Making a release version
From GO Wiki
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
- 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)
- 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.