Quickstart¶
We download some test data for the 32 tables from the address below and populate the Concept registry.
!wget -nc https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip
!unzip -n mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip
Show code cell output
--2025-02-16 19:48:36-- https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip
Resolving physionet.org (physionet.org)...
18.18.42.54
Connecting to physionet.org (physionet.org)|18.18.42.54|:443...
connected.
HTTP request sent, awaiting response...
200 OK
Length: 10786504 (10M) [application/zip]
Saving to: ‘mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip’
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Create a test instance:
!lamin init --storage ./test-omop --name test-omop --schema omop
→ initialized lamindb: anonymous/test-omop
Import omop:
import lamindb as ln
import omop as op
import pandas as pd
→ connected lamindb: anonymous/test-omop
Load the data into a Pandas DataFrame:
df = pd.read_csv(
"./mimic-iv-demo-data-in-the-omop-common-data-model-0.9/1_omop_data_csv/2b_concept.csv"
)
df.columns = df.columns.str.lower()
df.rename(columns={"concept_class_id": "concept_class"}, inplace=True)
df.head()
Show code cell output
| concept_id | concept_name | domain_id | vocabulary_id | concept_class | standard_concept | concept_code | valid_start_date | valid_end_date | invalid_reason | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 2000011360 | Caffeine Citrate 1 Syringe | Drug | mimiciv_drug_ndc | Prescription Drug | NaN | Caffeine Citrate 1 Syringe | 1970-01-01 | 2099-12-31 | NaN |
| 1 | 2000010536 | Acetaminophen | Drug | mimiciv_drug_ndc | Prescription Drug | NaN | ACETAMINOPHEN (RECTAL) | 1970-01-01 | 2099-12-31 | NaN |
| 2 | 2000011213 | Melatonin 1 MG | Drug | mimiciv_drug_ndc | Prescription Drug | NaN | melatonin 1 | 1970-01-01 | 2099-12-31 | NaN |
| 3 | 2000011355 | 0.9% Sodium Chloride 100 mL Bag | Drug | mimiciv_drug_ndc | Prescription Drug | NaN | 0.9% Sodium Chloride 100 mL Bag | 1970-01-01 | 2099-12-31 | NaN |
| 4 | 2000010313 | Vancomycin | Drug | mimiciv_drug_ndc | Prescription Drug | NaN | Vancomycin ophthalmic 50mg/ml bottle | 1970-01-01 | 2099-12-31 | NaN |
Populate the Concept registry:
concepts = [op.Concept(**row.to_dict()) for _, row in df.iterrows()]
for concept in concepts:
concept.save()
op.Concept.filter().first()
Show code cell output
Concept(concept_id=2000000000, concept_name='Stroke Volume Variation', domain_id='Measurement', vocabulary_id='mimiciv_mimic_generated', concept_class='Clinical Observation', standard_concept='S', concept_code='Stroke Volume Variation', valid_start_date=1970-01-01, valid_end_date=2099-12-31, invalid_reason='nan', created_by_id=1, space_id=1, created_at=2025-02-16 19:53:11 UTC)
Perform validation of new data.
op.Concept.validate(
["Stroke Volume Variation", "this concept does not exist"],
field=op.Concept.concept_name,
)
! 1 unique term (50.00%) is not validated for concept_name: 'this concept does not exist'
array([ True, False])