Phylogenetic Annotation Project

Note that this project was formerly called the Reference Genome Annotation Project.

Overview

The Phylogenetic Annotation Project performs annotation inferences across evolutionary related proteins based on known function of proteins within PANTHER [1] phylogenetic family trees.

PAINT (Phylogenetic Annotation and INference Tool)

PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO Phylogenetic Annotation Project to support inference of GO function terms (molecular function, cellular component and biological process) by homology.

Resources for PAINT annotation

PAINT Annotation principles

The PAINT Annotation principles page describes the PAINT annotation guidelines.

PAINT User Guide

The PAINT User Guide provides annotation guidelines for PAINT annotation as well as step-by-step instructions on how to use the PAINT tool.

PAINT trees curation status

The PAINT trees curation status page provides a list of all Panther trees and the history of their curation status.

PAINT Conference Calls

• Monthly, every First Tuesday of the month, 9 AM Pacific/6 PM Europe as of March 2019
• Link to the zoom is in the Google Calendar

• PAINT_Conference_Calls Agendas and Minutes

Reporting bugs or likely errors in the trees

Tree issues

If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues

PAINT issues

Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues

Pantree issues

Issues with the Pantree.org site should be reported at: https://github.com/pantherdb/PanTree

Pages to review

• http://wiki.geneontology.org/index.php/PAINT_annotation_working_group
• reference proteomes files: to be moved elsewhere
• Metrics: Discussion on annotation progress measurements
  • From 2017 Grant, suggestions for metrics:
    • fraction of human proteins in annotated families (PAINT progress)
    • impact: number of annotations added, for human and for other species
  • From a previous grant, see File:HowToCaptureMetrics3.doc
  • Other ideas (to be reviewed): Breath and Depth
    • • http://wiki.geneontology.org/index.php/GO_Reference_Genome_Meeting_Metric_Plan

Archived & retired Pages

Those pages are kept as reference but the information in them is not the most current information.

• Reference Genome Mailing list - disabled
• Electronic jamborees
• Annotation_pipeline By Judy, Suzi, Michael
• Ideas for publicizing Ref.Genome Annotation Data
• PAINT-GONUTS integration
• Reference Genome Annotation Project Summary
• Project timeline
• Reference_Genome Contact Persons from each database
• Reference Genome Progress Reports
• Procedure for selection of _target genes
• Procedure for filling Genome-Specific spreadsheets
• Tools for orthology determination: A summary of tools available to identify orthologs.
• SOP for determining ortholog (by database): The purpose of this page was to discuss the method by which each group establishes orthology between reference genome genes and human disease genes. We now collaborate with PANTHER to provide that. (Issues are different)
• Reference Genome Web Page Draft: We now have a real web page!
• List of potentially problematic families for all vs. all BLAST methods of orthology determination
• Running P-POD orthology tool on the reference genomes gene set by Kara Dolinski at Princeton - Nov2007.
• Reference_Genome_sequence_annotation: GFF3 sequence files for reference genome MODs
• Reference Genome Database Requirements Discussion
• Source_Forge_items_for_reference_genomes_(Retired)
• Reference Genome Publication Counts
• Review_of_trees-based_annotations_(Retired)
• GAF file 2.0 survey of contributing groups
• Reference Genome Software Plan to have some tracking system - supplanted with the db-version of Paint (2017)
• Ref_genome_Annotation_progress_ideas_(Retired)

Past Annotation _targets

• RefG annotation priorities of September 2009
• Lung_branching_morphogenesis_genes December 2009
• All PPOD clusters with at least one object from each of the twelve refG organisms
• _target Gene List: May 2008-Jan 2010
• Tree annotation progress 2010-2011
• RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation__targets: May- Sept 2011
• Wnt_signaling_Pathway June-Sept 2010
• Apoptosis Reference Genome _targets February-April 2011
• PAINT_-_Apoptosis_(Archived)
• PAINT - Apoptosis Nov 2013
• DNA repair family list: http://goo.gl/BaQxMC 2014
• http://dcn.spreadsheets.google.com/ccc?id=o16926456948884040128.4584390909151853752.07000735126025259412.442372083524637957

_target Gene List August 2006-April 2008

• Reference_Genome_Genes_(Retired)
• PAINT_trees_to_review (Retired)

Review Status

Last reviewed: 2021-07-01