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Hi, I've started addressing this issue in #163, that has already been merged for the next release which will be out soon.
Essentially with this change if you explicitly specify any of the recommended owl 2 file extensions from the export file dialog then there will be no '.owl' extension appended to the file.
The list of file extensions currently recognized are:
.owl - which is mostly a legacy from the old owl 1 spec
.ofn - as recommended for owl 2 functional-style syntax files
.owx - as recommended for owl 2 xml syntax
.omn - as recommenmded for owl 2 manchester syntax
.ttl - as recommended for RDF turtle notation
Notice however that the preferred extension must be specified by the user and is not automatically related to the syntax used in the exporter, so I'm not sure this change addressed this issue entirely. As an alternative we could look for the user-suggested file extension and preset the most appropriate syntax in the exporter.
As long as it always works the same ever time, it probably doesn't matter which way you do it! So either implementation of the format selection dictates file extension or fie extension selection (typed in) dictates format would work.
Given the current export workflow (file selection -> syntax and axiom selection) I think the latter is currently more intuitive.
I recently merged this in #165.
All Export Ontology resultant files seem to end in .owl, regardless of the format selected. For Turtle files it's typical to use .ttl, not .owl.
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