From a38f45c7c138753e4e29e9d91e104ecbf364d3ae Mon Sep 17 00:00:00 2001 From: William Hogan Date: Wed, 16 Oct 2024 08:20:22 -0500 Subject: [PATCH 1/2] updated qc.yml file to ODK 1.5.2 and actions@v4. Also fixes #248 --- .github/workflows/qc.yml | 6 +- docs/odk-workflows/ManageDocumentation.md | 1 + docs/odk-workflows/RepoManagement.md | 2 +- src/ontology/Makefile | 193 ++++++++++++++-------- src/ontology/imports/external_import.owl | 9 - src/ontology/omrse-edit.owl | 4 +- src/ontology/run.sh | 38 ++++- src/scripts/update_repo.sh | 5 +- src/sparql/class-count-by-prefix.sparql | 2 +- src/templates/external_import.tsv | 9 - 10 files changed, 170 insertions(+), 99 deletions(-) diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml index 4c560cf..110af6c 100644 --- a/.github/workflows/qc.yml +++ b/.github/workflows/qc.yml @@ -19,15 +19,15 @@ jobs: ontology_qc: # The type of runner that the job will run on runs-on: ubuntu-latest - container: obolibrary/odkfull:v1.4 + container: obolibrary/odkfull:v1.5.2 # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + - uses: actions/checkout@v3 - name: Run ontology QC checks env: DEFAULT_BRANCH: main - run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md index cf72dec..748a6f9 100644 --- a/docs/odk-workflows/ManageDocumentation.md +++ b/docs/odk-workflows/ManageDocumentation.md @@ -44,3 +44,4 @@ The documentation is _not_ automatically updated from the Markdown, and needs to Just make sure you give GitHub 2-5 minutes to build the pages! + diff --git a/docs/odk-workflows/RepoManagement.md b/docs/odk-workflows/RepoManagement.md index 701ce51..141bec3 100644 --- a/docs/odk-workflows/RepoManagement.md +++ b/docs/odk-workflows/RepoManagement.md @@ -2,7 +2,7 @@ ## Updating your ODK repository -Your ODK repositories configuration is managed in `src/ontology/omrse-odk.yaml`. Once you have made your changes, you can run the following to apply your changes to the repository: +Your ODK repositories configuration is managed in `src/ontology/omrse-odk.yaml`. The [ODK Project Configuration Schema](https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md) defines all possible parameters that can be used in this config YAML. Once you have made your changes, you can run the following to apply your changes to the repository: ``` diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 49653b4..078b681 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1,7 +1,7 @@ # ---------------------------------------- # Makefile for omrse # Generated using ontology-development-kit -# ODK Version: v1.4.3 +# ODK Version: v1.5.2 # ---------------------------------------- # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use omrse.Makefile instead @@ -15,6 +15,9 @@ # 2. [Refresh imports](all_imports) # 3. [Update repo to latest ODK](update_repo) +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= 6d7fdabc7e6d622e63f340c8f29791bf031e15c86faa2df55199cd04a497bc9f + # ---------------------------------------- # Standard Constants @@ -50,7 +53,7 @@ REPORT_PROFILE_OPTS = --profile $(ROBOT_PROFILE) OBO_FORMAT_OPTIONS = SPARQL_VALIDATION_CHECKS = equivalent-classes owldef-self-reference iri-range SPARQL_EXPORTS = basic-report class-count-by-prefix edges xrefs obsoletes synonyms -ODK_VERSION_MAKEFILE = v1.4.3 +ODK_VERSION_MAKEFILE = v1.5.2 TODAY ?= $(shell date +%Y-%m-%d) OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') @@ -65,6 +68,11 @@ FORMATS = $(sort owl obo json owl) FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full ) +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif + # ---------------------------------------- # Top-level targets # ---------------------------------------- @@ -75,12 +83,16 @@ RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full ) all: all_odk .PHONY: all_odk -all_odk: odkversion test all_assets +all_odk: odkversion config_check test custom_reports all_assets .PHONY: test test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt echo "Finished running all tests successfully." +.PHONY: test +test_fast: + $(MAKE_FAST) test + .PHONY: release_diff release_diff: $(REPORTDIR)/release-diff.md @@ -91,13 +103,52 @@ reason_test: $(EDIT_PREPROCESSED) .PHONY: odkversion odkversion: - echo "ODK Makefile version: $(ODK_VERSION_MAKEFILE) (this is the version of the ODK with which this Makefile was generated, \ - not the version of the ODK you are running)" &&\ - echo "ROBOT version (ODK): " && $(ROBOT) --version + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): mkdir -p $@ +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in omrse.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -187,11 +238,11 @@ validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) -sparql_test: omrse-base.owl catalog-v001.xml | $(REPORTDIR) +sparql_test: omrse-base.owl | $(REPORTDIR) ifneq ($(SPARQL_VALIDATION_QUERIES),) - $(ROBOT) verify --catalog catalog-v001.xml -i omrse-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) + $(ROBOT) verify -i omrse-base.owl --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) endif # ---------------------------------------- @@ -204,6 +255,14 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri $(URIBASE)/OMRSE_ --base-iri $(URIBASE)/omrse --print 5 -o $@ +check_for_robot_updates: + @cut -f2 "/tools/robot_report_profile.txt" | sort > $(TMPDIR)/sorted_tsv2.txt + @cut -f2 "$(ROBOT_PROFILE)" | sort > $(TMPDIR)/sorted_tsv1.txt + @comm -23 $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/sorted_tsv1.txt > $(TMPDIR)/missing.txt + @echo "Missing tests:" + @cat $(TMPDIR)/missing.txt + @rm $(TMPDIR)/sorted_tsv1.txt $(TMPDIR)/sorted_tsv2.txt $(TMPDIR)/missing.txt $(TMPDIR)/report_profile_robot.txt + # ---------------------------------------- # Release assets # ---------------------------------------- @@ -220,7 +279,7 @@ RELEASE_ASSETS = \ $(SUBSET_FILES) .PHONY: all_assets -all_assets: $(ASSETS) +all_assets: $(ASSETS) check_rdfxml_assets .PHONY: show_assets show_assets: @@ -228,7 +287,7 @@ show_assets: du -sh $(ASSETS) check_rdfxml_%: % - @check-rdfxml $< + @check-rdfxml $< .PHONY: check_rdfxml_assets check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) @@ -346,7 +405,7 @@ $(IMPORTDIR)/ogms_import.owl: $(MIRRORDIR)/ogms.owl $(IMPORTDIR)/ogms_terms_comb if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/ogms_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ remove --base-iri http://purl.obolibrary.org/obo/OGMS_ --base-iri http://purl.obolibrary.org/obo/BFO_ --base-iri http://purl.obolibrary.org/obo/OBI_ --axioms external --preserve-structure false --trim false \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/ogms_terms_combined.txt --select complement \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/ogms_terms_combined.txt --select complement \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi @@ -356,7 +415,7 @@ $(IMPORTDIR)/obib_import.owl: $(MIRRORDIR)/obib.owl $(IMPORTDIR)/obib_terms_comb if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ extract -T $(IMPORTDIR)/obib_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ remove --base-iri http://purl.obolibrary.org/obo/OBIB_ --base-iri http://purl.obolibrary.org/obo/OMIABIS_ --base-iri http://purl.obolibrary.org/obo/BFO_ --axioms external --preserve-structure false --trim false \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/obib_terms_combined.txt --select complement \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/obib_terms_combined.txt --select complement \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi @@ -434,9 +493,9 @@ recreate-%: no-mirror-recreate-%: $(MAKE) COMP=true IMP=false IMP_LARGE=false MIR=false PAT=true $(COMPONENTSDIR)/$*.owl -B -$(COMPONENTSDIR)/%: | $(COMPONENTSDIR) - touch $@ -.PRECIOUS: $(COMPONENTSDIR)/% +$(COMPONENTSDIR)/%.owl: | $(COMPONENTSDIR) + test -f $@ || touch $@ +.PRECIOUS: $(COMPONENTSDIR)/%.owl # ---------------------------------------- @@ -447,145 +506,135 @@ IMP=true # Global parameter to bypass import generation MIR=true # Global parameter to bypass mirror generation IMP_LARGE=true # Global parameter to bypass handling of large imports +ifeq ($(strip $(MIR)),true) ## ONTOLOGY: ro .PHONY: mirror-ro .PRECIOUS: $(MIRRORDIR)/ro.owl mirror-ro: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ro.owl --create-dirs -o $(MIRRORDIR)/ro.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/ro.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/ro.owl --create-dirs -o $(TMPDIR)/ro-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/ro-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: ogms .PHONY: mirror-ogms .PRECIOUS: $(MIRRORDIR)/ogms.owl mirror-ogms: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/ogms.owl --create-dirs -o $(MIRRORDIR)/ogms.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/ogms.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/ogms.owl --create-dirs -o $(TMPDIR)/ogms-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/ogms-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: obi .PHONY: mirror-obi .PRECIOUS: $(MIRRORDIR)/obi.owl mirror-obi: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obi.owl --create-dirs -o $(MIRRORDIR)/obi.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/obi.