SciKnowMine Web Application

The SciKnowMine system is a practical, open-source, text-mining-enabled digital library system for knowledge workers in biomedicine (including students, scientists, biocurators, doctors, etc.).

View on GitHub BMKEG

The Biomedical Knowledge Engineering Research Group (BMKEG) is part of the Intelligent Systems Division at the University of Southern California's Information Sciences Institute

Welcome to the SciKnowMine Technical Documentation.

The system is intended to provide an intuitive computational interface for the academic literature that supports practical high-level functions (document triage, clustering, information extraction, etc.), provides a development and deployment environment for computer science (CS) systems, libraries and solutions. Our initial deployment is focused on applying standard supervised machine learning techniques to document triage supporting the Mouse Genome Informatics Biocuration team at the Jackson Laboratory.

This website provides evolving, dynamic technical documentation for the SciKnowMine project in the form of different manuals, published as static evolving online blogs. This will evove and develop over time as we develop the system and its capabilities.

  1. Installation Manual
  2. System Organization
  3. Command Line - Set up
  4. Command Line - Working with Data
  5. Command Line - Reporting Functions
  6. Command Line - Deleting Data
  7. Command Line - Machine Learning
  8. Command Line Tools - Running Experiments
  9. Web Application - Running the System
  10. Web Application - Extracting text using LAPDF-Text
  11. Web Application - Performing the triage task
  12. Web Application - The Base Digital Library

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