- Link to i2b2 doc describing relevant topics
- Do not forget to plan for regular updates of your ontology
- What to do with deprecated codes?
- It is important to note that many COVID-19 related facts or observations, such as the diagnosis of COVID-19 (ICD-10-CM:U07.1), procedure codes for SARS-CoV-2 testing, laboratory codes for actual tests, etc., are brand-new and will not be in your i2b2 ontology unless you add them. It is crucial to do so in order to ensure that COVID-19 related observations flowing into your i2b2 are queriable by its users.
- New codes: https://docs.google.com/spreadsheets/d/1rbZfsZxsx16dsmleb7TFdM4lGQ-rypLG7IFcApwdAL0/edit?usp=sharing
- Innovations introduced in ACT’s COVID-19 ontology
- We draw a distinction between three terms used to name collections of concepts: vocabulary, terminology and ontology.
- A vocabulary is a collection of terms, without any implied relationship between them. For example, a list of drugs on US market is a vocabulary of drugs.
- A terminology begins with a vocabulary and adds child-parent (“is-a”) relationships. For example, you introduce the notion of Antibiotics and group certain drugs under that. And beta-blockers. And so on.
- An ontology goes one step further and introduces relationships other than is-a. For example, we can say that Acetaminophen “treats” headache. Here, “treats” is a relationship between the drug and a condition, and this relationship is not child-parent. That is what makes it an ontology.
- So technically, an i2b2 ontology is a terminology. However, the term “i2b2 ontology” is an enduring convention which we will continue to agree to use.