Difference between revisions of "Making a release version"

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(Making a pre-reasoned ontology from an XP file prior to release)
(Making a pre-reasoned ontology from an XP file prior to release)
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  in.obo < grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" | sed 's/^intersection_of\:/relationship\:/' > out.obo
 
  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.
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** Note 1: Relationships in differentia are not instantiated during step 1, but perhaps they should be ([https://sourceforge.net/tracker/index.php?func=detail&aid=2305594&group_id=36855&atid=418257 see this 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 10:14, 9 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:
in.obo < grep -v "intersection_of\: [Aa-Zz]*\:[0-9].* \!" | sed 's/^intersection_of\:/relationship\:/' > out.obo
  • 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), there are serious problems with redundancy flagging by the LPR when XP terms are present. However, the tests I've done so far suggest that this is safe in the absence of XP terms.