remove or modify usages of "non-redundant" relation-graph output

[turbomam]

The current 2+ relation-graph doesn't attempt to create non-redundant output because it never really did create non-redundant output.

see also

• https://github.com/microbiomedata/nmdc-ontology/issues/18

[turbomam]

$(ONT)-relation-graph.owl is a release artifact and is the input into several other targets

It is currently built by merging $(ONT)-nonredundant.ttl into $(ONT)-merged-labels.ttl

Let's try

• switching to relation-graph-cli, version: 2.3.2
• using the --output-file option as the sole output
• merging that input instead of $(ONT)-nonredundant.ttl

will it be unacceptably larger?

RELEASE_ARTEFACTS = $(ONT)-relation-graph.owl $(ONT).json $(ONT)-classes.json $(ONT).owl

$(ONT)-relation-graph.owl: $(ONT).owl $(ONT)-merged-labels.ttl
# build relation-graph from nmdc-merged.ttl file
# for relation-graph see https://github.com/balhoff/relation-graph  
# note, you may need to increase Java memory: export JAVA_OPTS=-Xmx16G
    @echo "\n** building $@ **"
    relation-graph --ontology-file $< \
        --reflexive-subclasses false \
        --equivalence-as-subclass false \
        --non-redundant-output-file $(ONT)-nonredundant.ttl \
        --redundant-output-file $(ONT)-redundant.ttl \
        --mode rdf
# merge in nmdco-merged for annotations
    $(ROBOT) merge \
        --input $(word 2, $^) \
        --input $(ONT)-nonredundant.ttl \
        annotate --ontology-iri $(ONTBASE)/$@ \
        $(ANNOTATE_ONTOLOGY_VERSION) \
        --output $@

[turbomam]

With non-redundant input:

-rw-rw-r-- 1 mark mark 13M Feb 15 12:18 nmdco-relation-graph.owl -rw-rw-r-- 1 mark mark 2.6M Feb 16 09:43 nmdco-classes.json

[turbomam]

With relation-graph 2.3 output:

-rw-rw-r-- 1 mark mark 66M Feb 16 09:38 nmdco-relation-graph.owl -rw-rw-r-- 1 mark mark 935K Feb 16 09:39 nmdco-classes.json