This project is a part of S2ORC. For S2ORC, we convert PDFs to JSON using Grobid and a custom TEI.XML to JSON parser. That TEI.XML to JSON parser (grobid2json) is made available here. We additionally process LaTeX dumps from arXiv. That parser (tex2json) is also made available here.
The S2ORC github page includes a JSON schema, but it may be easier to understand that schema based on the python classes in doc2json/s2orc.py.
This custom JSON schema is also used for the CORD-19 project, so those who have interacted with CORD-19 may find this format familiar.
Possible future components (no promises):
- Linking bibliography entries (bibliography consolidation) to papers in S2ORC
NOTE: Conda is shown but any other python env manager should be fine
Go here to install the latest version of miniconda.
Then, create an environment:
conda create -n doc2json python=3.8 pytest
conda activate doc2json
pip install -r requirements.txt
python setup.py developThe current grobid2json tool uses Grobid to first process each PDF into XML, then extracts paper components from the XML.
You will need to have Java installed on your machine. Then, you can install your own version of Grobid and get it running, or you can run the following script:
bash scripts/setup_grobid.shThis will setup Grobid, currently hard-coded as version 0.6.1. Then run:
bash scripts/run_grobid.shto start the Grobid server. Don't worry if it gets stuck at 87%; this is normal and means Grobid is ready to process PDFs.
The expected port for the Grobid service is 8070, but you can change this as well. Make sure to edit the port in both the Grobid config file as well as grobid/grobid_client.py.
There are a couple of test PDFs in tests/input/ if you'd like to try with that.
For example, you can try:
python doc2json/grobid2json/process_pdf.py -i tests/pdf/N18-3011.pdf -t temp_dir/ -o output_dir/This will generate a JSON file in the specified output_dir. If unspecified, the file will be in the output/ directory from your path.
If you want to process LaTeX, you also need to install the following libraries:
To process LaTeX, all files must be in a zip file, similar to the *.gz files you can download from arXiv.
A few examples are available under tests/latex/. For example, you can try:
python doc2json/grobid2json/process_tex.py -i test/latex/1911.02782.gz -t temp_dir/ -o output_dir/Again, this will produce a JSON file in the specified output_dir.
To process JATS XML, try:
python doc2json/jats2json/process_jats.py -i test/jats/PMC5828200.nxml -o output_dir/This will create a JSON file with the same paper id in the specified output directory.
The format of S2ORC releases have drifted over time. Use the load_s2orc function in doc2json/s2orc.py to try and load historic and currect S2ORC JSON.
To process PDFs, you will first need to start Grobid (defaults to port 8070). If you are processing LaTeX, no need for this step.
bash scripts/run_grobid.shThen, start the Flask app (defaults to port 8080).
python doc2json/flask/app.pyGo to localhost:8080 to upload and process papers.
Or alternatively, you can do things like:
curl localhost:8080/ -F file=@tests/pdf/N18-3011.pdfIf you use this utility in your research, please cite:
@inproceedings{lo-wang-2020-s2orc,
title = "{S}2{ORC}: The Semantic Scholar Open Research Corpus",
author = "Lo, Kyle and Wang, Lucy Lu and Neumann, Mark and Kinney, Rodney and Weld, Daniel",
booktitle = "Proceedings of the 58th Annual Meeting of the Association for Computational Linguistics",
month = jul,
year = "2020",
address = "Online",
publisher = "Association for Computational Linguistics",
url = "https://www.aclweb.org/anthology/2020.acl-main.447",
doi = "10.18653/v1/2020.acl-main.447",
pages = "4969--4983"
}
Contributions are welcome. Note the embarassingly poor test coverage. Also, please note this pipeline is not perfect. It will miss text or make errors on most PDFs. The current PDF to JSON step uses Grobid; we may replace this with a different model in the future.
Issues: contact [email protected] or [email protected]