Difference between revisions of "Phylogenetic Annotation Project"

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=Goal of the Reference Genome Annotation Project=
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''Note that this project was formerly called the Reference Genome Annotation Project.''
The GO consortium has established the complete annotation of 12 reference genomes as a priority goal. These reference genomes are:
 
  
<b><i>Arabidopsis thaliana</i>, <i>Caenorhabditis elegans</i>, <i>Danio rerio</i>, <i>Dictyostelium discoideum</i>, <i>Drosophila melanogaster</i>, <i>Escherichia coli</i>, <i>Gallus gallus</i>, <i>Homo sapiens</i>, <i>Mus musculus</i>,
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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.
<i>Rattus norvegicus</i>, <i>Saccharomyces cerevisiae</i>, <i>Schizosaccharomyces pombe</i></b>
 
  
The Reference Genome GO Annotation Team, with representatives from each genome annotation group, will coordinate annotation, facilitate implementation of GO Consortium annotation priorities, provide metrics to assess progress toward the goal of broad and deep annotation of the reference genomes. This group will be responsible for the coordination of the annotation of the twelve reference genomes. This group represents the annotation expertise within the GO consortium and provides key liaisons to the model organism databases the have primary responsibilities for the annotation of the reference genomes.
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=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] =
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=[[PAINT_User_Guide|PAINT User Guide]]=
  
==== [[Reference Genome Annotation Project Summary]]====
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=[[PAINT_SOP|PAINT Curation guidelines]] (SOP)=
  
==== [[Ref_Gen_pub_draft | Reference Genome Web Page Draft]]====
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=PAINT trees curation status=
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[http://pantree.org/tree/allTrees.jsp http://pantree.org/tree/allTrees.jsp]
  
----
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=[[PAINT_database_update_pipeline|PAINT Update pipeline]]=
=Communication=
 
====[[Reference Genome Mailing list]]====
 
  
==== [[Conference Calls]]====
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=[[PAINT_GAF_production|PAINT GAF production]]=
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==[[PAINT GAF QC-examples|PAINT GAF QC-examples]]==
  
====  [[Reference Genomes Meetings | Meetings]]====
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= [[PAINT Conference Calls]]=  
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* Monthly, every First Tuesday of the month, 9 AM Pacific/6 PM Europe as of March 2019
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* Link to the zoom is in the Google Calendar
  
----
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* [[PAINT_Conference_Calls]] Agendas and Minutes
=Annotation Targets=
 
===[http://dcn.spreadsheets.google.com/ccc?id=o16926456948884040128.4584390909151853752.07000735126025259412.442372083524637957 Target Gene List]===
 
  
* Access requires your email to be added to the system.  Email Rex if you would like to be added.
 
* This spreadsheet contains links to separate spreadsheets maintained by each of the reference genome groups.
 
  
===[[Procedure for selection of target genes]]===
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=Reporting bugs or likely errors in the trees=
  
===[[Procedure for filling Genome-Specific spreadsheets]]===
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==Tree issues==
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If a Panther tree needs to be reviewed, please create a ticket in the Panther GitHub tracker: https://github.com/pantherdb/Helpdesk/issues
  
----
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==PAINT issues==
=Gene Annotation=
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Issues with the PAINT tools should be reported in this tracker: https://github.com/pantherdb/db-PAINT/issues
===[[Annotation Consistency Issues]] ===
 
  
===[[Variant_annotation]] ===
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==Pantree issues==
*This page describes how each database handles suration of multiple forms of the same gene
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Issues with the Pantree.org site should be reported at: https://github.com/pantherdb/PanTree
  
===[[Other taxa annotations | Providing annotations to GOA in taxa other than you MOD's]] ===
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= PAINT family curation tracking=
* Please follow these instructions if you encounter a gene not from your database that you need to annotate.  
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http://pantree.org/tree/allTrees.jsp
  
===[[Reference Genome Gene Index | Gene Annotation wiki pages]]===
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=Pages to review=
* The purpose of these pages are to allow discussions of annotation and orthology issues related to particular genes. The individual gene pages are to be created as needed.
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* http://wiki.geneontology.org/index.php/PAINT_annotation_working_group
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* [[reference proteomes files]]: to be moved elsewhere
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* Metrics: Discussion on annotation progress measurements
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**From 2017 Grant, suggestions for metrics:
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*** fraction of human proteins in annotated families (PAINT progress)
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*** impact: number of annotations added, for human and for other species
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** From a previous grant, see [[Image:HowToCaptureMetrics3.doc|thumb|Description]]
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** Other ideas (to be reviewed): [[Metrics:_breath_and_depth_of_annotations |Breath and Depth]]
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**** http://wiki.geneontology.org/index.php/GO_Reference_Genome_Meeting_Metric_Plan
  
===[[Misused terms]]===
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=Archived & retired Pages=
* This page provides a list of often misused terms and (hopefully) an explanation as to how to use the term properly. This information should also be included in the 'comments' of the OBO file.
 
