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About NetMedEx

NetMedEx

NetMedEx is a Python-based tool designed to extract BioConcept entities (e.g., genes, diseases, chemicals, and species) from Pubtator files generated by Pubtator3. It calculates the frequency of BioConcept pairs (e.g., gene-gene, gene-chemical, chemical-disease) based on co-mentions in publications and generates a co-mention interaction network. These networks can be viewed in a browser or imported into Cytoscape for advanced visualization and analysis.

Getting Started

NetMedEx offers three ways for users to interact with the tool:

  1. Web Application (via Docker)
  2. Web Application (Local)
  3. Command-Line Interface (CLI)