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Table 1 Most commonly used relationships for annotation extension statements and examples of their usage

From: A method for increasing expressivity of Gene Ontology annotations using a compositional approach

Contextual relationships Example (gene product; primary GO term; annotation extension)
part_of C. elegans psf-1; nucleus; part_of(WBbt:0006804 body wall muscle cell)
occurs_in Mouse opsin-4; G-protein coupled photoreceptor activity; occurs_in(CL:0000740 retinal ganglion cell)
happens_during S. pombe wis4; stress-activated MAPK cascade; happens_during(GO:0071470 cellular response to osmotic stress)
Molecular relationships Example (gene product; primary GO term; annotation extension)
has_regulation_target Human suppressor of fused homolog SUFU; negative regulation of transcription factor import into nucleus; has_regulation_target(UniProtKB:P08151 zinc finger protein GLI1)
has_input S. pombe rlf2; protein localization to nucleus; has_input(PomBase:SPAC26H5.03 pcf2)
has_direct_input Human WNK4; chloride channel inhibitor activity; has_direct_input(UniProtKB:Q7LBE3 Solute carrier family 26 member 9)
  1. Molecular relations take an entity such as a gene, gene product, complex or chemical as an argument; contextual relations take an entity such as a cell type, anatomy term, developmental stage or a GO term as an argument. Entity names in italics are shown for clarity and are not part of the annotation extension format.