Retain definitions and xrefs from imports #1040
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PROBLEM: Definitions from imports with definition sources are stripped. This is because oboInOwl:hasDbXref's are removed and the definition source axioms depend on them. There's no way to drop only oboInOwl:hasDbXref triples within axioms with ROBOT. FIX: Keep oboInOwl:hasDbXrefs (and subsequently definitions) for ALL imports.
allenbaron
added
enhancement
imports
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@allenbaron -- we determined that we do not want the definitions included from external imports for several reasons, they increase the size of the ontology and any errors they may contain that violate our QC constraints are both out of our control to fix and gum up our release process. Other than SYMP and TRANS, we do not want to include the definitions, etc. from the other imports. |
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Some imports do have definitions with them (example: CHEBI). If we really want only definitions for SYMP and TRANS, we should probably remove the "definition" tag from the src/ontology/imports/annotations.txt file (which specifies the class annotations that should be retained for imports) and update our import procedure for SYMP and TRANS. |
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Maintenance and/or removal of definitions in imports was revised in PR #1052. |
This PR is an optional enhancement that will retain all oboInOwl:hasDbXref triples in all imports, thereby also retaining definitions.
Analysis of (minor) problem :
Definitions from imports with definition sources are stripped (e.g. SYMP, UBERON, CL, . This is because oboInOwl:hasDbXref's are removed and the definition source axioms depend on them.
There's no way to drop only oboInOwl:hasDbXref triples within definition axioms with ROBOT.
In order to retain definitions (when they have sources) all oboInOwl:hasDbXref statements must be retained.