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/obi.owl --create-dirs -o $(TMPDIR)/obi-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/obi-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: apollo_sv .PHONY: mirror-apollo_sv .PRECIOUS: $(MIRRORDIR)/apollo_sv.owl mirror-apollo_sv: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/apollo_sv.owl --create-dirs -o $(MIRRORDIR)/apollo_sv.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/apollo_sv.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/apollo_sv.owl --create-dirs -o $(TMPDIR)/apollo_sv-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/apollo_sv-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: obib .PHONY: mirror-obib .PRECIOUS: $(MIRRORDIR)/obib.owl mirror-obib: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/obib.owl --create-dirs -o $(MIRRORDIR)/obib.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/obib.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/obib.owl --create-dirs -o $(TMPDIR)/obib-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/obib-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: go .PHONY: mirror-go .PRECIOUS: $(MIRRORDIR)/go.owl mirror-go: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/go.owl --create-dirs -o $(MIRRORDIR)/go.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/go.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/go.owl --create-dirs -o $(TMPDIR)/go-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/go-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: oae .PHONY: mirror-oae .PRECIOUS: $(MIRRORDIR)/oae.owl mirror-oae: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/oae.owl --create-dirs -o $(MIRRORDIR)/oae.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/oae.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/oae.owl --create-dirs -o $(TMPDIR)/oae-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/oae-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: pco .PHONY: mirror-pco .PRECIOUS: $(MIRRORDIR)/pco.owl mirror-pco: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/pco.owl --create-dirs -o $(MIRRORDIR)/pco.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/pco.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/pco.owl --create-dirs -o $(TMPDIR)/pco-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/pco-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: bfo .PHONY: mirror-bfo .PRECIOUS: $(MIRRORDIR)/bfo.owl mirror-bfo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(MIRRORDIR)/bfo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/bfo.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/bfo.owl --create-dirs -o $(TMPDIR)/bfo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/bfo-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: oostt .PHONY: mirror-oostt .PRECIOUS: $(MIRRORDIR)/oostt.owl mirror-oostt: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/oostt.owl --create-dirs -o $(MIRRORDIR)/oostt.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/oostt.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/oostt.owl --create-dirs -o $(TMPDIR)/oostt-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/oostt-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: omo .PHONY: mirror-omo .PRECIOUS: $(MIRRORDIR)/omo.owl mirror-omo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/omo.owl --create-dirs -o $(MIRRORDIR)/omo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/omo.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/omo.owl --create-dirs -o $(TMPDIR)/omo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/omo-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: pno .PHONY: mirror-pno .PRECIOUS: $(MIRRORDIR)/pno.owl mirror-pno: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/pno.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/pno.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: d-acts .PHONY: mirror-d-acts .PRECIOUS: $(MIRRORDIR)/d-acts.owl mirror-d-acts: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then $(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/d-acts.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + $(ROBOT) convert -I http://purl.obolibrary.org/obo/iao/d-acts.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: geo .PHONY: mirror-geo .PRECIOUS: $(MIRRORDIR)/geo.owl mirror-geo: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/geo.owl --create-dirs -o $(MIRRORDIR)/geo.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/geo.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/geo.owl --create-dirs -o $(TMPDIR)/geo-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/geo-download.owl -o $(TMPDIR)/$@.owl ## ONTOLOGY: mf .PHONY: mirror-mf .PRECIOUS: $(MIRRORDIR)/mf.owl mirror-mf: | $(TMPDIR) - if [ $(MIR) = true ] && [ $(IMP) = true ]; then curl -L $(OBOBASE)/mf.owl --create-dirs -o $(MIRRORDIR)/mf.owl --retry 4 --max-time 200 &&\ - $(ROBOT) convert -i $(MIRRORDIR)/mf.owl -o $@.tmp.owl &&\ - mv $@.tmp.owl $(TMPDIR)/$@.owl; fi + curl -L $(OBOBASE)/mf.owl --create-dirs -o $(TMPDIR)/mf-download.owl --retry 4 --max-time 200 && \ + $(ROBOT) convert -i $(TMPDIR)/mf-download.owl -o $(TMPDIR)/$@.owl $(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) - if [ $(IMP) = true ] && [ $(MIR) = true ] && [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ cp $(TMPDIR)/mirror-$*.owl $@; fi; fi +else # MIR=false +$(MIRRORDIR)/%.owl: + @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." +endif @@ -668,9 +717,13 @@ ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< # ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) -# base: All the axioms as they are editted by the editors, excluding reasoning -$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) - $(ROBOT_RELEASE_IMPORT_MODE_BASE) \ +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri $(URIBASE)/OMRSE --axioms external --preserve-structure false --trim false \ $(SHARED_ROBOT_COMMANDS) \ annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ @@ -737,13 +790,16 @@ update_repo: update_docs: mkdocs gh-deploy --config-file ../../mkdocs.yaml -# Note to future generations: prepending ./ is a safety measure to ensure that -# the environment does not malicously set `CLEANFILES` to `\`. +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. .PHONY: clean clean: - [ -n "$(MIRRORDIR)" ] && [ $(MIRRORDIR) != "." ] && [ $(MIRRORDIR) != "/" ] && [ $(MIRRORDIR) != ".." ] && [ -d ./$(MIRRORDIR) ] && rm -rf ./$(MIRRORDIR)/* - [ -n "$(TMPDIR)" ] && [ $(TMPDIR) != "." ] && [ $(TMPDIR) != "/" ] && [ $(TMPDIR) != ".." ] && [ -d ./$(TMPDIR) ] && rm -rf ./$(TMPDIR)/* - [ -n "$(UPDATEREPODIR)" ] && [ $(UPDATEREPODIR) != "." ] && [ $(UPDATEREPODIR) != "/" ] && [ $(UPDATEREPODIR) != ".." ] && [ -d ./$(UPDATEREPODIR) ] && rm -rf ./$(UPDATEREPODIR)/* + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done rm -f $(CLEANFILES) .PHONY: help @@ -762,6 +818,7 @@ Core commands: * prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. * update_repo: Update the ODK repository setup using the config file omrse-odk.yaml * test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components * odkversion: Show the current version of the ODK Makefile and ROBOT. * clean: Delete all temporary files * help: Print ODK Usage information @@ -779,7 +836,7 @@ Imports management: Editor utilities: * validate_idranges: Make sure your ID ranges file is formatted correctly -* normalize_src: Load and safe your omrse-edit file after you to make sure its serialised correctly +* normalize_src: Load and save your omrse-edit file after you to make sure its serialised correctly * explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes * validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files * validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl index 6b07f9c..7bd7cf7 100644 --- a/src/ontology/imports/external_import.owl +++ b/src/ontology/imports/external_import.owl @@ -49,15 +49,6 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) diff --git a/src/ontology/omrse-edit.owl b/src/ontology/omrse-edit.owl index 392fab9..046281b 100644 --- a/src/ontology/omrse-edit.owl +++ b/src/ontology/omrse-edit.owl @@ -29,7 +29,7 @@ Import() Import() Import() Import() -Import() +Import() Annotation(dc:contributor "Barry Smith"@en) Annotation(dc:contributor "Chris Stoeckert"@en) Annotation(dc:contributor "Daniel Welch"@en) @@ -3588,4 +3588,4 @@ AnnotationAssertion(rdfs:label obo:IAO_0000412 "imported from"@en) AnnotationAssertion(owl:deprecated obo:OMIABIS_0000060 "true"^^xsd:boolean) AnnotationAssertion(owl:deprecated obo:OMIABIS_0001025 "true"^^xsd:boolean) AnnotationAssertion(owl:deprecated obo:OMIABIS_0001035 "true"^^xsd:boolean) -) \ No newline at end of file +) diff --git a/src/ontology/run.sh b/src/ontology/run.sh index 2718ff6..873e9bd 100644 --- a/src/ontology/run.sh +++ b/src/ontology/run.sh @@ -14,6 +14,8 @@ # # See README-editors.md for more details. +set -e + if [ -f run.sh.conf ]; then . ./run.sh.conf fi @@ -29,6 +31,22 @@ elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/tok GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") fi +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + ODK_IMAGE=${ODK_IMAGE:-odkfull} TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') if [ -n "$TAG_IN_IMAGE" ]; then @@ -40,16 +58,28 @@ ODK_TAG=${ODK_TAG:-latest} ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} ODK_DEBUG=${ODK_DEBUG:-no} +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + TIMECMD= if [ x$ODK_DEBUG = xyes ]; then # If you wish to change the format string, take care of using # non-breaking spaces (U+00A0) instead of normal spaces, to # prevent the shell from tokenizing the format string. - echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps." + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" fi +rm -f tmp/debug.log -VOLUME_BIND=$PWD/../../:/work +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND WORK_DIR=/work/src/ontology if [ -n "$ODK_BINDS" ]; then @@ -59,14 +89,14 @@ fi if [ -n "$USE_SINGULARITY" ]; then singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ - --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS" \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ --bind $VOLUME_BIND \ -W $WORK_DIR \ docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" else BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ - -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" fi diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index d426e47..38b7417 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -26,7 +26,8 @@ cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ mkdir -p $ROOTDIR/.github mkdir -p $ROOTDIR/.github/workflows -cp -n target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml +cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml @@ -35,5 +36,5 @@ cp target/$OID/.github/workflows/docs.yml $ROOTDIR/.github/workflows/docs.yml cp -n target/$OID/mkdocs.yaml $ROOTDIR/ echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" -echo "WARNING: Your QC workflows have not been updated automatically. Please update the ODK version number(s) in .github/workflows/qc.yml." + echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/sparql/class-count-by-prefix.sparql b/src/sparql/class-count-by-prefix.sparql index 0c4d284..a6a4851 100644 --- a/src/sparql/class-count-by-prefix.sparql +++ b/src/sparql/class-count-by-prefix.sparql @@ -7,4 +7,4 @@ SELECT ?prefix (COUNT(DISTINCT ?cls) AS ?numberOfClasses) WHERE FILTER (!isBlank(?cls)) BIND( STRBEFORE(STRAFTER(str(?cls),"http://purl.obolibrary.org/obo/"), "_") AS ?prefix) } -GROUP BY ?prefix +GROUP BY ?prefix \ No newline at end of file diff --git a/src/templates/external_import.tsv b/src/templates/external_import.tsv index e590759..19df716 100644 --- a/src/templates/external_import.tsv +++ b/src/templates/external_import.tsv @@ -10,15 +10,6 @@ BFO:0000054 owl:ObjectProperty BFO:0000055 owl:ObjectProperty BFO:0000066 owl:ObjectProperty BFO:0000067 owl:ObjectProperty -BFO:0000075 owl:ObjectProperty -BFO:0000117 owl:ObjectProperty -BFO:0000118 owl:ObjectProperty -BFO:0000121 owl:ObjectProperty -BFO:0000181 owl:ObjectProperty -BFO:0000132 owl:ObjectProperty -BFO:0000138 owl:ObjectProperty -BFO:0000139 owl:ObjectProperty -BFO:0000136 owl:ObjectProperty GEO:000000400 owl:Class GO:0007610 owl:Class GO:0008150 owl:Class From 29ed61d42a0ec9b410be5b2ed9b4055c09fe7af4 Mon Sep 17 00:00:00 2001 From: William Hogan Date: Mon, 25 Nov 2024 10:56:20 -0600 Subject: [PATCH 2/2] fixing a number of issues, including version of ODK in qc.yml, name of ontology in omrse-odk.yml, and re-import of old OMRSE stuff from d-acdts, which was causing reasoner error on build --- docs/odk-workflows/ManageDocumentation.md | 4 +- docs/odk-workflows/ReleaseWorkflow.md | 2 +- docs/odk-workflows/RepositoryFileStructure.md | 2 +- omrse-base.json | 290 +- omrse-base.obo | 92 +- omrse-base.owl | 480 +- omrse-full.json | 863 +-- omrse-full.obo | 338 +- omrse-full.owl | 880 +-- omrse.json | 863 +-- omrse.obo | 342 +- omrse.owl | 880 +-- src/ontology/Makefile | 16 +- src/ontology/imports/d-acts_import.owl | 5756 +---------------- src/ontology/imports/d-acts_terms.txt | 8 +- src/ontology/imports/external_import.owl | 1 + src/ontology/omrse-odk.yaml | 11 +- src/templates/external_import.tsv | 1 + 18 files changed, 765 insertions(+), 10064 deletions(-) diff --git a/docs/odk-workflows/ManageDocumentation.md b/docs/odk-workflows/ManageDocumentation.md index 748a6f9..522cb9b 100644 --- a/docs/odk-workflows/ManageDocumentation.md +++ b/docs/odk-workflows/ManageDocumentation.md @@ -38,9 +38,9 @@ The documentation is _not_ automatically updated from the Markdown, and needs to If everything was successful, you will see a message similar to this one: ``` - INFO - Your documentation should shortly be available at: https://ufbmi.github.io/OMRSE/ + INFO - Your documentation should shortly be available at: https://mcwdsi.github.io/OMRSE/ ``` -3. Just to double check, you can now navigate to your documentation pages (usually https://ufbmi.github.io/OMRSE/). +3. Just to double check, you can now navigate to your documentation pages (usually https://mcwdsi.github.io/OMRSE/). Just make sure you give GitHub 2-5 minutes to build the pages! diff --git a/docs/odk-workflows/ReleaseWorkflow.md b/docs/odk-workflows/ReleaseWorkflow.md index f329a84..2c7139f 100644 --- a/docs/odk-workflows/ReleaseWorkflow.md +++ b/docs/odk-workflows/ReleaseWorkflow.md @@ -44,7 +44,7 @@ Once your [CI checks](ContinuousIntegration.md) have passed, and your reviews ar ## Create a GitHub release -1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/ufbmi/OMRSE/releases). Then click "Draft new release" +1. Go to your releases page on GitHub by navigating to your repository, and then clicking on releases (usually on the right, for example: https://github.com/mcwdsi/OMRSE/releases). Then click "Draft new release" 1. As the tag version you **need to choose the date on which your ontologies were build.** You can find this, for example, by looking at the `omrse.obo` file and check the `data-version:` property. The date needs to be prefixed with a `v`, so, for example `v2020-02-06`. 1. You can write whatever you want in the release title, but we typically write the date again. The description underneath should contain a concise list of changes or term additions. 1. Click "Publish release". Done. diff --git a/docs/odk-workflows/RepositoryFileStructure.md b/docs/odk-workflows/RepositoryFileStructure.md index a798370..0debd1a 100644 --- a/docs/odk-workflows/RepositoryFileStructure.md +++ b/docs/odk-workflows/RepositoryFileStructure.md @@ -28,7 +28,7 @@ These are the current imports in OMRSE | oostt | http://purl.obolibrary.org/obo/oostt.owl | None | | omo | http://purl.obolibrary.org/obo/omo.owl | mirror | | pno | http://purl.obolibrary.org/obo/iao/pno.owl | mirror | -| d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | mirror | +| d-acts | http://purl.obolibrary.org/obo/iao/d-acts.owl | filter | | geo | http://purl.obolibrary.org/obo/geo.owl | None | | mf | http://purl.obolibrary.org/obo/mf.owl | None | diff --git a/omrse-base.json b/omrse-base.json index 3566cb5..04bd6c2 100644 --- a/omrse-base.json +++ b/omrse-base.json @@ -70,9 +70,9 @@ "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-14" + "val" : "2024-11-25" } ], - "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-08-14/omrse-base.json" + "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-11-25/omrse-base.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032", @@ -128,9 +128,6 @@ }, { "id" : "http://purl.obolibrary.org/obo/GO_0007610", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0008150", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000001", "type" : "CLASS" @@ -170,9 +167,6 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000578", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020022", - "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021001", "type" : "CLASS" @@ -5398,24 +5392,6 @@ "id" : "http://purl.obolibrary.org/obo/OBI_0001688", "type" : "PROPERTY", "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000009", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000020", "lbl" : "obsolete is-aggregate-of", @@ -5662,14 +5638,6 @@ "id" : "http://purl.obolibrary.org/obo/RO_0002087", "type" : "PROPERTY", "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002217", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002218", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", "type" : "PROPERTY", @@ -13317,7 +13285,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", - "lbl" : "definition", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -13334,7 +13301,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", - "lbl" : "definition source", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -13419,10 +13385,6 @@ "val" : "William R. Hogan" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/omrse/language-individuals/imports", - "type" : "PROPERTY", - "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/elements/1.1/contributor", "type" : "PROPERTY", @@ -13459,30 +13421,8 @@ "id" : "http://purl.org/dc/terms/source", "type" : "PROPERTY", "propertyType" : "ANNOTATION" - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0000412", - "lbl" : "imported from" - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000060", - "meta" : { - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001025", - "meta" : { - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001035", - "meta" : { - "deprecated" : true - } } ], "edges" : [ { - "sub" : "http://purl.obolibrary.org/obo/GO_0008150", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000015" - }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000000", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000578" @@ -13492,8 +13432,8 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000001", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000002", "pred" : "is_a", @@ -13512,8 +13452,8 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000004" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000005", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000006", "pred" : "is_a", @@ -13521,11 +13461,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000007", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000007", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000008", "pred" : "is_a", @@ -13548,8 +13484,8 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000010" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000011", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000012", "pred" : "is_a", @@ -13560,16 +13496,16 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000012" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000013", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000014", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000012" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000014", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000015", "pred" : "is_a", @@ -13609,19 +13545,19 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000051" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000025", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000026", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000027", "pred" : "is_a", @@ -13634,6 +13570,14 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000029", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000011" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000031", "pred" : "is_a", @@ -13646,6 +13590,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", + "pred" : "http://purl.obolibrary.org/obo/RO_0002351", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000034", "pred" : "is_a", @@ -13669,19 +13617,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000039", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000039", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000040", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000040", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000041", "pred" : "is_a", @@ -13710,10 +13650,38 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000047", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000048", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000049", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000049" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000050", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000051", + "pred" : "http://purl.obolibrary.org/obo/RO_0000052", + "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000052", "pred" : "is_a", @@ -13734,14 +13702,18 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000056", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000056", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000054" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000057", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000058", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000086" + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000057", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000055" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000059", "pred" : "is_a", @@ -13768,6 +13740,10 @@ "val" : "09/09/2017" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000062", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000063", "pred" : "is_a", @@ -13776,10 +13752,18 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000063", "pred" : "http://purl.obolibrary.org/obo/BFO_0000067", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000160" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000063", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000052" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000062" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000064", + "pred" : "http://purl.obolibrary.org/obo/RO_0000053", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000053" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000065", "pred" : "is_a", @@ -13856,10 +13840,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000085", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000086", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000001" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000087", "pred" : "is_a", @@ -13968,14 +13948,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000108", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000150" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000108", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000067", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000153" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000108", - "pred" : "http://purl.obolibrary.org/obo/RO_0000053", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000075" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000109", "pred" : "is_a", @@ -14114,8 +14086,8 @@ "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000012" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000129", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000050" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000130", "pred" : "is_a", @@ -14160,6 +14132,30 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000141", "pred" : "is_a", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000142", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", + "obj" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000143", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000028" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000143", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000219", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000144", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/IAO_0000028" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000144", + "pred" : "http://purl.obolibrary.org/obo/IAO_0000219", + "obj" : "http://purl.obolibrary.org/obo/PCO_0000020" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000145", "pred" : "is_a", @@ -14176,10 +14172,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000150" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000148", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000067", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000153" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000148", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -14340,6 +14332,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000034" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000172", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", + "obj" : "http://purl.obolibrary.org/obo/OGMS_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000173", "pred" : "is_a", @@ -14476,10 +14472,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000202", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000203", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000030" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000204", "pred" : "is_a", @@ -14596,6 +14588,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBIB_0000667" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000232", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000312", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000231" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000233", "pred" : "is_a", @@ -14832,6 +14828,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002031", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000104" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002031", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002030" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002032", "pred" : "is_a", @@ -14844,6 +14844,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002034", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002034", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002035" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002035", "pred" : "is_a", @@ -14856,14 +14860,30 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002037", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0021001" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002037", + "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", + "obj" : "http://purl.obolibrary.org/obo/OOSTT_00000074" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002038", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002038", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002035" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002038", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002036" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002039", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002039", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002036" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002040", "pred" : "is_a", @@ -14872,10 +14892,18 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002041", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002041", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002040" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002042", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002042", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002043" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002043", "pred" : "is_a", @@ -14892,6 +14920,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002046", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002031" + }, { + "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002046", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002044" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002047", "pred" : "is_a", @@ -15019,15 +15051,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00002072", - "pred" : "http://purl.obolibrary.org/obo/RO_0000052", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/PCO_0000020", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" + "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000048" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000507", "pred" : "type", @@ -16692,14 +16716,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000922", "pred" : "type", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002069" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000009", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000021", "pred" : "subPropertyOf", @@ -16724,10 +16740,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000276", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000056" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002217", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000263", "pred" : "inverseOf", diff --git a/omrse-base.obo b/omrse-base.obo index 5e37ac7..76bf71a 100644 --- a/omrse-base.obo +++ b/omrse-base.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omrse/releases/2024-08-14/omrse-base.owl +data-version: omrse/releases/2024-11-25/omrse-base.owl idspace: dc http://purl.org/dc/elements/1.1/ idspace: foaf http://xmlns.com/foaf/0.1/ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# @@ -27,13 +27,9 @@ property_value: dc:creator "William Hogan" xsd:string property_value: dc:description "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." xsd:string property_value: dc:title "Ontology for Modeling and Representation of Social Entities" xsd:string property_value: dc:type IAO:8000001 -property_value: owl:versionInfo "2024-08-14" xsd:string +property_value: owl:versionInfo "2024-11-25" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string -[Term] -id: GO:0008150 -is_a: BFO:0000015 - [Term] id: OMRSE:00000000 name: social security number @@ -48,7 +44,7 @@ id: OMRSE:00000001 name: human social role def: "A social role inhering in a human being." [] is_a: OMRSE:00000026 ! organism social role -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -71,7 +67,7 @@ is_a: OMRSE:00000002 ! party to a legal entity id: OMRSE:00000005 name: party to a marriage contract is_a: OMRSE:00000004 ! party to a legal agreement -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role [Term] id: OMRSE:00000006 @@ -82,8 +78,7 @@ is_a: OMRSE:00000002 ! party to a legal entity id: OMRSE:00000007 name: gender role def: "A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture." [] -is_a: BFO:0000023 -relationship: RO:0000052 OBI:0100026 +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Gender_role" xsd:string @@ -121,7 +116,7 @@ name: patient role def: "A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter." [] comment: In order to avoid the presumption of the formal structures and institutions of Western civilization, bearing a patient role does not entail that the organism presents at an official place of business, with an organization formally and legally registered with various gov't entities, with a person endowed by the gov't with certain certifications. is_a: OMRSE:00000010 ! human health care role -relationship: RO:0000052 OBI:0100026 +is_a: OMRSE:00000049 ! organism role property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "patient" xsd:string @@ -140,7 +135,7 @@ id: OMRSE:00000013 name: physician role def: "A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments." [] is_a: OMRSE:00000012 ! health care provider role -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "physician" xsd:string property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Physician" xsd:string @@ -150,7 +145,7 @@ id: OMRSE:00000014 name: nurse role def: "A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life." [] is_a: OMRSE:00000012 ! health care provider role -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000118 "nurse" xsd:string property_value: IAO:0000119 "based on: http://en.wikipedia.org/wiki/Nursing" xsd:string @@ -220,8 +215,8 @@ id: OMRSE:00000025 name: organization social role def: "A role in human social processes that inheres in an organization." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. +is_a: OMRSE:00000051 ! organization role is_a: OMRSE:00002072 ! role in human social processes -relationship: RO:0000052 OBI:0000245 property_value: IAO:0000117 "William R. Hogan" xsd:string [Term] @@ -231,8 +226,8 @@ def: "A role in human social processes that inheres in an organism." [] comment: Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist.\n\nDitto for its current descendants. comment: Includes animals as well as humans. For example, pet, assistance animal, animal grown for food, work animal, domesticated animal, K-9, etc. Human roles include gender role, party to legal entities, health care provider roles like doctor, nurse, etc. comment: Previous definition: A role in human social processes played by an organism. +is_a: OMRSE:00000049 ! organism role is_a: OMRSE:00002072 ! role in human social processes -relationship: RO:0000052 OBI:0100026 property_value: IAO:0000117 "William R. Hogan\nMathias Brochhausen" xsd:string [Term] @@ -262,6 +257,8 @@ is_obsolete: true id: OMRSE:00000030 name: human patient role def: "A patient role that inheres in a human being." [] +is_a: OMRSE:00000011 ! patient role +is_a: OMRSE:00000050 ! Homo sapiens role intersection_of: OMRSE:00000011 ! patient role intersection_of: RO:0000052 NCBITaxon:9606 @@ -289,6 +286,7 @@ name: aggregate of organizations def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" [] comment: It is often convenient to group organizations together that otherwise might not even interact with one another. is_a: BFO:0000040 +relationship: RO:0002351 OBI:0000245 property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string [Term] @@ -342,14 +340,12 @@ property_value: IAO:0000119 "Malcolm N. Shaw: International Law. Cambridge Unive id: OMRSE:00000039 name: smoker role def: "A role that inheres in an organism and is realized by habitually smoking tobacco products." [] -is_a: BFO:0000023 -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role [Term] id: OMRSE:00000040 name: intravenous drug user -is_a: BFO:0000023 -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role [Term] id: OMRSE:00000041 @@ -430,22 +426,28 @@ is_obsolete: true [Term] id: OMRSE:00000048 name: material entity role +is_a: BFO:0000023 intersection_of: BFO:0000023 intersection_of: RO:0000052 BFO:0000040 relationship: RO:0000052 BFO:0000040 {all_only="true"} +relationship: RO:0000052 BFO:0000040 [Term] id: OMRSE:00000049 name: organism role +is_a: OMRSE:00000048 ! material entity role intersection_of: OMRSE:00000048 ! material entity role intersection_of: RO:0000052 OBI:0100026 relationship: RO:0000052 OBI:0100026 {all_only="true"} +relationship: RO:0000052 OBI:0100026 [Term] id: OMRSE:00000050 name: Homo sapiens role +is_a: OMRSE:00000049 ! organism role intersection_of: OMRSE:00000049 ! organism role intersection_of: RO:0000052 NCBITaxon:9606 +relationship: RO:0000052 NCBITaxon:9606 relationship: RO:0000052 NCBITaxon:9606 {all_only="true"} [Term] @@ -454,6 +456,7 @@ name: organization role is_a: OMRSE:00000048 ! material entity role intersection_of: BFO:0000023 intersection_of: RO:0000052 OBI:0000245 +relationship: RO:0000052 OBI:0000245 relationship: RO:0000052 OBI:0000245 {all_only="true"} [Term] @@ -491,6 +494,7 @@ def: "An organization that is the bearer of a hospital role." [] is_a: OBI:0000245 intersection_of: OBI:0000245 intersection_of: RO:0000053 OMRSE:00000054 ! hospital role +relationship: RO:0000053 OMRSE:00000054 ! hospital role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -500,13 +504,13 @@ def: "An organization that is the bearer of a school role." [] is_a: OBI:0000245 intersection_of: OBI:0000245 intersection_of: RO:0000053 OMRSE:00000055 ! school role +relationship: RO:0000053 OMRSE:00000055 ! school role property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] id: OMRSE:00000058 name: student role def: "A human social role that, if realized, is realized by the process of formal education that the bearer undergoes." [] -is_a: