🌐 EcoDermDB User Manual

1. Who Can Use EcoDermDB?

EcoDermDB is designed for researchers in skin microbiome ecology, dermatologists, bioinformaticians, skincare product developers, and anyone interested in skin health and the skin microbiome. Whether you're conducting basic research, working in clinical practice, or developing functional skincare products, EcoDermDB provides rich data resources and visual analysis tools.

2. Website Overview

Website Overview

1. Navigation Bar

The top of the site features a global navigation bar with the following five menu options:

  • Home: Overview and entry point to the database
  • Search: Access the database search modules
  • Download: Download selected datasets
  • User Manual: This guide page
  • About: Background and team introduction

2. About Section

Below the navigation bar is a brief introduction highlighting EcoDermDB's core functions, data structure, and application value.

3. Data Overview

The middle section of the homepage displays the types and sources of data in EcoDermDB, including microbial species, growth conditions, and knowledge graphs. The bottom of the page includes links to related publications and contact information.

3. Search Functions Overview

EcoDermDB offers access to three main search modules from the homepage:

  1. Microbial Phenotype Module
  2. Skin Disease Module
  3. Skin Efficacy Module
Search Modules

4. Microbial Phenotype Module

(1) Global Search

Users can search microbial phenotype data by keywords such as:

  • Microbial genus and species (e.g., Arthrobacter mysorens, Cutibacterium acnes)
  • Microbial products (metabolites) like acetic acid, propionic acid
  • Aerobic/anaerobic classification
  • Growth conditions

Results: The system returns relevant microbes and uses knowledge graphs to show relationships.

The following is a display of search results for Nitrate and Arthrobacter mysorens

Search Results

(2) Advanced Search

This section provides two quick-access links:

  • Browse Microbes: Opens the Microbe Browser
  • Browse Metabolites: Opens the Metabolite Browser

4.1 Microbe Browser (Search for Microbe)

Microbe Browser

Function:

Displays all microbes in EcoDermDB with filtering and sorting options.

Filter fields include:

  • Taxonomy: Phylum, genus, species
  • Ecological traits: Habitat, oxygen preference, temperature, salinity (NaCl), pH
  • Nutritional needs: Carbon source, nitrogen source
  • Metabolic features: Antibiotic response, enzymatic reactions

All filters default to "All" and can be combined. Click Apply Filters (blue button) to update the table or Clear (red button) to reset filters.

Table fields include:

  • Microbe ID (EcoDermDB ID, clickable)
  • Microbe name
  • Taxonomy (phylum, genus, species)
  • Physiological traits (pH, temperature, salinity, oxygen preference)
  • Nutritional requirements
  • Habitat

Supports sorting by name, pH, temperature, salinity, etc.

Navigation:
Click a microbe ID or name to open the MicrobeCard (microbe detail page).

MicrobeCard

MicrobeCard Page Content

Each MicrobeCard includes the following seven sections:

  1. EcoDermDB Record Information
  2. Microbe Identification
  3. Taxonomy
  4. Phenotypic Traits
  5. Growth Conditions
  6. Related Metabolites (displayed via embedded knowledge graph)
  7. Genetic Information

Click the arrow next to each section header to expand or collapse details.

4.2 Metabolite Browser (Search for Metabolite)

Metabolite Browser

Function:

Displays all metabolites associated with microbes in EcoDermDB. Supports filtering and sorting.

Filter fields include:

  • Associated genus or species
  • Metabolite name
  • Common therapeutic uses
  • Related diseases
  • Antibiotic category
  • Enzyme information

Table fields include:

  • Metabolite ID (clickable)
  • Name, molecular formula, structure
  • Physicochemical properties
  • Related microbes
  • Disease associations

Supports sorting by name, associated microbes, or diseases.

Navigation:
Click a metabolite ID or name to open the MetaboliteCard (metabolite detail page).

MetaboliteCard

MetaboliteCard Page Content

Each MetaboliteCard includes the following six sections:

  1. Metabolite Record Information
  2. Metabolite Identification
  3. Physical Properties
  4. Associated Microbes (shown via knowledge graph)
  5. Therapeutic Applications
  6. References

Each section can be expanded or collapsed via the arrow next to its header.

5. Skin Disease Module

On the main disease search page, users can enter disease names, drug names, or targets into the search bar. The system will return related microbes.

Skin Disease Module

Page layout example (e.g., "Acne"):

  • Left panel: Displays disease category, name, type, and ICD-11 code
  • Center panel: Visualizes associated drugs (different colors for each)
  • Right panel: When a drug is selected, shows its detailed treatment info (disease ID, name, drug category)
  • Bottom table: Lists microbes associated with the disease; sortable and linked to MicrobeCard pages
Acne Page Layout

6. Skin Efficacy Module

This module allows users to search by skin function or cosmetic ingredients (e.g., "Anti-aging").

Skin Efficacy Module

Page layout:

  • Left panel: Displays efficacy category info
  • Center graph: Visualizes related cosmetic ingredients (colored by ingredient)
  • Right panel: Clicking an ingredient shows details (name, function, mechanism, INCI name, source)
  • Bottom table: Lists related microbes, sortable and linked to MicrobeCard pages
Efficacy Page Layout