[Experimental] Replace OWLTools with ODK ROBOT plugin #3476
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That file was supposedly used by "several of the subset" rules, but actually is not used anywhere.
Most subsets in Uberon are currently created by various OWLTools commands. Whenever possible, we replace them by corresponding ROBOT commands. * Subsets created by `--reasoner-query --make-ontology-from-results`: Replaced by `odk:subset --query`, using the ODK ROBOT plugin. * Subsets created by `--extract-ontology-subset --fill-gaps`: Replaced by `odk:subset --fill-gaps true`, using the ODK ROBOT plugin. * Subsets created by `--extract-ontology-subset` (without the `--fill-gaps` option, meaning that gaps should be spanned instead): Replaced by `extract --method subset`.
The -basic versions of the composite ontologies are currently produced mostly with OWLTools. Here we attempt to replace OWLTools by a ROBOT pipeline that does approximately the same tasks as the original OWLTools commands.
The list of prerequisites for the cumbo subset was bogus, with a missing space between prerequisites...
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This PR attempts to remove most of the remaining uses of OWLTools throughout the custom Makefile, using a proposed ODK ROBOT plugin where necessary.
One of the most important uses of OWLTools currently is for the production of ontology subsets, which is done using a variety of OWLTools commands:
1.
--extract-ontology-subsetUsed to extract a subset defined by a
oboInOwl:inSubsetannotation within the ontology. What we can use to replace this command with ROBOT depends on whether the--fill-gapsoption is used:1.1. without
--fill-gaps(e.g. for the “combo” subset)We can replace by the standard ROBOT command
robot extract --method subset(after manually extracting the list of classes annotated as belonging to the desired subset). One difference is that the ROBOT command does not include relationships by default, we must explicitly specify the relationships we want to see in the subset.1.2. with
--fill-gapsCannot be reproduced by any standard ROBOT command, but can be replaced by the
odk:subsetcommand of the proposed ROBOT ODK plugin.2.
--reasoner-query [...] --make-ontology-from-resultsUsed to extract a subset defined by a DL query (e.g.
'part of' some 'renal system'for therenal-minimalsubset). Cannot be reproduced by any standard ROBOT command, but can be replaced by theodk:subsetcommand (with the--queryoption) of the proposed ROBOT ODK plugin.3.
--mingraph --make-subset-by-propertiesUsed to create the
-basicversions of the composite ontologies (e.g.composite-metazoan-basic.owl. Cannot be exactly reproduced by any standard ROBOT command, but can be reasonably approximated by a combination of severalfilter/removeoperations (this is roughly similar to the standard ODK rule to create the ODK-defined-basicrelease artefacts).