OMRSE:00000086 ! human role within an organization property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -539,6 +543,7 @@ is_a: OMRSE:00000061 ! architectural structure intersection_of: OMRSE:00000061 ! architectural structure intersection_of: RO:0000053 BFO:0000034 relationship: OMRSE:00000068 OBI:0000245 {owl:versionInfo="09/09/2017"} ! is administered by +relationship: RO:0000053 BFO:0000034 property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -547,6 +552,7 @@ name: hospital facility def: "A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function." [] is_a: OMRSE:00000102 ! health care facility relationship: BFO:0000067 OMRSE:00000160 ! acute care encounter +relationship: RO:0000053 OMRSE:00000052 ! hospital function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "William Hogan" xsd:string @@ -555,6 +561,7 @@ id: OMRSE:00000064 name: school facility def: "A facility that is run by a school organization and is the bearer of a school function." [] is_a: OMRSE:00000062 ! facility +relationship: RO:0000053 OMRSE:00000053 ! school function property_value: IAO:0000117 "Mathias Brochhausen" xsd:string [Term] @@ -699,7 +706,6 @@ is_obsolete: true id: OMRSE:00000086 name: human role within an organization def: "A human social role that is created by a deontic declaration performed by an organization." [] -is_a: OMRSE:00000001 ! human social role property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000118 "human organizational role" xsd:string @@ -855,8 +861,6 @@ id: OMRSE:00000108 name: residential health care facility def: "A community living health care facility that provides health care services in a home-like setting" [] is_a: OMRSE:00000150 ! community living health care facility -relationship: BFO:0000067 OMRSE:00000153 ! assistive care encounter -relationship: RO:0000053 OMRSE:00000075 ! residence function property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000117 "William Hogan" xsd:string @@ -1007,7 +1011,7 @@ id: OMRSE:00000129 name: US physician assistant role def: "A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon." [] is_a: OMRSE:00000012 ! health care provider role -relationship: RO:0000052 NCBITaxon:9606 +is_a: OMRSE:00000050 ! Homo sapiens role [Term] id: OMRSE:00000130 @@ -1084,8 +1088,10 @@ replaced_by: male gender identity information content entity id: OMRSE:00000142 name: human traveling information def: "An information content entity that is about human travel." [] +is_a: IAO:0000030 intersection_of: IAO:0000030 intersection_of: IAO:0000136 APOLLO_SV:00000532 +relationship: IAO:0000136 APOLLO_SV:00000532 property_value: dc:contributor "Jie Zheng" xsd:string property_value: dc:creator "Amanda Hicks" xsd:string property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyURI @@ -1093,8 +1099,10 @@ property_value: IAO:0000119 "https://github.com/ufbmi/OMRSE/issues/79" xsd:anyUR [Term] id: OMRSE:00000143 name: household identifier +is_a: IAO:0000028 intersection_of: IAO:0000028 intersection_of: IAO:0000219 OMRSE:00000076 ! household +relationship: IAO:0000219 OMRSE:00000076 ! household property_value: dc:contributor "A symbol that denotes a specific household" xsd:string property_value: dc:contributor "Jie Zheng" xsd:string property_value: dc:creator "Amanda Hicks" xsd:string @@ -1103,8 +1111,10 @@ property_value: dc:creator "Amanda Hicks" xsd:string id: OMRSE:00000144 name: family identifier def: "A symbol that denotes a family." [] +is_a: IAO:0000028 intersection_of: IAO:0000028 intersection_of: IAO:0000219 PCO:0000020 +relationship: IAO:0000219 PCO:0000020 property_value: dc:contributor "Jie Zheng" xsd:string property_value: dc:creator "Amanda Hicks" xsd:string @@ -1136,7 +1146,6 @@ id: OMRSE:00000148 name: adult foster home facility def: "a facility that is run by an adult foster home organization and is the bearer of an adult foster home organization" [] is_a: OMRSE:00000150 ! community living health care facility -relationship: BFO:0000067 OMRSE:00000153 ! assistive care encounter relationship: RO:0000053 OMRSE:00000149 ! adult foster home function property_value: IAO:0000117 "Amanda Hicks" xsd:string @@ -1284,6 +1293,7 @@ name: health care function is_a: BFO:0000034 intersection_of: BFO:0000034 intersection_of: BFO:0000054 OGMS:0000097 +relationship: BFO:0000054 OGMS:0000097 [Term] id: OMRSE:00000173 @@ -1531,7 +1541,6 @@ property_value: IAO:0000118 "tumor summary staging" xsd:string id: OMRSE:00000203 name: cancer summary staging code def: "An information content entity that is the specified output of cancer summary staging." [] -is_a: IAO:0000030 property_value: IAO:0000111 "cancer summary staging code" xsd:string property_value: IAO:0000112 "The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture." xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string @@ -1879,6 +1888,7 @@ id: OMRSE:00000232 name: county smoking survey data def: "Survey data that is the specified output of a county smoking survey execution." [] is_a: OBIB:0000667 +relationship: OBI:0000312 OMRSE:00000231 ! county smoking survey execution property_value: dc:contributor "Hansi Zhang" xsd:string property_value: dc:contributor "Jiang Bian" xsd:string property_value: dc:contributor "Matthew Diller" xsd:string @@ -2417,6 +2427,7 @@ comment: Very broad. Covers everything from grade school to high school to coll is_a: IAO:0000104 intersection_of: IAO:0000104 intersection_of: BFO:0000051 OMRSE:00002030 ! educational objective +relationship: BFO:0000051 OMRSE:00002030 ! educational objective property_value: IAO:0000111 "educational plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000600 "A plan specification with one or more educational objectives." xsd:string @@ -2451,6 +2462,7 @@ comment: In the united states, also called "elementary education" comment: It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom. comment: Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation. is_a: OMRSE:00002031 ! educational program +relationship: BFO:0000051 OMRSE:00002035 ! primary education objective property_value: IAO:0000111 "primary education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "elementary education" xsd:string @@ -2484,6 +2496,7 @@ comment: Different degrees have different claims and obligations associated with is_a: IAO:0021001 intersection_of: IAO:0021001 intersection_of: OBI:0000299 OOSTT:00000074 +relationship: OBI:0000299 OOSTT:00000074 property_value: IAO:0000111 "awarding of an academic degree" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -2497,6 +2510,8 @@ is_a: OMRSE:00002031 ! educational program intersection_of: OMRSE:00002031 ! educational program intersection_of: BFO:0000051 OMRSE:00002035 ! primary education objective intersection_of: BFO:0000051 OMRSE:00002036 ! lower secondary education objective +relationship: BFO:0000051 OMRSE:00002035 ! primary education objective +relationship: BFO:0000051 OMRSE:00002036 ! lower secondary education objective property_value: IAO:0000111 "basic education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "http://uis.unesco.org/en/glossary-term/basic-education" xsd:string @@ -2509,6 +2524,7 @@ comment: It can still have action specifications as parts, and possibly other IC comment: Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects. comment: Requires successful completion of a primary education program as a pre-requisite. is_a: OMRSE:00002031 ! educational program +relationship: BFO:0000051 OMRSE:00002036 ! lower secondary education objective property_value: IAO:0000111 "lower secondary education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -2530,6 +2546,7 @@ comment: It can still have action specifications as parts, and possibly other IC comment: Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available. comment: Requires successful completion of a lower secondary education program as a pre-requisite. is_a: OMRSE:00002031 ! educational program +relationship: BFO:0000051 OMRSE:00002040 ! upper secondary education objective property_value: IAO:0000111 "upper secondary education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string @@ -2540,6 +2557,7 @@ comment: Includes college, university, community college, professional schools ( comment: Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one. comment: Requires successful completion of a secondary education program as a pre-requisite. is_a: OMRSE:00002031 ! educational program +relationship: BFO:0000051 OMRSE:00002043 ! higher education objective property_value: IAO:0000111 "higher education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000118 "post-secondary education plan specification" xsd:string @@ -2582,6 +2600,7 @@ comment: Vocational education programs are designed for learners to acquire the is_a: OMRSE:00002031 ! educational program intersection_of: OMRSE:00002031 ! educational program intersection_of: BFO:0000051 OMRSE:00002044 ! vocational education objective +relationship: BFO:0000051 OMRSE:00002044 ! vocational education objective property_value: IAO:0000111 "vocational education plan specification" xsd:string property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000119 "http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf" xsd:string @@ -2866,26 +2885,11 @@ id: OMRSE:00002072 name: role in human social processes def: "A role that inheres in some entity that is realized in a social act." [] comment: Previous definition: A role played by an entity in human social processes. -is_a: BFO:0000023 -relationship: RO:0000052 BFO:0000040 +is_a: OMRSE:00000048 ! material entity role relationship: RO:0000052 BFO:0000040 {all_only="true"} property_value: dc:contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string -[Term] -id: PCO:0000020 -is_a: OMRSE:00000022 ! aggregate of objectual organisms - -[Typedef] -id: OMIABIS:0000008 -is_a: oboInOwl:ObsoleteProperty -is_obsolete: true - -[Typedef] -id: OMIABIS:0000009 -is_a: oboInOwl:ObsoleteProperty -is_obsolete: true - [Typedef] id: OMRSE:00000020 name: obsolete is-aggregate-of @@ -3006,7 +3010,3 @@ domain: NCBITaxon:9606 range: OMRSE:00000274 ! personal data disclosure is_a: RO:0000056 -[Typedef] -id: RO:0002217 -is_a: oboInOwl:ObsoleteProperty - diff --git a/omrse-base.owl b/omrse-base.owl index eeca7b0..6a2fa97 100644 --- a/omrse-base.owl +++ b/omrse-base.owl @@ -11,10 +11,9 @@ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" - xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" - xmlns:language-individuals="http://purl.obolibrary.org/obo/omrse/language-individuals/"> + xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Barry Smith Chris Stoeckert Daniel Welch @@ -37,7 +36,7 @@ https://creativecommons.org/licenses/by/4.0/ This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt - 2024-08-14 + 2024-11-25 @@ -67,10 +66,7 @@ - - definition - definition - + @@ -94,9 +90,7 @@ - - definition source - + @@ -171,12 +165,6 @@ - - - - - - @@ -314,30 +302,6 @@ - - - - - true - - - - - - - - - true - - - - - - - - - - @@ -596,20 +560,6 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - - - - - - - - - @@ -805,14 +755,6 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - - - @@ -891,12 +833,6 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - @@ -1016,12 +952,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - + A social role inhering in a human being. Mathias Brochhausen William R. Hogan @@ -1089,12 +1020,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - + party to a marriage contract @@ -1112,13 +1038,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - - + A human social role borne by a human being being realized in behaviour which is considered socially appropriate for individuals of a specific sex in the context of a specific culture. Mathias Brochhausen http://en.wikipedia.org/wiki/Gender_role @@ -1202,12 +1122,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - + A role borne by an organism and that is realized by presenting to a health care provider in a clinical encounter. Amanda Hicks Mathias Brochhausen @@ -1263,12 +1178,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - + A health care role borne by a human being and realized by promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury and other physical and mental impairments. Mathias Brochhausen physician @@ -1282,12 +1192,7 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - - - - - + A health care role borne by a human being and realized by the care of individuals, families, and communities so they may attain, maintain, or recover optimal health and quality of life. Mathias Brochhausen nurse @@ -1453,13 +1358,8 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope + - - - - - - A role in human social processes that inheres in an organization. William R. Hogan Defined class that we will ultimately move to an application ontology. We are leaving here for now until we determine which application ontology: it is likely going to be an ontology that does not currently (2012-06-05) exist. @@ -1473,13 +1373,8 @@ Ditto for its current descendants. + - - - - - - A role in human social processes that inheres in an organism. William R. Hogan Mathias Brochhausen @@ -1542,6 +1437,8 @@ Ditto for its current descendants. + + A patient role that inheres in a human being. human patient role @@ -1596,6 +1493,12 @@ Ditto for its current descendants. + + + + + + An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common William R. Hogan Amanda Hicks @@ -1705,13 +1608,7 @@ However, Shaw explicates: - - - - - - - + A role that inheres in an organism and is realized by habitually smoking tobacco products. smoker role @@ -1721,13 +1618,7 @@ However, Shaw explicates: - - - - - - - + intravenous drug user @@ -1860,6 +1751,13 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + + @@ -1885,6 +1783,13 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + + @@ -1910,6 +1815,13 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + + @@ -1936,6 +1848,12 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + @@ -2006,6 +1924,12 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + An organization that is the bearer of a hospital role. Mathias Brochhausen hospital organization @@ -2028,6 +1952,12 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + An organization that is the bearer of a school role. Mathias Brochhausen school organization @@ -2038,7 +1968,6 @@ Note: this definition was taken over from "geopolitical organization". - @@ -2116,19 +2045,25 @@ Note: this definition was taken over from "geopolitical organization". - + + + + + + + An architectural structure that bears some function. Mathias Brochhausen facility - + - + 09/09/2017 @@ -2166,6 +2101,12 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + A health care facility that bears the function to provide acute and intensive healthcare services and that is run by a hospital organization and is the bearer of a hospital function. Mathias Brochhausen William Hogan @@ -2201,6 +2142,12 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + A facility that is run by a school organization and is the bearer of a school function. Mathias Brochhausen school facility @@ -2258,6 +2205,22 @@ Note: this definition was taken over from "geopolitical organization". + + + + + + + + + + + + + + + + A patient role that inheres an organism suffering one or more injuries. Amanda Hicks injured patient @@ -2408,6 +2371,26 @@ A patient sustaining an injury who has been admitted to the hospital, transferre + + + + + + + + + + + + + + + + + + + + A human or collection of humans that occupies a housing unit by storing their possessions there and habitually sleeping there thereby participating in the realization of that housing unit's residence function. Amanda Hicks Note in OMRSE it is the housing unit, not the people living there, that are the bearers of a "residence function". Note the distinction between being a residence and a resident. @@ -2581,7 +2564,6 @@ last accessed June 30, 2015 - @@ -3120,18 +3102,6 @@ last accessed June 30, 2015 - - - - - - - - - - - - A community living health care facility that provides health care services in a home-like setting Amanda Hicks William Hogan @@ -3475,12 +3445,7 @@ last accessed June 30, 2015 - - - - - - + A human health care provider role that inheres in a human being that is created by state licensing and that is realized by taking patient histories, performing physical exams, diagnosing illnesses, developing treatment plans, ordering lab tests, prescribing medications, counselling and educating patients, suturing wounds, and assisting in surgery under the supervision of a physician or a surgeon. US physician assistant role @@ -3638,6 +3603,13 @@ last accessed June 30, 2015 + + + + + + + An information content entity that is about human travel. https://github.com/ufbmi/OMRSE/issues/79 Jie Zheng @@ -3661,6 +3633,13 @@ last accessed June 30, 2015 + + + + + + + A symbol that denotes a specific household Jie Zheng Amanda Hicks @@ -3683,6 +3662,13 @@ last accessed June 30, 2015 + + + + + + + A symbol that denotes a family. Jie Zheng Amanda Hicks @@ -3742,12 +3728,6 @@ last accessed June 30, 2015 - - - - - - @@ -4096,6 +4076,12 @@ Somehow involves skilled nursing encounters + + + + + + health care function @@ -4502,7 +4488,6 @@ Somehow involves skilled nursing encounters - @@ -4970,6 +4955,17 @@ Somehow involves skilled nursing encounters + + + + + + + + + + + The Alachua county smoking survey execution. A survey execution that realizes the concretization of a smoking survey plan specification that is stratified by county. Mathias Brochhausen @@ -4994,6 +4990,12 @@ Somehow involves skilled nursing encounters + + + + + + The Alachua county smoking survey data. Survey data that is the specified output of a county smoking survey execution. Mathias Brochhausen @@ -5869,6 +5871,27 @@ Somehow involves skilled nursing encounters + + + + + + + + + + + + + + + + + + + + + Can be about any aspect of employment, such as salary, work location, or employer. A data item that is about a person's job role and/or its realization. Matthew Diller @@ -5983,6 +6006,17 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + educational objective specification An objective specification that describes the type of capability or capabilities to be imparted or improved by its realization, which is an educating (education process). William R. Hogan @@ -6007,6 +6041,12 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + educational plan