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
--2024-11-21 12:08:55-- 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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2024-11-21 12:09:20 (431 KB/s) - ‘mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip’ saved [10786504/10786504]
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Create a test instance:
!lamin init --storage ./test-omop --name test-omop --schema omop
→ connected 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.df()
Show code cell output
| concept_name | domain_id | vocabulary_id | concept_class | standard_concept | concept_code | valid_start_date | valid_end_date | invalid_reason | run_id | created_at | created_by_id | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| concept_id | ||||||||||||
| 2000000008 | Labs - Culture Sensitivity | Type Concept | mimiciv_mimic_generated | Meas Type | S | Labs - Culture Sensitivity | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.384799+00:00 | 1 |
| 2000000007 | Labs - Culture Organisms | Type Concept | mimiciv_mimic_generated | Meas Type | S | Labs - Culture Organisms | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.382081+00:00 | 1 |
| 2000000009 | Labs - Hemato | Type Concept | mimiciv_mimic_generated | Meas Type | S | Labs - Hemato | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.379918+00:00 | 1 |
| 2000000003 | Output Event | Type Concept | mimiciv_mimic_generated | Meas Type | S | Output Event | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.377184+00:00 | 1 |
| 2000000005 | Intravenous Continous | Type Concept | mimiciv_mimic_generated | Drug Type | S | Intravenous Continous | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.374340+00:00 | 1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 2000026215 | PRESUMPTIVE PEPTOSTREPTOCOCCUS SPECIES | Observation | mimiciv_micro_organism | Organism | nan | 80233 | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.171899+00:00 | 1 |
| 2000026242 | POSITIVE FOR UREAPLASMA UREALYTICUM | Observation | mimiciv_micro_organism | Organism | nan | 80261 | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.168634+00:00 | 1 |
| 2000026058 | ASPERGILLUS NIGER | Observation | mimiciv_micro_organism | Organism | nan | 80062 | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.166530+00:00 | 1 |
| 2000026098 | SACCHAROMYCES CEREVISIAE | Observation | mimiciv_micro_organism | Organism | nan | 80102 | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.164790+00:00 | 1 |
| 2000026124 | MYCELIA STERILIA | Observation | mimiciv_micro_organism | Organism | nan | 80130 | 1970-01-01 | 2099-12-31 | nan | None | 2024-11-21 12:11:23.163043+00:00 | 1 |
100 rows × 12 columns
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])