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Steps to get taxon exclusions from relation graph #2160

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Steps to get taxon exclusions from relation graph #2160

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d163c51
Steps to get taxon exclusions from relation graph
cmungall Nov 9, 2021
e491925
Merge branch 'master' into taxon-constraints-relation-graph-2137
matentzn Nov 12, 2021
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30 changes: 24 additions & 6 deletions src/ontology/uberon.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@ core.owl: $(OWLSRC)
# FIXED apparently our base does not contain phenoscape-ext!! (It does, through unreasoned)
#$(TMPDIR)/phenoscape-ext-src.owl: $(SRC)
# wget --no-check-certificate https://raw.githubusercontent.com/obophenotype/uberon-phenoscape-ext/master/phenoscape-ext.owl -O $@ && touch $@

# including the imports would lead to circularity, so we remove these here
#$(COMPONENTSDIR)/phenoscape-ext.owl: $(TMPDIR)/phenoscape-ext-src.owl core.owl
# owltools $(UCAT) $< --remove-imports-declarations -o -f functional $@
Expand Down Expand Up @@ -1713,8 +1713,8 @@ reports/robot_release_diff.md: $(TMPDIR)/$(ONT)-obo.obo $(TMPDIR)/$(ONT)-obo-mai

.PHONY: feature_diff
feature_diff: reports/robot_main_diff.md


########################
#### Utility commands ##

Expand Down Expand Up @@ -1745,7 +1745,6 @@ clean:
rm -rf ./uberon-base.*
rm -f uberon.owl uberon.obo core.owl BUILDLOGUBERON.txt unsat_all_explanation.md
rm -f ext.owl


explain:
$(ROBOT) explain --input $(TMPDIR)/unreasoned-composite-metazoan.owl --reasoner ELK \
Expand All @@ -1756,13 +1755,13 @@ explain:
# echo "skipping $@"

unsat: $(TMPDIR)/bundled-metazoan.owl_unsat.ofn $(TMPDIR)/cl_mondo_merged.owl_unsat.ofn

$(TMPDIR)/%_unsat.ofn: %
$(ROBOT) merge --input $< explain --reasoner ELK \
-M unsatisfiability --unsatisfiable random:3 --explanation [email protected] \
annotate --ontology-iri "$(ONTBASE)/$@" \
--output $@

cl_mondo_merged.owl:
$(ROBOT) merge -i uberon.owl -I $(URIBASE)/cl.owl -o $@

Expand Down Expand Up @@ -1873,6 +1872,24 @@ docs/releases.md: uberon-odk.yaml
# if http://purl.obolibrary.org/obo/mondo/releases/2021-01-01/mondo.owl exists, include it in overview.
# Use Github or obo purls (include switch that we can conficgue with ODK)

# ----------------------------------------
# TAXON CONSTRAINTS VIA RELATION GRAPH
# ----------------------------------------
# see https://github.com/obophenotype/uberon/issues/2137#issuecomment-963594082

# make a relationgraph ttl file (assumes RG 2.0 - may not be in ODK yet)
tmp/%.relationgraph.ttl: %.obo
relation-graph --ontology-file $< --equivalence-as-subclass true --output-subclasses true --reflexive-subclasses true --output-file $@
.PRECIOUS: tmp/%.relationgraph.ttl

tmp/%.rgmerged.ttl: tmp/%.relationgraph.ttl %.obo
robot merge -i $< -i $*.obo -o $@
.PRECIOUS: tmp/%.rgmerged.ttl

# This is currently hardcoded to a subset of species
tmp/class-taxon-exclusions.tsv: tmp/uberon-edit.rgmerged.ttl
robot query -i $< --tdb true --query ../sparql/taxon-violation-relation-graph.sparql $@

### Removing uberon_2 contraints
### refer to https://github.com/obophenotype/uberon/discussions/2158
remove_uberon_two_constraints:
Expand All @@ -1886,3 +1903,4 @@ explain_humans:

explain_humans_all:
$(ROBOT) merge -i ../../ext.owl -i contexts/context-human.owl explain --reasoner ELK -M unsatisfiability --unsatisfiable random:10 --explanation [email protected]

47 changes: 47 additions & 0 deletions src/sparql/taxon-violation-relation-graph.sparql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,47 @@
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

PREFIX human: <http://purl.obolibrary.org/obo/NCBITaxon_9606>
PREFIX mammal: <http://purl.obolibrary.org/obo/NCBITaxon_40674>
PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161>
PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162>

SELECT ?c ?cLabel ?p ?pLabel ?clsWithConstraint ?clsWithConstraintLabel ?taxonWithConstraint ?taxonWithConstraintLabel ?queryTaxon
WHERE {

?c ?p ?clsWithConstraint .

# NEVER IN
{
?clsWithConstraint never_in_taxon: ?taxonWithConstraint .
?queryTaxon
rdfs:subClassOf ?taxonWithConstraint
}
UNION
# ONLY IN
{
?clsWithConstraint in_taxon: ?taxonWithConstraint
FILTER NOT EXISTS { ?queryTaxon
rdfs:subClassOf ?taxonWithConstraint
}
}

# add to this as required
VALUES ?queryTaxon {
human: mammal:
}
OPTIONAL
{ ?c rdfs:label ?cLabel }
OPTIONAL
{ ?p rdfs:label ?pLabel }
OPTIONAL
{ ?clsWithConstraint rdfs:label ?clsWithConstraintLabel }
OPTIONAL
{ ?taxonWithConstraint rdfs:label ?taxonWithConstraintLabel }


FILTER isIRI(?c)


}