PAINT Annotation Update Huaiyu Mi for the PAINT

PAINT Annotation Update Huaiyu Mi for the PAINT Annotation Working Group GO Consortium Meetinbg March 16, 2014

Phylogenetic annotation • Integrate and review all experimentally-supported GO annotations for all genes in a gene family – QA of experimental annotations – QA of ontology • Annotate the phylogenetic tree with terms – Model of the evolution of function – Rules for how annotations should be “propagated” to homologous genes • Principled annotation of millions of genes that will never be assayed by experiment but are homologous to an experimentally assayed gene in another system • Fuller, richer and more relevant annotation of genes even in wellcharacterized organisms

IBA: Use multiple pieces of evidence in a phylogenetic tree Integration of experimental GO annotations Inheritance of inferred ancestral annotations to annotate extant genes (automatic) from different models (curated) Gaudet P et al. Brief Bioinform 2011; 12: 449 -462

Annotation comparison Gaudet et al. Briefings in Bioinformatics 2011

PAINT Annotation Software • Can be downloaded from the sourceforge: http: //sourceforge. net/projects/pantherdb/ • Is reaching a relatively stable status. • A web version of PAINT (js. PAINT) is being developed.

PAINT Annotation • A committed group of members participated in the annotation efforts. • Regular bi-weekly meetings. • PAINT User Guide expanded – http: //wiki. geneontology. org/index. php/PAINT_U ser_Guide

Resources • A wiki page for the working group: http: //wiki. geneontology. org/index. php/PAINT_annotation_working_group – Conference call minutes. – PAINT annotation user guide. – Annotation updates.

PAINT Curation Progress • 168 families have been annotated in PAINT (can be downloaded from PAINT svn). • 119 K annotations • Thru June 2013 – Re-annotation of PAINT families. • November-Feb – Apoptosis family annotations. • Current – DNA replication and repair

What have we learned • While literature curation allows a curator to annotate one or few genes at a time in great detail, PAINT curation provides a overview of the entire family across different species through an evolutionary view. • It is a great way to review and validate annotations, and identify mistakes at the same time.

PAINT Working Group Curation • Rama Balakrishnan • Karen Christie • Pascale Gaudet • Ranjana Kishore • Donghui Li • Huaiyu Mi • Monica Munoz-Torres • Li Ni • Paul Thomas Software • Suzanna Lewis • Anushya Muruganujan