Phylogenetic Annotation Project: Difference between revisions

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=Software/database development=
=Software/database development=


*'''[[Reference Genome Database Requirements Discussion]]'''
 
*'''[[RG:_Software|Reference Genome Software]]'''
*'''[[RG:_Software|Reference Genome Software]]'''
*'''[[RG_Software_group|Software group]]'''
*'''[[RG_Software_group|Software group]]'''
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* [[Running P-POD orthology tool on the reference genomes gene set]] by Kara Dolinski at Princeton - Nov2007.  
* [[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_sequence_annotation]]: GFF3 sequence files for reference genome MODs
* [[Reference Genome Database Requirements Discussion]]


==Past Annotation targets==
==Past Annotation targets==

Revision as of 13:22, 16 January 2018



PAINT : Software for tree annotation

The reference project group has developed a software to perform the annotations based on phylogenetic trees, PAINT.


PAINT Curation guidelines

PAINT_SOP



Annotation Priorities

  • RefG annotation priorities as of September 2009 (following GOC meeting held in Cambridge). Including procedure to propose new targets.

Annotation targets

PAINT Annotation target 2014

Please contact PAINT team to have access to the document.

Nov 2013 PAINT - Apoptosis

May- Sept 2011: RefG_Heart_Development_co-curation#Heart_Development_Transcription_Annotation_Targets

February-April 2011: Apoptosis Reference Genome Targets

June-Sept 2010: Wnt_signaling_Pathway

Selected refG target sets

  • PPOD clusters selected since April 2008
  • Manually curated target sets selected before April 2008

Target Gene List August 2006-April 2008

  • Access requires your email to be added to the system. Email Pascale if you would like to be added.
  • This spreadsheet contains links to separate spreadsheets maintained by each of the reference genome groups.



Scripts to ensure PAINT data integrity

Work in progress

PAINT annotation SOPs

GAFs for trees-based annotations

Standard Operating Procedure for Tree-based propagation of annotations

Reference Genomes Metrics | Metrics: Discussion on annotation progress measurements

Branding Ref.Genome Project

Ideas for publicizing Ref.Genome Annotation Data


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).

GAF file 2.0

The GAF file should contain 17 columns, and the meaning of columns 2, 12 and 17 have been modified. See that page for specifications.




Software/database development


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.


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?


Archived communication

Retired Pages

Those pages are kept as reference but the information in them is not the most current information.



Past Annotation targets