Phylogenetic Annotation Project
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.
- 2008-06-18 RefGen RefGenProgress_2008-06-18
- 2008-06-04 RefGen RefGenProgress_2008-06-04
- 2008-04-20 Second Reference Genome Annotation Meeting, Salt Lake City, UT [Minutes]
- 2007-09-27: First Reference Genome Annotation Meeting, Princeton, NJ [Minutes]
From May 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.
By Judy, Suzi, Michael
- Annotation QC problems
- Annotation completion Source Forge tracker [http://sourceforge.net/tracker/?group_id=36855&atid=1040173]
- IEA, ISS, IC Usage Discussion
- This page describes how each database handles suration of multiple forms of the same gene
- Please follow these instructions if you encounter a gene not from your database that you need to annotate.
- 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.
- 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.
Graphical views of the annotations:
All PPOD clusters with at least one object from each of the twelve refG organisms, including May targets
Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements
by Kara Dolinski at Princeton - Nov2007
- This page contains a description of the project and the requirements for providing files
The purpose of this page is to discuss general principles and problems with establishing orthology between reference genome genes and human disease genes.
A summary of tools available to identify orthologs.
GFF3 sequence files for reference genome MODs
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.