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README.md

README.md

Note: All programs require the OWL version of SNOMED CT (res_StatedOWLF_INT_20120731.owlf) in the ontologies folder. This version can be generated with the script that comes with the official SNOMED release.

The classes to reproduce the experiments described in the paper "Intra-Axiom Redundancies in SNOMED CT" are:

redundancy.RedundancyChecker

Runtime: several minutes for the list of concepts that must be redundant, ca. 6 hours for all concepts regarding supertypes, and ca. 12 hours with exhaustive search. Input: ontologies/res_StatedOWLF_INT_20120731.owlf; results/EquivalentSubconceptsAll.txt (for doList) Output: results/RedundantConceptsDisregarding.txt, results/RedundantConceptsRegarding.txt or RedundantConceptsRegardingExhaustive, depending on doSuperClasses and exhaustiveSearch

Checks for concepts whether they are redundant. Can be run to check all concepts (doAll), a list (doList) or a single concept only (doConcept). It can be run regarding or disregarding supertypes (doSuperClasses). Returns either only the first explanation per redundancy, or all explanations.

util.Util

Input: - Output: -

The Util class contains useful methods.

CornetsEquivalenceMethod

Runtime: several minutes, ca. 2 hours with Pellet Input: ontologies/res_StatedOWLF_INT_20120731.owlf Output: results/ClassesWithEquivalentClass.txt; results/Explanations.txt

Generates a list of all pairs of equivalent classes Can be run with Pellet to generate explanations for non-equivalent files (needs > 8 GB heap space; explanations = true)

ValidateRedundantConceptsCornet

Runtime: several minutes Input: ontologies/res_StatedOWLF_INT_20120731.owlf; results/RedundantConceptsRegarding.txt Output: results/EquivalentSubconceptsAll.txt

Generates a list (EquivalentSubconceptsAll.txt) of concepts that must be redundantly defined according to Cornet's method. This list can be taken as input for the RedundancyChecker (doList)

Final notes

  • All classes should be run with sufficient heap space (-Xmx2G)
  • Optimizations to all programs would be welcome