Difference between revisions of "Making a release version"

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(Saving implied links and removing foreign terms from in an XP file prior to release)
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= Saving implied links and removing foreign terms from in an XP file prior to release =
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= Making a pre-reasoned ontology from an XP file prior to release =
  
 
* Step 1: Save with 'save implied links' (save for presentation) selected.
 
* Step 1: Save with 'save implied links' (save for presentation) selected.
 
* Step 2: Add auto-defs using autodef.pl
 
* Step 2: Add auto-defs using autodef.pl
 
* Step 3: Strip out genus lines of intersections and convert differentiae to regular relationships.  To do this use:
 
* Step 3: Strip out genus lines of intersections and convert differentiae to regular relationships.  To do this use:
  grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" tmp.obo | sed 's/^intersection_of\:/relationship\:/' >
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  your_XP_ontology.obo < grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" | sed 's/^intersection_of\:/relationship\:/' > your_ontology_pre-reasoned.obo
 
** Note 1: Relationships in differentia are not instantiated during step 1  But perhaps they should be (see ticket*) .  This step instantiates them.
 
** 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)
 
** Note 2: It is vital to do this before step 4, otherwise highly dangerous dangling intersections result from disallowing dangling parents)

Revision as of 07:03, 8 December 2008

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 autodef.pl
  • Step 3: Strip out genus lines of intersections and convert differentiae to regular relationships. To do this use:
your_XP_ontology.obo < grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" | sed 's/^intersection_of\:/relationship\:/' > your_ontology_pre-reasoned.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