OMOP DB Population Simulation
A class for interacting with a test database using OMOP standard. It provides access to person, observation, and measurement data.
1"""
2A class for interacting with a test database using OMOP standard. It provides access to person, observation, and measurement data.
3"""
4from biomodel.database import OMOP_DB
5from biomodel.models import Framingham
6from biomodel.biomodel import OMOPId
7from pathlib import Path
8
9if __name__ == '__main__':
10 data_path = Path("/home/josalhor/Desktop/bioTwin/data/ukbiobank-simulation")
11
12
13 class TestDB(OMOP_DB):
14 """
15 A class for interacting with a test database using OMOP standard. It provides access to person, observation, and measurement data.
16 """
17
18 person_path = data_path / "person.csv"
19 observation_path = data_path / "observation.csv"
20 measurement_path = data_path / "measurement.csv"
21
22
23 coltot = OMOPId(4224820)
24 hdl = OMOPId(4011133)
25 tas = OMOPId(4152194)
26 tad = OMOPId(4154790)
27 smoke = OMOPId(1585856)
28 diab = OMOPId(35817874)
29
30 db = TestDB()
31 model = Framingham()
32
33 prediction = model.predict_population_time(
34 db,
35 {
36 "No smoke": {smoke: 0},
37 "No smoke & CH control": {smoke: 0, coltot: 180, hdl: 50},
38 "Full control": {
39 coltot: 180,
40 hdl: 50,
41 tas: 125,
42 tad: 80,
43 smoke: 0,
44 },
45 },
46 )
47
48 prediction.show_change()
