View source for Phylogenetic Annotation Project

''Note that this project was formerly called the Reference Genome Annotation Project.''

The Phylogenetic Annotation Project performs annotation inferences across evolutionary related proteins based on known function of proteins within PANTHER [http://pantherdb.org/] phylogenetic family trees. 

=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] =
=[[PAINT_User_Guide|PAINT User Guide]]=

=[[PAINT_SOP|PAINT Curation guidelines]]=

=[[PAINT_database_update_pipeline|PAINT Update pipeline]]=

=[[PAINT_GAF_production|PAINT GAF production]]=
==[[PAINT GAF QC-examples|PAINT GAF QC-examples]]==

= [[PAINT Conference Calls]]= 
* Monthly, every First Tuesday of the month, 9 AM Pacific/6 PM Europe as of March 2019
* Link to the zoom is in the Google Calendar

* [[PAINT_Conference_Calls]] Agendas and Minutes


=Reporting bugs or likely errors in the trees=

==Tree issues==
If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues

==PAINT issues==
Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues

==Pantree issues==
Issues with the Pantree.org site should be reported at: https://github.com/pantherdb/PanTree

= PAINT family curation tracking=
https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing. '''Not updated since Panther 12'''

=Pages to review=
* http://wiki.geneontology.org/index.php/PAINT_annotation_working_group
* [[reference proteomes files]]: to be moved elsewhere
* Metrics: Discussion on annotation progress measurements
**From 2017 Grant, suggestions for metrics: 
*** fraction of human proteins in annotated families (PAINT progress)
*** impact: number of annotations added, for human and for other species
** From a previous grant, see [[Image:HowToCaptureMetrics3.doc|thumb|Description]] 
** Other ideas (to be reviewed): [[Metrics:_breath_and_depth_of_annotations |Breath and Depth]]
**** http://wiki.geneontology.org/index.php/GO_Reference_Genome_Meeting_Metric_Plan

=Archived & retired Pages=

Those pages are kept as reference but the information in them is not the most current information. 
* [[Reference Genome Mailing list]] - disabled
* [[Electronic_jamborees| Electronic jamborees ]]
* [[Annotation_pipeline]] By Judy, Suzi, Michael
* [[Ideas for publicizing Ref.Genome Annotation Data]]
* [[PAINT-GONUTS integration]]
* [[Reference Genome Annotation Project Summary]]
* [[Progress_Reports#Reference_Genomes | 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_identifying_orthologs|Tools for orthology determination]]: A summary of tools available to identify orthologs. 
* [[Orthology discussion page|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)
* [[Ref_Gen_pub_draft | 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
* [[RG:_Software|Reference Genome Software]] Plan to have some tracking system - supplanted with the db-version of Paint (2017)
* [[Ref_genome_Annotation_progress_ideas_(Retired)]]


==Past Annotation targets==

* [[RefG annotation priorities]] of September 2009 
*[[Lung_branching_morphogenesis_genes]] December 2009
* [http://proto.informatics.jax.org/prototypes/GOgraphEX/PPOD12_Graphs/ All PPOD clusters with at least one object from each of the twelve refG organisms] 
*[http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en 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_(Archived)]]
* [[PAINT - Apoptosis]] Nov 2013
* DNA repair family list: http://goo.gl/BaQxMC 2014 
* http://dcn.spreadsheets.google.com/ccc?id=o16926456948884040128.4584390909151853752.07000735126025259412.442372083524637957 
Target Gene List August 2006-April 2008
* [[Reference_Genome_Genes_(Retired)]]
* [[PAINT_trees_to_review (Retired)]]

[[Category:PAINT]]