Phylogenetic Annotation Project

PAINT : Software for tree annotation

The reference project group has developed a software to perform the annotations based on phylogenetic trees.

• PAINT software

PAINT Curation guidelines

• PAINT_SOP

• 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.

Pages to review

• Scripts to ensure PAINT data integrity

• Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Orthology determination: Data used to make orthology calls

reference proteomes files

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.

New gene2geneproduct file

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).

Archived & retired Pages

Preretired pages! To discuss with DH and KVH

Gene pages

http://wiki.geneontology.org/index.php/Category:Reference_Genome_Genes > I forgot how those were created. They can probably all be removed. Can this be done in bulk?

Retired Pages

Those pages are kept as reference but the information in them is not the most current information.

• Reference Genome Mailing list - disabled
• Conference Calls - 2007-2011
• Electronic jamborees
• Annotation_pipeline By Judy, Suzi, Michael
• Ideas for publicizing Ref.Genome Annotation Data
• PAINT-GONUTS integration
• Reference Genome Annotation Project Summary
• Project timeline
• Reference_Genome Contact Persons from each database
• Reference Genome Progress Reports
• 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!
• List of potentially problematic families for all vs. all BLAST methods of orthology determination
• Running P-POD orthology tool on the reference genomes gene set by Kara Dolinski at Princeton - Nov2007.
• Reference_Genome_sequence_annotation: GFF3 sequence files for reference genome MODs
• Reference Genome Database Requirements Discussion
• Source_Forge_items_for_reference_genomes_(Retired)
• Reference Genome Publication Counts
• Review_of_trees-based_annotations_(Retired)
• GAF file 2.0 survey of contributing groups
• Reference Genome Software Plan to have some tracking system - supplanted with the db-version of Paint (2017)

Past Annotation targets

• RefG annotation priorities of September 2009
• Lung_branching_morphogenesis_genes December 2009
• All PPOD clusters with at least one object from each of the twelve refG organisms
• Target Gene List: May 2008-Jan 2010
• Tree annotation progress 2010-2011
• RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets: May- Sept 2011
• Wnt_signaling_Pathway June-Sept 2010
• Apoptosis Reference Genome Targets February-April 2011
• PAINT - Apoptosis Nov 2013
• DNA repair family list: http://goo.gl/BaQxMC 2014
• Target Gene List August 2006-April 2008