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Issue 125 relation graphs #198

Merged
merged 17 commits into from
Aug 28, 2020
Merged

Issue 125 relation graphs #198

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f5f498d
Compute relation graphs
Shalsh23 Aug 19, 2020
f692ea1
Load property graphs to blazegraph
Shalsh23 Aug 19, 2020
efcfbf4
Remove dosdp generated subsumer patterns
Shalsh23 Aug 19, 2020
9d47c82
Put both relation graphs in different locations in blazegraph
Shalsh23 Aug 20, 2020
c574e1c
Partial update to the queries to work with relation graphs; needs mor…
Shalsh23 Aug 20, 2020
44862e5
Add target for redundant property graph
Shalsh23 Aug 21, 2020
a338e2a
Add back targets using absences dodsdp pattern
Shalsh23 Aug 21, 2020
e8146a7
Remove dosdp patterns no longer being used
Shalsh23 Aug 21, 2020
bb3c0af
Need newer run.sh to use relation-graph tool
balhoff Aug 21, 2020
7819f50
Update Jenkinsfile
balhoff Aug 21, 2020
ffdaacf
Update pipeline-tools docker image version
Shalsh23 Aug 21, 2020
1a175f2
Merge pull request #199 from phenoscape/shalsh-patch
balhoff Aug 21, 2020
f703e72
Need to set memory for relation-graph tool.
balhoff Aug 21, 2020
0666fbb
Merge branch 'master' into issue-125-relation-graphs
balhoff Aug 21, 2020
75238c5
Update Makefile
balhoff Aug 22, 2020
84efcf8
Merge absences into kb-tbox
Shalsh23 Aug 25, 2020
e0b1a9d
Disable semantic similarity component
Shalsh23 Aug 25, 2020
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136 changes: 9 additions & 127 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -205,38 +205,21 @@ $(BUILD_DIR)/phenoscape-kb-tbox-classified-pre-absence-reasoning.ofn: $(BUILD_DI
# ----------

# Generate phenoscape-kb-tbox.ofn
$(BUILD_DIR)/phenoscape-kb-tbox.ofn: $(BUILD_DIR)/bio-ontologies-classified.ttl \
$(BUILD_DIR)/defined-by-links.ttl \
$(BUILD_DIR)/phenex-tbox.ofn \
$(BUILD_DIR)/anatomical-entity-presences.ofn \
$(BUILD_DIR)/anatomical-entity-absences.ofn \
$(BUILD_DIR)/anatomical-entity-partOf.ofn \
$(BUILD_DIR)/hasParts.ofn \
$(BUILD_DIR)/anatomical-entity-hasPartsInheringIns.ofn \
$(BUILD_DIR)/anatomical-entity-phenotypeOfs.ofn \
$(BUILD_DIR)/anatomical-entity-phenotypeOf-partOf.ofn \
$(BUILD_DIR)/anatomical-entity-phenotypeOf-developsFrom.ofn
$(BUILD_DIR)/phenoscape-kb-tbox.ofn: $(BUILD_DIR)/bio-ontologies-classified.ttl $(BUILD_DIR)/defined-by-links.ttl $(BUILD_DIR)/phenex-tbox.ofn
$(ROBOT) merge \
-i $(BUILD_DIR)/bio-ontologies-classified.ttl \
-i $(BUILD_DIR)/defined-by-links.ttl \
-i $(BUILD_DIR)/phenex-tbox.ofn \
-i $(BUILD_DIR)/anatomical-entity-presences.ofn \
-i $(BUILD_DIR)/anatomical-entity-absences.ofn \
-i $(BUILD_DIR)/anatomical-entity-partOf.ofn \
-i $(BUILD_DIR)/hasParts.ofn \
-i $(BUILD_DIR)/anatomical-entity-hasPartsInheringIns.ofn \
-i $(BUILD_DIR)/anatomical-entity-phenotypeOfs.ofn \
-i $(BUILD_DIR)/anatomical-entity-phenotypeOf-partOf.ofn \
-i $(BUILD_DIR)/anatomical-entity-phenotypeOf-developsFrom.ofn \
convert --format ofn \
-o [email protected] \
&& mv [email protected] $@

# ----------

# *** Subsumers ***

# -----
$(BUILD_DIR)/bio-ontologies-property-graphs.ttl : $(BUILD_DIR)/bio-ontologies-merged.ttl
relation-graph --ontology-file $< \
--non-redundant-output-file $@ \
--redundant-output-file $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl \
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--mode rdf

