Difference between revisions of "Phylogenetic Annotation Project"

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[[Category:Reference Genome]] [[Category:Working Groups]]
''Note that this project was formerly called the Reference Genome Annotation Project.''


=PAINT : Phylogenetic Annotation INference Tool=
=Overview=
The reference project group has developed a software to perform the annotations based on phylogenetic trees.  
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]]
* [[PAINT_User_Guide]]
= PAINT (Phylogenetic Annotation and INference Tool) =
PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO [[Phylogenetic Annotation Project]] to support inference of GO function terms (molecular function, cellular component and biological process) by homology.


==Resources for PAINT annotation==


=PAINT Curation guidelines=
===[[PAINT annotation guidelines|PAINT Annotation principles]]===
* [[PAINT_SOP]]
The [[PAINT SOP|PAINT Annotation principles]] page describes the PAINT annotation guidelines.


* PAINT family list: https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing. '''Not updated since Panther 12'''
===[[PAINT_User_Guide|PAINT User Guide]]===
The [[PAINT_User_Guide|PAINT User Guide]] provides annotation guidelines for PAINT annotation as well as step-by-step instructions on how to use the PAINT tool.


=Pages to review=
===[http://pantree.org/tree/allTrees.jsp PAINT trees curation status]===
* [[Scripts to ensure PAINT data integrity]]
The [http://pantree.org/tree/allTrees.jsp PAINT trees curation status] page provides a list of all Panther trees and the history of their curation status.
 
=[[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


*[[Reference Genomes Metrics]] | Metrics: Discussion on annotation progress measurements
* [[PAINT_Conference_Calls]] Agendas and Minutes




=Reporting bugs or likely errors in the trees=


* Orthology determination: Data used to make orthology calls
==Tree issues==
** [[reference proteomes files]]
If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues
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]]
==PAINT issues==
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).  
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


=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=
=Archived & retired Pages=
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Those pages are kept as reference but the information in them is not the most current information.  
Those pages are kept as reference but the information in them is not the most current information.  
* [[Reference Genome Mailing list]] - disabled
* [[Reference Genome Mailing list]] - disabled
* [[Conference Calls]] - 2007-2011
* [[Electronic_jamborees| Electronic jamborees ]]
* [[Electronic_jamborees| Electronic jamborees ]]
* [[Annotation_pipeline]] By Judy, Suzi, Michael
* [[Annotation_pipeline]] By Judy, Suzi, Michael
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* [[GAF file 2.0]] survey of contributing groups
* [[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)
* [[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)]]




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* [[Wnt_signaling_Pathway]] June-Sept 2010
* [[Wnt_signaling_Pathway]] June-Sept 2010
* [[Apoptosis Reference Genome Targets]] February-April 2011
* [[Apoptosis Reference Genome Targets]] February-April 2011
* [[PAINT_-_Apoptosis_(Archived)]]
* [[PAINT - Apoptosis]] Nov 2013
* [[PAINT - Apoptosis]] Nov 2013
* DNA repair family list: http://goo.gl/BaQxMC 2014  
* 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]
* http://dcn.spreadsheets.google.com/ccc?id=o16926456948884040128.4584390909151853752.07000735126025259412.442372083524637957  
Target Gene List August 2006-April 2008
* [[Reference_Genome_Genes_(Retired)]]
* [[Reference_Genome_Genes_(Retired)]]
* [[PAINT_trees_to_review (Retired)]]
== Review Status ==
Last reviewed: 2021-07-01
[[Category:PAINT]]

Latest revision as of 01:50, 1 July 2021

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

Overview

The Phylogenetic Annotation Project performs annotation inferences across evolutionary related proteins based on known function of proteins within PANTHER [1] phylogenetic family trees.

PAINT (Phylogenetic Annotation and INference Tool)

PAINT is a Java software application for supporting inference of ancestral as well as present-day characters (represented by ontology terms) in the context of a phylogenetic tree. PAINT is currently being used in the GO Phylogenetic Annotation Project to support inference of GO function terms (molecular function, cellular component and biological process) by homology.

Resources for PAINT annotation

PAINT Annotation principles

The PAINT Annotation principles page describes the PAINT annotation guidelines.

PAINT User Guide

The PAINT User Guide provides annotation guidelines for PAINT annotation as well as step-by-step instructions on how to use the PAINT tool.

PAINT trees curation status

The PAINT trees curation status page provides a list of all Panther trees and the history of their curation status.

PAINT Update pipeline

PAINT GAF production

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


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

Pages to review

Archived & retired Pages

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


Past Annotation targets

Target Gene List August 2006-April 2008

Review Status

Last reviewed: 2021-07-01