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README.md

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What these file?

To extract the gene name using API in PubTator:

  • PubTator_read.py is reading gene name from "Export Annotations".
  • PubTator_submit.py is transforme pdf into json,then submit json to API.
  • PubTator_retrieve.py is retrieve what has handled json by a session number.
  • pdf_file was used storage your upload pdf.

How to use it?

Export Annotations

  1. run it in command line
python PubTator_retrieve.py
  1. Input your need format, type, identifiers in order
  2. then gene name output in the gene_name.csv

Submit your pdf

  1. Taking your all pdf into pdf_file" (this step is important)
  2. run it in command line
python PubTator_submit.py
  1. All successful submit was storage into SessionNumber.txt

Retrieve your upload file

  1. run it in command line
python PubTator_retrieve.py
  1. All gene name was taked into the gene_name.csv