2. Tutorials

The tutorials go deeper than the Quick Start: each one focuses on a specific service or use-case and shows realistic, end-to-end workflows.

• KEGG — pathway retrieval, KGML parsing, and gene/compound look-up

• BioModels — searching and downloading curated SBML models

• Protein — combining multiple services to profile a single protein

• Compound — exploring chemical entities via ChEBI, ChEMBL, and Rhea

• Convertor — ID mapping across databases

• BioMart — building queries and retrieving genomic data

Contributions of new tutorials are welcome.

• 2.1. KEGG Tutorial
  • 2.1.1. Introduction
  • 2.1.2. Searching for an organism
  • 2.1.3. Look for pathways (by name)
  • 2.1.4. Look for pathway (by genes i.e., IDs or usual name)
  • 2.1.5. Introspecting a pathway
  • 2.1.6. Building a histogram of all relations in human pathways
• 2.2. Biomodels tutorial
• 2.3. Protein test case study
  • 2.3.1. Get a unique identifier and gene names from a name
  • 2.3.2. Getting the fasta sequence
  • 2.3.3. Using BLAST on the sequence
  • 2.3.4. Searching for relevant pathways
  • 2.3.5. Searching for binary Interactions
  • 2.3.6. What’s next ?
• 2.4. Manipulating compound identifiers
  • 2.4.1. Retrieve a compound identifier from KEGG, ChEBI and ChEMBL
• 2.5. Mapping identifiers
  • 2.5.1. Convert from KEGG ID to ChEBI (compound)
  • 2.5.2. convert from KEGG ID to UniProt and vice versa (gene)
• 2.6. BioMart service