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Issue 125 relation graphs #198

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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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2 changes: 1 addition & 1 deletion Jenkinsfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
pipeline {
agent {
docker {
image 'phenoscape/pipeline-tools:v1.1'
image 'phenoscape/pipeline-tools:v1.3.1'
label 'zeppo'
}
}
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135 changes: 18 additions & 117 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ JVM_ARGS=JVM_ARGS=-Xmx80G
ARQ=$(JVM_ARGS) arq
RIOT=riot
BLAZEGRAPH-RUNNER=JAVA_OPTS=-Xmx80G blazegraph-runner
RELATIONGRAPH=JAVA_OPTS=-Xmx160G relation-graph

BIO-ONTOLOGIES=ontologies.ofn
# Path to data repo; must be separately downloaded/cloned
Expand All @@ -34,8 +35,8 @@ clean:
# 1. KB build
# 2. Semantic similarity


all: kb-build ss-scores-gen $(DB_FILE)
# disabled semantic similarity component
all: kb-build $(DB_FILE)

# ########## # ##########
# ########## # ##########
Expand Down Expand Up @@ -205,38 +206,26 @@ $(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)/anatomical-entity-absences.ofn $(BUILD_DIR)/phenex-tbox.ofn
$(ROBOT) merge \
-i $(BUILD_DIR)/bio-ontologies-classified.ttl \
-i $(BUILD_DIR)/defined-by-links.ttl \
-i $(BUILD_DIR)/anatomical-entity-absences.ofn \
-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
$(RELATIONGRAPH) --ontology-file $< \
--non-redundant-output-file $@ \
--redundant-output-file $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl \
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--mode rdf

# -----
# Built along with $(BUILD_DIR)/bio-ontologies-property-graphs.ttl
$(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl: $(BUILD_DIR)/bio-ontologies-property-graphs.ttl
touch $@

$(BUILD_DIR)/defined-by-links.ttl: $(BUILD_DIR)/bio-ontologies-merged.ttl $(SPARQL)/isDefinedBy.sparql
$(ROBOT) query \
Expand All @@ -245,16 +234,6 @@ $(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
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mkdir -p $(dir $@) \
&& dosdp-tools generate \
Expand All @@ -265,70 +244,6 @@ $(BUILD_DIR)/anatomical-entity-absences.ofn: $(BUILD_DIR)/anatomical-entities.tx
[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) \
Expand All @@ -340,15 +255,6 @@ $(BUILD_DIR)/anatomical-entities.txt: $(BUILD_DIR)/bio-ontologies-classified.ttl
&& 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 @@ -686,21 +592,16 @@ $(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)/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)/bio-ontologies-property-graphs.ttl $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl \
$(BUILD_DIR)/phylopics.owl \
$(BUILD_DIR)/vto_ncbi_common_names.owl \
$(BUILD_DIR)/build-time.ttl
$(BUILD_DIR)/vto_ncbi_common_names.owl \
$(BUILD_DIR)/build-time.ttl
rm -f $@ && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --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/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 && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/gene" $(BUILD_DIR)/corpus-ics-genes.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/gene" $(BUILD_DIR)/gene-expect-scores.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/sim/gene" $(BUILD_DIR)/gene-pairwise-sim.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/property_graphs/non-redundant" $(BUILD_DIR)/bio-ontologies-property-graphs.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/property_graphs/redundant" $(BUILD_DIR)/bio-ontologies-redundant-property-graphs.ttl && \
$(BLAZEGRAPH-RUNNER) load --informat=rdfxml --journal=$@ --properties=$< --graph="http://purl.org/phenoscape/phylopics.owl" $(BUILD_DIR)/phylopics.owl && \
$(BLAZEGRAPH-RUNNER) load --informat=rdfxml --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/" $(BUILD_DIR)/vto_ncbi_common_names.owl && \
$(BLAZEGRAPH-RUNNER) load --informat=turtle --journal=$@ --properties=$< --graph="http://kb.phenoscape.org/" $(BUILD_DIR)/build-time.ttl
Expand Down
23 changes: 0 additions & 23 deletions patterns/has_part.yaml
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23 changes: 0 additions & 23 deletions patterns/has_part_inhering_in.yaml
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23 changes: 0 additions & 23 deletions patterns/implies_presence_of.yaml
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23 changes: 0 additions & 23 deletions patterns/part_of.yaml
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23 changes: 0 additions & 23 deletions patterns/phenotype_of.yaml
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18 changes: 0 additions & 18 deletions patterns/phenotype_of_develops_from.yaml
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18 changes: 0 additions & 18 deletions patterns/phenotype_of_part_of.yaml
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2 changes: 1 addition & 1 deletion run.sh
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Expand Up @@ -7,7 +7,7 @@
# Usage example
# ./run.sh make all

IMAGE_VERSION=v1.1
IMAGE_VERSION=v1.3.1

# cd pipeline_dir
# docker pull phenoscape/pipeline-tools:$IMAGE_VERSION
Expand Down
2 changes: 1 addition & 1 deletion sparql/absences.sparql
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Expand Up @@ -8,7 +8,7 @@ PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT DISTINCT ?taxon (ps:has_absence_of AS ?p) ?entity
WHERE {
?taxon ps:exhibits_state/ps:describes_phenotype/rdfs:subClassOf/ps:absence_of ?phenotypeEntity .
?entity ^ps:implies_presence_of_some/rdfs:subClassOf/ps:implies_presence_of_some ?phenotypeEntity .
?phenotypeEntity ps:implies_presence_of|^rdfs:subClassOf ?entity .
?entity rdfs:isDefinedBy <http://purl.obolibrary.org/obo/uberon.owl> .
?taxon rdfs:isDefinedBy <http://purl.obolibrary.org/obo/vto.owl> .
}
2 changes: 1 addition & 1 deletion sparql/presences.sparql
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Expand Up @@ -6,7 +6,7 @@ WHERE {
?taxon <http://www.w3.org/2000/01/rdf-schema#isDefinedBy> <http://purl.obolibrary.org/obo/vto.owl> .
?entity <http://www.w3.org/2000/01/rdf-schema#isDefinedBy> <http://purl.obolibrary.org/obo/uberon.owl> .

?taxon <http://purl.org/phenoscape/vocab.owl#exhibits_state>/<http://purl.org/phenoscape/vocab.owl#describes_phenotype>/(<http://www.w3.org/2000/01/rdf-schema#subClassOf>)/<http://purl.org/phenoscape/vocab.owl#implies_presence_of_some> ?entity .
?taxon ps:exhibits_state/ps:describes_phenotype/ps:implies_presence_of ?entity .

#?taxon rdfs:subClassOf* <http://purl.obolibrary.org/obo/VTO_0000001> .
#?entity rdfs:subClassOf* <http://purl.obolibrary.org/obo/UBERON_0001062>
Expand Down