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Adding direct links to entities based on EQs #3480

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Adding direct links to entities based on EQs #3480

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f2d306d
EQ Work
matentzn Dec 8, 2021
57bcc69
adding upheno
matentzn Dec 11, 2021
5cd1866
Update mp-odk.yaml
matentzn Dec 11, 2021
f27e2bc
Update relationships code
matentzn Dec 11, 2021
2af2190
Delete eq.owl
matentzn Dec 11, 2021
3615964
Merge branch 'main' into relation-graph-eq
matentzn Mar 4, 2022
81b4fc6
Update ODK
matentzn Mar 4, 2022
bd13855
Update method
matentzn Mar 4, 2022
026f13b
Update qc.yml
matentzn Mar 4, 2022
082aa3b
Add dynamic pheno make component
matentzn Mar 4, 2022
dd8aeca
Next update to pipeline
matentzn Mar 4, 2022
646e94d
Update eq-relations.owl
matentzn Mar 4, 2022
d134adf
Remove uPheno module
matentzn Mar 4, 2022
e6b34cd
Merge branch 'main' into relation-graph-eq
matentzn Mar 4, 2022
85fccb3
Delete upheno_import.owl
matentzn Mar 4, 2022
5caeb34
Delete upheno_terms.txt
matentzn Mar 4, 2022
e89cc0f
Update additional eqs
matentzn Mar 27, 2022
ab17c76
Merge branch 'main' into relation-graph-eq
matentzn Apr 8, 2022
ff5d028
Update Makefile
matentzn Apr 8, 2022
5619538
Update pheno.Makefile
matentzn Apr 8, 2022
a510bf4
Update pheno.Makefile
matentzn Apr 8, 2022
d92db74
Adding go plus and additional relation
matentzn Apr 10, 2022
ba10279
Added sparql-based occurs in materialisation
matentzn Apr 18, 2022
c144bb2
Update eq-relations.owl
matentzn Apr 18, 2022
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30 changes: 28 additions & 2 deletions src/ontology/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ TODAY ?= $(shell date +%Y-%m-%d)
OBODATE ?= $(shell date +'%d:%m:%Y %H:%M')
VERSION= $(TODAY)
ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
OTHER_SRC = $(PATTERNDIR)/definitions.owl
OTHER_SRC = $(PATTERNDIR)/definitions.owl $(COMPONENTSDIR)/eq-relations.owl
ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt
PATTERNDIR= ../patterns
PATTERN_TESTER= dosdp validate -i
Expand Down Expand Up @@ -307,6 +307,32 @@ no-mirror-refresh-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B


# ----------------------------------------
# Components
# ----------------------------------------
# Some ontologies contain external and internal components. A component is included in the ontology in its entirety.

COMP=true # Global parameter to bypass component generation

.PHONY: all_components
all_components: $(OTHER_SRC)

.PHONY: recreate-components
recreate-components:
$(MAKE) IMP=true MIR=true PAT=true IMP_LARGE=true all_components -B

.PHONY: recreate-%
recreate-%:
$(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=true $(COMPONENTSDIR)/$*.owl -B

$(COMPONENTSDIR)/%: | $(COMPONENTSDIR)
touch $@
.PRECIOUS: $(COMPONENTSDIR)/%





# ----------------------------------------
# Mirroring upstream ontologies
# ----------------------------------------
Expand Down Expand Up @@ -335,7 +361,7 @@ mirror-pr: | $(TMPDIR)
.PHONY: mirror-go
.PRECIOUS: $(MIRRORDIR)/go.owl
mirror-go: | $(TMPDIR)
if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(URIBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 && $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi
if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/go/go-base.owl -o [email protected] && mv [email protected] $(TMPDIR)/[email protected]; fi


## ONTOLOGY: uberon
Expand Down
2 changes: 2 additions & 0 deletions src/ontology/catalog-v001.xml
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Expand Up @@ -10,6 +10,8 @@
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/imports/pr_import.owl" uri="imports/pr_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/imports/ro_import.owl" uri="imports/ro_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/imports/uberon_import.owl" uri="imports/uberon_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/imports/upheno_import.owl" uri="imports/upheno_import.owl"/>
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/components/eq-relations.owl" uri="components/eq-relations.owl"/>
<uri id="Automatically generated entry, Timestamp=1569338358152" name="http://purl.obolibrary.org/obo/mp/patterns/definitions.owl" uri="../patterns/definitions.owl"/>
</group>
</catalog>
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