Difference between revisions of "Phylogenetic Annotation Project"

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''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_User_Guide|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.


=PAINT trees curation status=
==Resources for PAINT annotation==
 
==[[PAINT_User_Guide|PAINT User Guide]]==
 
==PAINT trees curation status==
List of all tree, and the history of their curation status
[http://pantree.org/tree/allTrees.jsp http://pantree.org/tree/allTrees.jsp]
[http://pantree.org/tree/allTrees.jsp http://pantree.org/tree/allTrees.jsp]



Revision as of 01:40, 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 User Guide

PAINT trees curation status

List of all tree, and the history of their curation status http://pantree.org/tree/allTrees.jsp

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

PAINT family curation tracking

http://pantree.org/tree/allTrees.jsp

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