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 (zebrafish)
- 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
First Reference Genome Annotation Meeting, Princeton, NJ, Sept 26, 27, 2007
[Agenda]
Annotation Targets
The Reference Genome Target Gene List
The spreadsheet is located at
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.
Web sites with lists of disease genes
Communication
Reference Genome Mailing list
The Reference Genome GO Annotation Team uses an email discussion list to facilitate communication. The list is open to curators of the identified reference genomes involved in reference genome annotation.
To join the list send an email to:
refgenome-request@geneontology.org
In the body of the message add the line:
subscribe <insert your email address>
To access the email archive for this mailing list:
http://www.geneontology.org/GO.list.refgenome.shtml
Reference Genome Conference Calls
The second Tuesday of each month; alternate times: 8 AM/11AM Pacific time
Minutes of Reference Genome Phone Conferences
RefGenome11Sept07_Phone_Conference.doc
RefGenome07Aug07_Phone_Conference.doc
RefGenome10July07_Phone_Conference.doc
RefGenome12Jun07_Phone_Conference.doc
RefGenome24Jan07_Phone_Conference.doc
Annotation Progress
Graphical views of the annotations
Graphical views of the annotations of the reference genome target genes can be viewed here:
Discussion on annotation progress measurements
For recent summary of some of the issues please open "HowToCaptureMetrics3" file. File:HowToCaptureMetrics3.doc
- Guidelines for counting gene products
- Annotation progress
- Breath and Depth
- Reference Genome Publication Counts
- Source Forge items for reference genomes
A summary of how each group is completing columns L,M,N,O for publications metrics.
Orthology determination
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.
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.
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.