jamesaoverton
commented
2 years ago ROBOT has a QuotedEntityChecker which tries to handle quoted labels like Protege does during OWLAPI's Manchester parsing. We've seen lots of problems with quoting and unquoting for ROBOT templates because of differences in CSV flavours, Excel weirdness, quote characters in ontology term labels, etc. I've never seen anyone try to use a value expression in a ROBOT template. So you're right to suspect ROBOT's quotation handling.
But I did make this work. I started with the file you linked to, added a row for 'has atomic number', changed 'A definition' to 'A obo:definition' just so the file would be self-contained, and kept just one example row. I also had to add a closing quotation mark to the definition column for the example -- many of your definitions start with a double-quote but the matching double-quote is missing from the end of the cell.
Ontology ID Label CLASS TYPE Logical Type Parent Class Def definition Domain Range
ID LABEL CLASS_TYPE TYPE CI SC % A obo:definition DOMAIN RANGE
obo:RBO_2000 has atomic number data property obo:RBO_00005001 xsd:nonNegativeInteger
obo:RBO_2001 mass number data property obo:RBO_00005001 xsd:nonNegativeInteger
obo:RBO_00000008 He-4 ion radiation subclass class obo:RBO_00005001 "('has atomic number' value ""2""^^xsd:nonNegativeInteger) and ('mass number' value ""4""^^xsd:nonNegativeInteger)" "Atomic nuclei, each with 2 protons and 2 neutrons with kinetic energy imparted by natural or artificial means (such as by a particle accelerator)"When I ran robot template -t rbo.tsv -o rbo.owl I saw a proper logical axiom for obo:RBO_00000008. So ROBOT can handle the value expressions, but the quoting is delicate.
reality
We are trying to use class expressions to establish sc of axioms for classes in a template, e.g.
in a column with "SC %" as the definition. In the file produced by robot, instead of having these class expression as subclassof axioms, the classes appear as subclasses of empty classes with an "rdfs:about" property of a string equivalent to the class expression in the template, e.g.:
In the OWL file, the classes look like this:
If I try to make a new axiom in Protege with the class expression as it appears in the file, it works fine, which implies that OWLAPI can parse it. I also tried removing the surrounding " from the axioms in the file, which didn't work. My guess would be some kind of encoding or processing of the quote symbols?
You can see the template here: https://github.com/Radiobiology-Informatics-Consortium/RBO/blob/luke-testing/src/templates/RBO_nuclei.tsv (and the owl file is also in that dir)
Thanks a lot in advance!