Classification lost in -simple version when named EC pairs present in the master file

From dosu...@gmail.com on March 04, 2013 03:31:22

= What steps will reproduce the problem? =

ontology-release-runner --reasoner hermit flybase_controlled_vocabulary_xp.obo --allow-equivalent-pairs --no-subsets --simple --allow-overwrite --outdir oort

You can grab the master file from here:
http://kyala.gen.cam.ac.uk/svn/ontologies/ontologies/trunk/flybase_controlled_vocabulary_xp.obo

It contains named pairs of equivalent classes from ChEBI AND FBcv.

= What is the expected output? What do you see instead? =

I expected the -simple versions to have FBcv terms with classification to root, including some inference from ChEBI. Instead, all classification of these terms is lost, including asserted classification from FBcv.


= What version of the product are you using? On what operating system? =

Ubuntu 2.6.32-45-server
OWLTOOLS SVN Revision: 1132

Original issue: http://code.google.com/p/owltools/issues/detail?id=54

Reproduce the command with ontology-release-runner, the HermiT reasoner, and the supplied flybase_controlled_vocabulary_xp.obo master file. Compare the generated -simple output with the expected FBcv classification to determine where asserted and inferred classifications are lost when named equivalent-class pairs from ChEBI and FBcv are present.