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.''


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 : Software for tree annotation=
=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] =
The reference project group has developed a software to perform the annotations based on phylogenetic trees.
=[[PAINT_User_Guide|PAINT User Guide]]=


* [[PAINT]] software
=[[PAINT_SOP|PAINT Curation guidelines]]=


=PAINT Curation guidelines=
* [[PAINT_SOP]]
* PAINT family list based on number of genes, duplication nodes and GO terms: https://docs.google.com/spreadsheets/d/1uHgcaXO7t9__9GuXgBibT0H-YlnU252IsRGWIyhCWN8/edit?usp=sharing. The family is usually easier to PAINT if there are less duplication nodes, but please select ones that have more GO terms and more genes (>100)
Please contact PAINT team to have access to the document.
=[[Scripts to ensure PAINT data integrity]]=
==PAINT annotation SOPs==
====[[PAINT_SOP |Standard Operating Procedure for Tree-based propagation of annotations]]====
* [[PAINT-GONUTS integration]]
==[[Reference Genomes Metrics]] | Metrics: Discussion on annotation progress measurements==
=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.
====New [[gene2geneproduct file]]====
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).
=Software/database development=
*'''[[RG:_Software|Reference Genome Software]]'''
*'''[[RG_Software_group|Software group]]'''
*'''[[PAINT_SOP|PAINT]]'''
The purpose of this page is to discuss features and requirements that would be desirable in a database used to replace the existing Google Spreadsheet system for managing target genes, their annotations and metrics.


= 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
* [[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
**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=


Preretired pages! To discuss with DH and KVH
===Gene pages===
http://wiki.geneontology.org/index.php/Category:Reference_Genome_Genes
> I forgot how those were created. They can probably all be removed. Can this be done in bulk?
==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
* [[ Ideas for publicizing Ref.Genome Annotation Data ]]
* [[Ideas for publicizing Ref.Genome Annotation Data]]
* [[PAINT-GONUTS integration]]
* [[Reference Genome Annotation Project Summary]]
* [[Reference Genome Annotation Project Summary]]
* [[Progress_Reports#Reference_Genomes | Project timeline]]
* [[Progress_Reports#Reference_Genomes | Project timeline]]
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* [[Review_of_trees-based_annotations_(Retired)]]
* [[Review_of_trees-based_annotations_(Retired)]]
* [[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)
* [[Ref_genome_Annotation_progress_ideas_(Retired)]]


==Past Annotation targets==
==Past Annotation targets==
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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)]]
* [[PAINT_trees_to_review (Retired)]]

Revision as of 14:36, 19 January 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 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