Making a release version

From GO Wiki
Revision as of 06:04, 8 December 2008 by Dosumis (talk | contribs) (Making a pre-reasoned ontology from an XP file prior to release)

Jump to: navigation, search

Making a pre-reasoned ontology from an XP file prior to release

  • Step 1: Save with 'save implied links' (save for presentation) selected.
  • Step 2: Add auto-defs using
  • Step 3: Strip out genus lines of intersections and convert differentiae to regular relationships. To do this use:
in.obo < grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" | sed 's/^intersection_of\:/relationship\:/' > out.obo
    • Note 1: Relationships in differentia are not instantiated during step 1 But perhaps they should be (see ticket*) . This step instantiates them.
    • Note 2: It is vital to do this before step 4, otherwise highly dangerous dangling intersections result from disallowing dangling parents)
  • Step 4: Strip out foriegn terms. To do this: Save with filter selecting terms that have <insert ID prefix of your ontology>.

Check 'always save properties'. Do not check 'allow dangling parents'

  • Step 5: Save with filter to strip redundancy.
    • Note - relies on redundancy filters being good. Currently (12/08), they are good for