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The Gene Ontology Consortium launched the GO-PAINT project (PhylogeneticAnnotation and INference Tool) 9 years ago and is currently being used in theGO Reference Genome Annotation Project to support inference of GO functionterms (molecular function, cellular component and biological process) byhomology. PAINT uses a phylogenetic model to infer gene function by homology, aprocess that requires manual curation of experienced biocurators. Tremendousamount of time and efforts have been spent on the GO-PAINT project yieldingmore than 4000 fully annotated phylogenetic families with more than 170,000annotations. These preliminary data have thus enabled potential algorithmicrepresentation and automatic solvation of the additional 9000 unannoatedphylogenetic families. Here we present an automated pipeline for phylogeneticannotation and inference, which simulates the standard annotation procedures ofcurators and models the curators' decisions during the manual curation process.The pipeline has been built into the newest version of PAINT software availableat http://www.pantherdb.org/downloads/index.jsp. The standalone automationpipeline and datasets are available athttps://github.com/haimingt/GO-PAINT-automation

Automation of gene function prediction through modeling human curators' decisions in GO phylogenetic annotation project