From eb60278b71a11fa51047ea6716a7bbb4e21478e6 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 12 Mar 2024 15:26:03 -0400 Subject: [PATCH 1/3] Update ODK config --- src/ontology/phenio-odk.yaml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/src/ontology/phenio-odk.yaml b/src/ontology/phenio-odk.yaml index 159062f..e889d98 100644 --- a/src/ontology/phenio-odk.yaml +++ b/src/ontology/phenio-odk.yaml @@ -72,12 +72,6 @@ components: # make_base: TRUE # base_iris: # - http://purl.obolibrary.org/obo/FAO_ - - filename: ddpheno.owl - source: http://purl.obolibrary.org/obo/ddpheno.owl - make_base: TRUE - base_iris: - - http://purl.obolibrary.org/obo/ddpheno# - - http://purl.obolibrary.org/obo/DDPHENO_ - filename: emapa.owl source: http://purl.obolibrary.org/obo/emapa.owl make_base: TRUE @@ -140,6 +134,8 @@ components: - http://purl.obolibrary.org/obo/XPO_ - http://purl.obolibrary.org/obo/ZP_ - http://purl.obolibrary.org/obo/FYPO_ + - http://purl.obolibrary.org/obo/DDPHENO_ + - http://purl.obolibrary.org/obo/DDANAT_ - filename: wbbt.owl source: http://purl.obolibrary.org/obo/wbbt.owl make_base: TRUE From 6f613e1fafa51b790fff9ac52ecf241cad23d92d Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 12 Mar 2024 15:28:16 -0400 Subject: [PATCH 2/3] Update additional configs --- src/ontology/catalog-v001.xml | 2 -- src/ontology/phenio-edit.owl | 1 - 2 files changed, 3 deletions(-) diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml index 2594850..ad0e94a 100644 --- a/src/ontology/catalog-v001.xml +++ b/src/ontology/catalog-v001.xml @@ -61,8 +61,6 @@ - - diff --git a/src/ontology/phenio-edit.owl b/src/ontology/phenio-edit.owl index 9e3940d..3681815 100644 --- a/src/ontology/phenio-edit.owl +++ b/src/ontology/phenio-edit.owl @@ -12,7 +12,6 @@ Prefix(dcterms:=) Ontology( Import() -Import() Import() #Import() Import() From 5e4c3bf242a9e996f473ece738a769cdeb06ac0b Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Tue, 12 Mar 2024 15:29:46 -0400 Subject: [PATCH 3/3] Update repo files --- docs/odk-workflows/RepositoryFileStructure.md | 1 - src/ontology/Makefile | 21 +++---------------- 2 files changed, 3 insertions(+), 19 deletions(-) diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index 137f938..6c9b6ef 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -46,7 +46,6 @@ These are the components in PHENIO | Filename | URL | | -------- | --- | | bfo.owl | http://purl.obolibrary.org/obo/bfo.owl | -| ddpheno.owl | http://purl.obolibrary.org/obo/ddpheno.owl | | emapa.owl | http://purl.obolibrary.org/obo/emapa.owl | | fbbt.owl | http://purl.obolibrary.org/obo/fbbt.owl | | go.owl | http://purl.obolibrary.org/obo/go.owl | diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 9fa8b42..0cce16c 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -10,7 +10,7 @@ # More information: https://github.com/INCATools/ontology-development-kit/ # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 1126eedd8e58276f7dc4423f54c5463ff19cc8d1c79755b1eb65763cea44fb0f +CONFIG_HASH= ff6f93caf8c93bf6c4c5c663944a984e193688503d790d719a90a5de2d147045 # ---------------------------------------- @@ -53,7 +53,7 @@ OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') VERSION= $(TODAY) ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ -OTHER_SRC = $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/ddpheno.owl $(COMPONENTSDIR)/emapa.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl +OTHER_SRC = $(COMPONENTSDIR)/bfo.owl $(COMPONENTSDIR)/emapa.owl $(COMPONENTSDIR)/fbbt.owl $(COMPONENTSDIR)/go.owl $(COMPONENTSDIR)/hsapdv.owl $(COMPONENTSDIR)/mondo.owl $(COMPONENTSDIR)/mpath.owl $(COMPONENTSDIR)/nbo.owl $(COMPONENTSDIR)/ro.owl $(COMPONENTSDIR)/uberon.owl $(COMPONENTSDIR)/upheno.owl $(COMPONENTSDIR)/wbbt.owl $(COMPONENTSDIR)/zfa.owl ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl @@ -454,21 +454,6 @@ $(COMPONENTSDIR)/bfo.owl: component-download-bfo.owl .PRECIOUS: $(COMPONENTSDIR)/bfo.owl -.PHONY: component-download-ddpheno.owl -component-download-ddpheno.owl: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/ddpheno.owl \ - remove --base-iri http://purl.obolibrary.org/obo/ddpheno# --base-iri http://purl.obolibrary.org/obo/DDPHENO_ --axioms external --preserve-structure false --trim false \ - annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi - -$(COMPONENTSDIR)/ddpheno.owl: component-download-ddpheno.owl - if [ $(COMP) = true ]; then if cmp -s $(TMPDIR)/component-download-ddpheno.owl.owl $(TMPDIR)/component-download-ddpheno.owl.tmp.owl ; then echo "Component identical."; \ - else echo "Component is different, updating." &&\ - cp $(TMPDIR)/component-download-ddpheno.owl.owl $(TMPDIR)/component-download-ddpheno.owl.tmp.owl &&\ - $(ROBOT) annotate -i $(TMPDIR)/component-download-ddpheno.owl.owl --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@; fi; fi - -.PRECIOUS: $(COMPONENTSDIR)/ddpheno.owl - - .PHONY: component-download-emapa.owl component-download-emapa.owl: | $(TMPDIR) if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/emapa.owl \ @@ -606,7 +591,7 @@ $(COMPONENTSDIR)/uberon.owl: component-download-uberon.owl .PHONY: component-download-upheno.owl component-download-upheno.owl: | $(TMPDIR) if [ $(MIR) = true ] && [ $(COMP) = true ]; then $(ROBOT) merge -I http://purl.obolibrary.org/obo/upheno/v2/upheno.owl \ - remove --base-iri http://purl.obolibrary.org/obo/UPHENO_ --base-iri http://purl.obolibrary.org/obo/HP_ --base-iri http://purl.obolibrary.org/obo/MP_ --base-iri http://purl.obolibrary.org/obo/WBPhenotype_ --base-iri http://purl.obolibrary.org/obo/XPO_ --base-iri http://purl.obolibrary.org/obo/ZP_ --base-iri http://purl.obolibrary.org/obo/FYPO_ --axioms external --preserve-structure false --trim false \ + remove --base-iri http://purl.obolibrary.org/obo/UPHENO_ --base-iri http://purl.obolibrary.org/obo/HP_ --base-iri http://purl.obolibrary.org/obo/MP_ --base-iri http://purl.obolibrary.org/obo/WBPhenotype_ --base-iri http://purl.obolibrary.org/obo/XPO_ --base-iri http://purl.obolibrary.org/obo/ZP_ --base-iri http://purl.obolibrary.org/obo/FYPO_ --base-iri http://purl.obolibrary.org/obo/DDPHENO_ --base-iri http://purl.obolibrary.org/obo/DDANAT_ --axioms external --preserve-structure false --trim false \ annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $(TMPDIR)/$@.owl; fi $(COMPONENTSDIR)/upheno.owl: component-download-upheno.owl