Biomedical-CaseOLAP-PD/03_run_mesh2pmid.py at main · CaseOLAP/Biomedical-CaseOLAP-PD · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
'''
The purpose of this file is to map MeSH Terms (metadata) to PMIDs
'''
from caseolap._03_mesh2pmid import *


'''
Parameters
'''
### Input
parsed_data_inputfile = "./data/pubmed.json"

### Output
mesh2pmid_outputfile = "./data/mesh2pmid.json"    # {"MeSH Term":[PMID1,...], ...}
mesh2pmid_statfile = "./data/mesh2pmid_stat.json" # {"MeSH Term": #PMIDs, ...}
logFilePath = "./log/mesh2pmid_log.txt"           # Logs mapping progress


'''
Main Code
'''
if __name__ == '__main__':

    # Open log file
    logfile = open(logFilePath, "w")

    # Initialize class
    mesh2PMID = MeSH2PMID()

    # Map MeSH to PMID
    mesh2PMID.mesh2pmid_mapping(parsed_data_inputfile,mesh2pmid_outputfile,logfile)

    # Map MeSH to #PMIDs
    mesh2PMID.mesh2pmid_mapping_stat(mesh2pmid_statfile,logfile)

    # Close log file
    logfile.close()