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BenGlicksberg / ROMOP

R package to easily interface with OMOP-formatted EHR data.
MIT License
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Find patients via OMOP concept ID #9

Open dramacloak opened 4 years ago

dramacloak commented 4 years ago

So I have a concept_id for bladder cancer that is 197508 in OMOP. In the concept table it looks like:

sql <- render("SELECT * FROM concept where concept_id = '197508'") querySql(con,sql) CONCEPT_ID CONCEPT_NAME DOMAIN_ID VOCABULARY_ID CONCEPT_CLASS_ID STANDARD_CONCEPT CONCEPT_CODE VALID_START_DATE VALID_END_DATE INVALID_REASON 1 197508 Malignant tumor of urinary bladder Condition SNOMED Clinical Finding S 399326009 1970-01-01 2099-12-31 

person_id condition_start_datetime visit_occurrence_id             condition_source_value condition_concept_vocabulary
1:       id               date                   1 Malignant tumor of urinary bladder                       SNOMED
   condition_concept_code             condition_concept_name condition_source_vocabulary condition_source_code
1:              399326009 Malignant tumor of urinary bladder                      SNOMED             399326009
                condition_source_name                               condition_type condition_status_type
1: Malignant tumor of urinary bladder Condition tested for by diagnostic procedure                Domain

However, I can’t find any patients using the OHDSI concept ID, but I can find them using the SNOMED concept ID:

patient_list <- findPatients(strategy_in="direct", vocabulary_in = "SNOMED", codes_in = "197508") Error: none of the inclusion criteria were able to map to the ontology. Please check terms and try again. patient_list <- findPatients(strategy_in="mapped", vocabulary_in = "SNOMED", codes_in = "197508") Error: none of the inclusion criteria were able to map to the ontology. Please check terms and try again. patient_list <- findPatients(strategy_in="mapped", vocabulary_in = "SNOMED", codes_in = "399326009") Connecting using Oracle driver

  • using THIN to connect Connecting using Oracle driver
  • using THIN to connect Connecting using Oracle driver
  • using THIN to connect [1] "1840 patients found that meet the inclusion criteria."

Is it possible to use findPatients by searching the OMOP concept_id’s like ‘197508’?

dramacloak commented 4 years ago

Direct is looking at source_concept_id Mapped is looking at regular concept_id Ideally, there would be a third option searching the OMOP concept_id where we wouldn't need to know the source vocabulary