Workflow for ScreenIT usign softcite

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.