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PubMed_DDI: identifying drug-drug interaction related information from PubMed literature

Version 2 2017-03-01, 22:19
Version 1 2017-03-01, 22:16
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posted on 2017-03-01, 22:19 authored by Feng ChengFeng Cheng
PubMed_DDi: identifying drug-drug interaction related information from PubMed literature

The process of the application is classified into three modules: 
Module 1: downloading DDI related substances, 
Module 2: random sampling and p-value calculation, and 
Module 3:exporting the significant compound and protein terms. 
Module 1 is performed in step 1 and Modules 2 and 3 are performed in step2. 
The detailed commands to compile and execute source code are as follows:
Here, we use Ibuprofen as an example.
1. Module 1
        python step_1_download_Substance.py drugNameList_original para.txt
In this step, please make sure that the Biopython package is installed.
        There are five output files which are:
ibuprofen_PMID_Substances.txt
ibuprofen_result_1_compounds.txt (DDI-related)
ibuprofen_result_1_proteins.txt (DDI-related)
ibuprofen_result_2_compounds.txt (DDI-unrelated)
ibuprofen_result_2_proteins.txt (DDI-unrelated)

2. Modules 2 and 3
In this step, please make sure that the scipy and numpy packages are installed.
Run the python script:
python step_2_randomSampling_pValue_output.py ibuprofen_result_1_compounds.txt ibuprofen_result_2_compounds.txt ibuprofen_result_1_proteins.txt ibuprofen_result_2_proteins.txt para.txt "Ibuprofen"

There are four output files containing the compounds and proteins information for Ibuprofen related DDI which are:
Ibuprofen_temp_result1_Substance_compounds_cutoff_1.txt
Ibuprofen_temp_result1_Substance_compounds_cutoff_1_p_0.1.txt
Ibuprofen_temp_result1_Substance_proteins_cutoff_1.txt
Ibuprofen_temp_result1_Substance_proteins_cutoff_1_p_0.1.txt

Funding

the Ed and Ethel Moore Alzheimer's Disease Research Program of Florida Department of Health (Award No: 7AZ23) to Feng Cheng

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