Appendix

• Glossary
  • Short Reads and BAM
  • Genetic variants and VCF
• Use of Ontologies in GA4GH API
  • Examples for OntologyTerm use
    • Why should we use an ontology term?
    • Ontology Lookup Service
    • What is the minimum attribute requirement for OntologyTerm in GA4GH?
    • Ontology Selection and Overlap
  • Examples
    • Genotypic sex
    • Sequence Ontology
    • Human Phenotype ontology
    • Body part (Uberon)
    • Human disease ontology
    • Experimental factor ontology
    • Unit Ontology
• The JSON Format
  • GA4GH JSON Serialization
  • Serialization example
• Google Protocol Buffers
  • What does the GA4GH web API take from Protocol Buffers?
  • How does the GA4GH web API use Protocol Buffer schemas?
  • How does the GA4GH Web API use Protocol Buffers?
• Code samples (stub)
• Generating API Definitions
  • Installing Prerequisites
  • Compiling Swagger Documentation
  • Using Generated Definitions