Phylogenetic Annotation Project

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Goal of the Reference Genome Annotation Project

The GO consortium has established the complete annotation of 12 reference genomes as a priority goal. These reference genomes are:

Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Dictyostelium discoideum, Drosophila melanogaster, Escherichia coli, Gallus gallus, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Schizosaccharomyces pombe

The Reference Genome GO Annotation Team, with representatives from each genome annotation group, will coordinate annotation, facilitate implementation of GO Consortium annotation priorities, provide metrics to assess progress toward the goal of broad and deep annotation of the reference genomes. This group will be responsible for the coordination of the annotation of the twelve reference genomes. This group represents the annotation expertise within the GO consortium and provides key liaisons to the model organism databases the have primary responsibilities for the annotation of the reference genomes.

More information

Reference Genome Annotation Project Summary

Reference_Genome Contact Persons from each database

Progress Reports

  • April 20, 2008 Second Reference Genome Annotation Meeting, Salt Lake City, UT [Minutes]
  • Sept 27, 2007: First Reference Genome Annotation Meeting, Princeton, NJ [Minutes]


Reference Genome Mailing list

Conference Calls


Electronic jamborees

Annotation Targets

Panther gene lists

From May 2008

Target Gene List (May 2008-)

Target Gene List August 2006-April 2008

  • Access requires your email to be added to the system. Email Pascale if you would like to be added.
  • This spreadsheet contains links to separate spreadsheets maintained by each of the reference genome groups.

Procedure for selection of target genes

Procedure for filling Genome-Specific spreadsheets

Gene Annotation

GAFs for trees-based annotations

Standard Operating Procedure for Tree-based propagation of annotations


By Judy, Suzi, Michael

Annotation Quality control

Annotation Consistency Issues

Improving GO terms and definitions

Misused terms

This page provides a list of often misused terms and (hopefully) an explanation as to how to use the term properly. This information should also be included in the 'comments' of the OBO file.


  • This page describes how each database handles curation of multiple forms of the same gene

Providing annotations to GOA in taxa other than you MOD's

  • Please follow these instructions if you encounter a gene not from your database that you need to annotate.

Gene Annotation wiki pages

  • The purpose of these pages are to allow discussions of annotation and orthology issues related to particular genes. The individual gene pages are to be created as needed.

Annotation Progress

Lung Development related Gene Annotation Progress

Graphical views of the annotations:

Selected refG target sets

  • PPOD clusters selected since April 2008
  • Manually curated target sets selected before April 2008

All PPOD clusters with at least one object from each of the twelve refG organisms

Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Orthology determination

List of potentially problematic families for all vs. all BLAST methods of orthology determination

Data used to make orthology calls

reference proteomes files

At the July 2009 Quest for Orthologs meeting, it was agreed to decide upon a standard set of genomes, and compile "complete" sets of protein coding genes for each genome, and a representative protein sequence for each gene.

New gene2geneproduct file

At the April 2009 Reference Genome meeting it was decided to create a new file to replace the GP2protein file, called 'gene2geneproduct'. Specifications can be found on this page (will be added soon).

GAF file 2.0

The GAF file should contain 17 columns, and the meaning of columns 2, 12 and 17 have been modified. See that page for specifications.

Data used for Running P-POD orthology tool on the reference genomes gene set

by Kara Dolinski at Princeton - Nov2007

  • This page contains a description of the project and the requirements for providing files for the P-POD analysis.

GFF3 sequence files for reference genome MODs


Software/database development

The purpose of this page is to discuss features and requirements that would be desirable in a database used to replace the existing Google Spreadsheet system for managing target genes, their annotations and metrics.

Branding Ref.Genome Project

Ideas for publicizing Ref.Genome Annotation Data

Retired Pages

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

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 and POPOD to provide that. (Issues are different)

Reference Genome Web Page Draft

  • We now have a real web page!