osm

OpenSciMetrics

OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.

Dashboard

The Open Science Metrics Dashboard visualizes data sharing and code sharing trends across biomedical research funders and journals, based on analysis of PubMed Central publications.

Live Dashboard: https://www.opensciencemetrics.org

Features

• Splitting Variables: View trends by Journal or Funder
• Presets: Quick selection of top journals/funders by data sharing count or percent
• Aggregation Metrics: Data Sharing %, Code Sharing %, article counts
• Interactive Charts: Toggle individual lines, hover for details
• Year Range Filter: Focus on specific time periods (default: 2010-2024)

CLI Tool (Legacy)

The repository also contains a command line tool for processing individual PDFs and XMLs. Note: This tool is not currently being actively maintained.

With docker-compose and python >=3.11 installed:

pip install .
osm -f path/to/pdf-or-xml -u uuid

For processing many files, start docker-compose dependencies separately:

docker compose up  # In one terminal
osm -f path/to/pdf-or-xml -u uuid --user-managed-compose  # In another terminal

Contributing

To set up a development environment:

pip install -e .
docker compose -f compose.yaml -f compose.development.override.yaml up --build

In another terminal:

export OSM_API="http://localhost:80"
osm -f path/to/pdf-or-xml -u uuid --user-managed-compose

Pre-commit Hooks

Pre-commit runs checks on every commit. To install:

pip install pre-commit
pre-commit install

Apple Silicon Notes

On Apple silicon, you must use emulation:

export DOCKER_DEFAULT_PLATFORM=linux/amd64
docker pull mongo:4.4.6

Note: PDF parsing does not work on Apple silicon.

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