SNOMED International | Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) | Demographics, Diagnoses, Procedures, Measurements, Medications |
| Regenstrief Institute | Logical Observation Identifiers Names and Codes (LOINC) | Measurements (Laboratory Tests, Vital Signs) |
| US Food and Drug Administration (FDA) | National Drug Code (NDC) | Medications |
| US National |
| Center for Health Statistics (NCHS) | International Classification of Diseases (ICD) | Diagnoses (ICD9-CM, ICD10-CM), Procedures (ICD9-PROC, ICD10-PCS) |
| US National Library of Medicine | RxNorm (part of UMLS) |
| Medications | ||
| US National Library of Medicine | Unified Medical Language System (UMLS) | Demographics, Diagnoses, Procedures, Measurements, Medications |
| US Veterans Administration |
| VA Classes |
| Medications |
Do all i2b2 instances always have the same ontology?
...
| Name | Description | Included Domains (I don't think all domains can be listed, or it will be hard to understand. I think this merges with description and tries to convey the level of detail and comprehensiveness). | Target Data Model |
|---|---|---|---|
| i2b2 demo ontology | default metadata from i2b2 authors | fixme | i2b2 Common Data Model (star-schema); default CRC database has matching concepts |
| ACT ontology | ENACT project | fixme | i2b2 Common Data Model (star-schema) | ; ACT CRC demo database has matching concepts
| ACT-on-OMOP ontology | ENACT project | fixme | i2b2 Common Data Model (star-schema), but modified with views into the OMOP Common Data Model; CRC database loaded with SYNPUF demo data has matching concepts |
...
. |
|---|
...
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.
How about a thumbnail description of these ontologies? How do they differ from each other?
Sure. Here is a table describing the major differences among them.
| Target Data Model | |||
|---|---|---|---|
| i2b2 demo ontology | default metadata from i2b2 authors | fixme | i2b2 Common Data Model (star-schema); default CRC database has matching concepts |
| ACT ontology | ENACT project | fixme | i2b2 Common Data Model (star-schema); ACT CRC demo database has matching concepts |
| ACT-on-OMOP ontology | ENACT project | fixme | i2b2 Common Data Model (star-schema), but modified with views into the OMOP Common Data Model; CRC database loaded with SYNPUF demo data has matching concepts |
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 data architecture, so if you are using this format locally, then ACT on OMOP will be the most relevant.
...
You just mentioned Domains. What do you mean by that?
...
