Phylogenetic Annotation Project: Difference between revisions

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


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


=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] =
=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] =
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=[[PAINT_SOP|PAINT Curation guidelines]]=
=[[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 family curation tracking=
= PAINT family curation tracking=
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=Pages to review=
=Pages to review=
* [[Scripts to ensure PAINT data integrity]]
* 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* [[Scripts to ensure PAINT data integrity]] ('touch-up'; incomplete and out of date; need to find the correct location of this documentation)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
* Metrics: Discussion on annotation progress measurements
* Metrics: Discussion on annotation progress measurements
 
**From 2017 Grant, suggestions for metrics:  
2018-01-17
*** fraction of human proteins in annotated families (PAINT progress)
From 2017 Grant, suggestions for metrics:  
*** impact: number of annotations added, for human and for other species
- fraction of human proteins in annotated families (PAINT progress)
** From a previous grant, see [[Image:HowToCaptureMetrics3.doc|thumb|Description]]  
- impact: number of annotations added, for human and for other species
** 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
 
For a summary of some of the issues please open "HowToCaptureMetrics3" file.
[[Image:HowToCaptureMetrics3.doc|thumb|Description]] (not sure this is still up to date)
* [[Metrics:_breath_and_depth_of_annotations |Breath and Depth]]
 
 
* 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.
 
 
 
 
=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]] - 2007-2011
* [[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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* [[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)]]

Revision as of 12:38, 24 August 2018

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 [1] phylogenetic family trees.

Phylogenetic annotation overview

PAINT User Guide

PAINT Curation guidelines

PAINT Update pipeline

PAINT GAF production

PAINT_GAF_QC-examples

PAINT family curation tracking

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

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

Retrieved from "https://wiki.geneontology.org/index.php?title=Phylogenetic_Annotation_Project&oldid=71052"