Documentation
Overview PubMed Integration CMID Research Kit Sample Management Compound Analysis Batch Processing API Reference Deployment Guide
CMID Research Intelligence Kit
Version 2.0

Comprehensive Mushroom Intelligence Dashboard Integration

Note: The CMID Research Intelligence Kit is included with your installation and provides pre-curated data on medicinal mushrooms.

Overview

The Comprehensive Mushroom Intelligence Dashboard (CMID) Research Intelligence Kit is a specialized collection of pre-curated data on medicinal mushrooms, their compounds, and associated research literature. This integration enhances the Mycology Research Pipeline with validated, high-quality research data that can be used as a foundation for your own investigations.

What's Included in the Kit

Species Information

Detailed information on key medicinal mushroom species, including taxonomic classification, common names, and basic biological properties.

Compound Data

Chemical compound information, including molecular structures, bioactivity profiles, and known medicinal properties.

Research Citations

Curated research citations from peer-reviewed journals, linked to PubMed records for further exploration.

Data Files Included

File Name Description Records
CMID_v2_Expanded_Species.csv Comprehensive species information 50+
CMID_v2_Compound_Structure_Matrix.csv Compound chemical structures and properties 200+
CMID_v2_PubMed_Citations.csv Curated PubMed citations 500+
CMID_v2_Bioactivity_Profiles.csv Bioactivity measurements for compounds 150+
CMID_v2_Traditional_Uses.csv Historical and traditional usage information 100+

Using the CMID Data

The CMID Research Intelligence Kit is automatically integrated with the Mycology Research Pipeline, making the data available throughout the platform. You can:

  • Browse pre-loaded species information in the Samples section
  • View compound data and molecular structures in the Compound Analysis tools
  • Access curated citations in the Literature section
  • Use the data as a baseline for comparison with your own research results

Importing CMID Data

The CMID Research Intelligence Kit comes pre-installed with the Mycology Research Pipeline. To import or update the data, you can use the provided import script: 

python import_research_kit.py -v

This command will import all the data from the kit into your database, creating or updating records as appropriate. The script is designed to be idempotent, so running it multiple times will not create duplicate records.

Import Options

The import script provides several options for customizing the import process:

  • -v, --verbose: Display detailed information during import
  • --species-only: Import only species data
  • --compounds-only: Import only compound data
  • --citations-only: Import only citation data
  • --force: Force overwrite of existing records

Extending the CMID Dataset

The CMID Research Intelligence Kit is designed to be extensible. You can add your own data to complement the pre-curated information:

  1. Add New Species: Create new species entries in the system, following the same data structure as the CMID species.
  2. Add New Compounds: Add your own compound data, linking it to appropriate species and including molecular structure information.
  3. Add Citations: Use the PubMed integration to add relevant research papers to the system, which will be included alongside the CMID citations.

Data Sources

The CMID Research Intelligence Kit data is compiled from multiple authoritative sources:

  • Peer-reviewed scientific publications
  • Mycological research databases
  • Taxonomic authorities
  • Chemical compound databases
  • Traditional medicine references

Attribution and Licensing

The CMID Research Intelligence Kit is developed by Michael Crowe and is included with the Mycology Research Pipeline under the following terms:

  • The data may be used for research and educational purposes
  • Any publications using the data should cite "Crowe Logic CMID Research Intelligence Kit v2.0"
  • Commercial use requires a separate license, please contact for details

Updates and Versions

The CMID Research Intelligence Kit is updated periodically with new data and corrections. Your installation includes version 2.0, released in 2025.

To check for updates, visit: https://www.mycology-research-pipeline.org/cmid-updates