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Guidelines for annotating transporter activity

Pathway Editor

The activity unit for a transmembrane transporter is:

  • MF: 'enables' a child of transmembrane transporter activity GO:0022857
  • Context:
  • The movement of the small molecule substrate is represented by:
    • small molecule (ChEBI) + ‘input of’ + the start location of the small molecule, captured with the relation 'located in'
    • the transporter activity + ‘has output’ the small molecule (ChEBI) + the end location of the small molecule, captured with the relation 'located in'
  • BP 'part of' the BP in which this transporter activity participates
  • CC 'occurs in' a child of membrane (GO:0016020), e. g.: lysosomal membrane (GO:0005765).

Example: SLC17A9 transports ATP to the lysosomal lumen

Form Editor

The activity unit for a transmembrane transporter is:

  • MF: a child of transmembrane transporter activity GO:0022857
  • Context: The movement of the small molecule substrate is represented by:
  • 'has input’ the small molecule (ChEBI)
  • BP 'part of' the BP in which this transporter activity participates
  • CC 'occurs in' a child of membrane (GO:0016020), e. g.: lysosomal membrane (GO:0005765)

Example: SLC17A9 transports ATP to the lysosomal lumen

Differences between GO-CAM and standard annotation of a transmembrane transporter activity

In standard annotation (captured with the Noctua Form or Protein2GO), the localization of the molecule is not captured; neither is the output of the transporter, since that output relates to the localization of the molecule transported.

Review information

Review date: 2023-07-20

Reviewed by:Cristina Casals, Pascale Gaudet, Patrick Masson