Ontology CVS Directory Layout Overhaul

From GO Public

1 Rationale
2 Timeline
- 2.1 Immediate timeline
- 2.2 Future changes
3 Proposed new layout
4 Software/Admin TODO
5 Derived files in CVS
6 FAQ
- 6.1 will this break scripts / configurations or lead to dead or stale links?
- 6.2 when should I change my scripts / configuration?
7 See Also

[edit] 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.

[edit] Timeline

[edit] Immediate timeline

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

This will be tied in with the introduction of the regulates relation

Midnight Pacific time March 18 (8 am, 3/19 Jen's time) : Begin freeze.
- Jen merges electron transport changes into gene_ontology_edit.obo, then let's Chris know that he can start file conversion
- This marks the last ever manual edit to gene_ontology_edit.obo
March 19: Add regulates relations - keep in scratch/ then cp to gene_ontology_write
March 20: Switch edit files: gene_ontology_write.obo open for business.
- Editors (David, Tanya, Jen only) can edit new file for QC purposes only. However, new changes remain largely invisible to general public
March 20-25: Switch script to use gene_ontology_write as source. See software TODO below
Freeze period will last until March 25th, x am Pacific when Chris puts up gene_ontology_write.obo as editor's file. Chris will email go list to say that new file is available for editing.
March 26+: Announce changes to community

[edit] Future changes

Dates to be determined

Extract slims from for-public version
- (retain in go_write for ease of maintenance)
Introduce stanza timestamps to write version
Add a obof1.3 export directory

[edit] Proposed new layout

The layout here is for the cvs tree. This is also reflected in the public URLs for GO. E.g the following are equivalent:

go/ontology/gene_ontology_edit.obo (CVS)
http://www.geneontology.org/ontology/gene_ontology_edit.obo (WWW)

This is the proposed structure:

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 will be fully supported throughout 2008 and possibly indefinitely
  
    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!

There is further explanation here:
http://wiki.geneontology.org/index.php/Thaw_Mail

[edit] Software/Admin TODO

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

The sequence of events is as follows:

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)
generate obo_format_1_0/gene_ontology.1_0.obo
- using obo2obo
generate deprecated files
- using cp
cvs commit