Get started

Prepare virtual environment

$ cd path/to/PMCFigureX
$ git clone https://github.com/yfpeng/PMCFigureX.git
$ cd path/to/PMCFigureX
$ virtualenv -p python3 /path/to/venv
$ source /path/to/venv
$ pip -r requirements

Download pre-trained models

1. Download pre-trained model for figure separation at https://github.com/apple2373/figure-separator
2. Donwload the CXR/CT classifier at https://github.com/ncbi-nlp/COVID-19-CT-CXR/releases/tag/v20200610

Prepare source file

1. Go to https://pubmed.ncbi.nlm.nih.gov/
2. Search disease. For example Atelectasis [all_field]. Note: PubMed will automatically find synonyms of atelectasis, e.g., "pulmonary atelectasis"[MeSH Terms] OR ("pulmonary"[All Fields] AND "atelectasis"[All Fields]) OR "pulmonary atelectasis"[All Fields] OR "atelectasis"[All Fields]
3. On the left, click "Free full text"
4. Click "Save" and choose the "CSV" format: /path/to/Atelectasis.export.csv

Convert PubMed export file

$ python figurex_db/convert_pubmed_search_output.py \
    -s /path/to/Atelectasi.export.csv \
    -d /path/to/Atelectasi.export.tsv

Run the script

Change the paths in run_keys_db.sh

disease='Atelectasis'
source_dir=$HOME'/path/to/PMCFigureX'
venv_dir=$HOME'/path/to/venv'
top_dir=$HOME'/path/to/Atelectasi.export.tsv'

$ bash run_keys_db.sh step1 step2 step3 step4 step5 step6 step7 step8

The output is at /path/to/Atelectasis.figure_text.json

Acknowledgments

This work was supported by NLM under award number 4R00LM013001 and the Intramural Research Programs of the National Institutes of Health. It was als supported by the Google COVID-19 Research Grant.