FAQ & Tutorials
Frequently Asked Questions
What is an opportunistic pathogen?
Opportunistic pathogens are microorganisms that typically don't cause disease in people with healthy immune systems but can cause serious infections in individuals with weakened immunity. These pathogens "take advantage" of opportunities such as a compromised immune system, breached barriers (like skin or mucous membranes), or altered microbiota (such as after antibiotic treatment).
How do I search for specific pathogens?
You can search for pathogens using the search box on our home page. Select a category (Organism, Diseases, Genes, Metabolites, or Tissue) from the dropdown menu, enter your search term in the input field dropdown, and click the "Search" button. The results will be displayed in a table format on the search results page.
What information is available for each pathogen?
Our database provides comprehensive information about each pathogen, including:
- Taxonomic classification
- Associated diseases
- Relevant genes
- Metabolic pathways
- Affected tissues
- Interactive network visualizations showing relationships between these elements
What do 🏥 and 🔗 symbols denote?
An organism present in the NHSN organism list is marked with a hospital icon (🏥). (b) An organism represented in the gcPathogen database is marked with a link icon (🔗), which provides direct access to the corresponding gcPathogen entry.
Can I contribute to the database?
Yes, we welcome contributions from researchers and experts in the field. If you have data or information that you believe would enhance our database, please contact us through the Contact Us page. Our team will review your submission and work with you to incorporate valuable additions to the database.
How can I access SigMine for my problem of interest
Write an email to the corresponding author
Tutorials
1. Navigating the Database
Our website features a simple navigation menu at the top of each page, allowing you to easily access different sections:
- Home: The main page with search functionality and featured pathogens
- About: Information about the project and team members
- FAQ/Tutorials: Answers to common questions and guides on using the database
- Contact Us: Form to get in touch with our team
2. Searching the Database
To search for information in our database:
- Go to the Home page
- In the "Search the Database" box, select a category from the dropdown menu
- Enter your search term in the input field
- Click the "Search" button
- View the results in the table on the search results page
3. Viewing Pathogen Information
After performing a search:
- Browse the results table to find the pathogen of interest
- Click the "View Cluster" button in the Action column
- Explore the interactive network visualization showing relationships between the pathogen, diseases, genes, metabolites, and tissues
4. Using Advanced Filters
To narrow down your search results:
- Perform an initial search
- Use the filter options above the results table
- Apply multiple filters to refine your results based on specific criteria
5. Getting Help
If you need assistance while using the database:
- Check this FAQ/Tutorials page for answers to common questions
- Use the Oppa chatbot (bottom-right corner) for immediate help
- Contact our team through the Contact Us page for more complex inquiries
