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.

Reference Genome Annotation Project Summary

Reference Genome Web Page Draft

Progress Reports

  • 2008-04-20 Second Reference Genome Annotation Meeting, Salt Lake City, UT [Minutes]
  • 2007-09-27: First Reference Genome Annotation Meeting, Princeton, NJ [Minutes]


Reference Genome Mailing list

Conference Calls


Electronic jamboree

Annotation Targets

From May 2008

PPOD Target Gene List

Old Target Gene List August 2006-April 2008

  • Access requires your email to be added to the system. Email Rex 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


By Judy, Suzi, Michael

Annotation Consistency Issues


  • This page describes how each database handles suration 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.

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.


  • Those reports are generated with the GOOSE SQL interface and provide lists of potentially mis-annotated genes.

Annotation Progress

Graphical views of the annotations:

Based on orthology calls in 'old' google spreadsheet

PPOD clusters associated with the 'old' refG set (based on object ids shared by refG set and PPOD cluster)

All PPOD clusters with at least one object from each of the twelve refG organisms, including May targets

June PPOD clusters

Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Orthology determination

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

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

SOP for determining ortholog (by database)

The purpose of this page is to discuss general principles and problems with establishing orthology between reference genome genes and human disease genes.

Tools for orthology determination

A summary of tools available to identify orthologs.

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.