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Add gap-fill option to subset method in extract #1128
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This would be useful (as would a general specification of an algo for graph traversal using the UberGraph redundant graph). |
Of your two options, this is clearer to me:
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I am creating this issue as a continuation of @gouttegd's comment here:
robot
extract
has a subset method described here, which is most useful. In the terminology of owltools, this method implements "gap spanning". owltools had an additional option when making subsets, "gap filling". This would add all intermediate nodes and edges between terms in the subset.this can be illustrated using the test subset ontology
let's make a subset:
cat > SUBSET ONT:1 ONT:4
we can then look at the difference between the two commands:
gap-spanned.obo:
note that the part-of between 4 and 1 is not asserted, it is entailed
gap-filled:
Proposal:
either a
--method
option called something likeintermediate-filled-subset
extract
that is only applicable forsubset
called something like--include-intermediate-nodes
(we should name this carefully, the owltools terminology of gap filling/spanning is not great)
unlike the default subset approach which connects subset terms via entailed edges, this would traverse all intermediate nodes via direct edges.
Algorithm:
Here
<s P o>
means that there exists a relation graph direct or indirect edge<s p o>
such thatp
is inP
orp
isrdfs:subClassOf
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