UCL/H OMOP course
- Using a standard makes it much easier to share data
- OMOP uses concepts to link dated to standard vocabularies
- R can be used to join and interrogate data
- Understand that nearly everything in a hospital can be represented
by an OMOP concept_id.
- Know that OMOP data usually includes the OMOP concept table and
other data from the vocabularies
- Be able to look up concepts by their name
- Know that patient conditions are stored in the condition_occurrence
table
- know that measurements are mainly lab results and other records like
pulse rate
- know observations are other facts obtained through questioning or
direct observation
- understand concept ids identify the measure or observation, values
are stored in value_as_number or value_as_concept_id
- be able to join to the concept table to find a particular
measurement or observation concept by name
- understand that different clinical questions can be answered by
querying by patient and/or visit, or summing across all records
- Know that a visit is a period of time and patients can have multiple
visits
- Understand that multiple measurements, conditions etc. can occur
within and between visits
- Understand that for some analyses you will want to look within
visits and for other analyses to sum across visits
- Know that visits are recorded in the visit_occurrence table
- Know each visit is unique to a person
- Understand that other tables link to visits
- Understand how visits can be used to find co-occurrence of other
events
- Know that exposure of a patient to medications is mainly stored in
the drug_exposure table
- Understand that drug concepts can be at different levels of
granularity
- Understand that source values are mapped to a standard
vocabulary
- Use
.md files for episodes when you want static
content
- Use
.Rmd files for episodes when you need to generate
output
- Run
sandpaper::check_lesson() to identify any issues
with your lesson
- Run
sandpaper::build_lesson() to preview your lesson
locally
