Ontology CVS Directory Layout Overhaul 2007 (Archived)

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Rationale

The current layout is confusing, with the edit file serving two purposes: an editors version and an obof1.2 version

Purpose: provide buffer between ontology users and editors to allow implementation of new features in a way that is non-disruptive

Currently we have

 go/
   ontology/
     gene_ontology.obo
     gene_ontology_edit.obo

this was designed to be a separate editors and for-public version of the ontology. However, the editors version has been advertised as the file to download for the public wishing to get obof1.2 features.

Timeline

The new layout will be phased in from March 18-25 2007.

Proposed new layout

go/
  ontology/
 
    gene_ontology.obo            
        -- The current for-public version of GO.
        -- Format: obof1.0 (currently)
        -- We reserve the right to switch to obof1.2, and any future versions,
        -- given sufficient lead time for file consumers to change software.
        -- If you wish to use a file that is *guaranteed* to be obof1.0, please consider
        -- go/ontology/obo_format_1_0/gene_ontology.1_0.obo
 
    gene_ontology_edit.obo       
        -- ** DEPRECATED [March 25 2008] **
        -- Format: obof1.2
        -- Use of this file is no longer recommended after March 25 2008
        -- Please use go/ontology/obo_format_1_2/gene_ontology.1_2.obo instead
        -- (the contents should be identical)
        -- This file path / URL will no longer be supported in 2009
 
    obo_format_1_0/
 
      README
          -- contains links to obof1.0 documentation
      
      gene_ontology.1_0.obo
          -- Format: obof1.0
          -- Recommended instead of: go/ontology/gene_ontology.obo
 
    obo_format_1_2/
 
      README
          -- contains links to obof1.2 documentation
 
      gene_ontology.1_2.obo        
          -- Format: obof1.2
          -- Must be used instead of: go/ontology/gene_ontology.obo
 
    editors/
 
      README
 
      gene_ontology_write.obo
          -- You should only use this file path if you are editing the live ontology.
          -- We do not recommend use of this file for non-editors. The file may
          -- contain experimental new features or tags that are filtered out in
          -- the for-public version.
          -- Caveat emptor!

Software/Admin TODO

Fix scripts for updating .obo files and .go files.

The sequence of events is as follows:

  1. generate obo_format_1_2/gene_ontology.1_2.obo
    • at first this will be a direct cp of editors/gene_ontology_write.obo
    • in the future it may use obo2obo (for example, to separate out slims)
  1. generate obo_format_1_0/gene_ontology.1_0.obo
    1. using obo2obo
  2. generate deprecated files
    1. using cp
  3. cvs commit

See Also

Versioning_Proposal