ontodev / robot

ROBOT is an OBO Tool
http://robot.obolibrary.org
BSD 3-Clause "New" or "Revised" License
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Add INFERRED as relationship column qualifier for robot export #697

Open cmungall opened 4 years ago

cmungall commented 4 years ago

In addition to ANON, NAMED, ANY, we would add INFERRED_ALL, INFERRED_DIRECT

A reasoner could be passed on command line in the usual way

For subClassOf this is a trivial reasoner API call. _ALL/_DIRECT would map to the isDirect parameter.

For ObjectProperties, this would use the EMR (as is used in materialize). @balhoff may have a faster implementation we can swap in.

A test/illustration:

[Term]
id: GO:0005654 ! nucleoplasm
name: nucleoplasm
is_a: GO:0110165 ! cellular anatomical entity
relationship: BFO:0000050 GO:0031981 ! part of nuclear lumen

[Term]
id: GO:0031981 ! nuclear lumen
name: nuclear lumen
is_a: GO:0070013 ! intracellular organelle lumen
relationship: BFO:0000050 GO:0005634 ! part of nucleus

[Term]
id: GO:0005634 ! nucleus
name: nucleus
is_a: GO:0043231 ! intracellular membrane-bounded organelle

For nucleoplasm:

@balhoff - this could also be useful for materializing taxon constraints

may also be useful for kpmp work

cmungall commented 3 years ago

this would be particularly useful for in_taxon and never_in_taxon fields