Has part

Overview and Scope of Use

• This relation is used in GO-CAMs but not in standard annotation extensions.
• For protein-containing complex annotations, 'has part' is used in GO-CAM to relate GO protein-containing complexes with their component genes or gene products. Note that in standard annotations, members of a protein complex are captured as a CC annotation using the 'part of' relation.

Ontology Usage Guidelines

In the ontology, 'has part' has been used to capture:

• MFs that are subfunctions of other MFs, such as GO:0003700 'DNA-binding transcription factor activity' has part GO:0000976 'transcription cis-regulatory region binding' and 'polysaccharide immune receptor activity' has part GO:0030247 'polysaccharide binding'.
• MFs that are subfunctions of BPs, such as GO:0061621 'canonical glycolysis' has part 'glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity'

Relations Ontology (RO) term

BFO_0000051 has input

• Note that while this relation is from BFO, it is instantiated in RO.

Current situation

• Ontology: 'has part' is used in the ontology, but that is not satisfactory because 1. relation with the larger term not visible in most tool, and (2) we would need to instantiate the annotations to the 'part' term, since these are not inferred from the GO hierarchy - for eg:
• tx fact act
  • has part DNA binding
• In GO-CAM annotations:
  1. 'has part' is not a causal relation, so in the pathway editor it is not available to link 2 MFs
  2. 'has part' is used to link MF to MF is allowed in Shex and a few models use is (how many? production?)
  3. 'has part' is used to link member components of protein-containing complexes
• Standard annotations
  • not in P2GO
  • may be used in Noctua (to be confirmed)

Proposal

Remove usage of 'has part' in the ontology and in annotations, except for member components of protein-containing complexes

Review Status

Last reviewed:

Reviewed by: