This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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GAFs output from PAINT need to conform to GAF spec 2.1 #49
Currently, the rest of the pipeline is using GAF 2.1, whil PAINT is apparently still using 2.0.
The closure of this issue would be either
This is either and enhancement or bug depending on which of the above it is.