INCATools / INCATools/ontology-development-kit

v1.5 Stripping excess annotation properties from imports is removing annotated RO role chains

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Description

for example - from RO:

>[Typedef]
id: RO:0002216
name: capable of part of
def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." []
property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165
property_value: IAO:0000118 "has function in" xsd:string
property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/
holds_over_chain: RO:0002215 BFO:0000050 {RO:0002582="true"}
is_a: RO:0002328 ! functionally related to
is_a: RO:0002500 ! causal agent in process

Default annotation properties to keep seem to be just label and definition (I can see why this might be desirable), but this causes the annotated role chain to be stripped out. This causes some loss of inference in FBbt.

I can fix this by amending my -odk.yaml file to have the following under import_group, but I think logical axioms should probably not be stripped out of imports at all.
> annotation_properties:
- RO:0002582
- rdfs:label
- IAO:0000115

Contributor guide

Open the contributing guide

Research direction

Start with the import_group.annotation_properties handling in the -odk.yaml configuration and reproduce the RO:0002216 example, checking whether the annotated holds_over_chain axiom is removed. Trace how imported annotation properties are selected and define done as preserving the role-chain annotation and resulting inference without requiring a per-import override.

Written by the indexing model from the issue text.

Assessment

Tech stack
yaml
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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