To enable comparisons of software mention extraction, we have a shared list of DOIs:
This repo uses that shared list of PMCIDs, runs a full crawl, grobid conversion, extraction, and an export to a csv file (one row per mention).
The repo is setup to run via docker-compose:
docker-compose up
The software-mention server is run (from a docker image) and listens on port 8060.
The software-mention client is built using the Dockerfile. Connect to the software-mention client using:
docker exec -it client_software_mentions /bin/bash
Run the pipeline with:
cd workspaces
python3 screen_it_pipeline.py
The .devcontainer folder also contains a setup that works using dev containers on vscode.