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. | |||
=[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] = | =[[Phylogenetic_annotation_overview|Phylogenetic annotation overview]] = | ||
| Line 11: | Line 9: | ||
=[[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= | ||
| Line 16: | Line 19: | ||
=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* [[Scripts to ensure PAINT data integrity]] ('touch-up'; incomplete and out of date; need to find the correct location of this documentation) | |||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: | **From 2017 Grant, suggestions for metrics: | ||
| Line 23: | Line 27: | ||
*** impact: number of annotations added, for human and for other species | *** impact: number of annotations added, for human and for other species | ||
** From a previous grant, see [[Image:HowToCaptureMetrics3.doc|thumb|Description]] | ** 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= | ||
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- | * [[Conference Calls]] - 2007-2016 | ||
* [[Electronic_jamborees| Electronic jamborees ]] | * [[Electronic_jamborees| Electronic jamborees ]] | ||
* [[Annotation_pipeline]] By Judy, Suzi, Michael | * [[Annotation_pipeline]] By Judy, Suzi, Michael | ||
| Line 73: | Line 69: | ||
* [[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 | |||
* [[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
- 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 File:HowToCaptureMetrics3.doc
- Other ideas (to be reviewed): Breath and Depth
- From 2017 Grant, suggestions for metrics:
Archived & retired Pages
Those pages are kept as reference but the information in them is not the most current information.
- Reference Genome Mailing list - disabled
- Conference Calls - 2007-2016
- Electronic jamborees
- Annotation_pipeline By Judy, Suzi, Michael
- Ideas for publicizing Ref.Genome Annotation Data
- PAINT-GONUTS integration
- Reference Genome Annotation Project Summary
- Project timeline
- Reference_Genome Contact Persons from each database
- Reference Genome Progress Reports
- Procedure for selection of target genes
- Procedure for filling Genome-Specific spreadsheets
- Tools for orthology determination: A summary of tools available to identify orthologs.
- 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)
- Reference Genome Web Page Draft: We now have a real web page!
- List of potentially problematic families for all vs. all BLAST methods of orthology determination
- Running P-POD orthology tool on the reference genomes gene set by Kara Dolinski at Princeton - Nov2007.
- Reference_Genome_sequence_annotation: GFF3 sequence files for reference genome MODs
- Reference Genome Database Requirements Discussion
- Source_Forge_items_for_reference_genomes_(Retired)
- Reference Genome Publication Counts
- Review_of_trees-based_annotations_(Retired)
- GAF file 2.0 survey of contributing groups
- 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
- RefG annotation priorities of September 2009
- Lung_branching_morphogenesis_genes December 2009
- All PPOD clusters with at least one object from each of the twelve refG organisms
- Target Gene List: May 2008-Jan 2010
- Tree annotation progress 2010-2011
- RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets: May- Sept 2011
- Wnt_signaling_Pathway June-Sept 2010
- Apoptosis Reference Genome Targets February-April 2011
- PAINT_-_Apoptosis_(Archived)
- PAINT - Apoptosis Nov 2013
- 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