Quickstart¶
We download some test data for the 32 tables from the address below and populate the Concept registry.
!wget https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip
!unzip mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip
Show code cell output
--2024-09-16 13:50:00-- 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 --schema omop
→ connected lamindb: anonymous/test-omop
Import omop:
import omop as oo
import pandas as pd
Load the data into a 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 = [oo.Concept(**row.to_dict()) for _, row in df.iterrows()]
for concept in concepts:
concept.save()
oo.Concept.df()
Show code cell output
→ connected lamindb: anonymous/test-omop
| concept_name | domain_id | vocabulary_id | concept_class | standard_concept | concept_code | valid_start_date | valid_end_date | invalid_reason | |
|---|---|---|---|---|---|---|---|---|---|
| concept_id | |||||||||
| 2000000000 | Stroke Volume Variation | Measurement | mimiciv_mimic_generated | Clinical Observation | S | Stroke Volume Variation | 1970-01-01 | 2099-12-31 | nan |
| 2000000002 | dynes.sec.cm-5/m2 | Unit | mimiciv_mimic_generated | Unit | S | dynes.sec.cm-5/m2 | 1970-01-01 | 2099-12-31 | nan |
| 2000000003 | Output Event | Type Concept | mimiciv_mimic_generated | Meas Type | S | Output Event | 1970-01-01 | 2099-12-31 | nan |
| 2000000004 | Intravenous Bolus | Type Concept | mimiciv_mimic_generated | Drug Type | S | Intravenous Bolus | 1970-01-01 | 2099-12-31 | nan |
| 2000000005 | Intravenous Continous | Type Concept | mimiciv_mimic_generated | Drug Type | S | Intravenous Continous | 1970-01-01 | 2099-12-31 | nan |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 2000001084 | Other|Ascites|Hematology | Measurement | mimiciv_meas_lab_loinc | Lab Test | nan | 51123 | 1970-01-01 | 2099-12-31 | nan |
| 2000001085 | RBC, Ascites|Ascites|Hematology | Measurement | mimiciv_meas_lab_loinc | Lab Test | nan | 51127 | 1970-01-01 | 2099-12-31 | nan |
| 2000001086 | Absolute Lymphocyte Count|Blood|Hematology | Measurement | mimiciv_meas_lab_loinc | Lab Test | nan | 51133 | 1970-01-01 | 2099-12-31 | nan |
| 2000001087 | ADP|Blood|Hematology | Measurement | mimiciv_meas_lab_loinc | Lab Test | nan | 51135 | 1970-01-01 | 2099-12-31 | nan |
| 2000001088 | Arachadonic Acid|Blood|Hematology | Measurement | mimiciv_meas_lab_loinc | Lab Test | nan | 51142 | 1970-01-01 | 2099-12-31 | nan |
100 rows × 9 columns