  
===[[Reference_Genome_Database_Reports]]===
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Those pages are kept as reference but the information in them is not the most current information.
* Those reports are generated with the GOOSE SQL interface and provide lists of potentially mis-annotated genes.  
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* [[Reference Genome Mailing list]] - disabled
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* [[Electronic_jamborees| Electronic jamborees ]]
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* [[Annotation_pipeline]] By Judy, Suzi, Michael
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* [[Ideas for publicizing Ref.Genome Annotation Data]]
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* [[PAINT-GONUTS integration]]
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* [[Reference Genome Annotation Project Summary]]
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* [[Progress_Reports#Reference_Genomes | Project timeline]]
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* [[Reference_Genome Contact Persons from each database]]
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* [[Reference Genome Progress Reports]]
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* [[Procedure for selection of target genes]]
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* [[Procedure for filling Genome-Specific spreadsheets]]
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* [[Tools_for_identifying_orthologs|Tools for orthology determination]]: A summary of tools available to identify orthologs.
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* [[Orthology discussion page|SOP for determining ortholog (by database)]]: The purpose of this page was to discuss the method by which each group establishes orthology between reference genome genes and human disease genes. We now collaborate with PANTHER to provide that. (Issues are different)
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* [[Ref_Gen_pub_draft | Reference Genome Web Page Draft]]: We now have a real web page!
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* [[List of potentially problematic families for all vs. all BLAST methods of orthology determination]]
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* [[Running P-POD orthology tool on the reference genomes gene set]] by Kara Dolinski at Princeton - Nov2007.
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* [[Reference_Genome_sequence_annotation]]: GFF3 sequence files for reference genome MODs
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* [[Reference Genome Database Requirements Discussion]]
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* [[Source_Forge_items_for_reference_genomes_(Retired)]]
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* [[Reference Genome Publication Counts]]
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* [[Review_of_trees-based_annotations_(Retired)]]
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* [[GAF file 2.0]] survey of contributing groups
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* [[RG:_Software|Reference Genome Software]] Plan to have some tracking system - supplanted with the db-version of Paint (2017)
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* [[Ref_genome_Annotation_progress_ideas_(Retired)]]
  
----
 
  
=Annotation Progress=
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==Past Annotation targets==
=== [http://www.geneontology.org/images/RefGenomeGraphs/ Graphical views of the annotations] ===
 
  
===[[Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements]]===
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* [[RefG annotation priorities]] of September 2009
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*[[Lung_branching_morphogenesis_genes]] December 2009
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* [http://proto.informatics.jax.org/prototypes/GOgraphEX/PPOD12_Graphs/ All PPOD clusters with at least one object from each of the twelve refG organisms]
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*[http://spreadsheets.google.com/ccc?key=pZhlLFuj8ewDe799QTmxzCA&hl=en Target Gene List]: May 2008-Jan 2010
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*[[Tree annotation progress]] 2010-2011
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* [[RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets]]: May- Sept 2011
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* [[Wnt_signaling_Pathway]] June-Sept 2010
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* [[Apoptosis Reference Genome Targets]] February-April 2011
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* [[PAINT_-_Apoptosis_(Archived)]]
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* [[PAINT - Apoptosis]] Nov 2013
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* DNA repair family list: http://goo.gl/BaQxMC 2014
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* http://dcn.spreadsheets.google.com/ccc?id=o16926456948884040128.4584390909151853752.07000735126025259412.442372083524637957
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Target Gene List August 2006-April 2008
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* [[Reference_Genome_Genes_(Retired)]]
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* [[PAINT_trees_to_review (Retired)]]
  
----
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[[Category:PAINT]]
=Orthology determination=
 
 
 
====[[Running P-POD orthology tool on the reference genomes gene set]] ====
 
by Kara Dolinski at Princeton - Nov2007
 
* This page contains a description of the project and the requirements for providing files
 
 
 
==== [[Orthology discussion page|SOP for determining ortholog (by database)]]====
 
 
 
The purpose of this page is to discuss general principles and problems with establishing orthology between reference genome genes and human disease genes.
 
 
 
====[[Tools_for_identifying_orthologs|Tools for orthology determination]]====
 
 
 
A summary of tools available to identify orthologs.
 
 
 
----
 
 
 
=Software/database development=
 
 
 
*'''[[Reference Genome Database Requirements Discussion]]'''
 
*'''[[RG_Software_group]]'''
 
 
 
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.
 
 
 
 
 
 
 
 
 
 
 
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Latest revision as of 05:31, 13 April 2021

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 (SOP)

PAINT trees 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