Proposed Developments to the GAF annotation format

• Relationships between annotation objects and ontology terms
  • Easily accomodated using qualifier column
  • For multi-organism processes, the role an organism is playing in a process

• Protein Complex ids as GO annotation objects

• Annotation Extension field, column 16 - Annotation_Cross_Products

• Evidence Code Ontology (ECO)

Developments to the GO annotation line that cannot be captured in the GAF format are explored here: LEGO-style annotation ideas