Re: [Obo-owltools] Issue 47 in owltools: TaxonConstraintsEngine deprecated

[<owl...@go...>]

Comment #7 on issue 47 by cmung...@gmail.com: TaxonConstraintsEngine  
deprecated
http://code.google.com/p/owltools/issues/detail?id=47

the uberon release (now fixed) uses SpeciesSubsetterUtil, which uses OWL  
reasoning to exclude classes.

 From the javadoc:

  * This implements species subsetting (module generation) using
  * OWL reasoning.
  *
  * The procedure is
  *
  * 1. to assert
  *      Thing SubClassOf in_taxon some My-taxon-of-interest
  *
  * 2. Remove all unsatisfiable classes.
  *
  * This is a somewhat brutal way of doing things. A more
  * elegant approach would be to test every class (C in_taxon some T),
  * but this would be a little slower. But it avoids stating falsehoods.
  *
  * The current approach requires removing all taxon-crossing
  * relationships first to avoid removing too many
  * (e.g. if C is unsatisfiable, then homologous_to some C is
  * also unsatisfiable, we don't want to remove the homologs).
  *
  * A few of these are hardcoded in the module, but the user
  * should be careful to remove others depending on their ontology.
  *
  * See: https://github.com/obophenotype/uberon/wiki/Taxon-constraints

-- 
You received this message because this project is configured to send all  
issue notifications to this address.
You may adjust your notification preferences at:
https://code.google.com/hosting/settings