Annotation guidelines for annotating complexes as annotation objects

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Annotation guidelines for annotating Complexes as objects

Since its inception, GO has annotated gene products (i.e. proteins or RNA) as the object of annotation. The GOC has recognized the importance of capturing function and process annotations for macromolecular complexes as objects. This document provides guidelines for annotation complexes.

  1. Column 2 of GAF should have a stable ID of the macromolecular complex. So far IntAct ID or PRO ID are allowed.
  2. Since there is overlap between GO and IntAct complexes, no need to restate that the Intact complex is_a GO complex. It is okay to annotate that the IntAct Complex to CC terms like mitochondrion or cytoplasm or to say that the IntAct complex is a specific type of a generic GO complex. IPI cannot be used for this anntoation since With column is mandatory for IPI. IDA ? Discuss further?
  3. Do not annotate complexes that have been inferred by chemogenomics. IntAct will use ECO terms to prevent export of such complexes.
  4. If IntAct has Exp evidence for a mouse complex and has inferred the complex for human using ISO, should the human complex get GO annotations in MF and BP? It is okay for human complex to get MF/BP but the evidence code should be ISS (may be a new evidence to say the complexes are conserved)