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.''
''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 [http://pantherdb.org/] phylogenetic family 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.  
= 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.


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


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


===[[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.


= PAINT family curation tracking=
===[http://pantree.org/tree/allTrees.jsp PAINT trees curation status]===
https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing. '''Not updated since Panther 12'''
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
 
* [[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


=Pages to review=
=Pages to review=
* http://wiki.geneontology.org/index.php/PAINT_annotation_working_group
* http://wiki.geneontology.org/index.php/PAINT_annotation_working_group
* [[Scripts to ensure PAINT data integrity]] ('touch-up'; incomplete and out of date; need to find the correct location of this documentation)
* [[reference proteomes files]]: to be moved elsewhere
* [[reference proteomes files]]: to be moved elsewhere
* Metrics: Discussion on annotation progress measurements
* Metrics: Discussion on annotation progress measurements
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** Other ideas (to be reviewed): [[Metrics:_breath_and_depth_of_annotations |Breath and Depth]]
** 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
**** http://wiki.geneontology.org/index.php/GO_Reference_Genome_Meeting_Metric_Plan
=Archived & retired Pages=
=Archived & retired Pages=


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]] - 2007-2016
* [[Electronic_jamborees| Electronic jamborees ]]
* [[Electronic_jamborees| Electronic jamborees ]]
* [[Annotation_pipeline]] By Judy, Suzi, Michael
* [[Annotation_pipeline]] By Judy, Suzi, Michael
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* [[Reference_Genome_Genes_(Retired)]]
* [[Reference_Genome_Genes_(Retired)]]
* [[PAINT_trees_to_review (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