Phylogenetic Annotation Project
- 1 Goal of the Reference Genome Annotation Project
- 2 Progress Reports
- 3 Communication
- 4 Annotation Targets
- 5 Gene Annotation
- 5.1 GAFs for trees-based annotations
- 5.2 Standard Operating Procedure for Tree-based propagation of annotations
- 5.3 Annotation_pipeline
- 5.4 Annotation Quality control
- 5.5 Annotation Consistency Issues
- 5.6 Misused terms
- 5.7 Variant_annotation
- 5.8 Providing annotations to GOA in taxa other than you MOD's
- 5.9 Gene Annotation wiki pages
- 6 Annotation Progress
- 6.1 Lung Development related Gene Annotation Progress
- 6.2 Graphical views of the annotations:
- 6.3 Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements
- 7 Orthology determination
- 7.1 List of potentially problematic families for all vs. all BLAST methods of orthology determination
- 7.2 Data used to make orthology calls
- 8 Software/database development
- 9 Retired Pages
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.
- January 2010 RefGen Reference_Genome_January_2010
- December 2009 RefGen Reference_Genome_December_2009
- November 2009 RefGen Reference_Genome_November_2009
- October 2009 RefGen Reference_Genome_October_2009
- September 2009 RefGen Reference_Genome_September_2009
- July 2009 RefGen RefGenProgress_2009-07
- June 2009 RefGen RefGenProgress_2009-06
- May 2009 RefGen RefGenProgress_2009-05
- April 2009 RefGen RefGenProgress_2009-04
- April 1, 2009 Third Reference Genome Annotation Meeting, Eugene, OR Agenda and Minutes
- March 2009 RefGen RefGenProgress_2009-03
- February 2009 RefGen RefGenProgress_2009-02
- September 2008 RefGen RefGenProgress_2008-09-10
- August 2008 RefGen RefGenProgress_2008-08-13
- July 2008 RefGen RefGenProgress_2008-07-18
- June 2008 RefGen RefGenProgress_2008-06-18
- May 2008 RefGen RefGenProgress_2008-06-04
- April 20, 2008 Second Reference Genome Annotation Meeting, Salt Lake City, UT [Minutes]
- Sept 27, 2007: First Reference Genome Annotation Meeting, Princeton, NJ [Minutes]
From May 2008
Target Gene List (May 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.
By Judy, Suzi, Michael
Annotation Quality control
- Annotation QC
- Annotation completion Source Forge tracker [http://sourceforge.net/tracker/?group_id=36855&atid=1040173]
- Reference_Genome_Database_Reports. Those reports are generated with the GOOSE SQL interface and provide lists of potentially mis-annotated genes.
Annotation Consistency Issues
- Annotation consistency: IEA, ISS, IC Usage Discussion: Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly VanAuken
- Annotation consistency: IDA or IC for processes: Tanya Berardini, Emily Dimmer, Pascale Gaudet, David Hill, Chris Mungall, Kimberly VanAuken, Ruth Lovering
- Annotation consistency: HTP Annotation of high throughput experiments, including microarray data SGD GO HTP guidelines : Stacia Engel, Emily Dimmer, Val Wood, Ruth Lovering
- Annotation consistency: Using IEP, including microarray data, and heat shock protein example: Emily Dimmer, Stacia Engel, Pascale Gaudet, Ruth Lovering, Varsha Khodiyar, Val Wood
- Annotation consistency: x protein binding and with : Becky Foulger, David Hill
- Annotation consistency: xx binding in the context of gene product: example is 'co-enzyme binding' from electronic jamboree : Pascale Gaudet, David Hill, Victoria Petri,
- Annotation consistency: 'Response to' terms: Check that all databases use evidence codes correctly for those terms. Tanya Berardini, Emily Dimmer, Pascale Gaudet, Ruth Lovering
Improving GO terms and definitions
- Annotation consistency: Clarification of oligomerization, dimerization, protein complex assembly: Debby Siegele
- Annotation consistency: chaperone activity definition: clarify the definitions of unfolded/misfolded protein binding and add chaperone activity as a synonym to both of the terms. Also add ‘de novo’ synonym to ‘unfolded protein binding’. Victoria Petri
- Binding terms working group
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
- 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.
Graphical views of the annotations:
- PPOD clusters selected since April 2008
- Manually curated target sets selected before April 2008
Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements
Data used to make orthology calls
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.
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).
The GAF file should contain 17 columns, and the meaning of columns 2, 12 and 17 have been modified. See that page for specifications.
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
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.
Those pages are kept as reference but the information in them is not the most current information.
A summary of tools available to identify orthologs.
- 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)
- We now have a real web page!