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Overview PubMed Integration Sample Management Compound Analysis Batch Processing API Reference Deployment Guide
PubMed Integration
Version 1.0

Scientific Literature Integration

Note: The PubMed integration requires an active internet connection to fetch the latest scientific literature.

Overview

The Mycology Research Pipeline integrates with the National Center for Biotechnology Information (NCBI) PubMed database to provide up-to-date scientific literature related to mycological research. This integration enables researchers to:

  • Automatically fetch relevant research papers for fungal species
  • Associate scientific literature with samples in the database
  • Filter and search through a curated collection of mycology research
  • Export citation data for use in publications

Key Features

Automated Literature Search

The system automatically generates optimized search queries for different fungal species to find the most relevant scientific papers in the PubMed database.

Research Storage

Literature references are stored in the database and associated with relevant samples, allowing for efficient organization and retrieval of research material.

Advanced Filtering

Filter literature by species, publication year, journal, and keywords to quickly find the most relevant research for your work.

Export Capabilities

Export citations in various formats for use in publications, bibliographic software, or research notes.

Using the PubMed Integration

Accessing the Literature Page

The main interface for accessing scientific literature is the Literature page. From here, you can:

  • Browse all literature references in the database
  • Filter references by species, year, and other criteria
  • Perform custom searches
  • Fetch new literature from PubMed

Fetching Literature for a Sample

To fetch scientific literature for a specific sample:

  1. Navigate to the sample details page
  2. Click the dropdown menu in the Compounds section
  3. Select "Update Literature References"
  4. The system will automatically search PubMed for relevant papers based on the sample's species
  5. New references will be displayed in the Scientific Literature section

Custom Literature Searches

To perform a custom search for scientific literature:

  1. Navigate to the Literature page
  2. Scroll down to the "Custom Literature Search" section
  3. Enter your PubMed query using standard PubMed syntax
  4. Select the maximum number of results to return
  5. Optionally associate the results with a sample
  6. Click "Search Literature"
Tips for Effective Searches
  • Use Boolean operators (AND, OR, NOT) to refine your search
  • Include specific terms related to medicinal properties when relevant
  • Use quotes around phrases to search for exact matches
  • Include publication date ranges using [PDAT] field tags
  • Specify article types with [PT] field tags

CMID Research Intelligence Kit Integration

The system includes integration with the Comprehensive Mushroom Intelligence Dashboard (CMID) Research Intelligence Kit, which provides pre-curated scientific literature and compound information for medicinal mushrooms.

Importing CMID Data

The CMID data can be imported using the provided import script: 

python import_research_kit.py -v

This script will import species information, compound data, and literature references from the CMID Research Kit into the Mycology Research Pipeline database.

Command-line Interface

For batch operations and automation, you can use the provided command-line tool: 

python fetch_mycology_literature.py -e your.email@example.com

For more options and information, run: 

python fetch_mycology_literature.py --help

API Access

The PubMed integration functionality is also available through the API for programmatic access. See the API Testing page for more information on how to use these endpoints.

Current Limitations

  • PubMed imposes rate limits on API requests, which may affect bulk operations
  • Abstract retrieval requires additional API calls and may not be available for all articles
  • The system currently does not support full-text retrieval for papers
  • Citation export is limited to CSV and JSON formats

Future Enhancements

  • Integration with additional scientific databases (Scopus, Web of Science)
  • Full-text retrieval for open access articles
  • Natural language processing for more intelligent search and filtering
  • Citation network visualization
  • Additional export formats (BibTeX, RIS)