Phylogenetic Annotation Project
- 1 Reference Genome Annotation Project: Purpose
- 2 Communications
- 3 PAINT : Software for tree annotation
- 4 PAINT Curation guidelines
- 5 Data availability
- 6 Annotation Priorities
- 6.1 Annotation targets
- 6.2 Past Annotation targets
- 7 Scripts to ensure PAINT data integrity
- 8 Work in progress
- 9 Orthology determination
- 9.1 List of potentially problematic families for all vs. all BLAST methods of orthology determination
- 9.2 Data used to make orthology calls
- 10 Software/database development
- 11 Retired Pages
Reference Genome Annotation Project: Purpose
- Comprehensive information about the group's purpose and objectives can be found at Reference Genome Annotation Project Summary
- 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.
PAINT : Software for tree annotation
The reference project group has developed a software to perform the annotations based on phylogenetic trees, PAINT.
PAINT Curation guidelines
- PAINT-generated GAF files are on the cvs repository :
- By Species: http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/gene-associations/submission/#dirlist
- Viewing reference genome annotations in AmiGO
- Reference GO:0000033: 
- RefG annotation priorities as of September 2009 (following GOC meeting held in Cambridge). Including procedure to propose new targets.
PAINT Annotation target 2014
- DNA repair family list: http://goo.gl/BaQxMC
- PAINT family list based on number of genes, duplication nodes and GO terms: https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing. The family is usually easier to PAINT if there are less duplication nodes, but please select ones that have more GO terms and more genes (>100)
Please contact PAINT team to have access to the document.
Nov 2013 PAINT - Apoptosis
May- Sept 2011: RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets
February-April 2011: Apoptosis Reference Genome Targets
June-Sept 2010: Wnt_signaling_Pathway
Past Annotation targets
Lung_branching_morphogenesis_genes Annotation Progress
From May 2008
Target Gene List (May 2008-Jan 2010)
- PPOD clusters selected since April 2008
- Manually curated target sets selected before 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.
Work in progress
PAINT annotation SOPs
Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements
Branding Ref.Genome Project
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.
- Annotation_pipeline By Judy, Suzi, Michael
- Reference_Genome Contact Persons from each database
- Procedure for selection of target genes
- Procedure for filling Genome-Specific spreadsheets
- 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 to provide that. (Issues are different)
- Reference Genome Web Page Draft: We now have a real web page!