Help & Development

Getting Help

If you need assistance with any prismAId tool, you can:

• Open an Issue on our GitHub repository.
• Discuss in the Matrix Support Room: prismAId Support Room .
• Stay Updated with New Releases: Follow the prismAId Announcements Room for the latest updates and release notifications.

Common Issues

General Issues

• Path Problems: Most crashes occur due to incorrect paths in configurations, such as typos or non-existent directories.
• API Keys: These may be loaded either through system variables or directly in configurations. When both are provided, the configuration values take priority.
• Software Bugs: For troubleshooting software issues, submit an issue on the GitHub repository.
• Feature Requests: To submit requests for new functionalities, participate in GitHub Discussions.

Download Tool Issues

• Zotero Authentication Errors: Verify your user ID and API key, ensuring the API key has appropriate permissions.
• Collection Not Found: Check that the collection/group path uses the correct format and exists in your Zotero library.
• Download Failures: If some PDFs fail to download, check if they are actually available/accessible in your Zotero library.

Convert Tool Issues

• Conversion Quality: PDF conversion may result in imperfect text extraction due to limitations of the PDF format. Always check converted files.
• Unsupported Formats: Ensure you’re using supported file formats (PDF, DOCX, HTML).
• Character Encoding: Some converted texts may display encoding issues with special characters.

Review Tool Issues

• Debugging Information: Control the level of debugging information via the log_level parameter in the project configuration.
• Partial Results: If only the first few entries of a review are processed, check the Token Per Minute (TPM) limits in your configuration.
• Response Format Errors: Ensure your prompt and review sections are well-structured to guide the AI to produce correctly formatted outputs.
• Token Limits: Very large documents may exceed model token limits; consider splitting or summarizing them.

Contributing

How to Contribute

We welcome contributions to improve any aspect of the prismAId toolkit, whether you’re fixing bugs, adding features, or enhancing documentation:

• Branching Strategy: Create a new branch for each set of related changes and submit a pull request via GitHub.
• Code Reviews: All submissions undergo thorough review to maintain code quality.
• Community Engagement: Connect with us through GitHub issues and discussions for feature requests, suggestions, or questions. - Discuss in the Matrix prismAId Support Room or follow the prismAId Announcements Room for the latest updates and release notifications.

Guidelines

For detailed contribution guidelines, see our CONTRIBUTING.md and CODE_OF_CONDUCT.md.

Software Stack

prismAId is developed in Go, selected for its simplicity and efficiency with concurrent operations. We prioritize the latest stable Go releases to incorporate improvements.

Technical Foundation

prismAId leverages the alembica pure Go package to manage interactions with Large Language Models. This foundation allows us to concentrate on developing robust protocol-based information extraction tools while alembica handles the standardized communication with various LLMs through consistent JSON data schemas, ensuring reliability and interoperability across different AI services.

Toolkit Architecture

The prismAId toolkit is structured as a set of modular tools (Download, Convert, Review) that can be used together or independently:

• Go Module: Core logic and API access for all tools are implemented in Go.
• Cross-Language Support: Each tool is accessible through:
  • Python Package: Python wrapper around a C shared library compiled from the Go code.
  • R Package: Contains a C shared library with an intermediate C wrapper, enabling R interaction.
  • Julia Package: Contains a C shared library with Julia bindings for direct integration.
• Self-Contained Binaries: Simplifies setup by packaging all dependencies within the binaries.
• Cross-Platform Compatibility: Fully operational across Windows, macOS, and Linux.

Development Philosophy

• Modularity: Tools that work together but can be used independently.
• Open Source: We value community contributions and transparency.
• CI/CD Pipelines: Automated testing and deployment maintain quality and reliability.

Open Science Support

prismAId actively supports Open Science principles through:

1. Transparency and Reproducibility
   • prismAId enhances transparency, making analyses understandable and reproducible, with consistent results across systematic reviews.
   • Detailed logs and records improve reproducibility.
2. Accessibility and Collaboration
   • An open-source, openly licensed tool fostering collaboration and participation.
   • Long-term accessibility through Zenodo.
3. Efficiency and Scalability
   • Efficient data handling enables timely, comprehensive reviews.
   • Modular tools allow flexible workflows adapted to different research needs.
4. Quality and Accuracy
   • Explicit prompts define information clearly, ensuring consistent, reliable reviews.
   • Separate tools for each workflow step improve focus and quality.
5. Ethics and Bias Reduction
   • Transparent design minimizes biases, with community oversight supporting ethical standards.
6. Scientific Innovation
   • Standardized, reusable methods facilitate innovation, cumulative knowledge, and rapid knowledge dissemination.