SciMiner Legacy (v1.1)

Enhanced Perl/CGI biomedical literature mining tool with modernized web interface.

Overview

SciMiner 1.1 is the enhanced version of the original SciMiner text mining tool. It provides dictionary- and rule-based biomedical literature mining for target identification and functional enrichment analysis from PubMed literature.

Live: https://hurlab.med.und.edu/SciMiner1.1/

What's New in v1.1 (vs Classic)

• Security: Bcrypt password hashing (with legacy fallback for migration)
• Deployment: Tomcat CGI servlet (vs Apache httpd)
• Configuration: Centralized Config.pm with environment variables
• Logging: Structured Logger.pm (DEBUG/INFO/WARN/ERROR)
• UI: Modernized responsive interface with topbar navigation
• Testing: 8-test Perl test suite

Features

• PubMed full-text and abstract mining
• Gene/protein target identification via dictionary and rule-based NLP
• Functional enrichment analysis:
  • Gene enrichment (Fisher's exact test)
  • Gene Ontology (GO) enrichment
  • MeSH term enrichment
  • Pathway enrichment (KEGG, Reactome)
  • Protein-Protein Interaction (PPI) network analysis
• Query comparison and merging
• Interactive network visualization (Cytoscape.js)
• EndNote citation export

Tech Stack

Component	Technology
Backend	Perl 5.38, CGI::Application
Database	MySQL 8.0 (shared with Classic)
Templates	HTML::Template
Auth	Bcrypt (Crypt::Eksblowfish::Bcrypt)
Network Viz	Cytoscape.js 3.30
Web Server	Apache Tomcat 9.0 (CGI servlet) + Nginx
Frontend	HTML5, CSS3 (custom sciminer-modern.css)

Directory Structure

SciMiner1.1/
├── index.html                    # Landing page
├── css/sciminer-modern.css       # Modern stylesheet
├── favicon.svg                   # Shared favicon
├── WEB-INF/
│   ├── web.xml                   # Tomcat CGI servlet config
│   └── cgi/                      # CGI scripts and templates
│       ├── *Launch.cgi           # Entry points (login + content)
│       ├── *.cgi                 # Processing scripts
│       ├── *Index.tmpl           # Login/wrapper templates
│       ├── *.tmpl                # Content templates
│       ├── shared_header.tmpl    # Topbar navigation
│       ├── shared_footer.tmpl    # Footer with version links
│       ├── SciMinerUI.pm         # Perl module for topbar/footer
│       ├── MinimalApp*.pm        # CGI::Application modules
│       └── sciminer.js           # Client-side JavaScript
├── SciMiner/                     # Public static files
│   ├── Images/                   # UI icons and logos
│   ├── Files/                    # User manual, supplementary files
│   ├── Samples/                  # Sample query results
│   ├── intro2.html               # Introduction page
│   ├── contact2.html             # Contact page
│   └── download.html             # Download page
├── annotation/SciMinerDB/        # Backend data and config
│   ├── annotationENV.ini         # Configuration (not in repo)
│   ├── Modules/Annotation/       # Core Perl modules
│   │   ├── SciMiner.pm           # Main mining engine (~32K lines)
│   │   ├── Config.pm             # Configuration management
│   │   ├── SciMinerSecurity.pm   # Bcrypt authentication
│   │   └── Logger.pm             # Structured logging
│   └── Scripts/                  # Utility scripts
├── scripts/                      # Setup and migration scripts
└── t/                            # Perl test suite

Setup

Prerequisites

• Perl 5.38+
• MySQL 8.0+
• Apache Tomcat 9.0+ (with CGI servlet enabled)
• Nginx (reverse proxy)

Required Perl Modules

cpan install CGI CGI::Application CGI::Session HTML::Template
cpan install DBI DBD::mysql
cpan install LWP::UserAgent JSON XML::LibXML
cpan install Crypt::Eksblowfish::Bcrypt
cpan install Spreadsheet::WriteExcel Boulder::Medline Text::NSP

Configuration

# Copy template and configure
cp annotation/SciMinerDB/annotationENV.template.ini annotation/SciMinerDB/annotationENV.ini
chmod 600 annotation/SciMinerDB/annotationENV.ini
# Edit with your database credentials and paths

Tomcat Configuration

The WEB-INF/web.xml configures the CGI servlet. Ensure Tomcat has:

• privileged="true" in the Context configuration
• Perl installed at /usr/bin/perl

Database

SciMiner 1.1 shares the sciminer MySQL database with Classic. Key tables:

• user — User accounts (with password_hash for bcrypt)
• query — Mining queries and results
• analysis — Enrichment analysis results

Adding columns (like password_hash) does not affect Classic's functionality.

Other Versions

Version	Description	URL
Classic	Original Perl/CGI (stable)	/SciMiner/
v1.1	Enhanced Perl/CGI with modern UI	/SciMiner1.1/
v2.0	Python/React platform (development)	/SciMiner2.0/

Citation

Hur J, Schuyler AD, States DJ, Feldman EL: SciMiner: web-based literature mining tool for target identification and functional enrichment analysis. Bioinformatics 2009, 25(6):838-840.

License

Developed by Hur Lab, University of North Dakota School of Medicine & Health Sciences.