Save implied links (for presentation) doesn't save differentiae as relationships. I think it should. A major reason we need the save implied links function is to allow user to group via part_of and is_a relations without taking intersection_of lines into account. If we don't instantiate differentiae as relationships, then some part_of relations will be inaccessible to those users who ignore intersection_of lines.
I've entered this as a bug rather than a feature request as I think the current behavior is un-intuitive enough to be considered a misfeature and is likely to cause problems for any release cycle that includes saving implied links. It took some testing for me to work out what it was going on.
(Note - no problem for how save implied links deals with genus - either converted straight to is_a or changed to place term at most appropriate position in the hierarchy).
[Hacky Workaround
This removes all intersection lines, converting differentiae to relationships following saving implied links:
grep -v "intersection_of\: [Aa-Zz]+\:[0-9]+ \!" fly_anatomy_pre-reasoned.obo | sed 's/^intersection_of\:/relationship\:/' > fly_anatomy_prereasoned_noXP.obo
]
a more general solution that materialized the relationship tags and preserves the intersection_ofs
http://github.com/cmungall/obo-scripts/raw/master/obo-add-relationships-from-xps.pl
from
http://github.com/cmungall/obo-scripts
this is only temporary - oe should have the required functionality