Mock-ups of new GOC Annotation pages (Deprecated): Difference between revisions

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These pages are drafts of new GO Annotation pages for the GO Consortium website, that will eventually replace and improve upon the information provided by current documentation pages:
#REDIRECT [[Defunct]]


* http://www.geneontology.org/GO.annotation.shtml (Annotation Guide)
[[Category:Annotation]]
 
  This page lists the content of the website overhaul done in 2011. Note that most links are dead.
 
 
Drafts of new GO Annotation pages are being prepared for the GO Consortium website. These will eventually replace and improve upon the information provided by current documentation pages listed below:
 
* [http://www.geneontology.org/GO.annotation.shtml Annotation Guide] CONTENT MOVED TO: [[Introduction to the GO Consortium annotation set]]
 
* [http://www.geneontology.org/GO.evidence.shtml Evidence Codes] Include Flow Chart? Need to include new PAINT evidence types. State objective of concordance with ECO?
 
* [http://www.geneontology.org/GO.annotation.conventions.shtml Conventions] CONTENT MOVED TO: [[Qualifiers]],[[Database Objects]], [[References]]
 
* [http://www.geneontology.org/GO.annotation.SOP.shtml SOPs] CONTENT MOVED TO: [[Guidelines for literature-based curation]], [[Guidelines for electronic annotation methods]], [[Guidelines for manual, sequence based curation]], [[How External Communities can contribute annotations to the GO Consortium]]
 
* [http://www.geneontology.org/GO.annotation.species_db.shtml Species, Databases]
 
* [http://www.geneontology.org/GO.annotation_qc.shtml QC Checks]. Perhaps the Annotation Quality Control section of: [http://www.geneontology.org/GO.format.annotation.shtml| File Format] could be displayed in this page
 
* [http://www.geneontology.org/GO.format.annotation.shtml File Format]
 
* [http://www.geneontology.org/cgi-bin/references.cgi GO Reference Collection] As this lists GO_REFs, which are just one of the references allowed in the GO annotation format, perhaps this could be linked to from a new [[References]] page?
 
 
----


* http://www.geneontology.org/GO.annotation.conventions.shtml


* http://www.geneontology.org/GO.annotation.SOP.shtml




'''New Annotation Documentation Layout'''
'''New Annotation Documentation Layout'''


[[Annotation Guidelines]]
Perhaps we could have an introduction to a generic GO annotation, with tabs displaying documentation for each of the fields; including:
 
--[[Database Objects]]
 
-- [[Qualifiers]]
 
-- [[References]]
 
-- [http://www.geneontology.org/GO.evidence.shtml Evidence Codes]
 
-- [[With field]]
 
--[[Annotation assigned_by]]


Contents:
--[[Annotation Extension]]
* what information a GO annotation does/should include
* Has child pages dealing specifically with literature-based and electronic annotation methods


[[Introduction to the GO Consortium annotation set]]
[[Introduction to the GO Consortium annotation set]]
Line 20: Line 52:
[[How External Communities can contribute annotations to the GO Consortium]]
[[How External Communities can contribute annotations to the GO Consortium]]


Contents:
[[Annotation Guidelines]]
* How communities can interact with the GO Consortium, either contributing or feeding back on annotations. Include annotation resources
 
-- [[Guidelines for literature-based curation]]
 
-- [[Guidelines for electronic annotation methods]]
 
-- [[Guidelines for manual, sequence based curation]]
 
[[GO Annotation Usage Guidelines]]
 
 
 
I realize that its not a page for the annotation group, however should one be created that deals with how to requesting new GO terms? Suggestions for content here: [[Requesting new GO terms]]
 
The Annotation Quality Control section of: http://www.geneontology.org/GO.format.annotation.shtml could be displayed as a separate page, and include a link to the Annotation QC page that Amelia has now generated - http://www.geneontology.org/GO.annotation_qc.shtml
 


[[Annotation Usage Guidelines]]
----


Possible Contents:
[[GO annotation fields required for correct display]]
*  "response_to" annotations with IEP vs other codes, (targets/mediators): Harold
*  Use of IEP annotations
*  Use of IEA annotations
*  Use of ND annotations
*  Qualified annotations


*  Identifier mapping resources
[[Technical Priorities for Annotation Groups]]
*  Tools, e.g. BLAST2GO for annotation prediction?

Revision as of 18:36, 6 March 2020

Redirect to:


  This page lists the content of the website overhaul done in 2011. Note that most links are dead.


Drafts of new GO Annotation pages are being prepared for the GO Consortium website. These will eventually replace and improve upon the information provided by current documentation pages listed below:

  • Evidence Codes Include Flow Chart? Need to include new PAINT evidence types. State objective of concordance with ECO?
  • QC Checks. Perhaps the Annotation Quality Control section of: File Format could be displayed in this page
  • GO Reference Collection As this lists GO_REFs, which are just one of the references allowed in the GO annotation format, perhaps this could be linked to from a new References page?





New Annotation Documentation Layout

Perhaps we could have an introduction to a generic GO annotation, with tabs displaying documentation for each of the fields; including:

--Database Objects

-- Qualifiers

-- References

-- Evidence Codes

-- With field

--Annotation assigned_by

--Annotation Extension

Introduction to the GO Consortium annotation set

How External Communities can contribute annotations to the GO Consortium

Annotation Guidelines

-- Guidelines for literature-based curation

-- Guidelines for electronic annotation methods

-- Guidelines for manual, sequence based curation

GO Annotation Usage Guidelines


I realize that its not a page for the annotation group, however should one be created that deals with how to requesting new GO terms? Suggestions for content here: Requesting new GO terms

The Annotation Quality Control section of: http://www.geneontology.org/GO.format.annotation.shtml could be displayed as a separate page, and include a link to the Annotation QC page that Amelia has now generated - http://www.geneontology.org/GO.annotation_qc.shtml



GO annotation fields required for correct display

Technical Priorities for Annotation Groups