/cytreg

This repository contains the python scripts used to retrieve PubMed articles containing at least a combination of a TF, a cytokine, and an assay. Additionally has the cytokine and TF name lists used to query PubMed.

Primary LanguagePython

CytReg

This repository contains the python scripts used to retrieve PubMed articles containing at least one combination of a TF, a cytokine, and an assay. Additionally has the cytokine and TF name lists used to query PubMed.

Description of Files

  • nih_eutils_defs.py
     holds definitions of assays and functions to create the TF and cytokine dictionaries
  • nih_eutils_tf_pmid.py
     downloads PubMed articles XLM files containing at least a TF, cytokine and assay
  • post_process_pmids.py
     extracts all TF, cytokine and assays found in a given XML file  

Usage

  1. nih_eutils_tf_pmid
    python nih_eutils_tf_pmid.py tf_names.txt cyt_names.txt output_directory

  2. post_process_pmids.py
    python post_process_pmids.py -xml ../xml_directory -tf_list tf_names.txt cyt_names.txt -match xml -ofile output_file -a