$(BUILD_DIR)/defined-by-links.ttl: $(BUILD_DIR)/bio-ontologies-merged.ttl $(SPARQL)/isDefinedBy.sparql
$(ROBOT) query \
Expand All @@ -245,110 +228,6 @@ $(BUILD_DIR)/defined-by-links.ttl: $(BUILD_DIR)/bio-ontologies-merged.ttl $(SPAR
--input $< \
--query $(SPARQL)/isDefinedBy.sparql $@

$(BUILD_DIR)/anatomical-entity-presences.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/implies_presence_of.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/implies_presence_of.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-absences.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/absences.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/absences.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-partOf.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/part_of.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/part_of.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/hasParts.ofn: $(BUILD_DIR)/anatomical-entities.txt $(BUILD_DIR)/qualities.txt patterns/has_part.yaml
mkdir -p $(dir $@) \
&& sed '1d' $(BUILD_DIR)/qualities.txt > $(BUILD_DIR)/qualities--header.txt \
&& cat $(BUILD_DIR)/anatomical-entities.txt $(BUILD_DIR)/qualities--header.txt > $(BUILD_DIR)/anatomical-entities++qualities.txt \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/has_part.yaml \
--infile=$(BUILD_DIR)/anatomical-entities++qualities.txt \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-hasPartsInheringIns.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/has_part_inhering_in.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/has_part_inhering_in.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-phenotypeOfs.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/phenotype_of.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/phenotype_of.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-phenotypeOf-partOf.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/phenotype_of_part_of.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/phenotype_of_part_of.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

$(BUILD_DIR)/anatomical-entity-phenotypeOf-developsFrom.ofn: $(BUILD_DIR)/anatomical-entities.txt patterns/phenotype_of_develops_from.yaml
mkdir -p $(dir $@) \
&& dosdp-tools generate \
--generate-defined-class=true \
--obo-prefixes=true \
--template=patterns/phenotype_of_develops_from.yaml \
--infile=$< \
[email protected] \
&& mv [email protected] $@

# -----

# Generate anatomical-entities.txt
$(BUILD_DIR)/anatomical-entities.txt: $(BUILD_DIR)/bio-ontologies-classified.ttl $(BUILD_DIR)/defined-by-links.ttl $(SPARQL)/anatomicalEntities.sparql
$(ARQ) \
-q \
--data=$< \
--data=$(BUILD_DIR)/defined-by-links.ttl \
--results=TSV \
--query=$(SPARQL)/anatomicalEntities.sparql > [email protected] \
&& sed 's/^\?//' -i [email protected] \
&& mv [email protected] $@

# Generate qualities.txt
$(BUILD_DIR)/qualities.txt: $(BUILD_DIR)/bio-ontologies-classified.ttl $(SPARQL)/qualities.sparql
$(ROBOT) query \
-i $< \
--use-graphs true \
--query $(SPARQL)/qualities.sparql [email protected] \
&& mv [email protected] $@

# -----

# ----------

Expand Down Expand Up @@ -686,6 +565,7 @@ $(BUILD_DIR)/build-time.ttl: $(SPARQL)/build-time.sparql
$(DB_FILE): $(BLAZEGRAPH_PROPERTIES) \
$(BUILD_DIR)/phenoscape-kb.ttl \
$(BUILD_DIR)/subclass-closure.ttl $(BUILD_DIR)/instance-closure.ttl \
$(BUILD_DIR)/bio-ontologies-property-graphs.ttl $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl \
$(BUILD_DIR)/corpus-ics-taxa.ttl $(BUILD_DIR)/taxa-expect-scores.ttl $(BUILD_DIR)/taxa-pairwise-sim.ttl \
$(BUILD_DIR)/corpus-ics-genes.ttl $(BUILD_DIR)/gene-expect-scores.ttl $(BUILD_DIR)/gene-pairwise-sim.ttl \
$(BUILD_DIR)/phylopics.owl \
Expand All @@ -695,6 +575,8 @@ $(DB_FILE): $(BLAZEGRAPH_PROPERTIES) \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/" $(BUILD_DIR)/phenoscape-kb.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/closure" $(BUILD_DIR)/subclass-closure.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/closure" $(BUILD_DIR)/instance-closure.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/property_graphs" $(BUILD_DIR)/bio-ontologies-property-graphs.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/property_graphs" $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl && \
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$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/taxa" $(BUILD_DIR)/corpus-ics-taxa.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/taxa" $(BUILD_DIR)/taxa-expect-scores.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/taxa" $(BUILD_DIR)/taxa-pairwise-sim.ttl && \
Expand Down