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

2. Input your need format, type, identifiers in order
3. 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

3. All successful submit was storage into SessionNumber.txt

Retrieve your upload file

1. run it in command line

python PubTator_retrieve.py

2. All gene name was taked into the gene_name.csv