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phyloref / jphyloref

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Phyloref status extraction now works whether start/end dates are interpreted as Annotations or Datatype Properties #24

Closed gaurav closed 3 years ago

gaurav commented 6 years ago

hasIntervalStartDate should be interpreted by OWLAPI as an AnnotationProperty, but it is sometimes interpreted as an OWLDataProperty. (This also applies to hasIntervalEndDate.) We appear to have a consistent example of this: the Brochu 2003 example file is interpreted as an Annotation Property when the OWL is generated by the Curation Tool and rdfpipe, but it is interpreted as a Datatype Property when the OWL is generated by the Clade Ontology test suite (see Gist for these files). This PR provides one quick-and-dirty workaround, which is to simply look for both annotation properties or datatype properties, but it's only the first step in (1) figuring out why this is happening, and (2) writing a test to make sure that this doesn't keep happening, as these issues are difficult to debug.

Do not merge: This is not a good fix for this problem, and I still need to figure out why we need this additional code to make this work for the Curation Tool. Also, this is just crying out for an automated test, so this is a good excuse to finally give JPhyloRef a test suite (probably in a different PR).

gaurav commented 3 years ago

We haven't had this problem in a while and the code has changed dramatically since I wrote this PR, so it's both no longer needed and is hopelessly out of date. Closing.