specification A plan specification with an educational objective specification as part. William R. Hogan @@ -6037,6 +6077,17 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + completing a program of education An educating that realizes a concretization of some program of education. William R. Hogan @@ -6126,6 +6177,12 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + primary education plan specification An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts. William R. Hogan @@ -6182,6 +6239,12 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + awarding of an academic degree A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree. William R. Hogan @@ -6210,6 +6273,18 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + + basic education plan specification An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification. William R. Hogan @@ -6262,6 +6337,23 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + + + + + + + lower secondary education plan specification An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts. William R. Hogan @@ -6328,6 +6420,23 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + + + + + + + upper secondary education plan specification An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts. William R. Hogan @@ -6380,6 +6489,23 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + + + + + + + + + + + + higher education plan specification William R. Hogan post-secondary education plan specification @@ -6448,6 +6574,12 @@ This addition to the definition notwithstanding, we do not intend to incorporate + + + + + + vocational education plan specification An educational plan specification that has a vocational objective specification as part. William R. Hogan @@ -7028,13 +7160,7 @@ It indicates that a person has completed only early childhood education and noth - - - - - - - + @@ -7058,9 +7184,7 @@ It indicates that a person has completed only early childhood education and noth - - - + @@ -12395,18 +12519,6 @@ It indicates that a person has completed only early childhood education and noth /////////////////////////////////////////////////////////////////////////////////////// --> - - imported from - - - true - - - true - - - true - non-binary gender identity datum A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender. diff --git a/omrse-full.json b/omrse-full.json index 3e4dbad..1ddb4d4 100644 --- a/omrse-full.json +++ b/omrse-full.json @@ -67,31 +67,11 @@ "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-14" + "val" : "2024-11-25" } ], - "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-08-14/omrse-full.json" + "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-11-25/omrse-full.json" }, "nodes" : [ { - "id" : "http://purl.obolibary.org/obo/IAO_0021001", - "lbl" : "obsolete_deontic document act", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my filling in an immigration form, a judge's signing and stamping a court order" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "lbl" : "software development", "type" : "CLASS", @@ -7280,91 +7260,6 @@ "val" : "Amanda Hicks" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020025", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obligor role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "duty holder role (IAO:210016)" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020026", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obligee role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "claimant role (IAO:0021013)" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020027", - "lbl" : "owner role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBIB/ICO community" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/d-acts/d-acts/issues/29" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021000", - "lbl" : "obsolete_claim", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021001", "lbl" : "deontic document act", @@ -7381,29 +7276,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021002", - "lbl" : "obsolete_document act", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my filling in an immigration form, a judge's signing and stamping a court order" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibary.org/obo/IAO_0021001" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021003", "lbl" : "social act", @@ -7421,95 +7293,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021004", - "lbl" : "obsolete_socio-legal generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021005", - "lbl" : "obsolete_deontic declaration", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "deontic declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "status function declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021006", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021007", - "lbl" : "document act input document", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021008", - "lbl" : "deontic role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Neil Otte" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021009", "lbl" : "deontic declaration", @@ -7523,244 +7306,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021010", - "lbl" : "obsolete_obligation", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021013", - "lbl" : "claimant role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A." - }, - "comments" : [ "Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. \nhttps://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021014", - "lbl" : "obsolete_declaration executive role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021015", - "lbl" : "obsolete_document template creator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." - }, - "comments" : [ "not that the \"template\" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021016", - "lbl" : "duty holder role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021017", - "lbl" : "obsolete_claimant role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings concretizing a claim." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021018", - "lbl" : "obsolete_obligator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings concretizing an obligation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021019", - "lbl" : "privilege holder role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021020", - "lbl" : "obsolete_declaration target", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021021", - "lbl" : "document act template creator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021022", - "lbl" : "deontic declaration performer role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "declaration performer role" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021023", - "lbl" : "power role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021030", - "lbl" : "obsoleted_document act target", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021031", "lbl" : "document act performer role", @@ -7777,73 +7322,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021032", - "lbl" : "obsolete_obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021033", - "lbl" : "obsolete_obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021102", - "lbl" : "standing declaration", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act that postulates a socio-legal fact for a specified group of people or organizations." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enactment" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021300", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "John Judkins" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", @@ -8385,7 +7863,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." + "val" : "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -8940,11 +8418,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "lbl" : "collection of organisms", + "lbl" : "aggregate of objectual organisms", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An object aggregate of organisms." + "val" : "An object aggregate of objectual organisms." }, "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ] } @@ -8955,8 +8433,7 @@ "meta" : { "definition" : { "val" : "An object aggregate all of whose components are human beings." - }, - "comments" : [ "An object aggregate all of whose components are human beings." ] + } } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000024", @@ -9088,14 +8565,8 @@ }, "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan\nAmanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl" } ] } }, { @@ -13795,9 +13266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" @@ -14002,10 +13470,7 @@ "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485219" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485220" + "val" : "_:genid2147485116" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" @@ -14105,34 +13570,6 @@ "val" : "http://purl.obolibrary.org/obo/uo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - } ], - "deprecated" : true - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", "type" : "CLASS" @@ -14272,9 +13709,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "realized_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" @@ -14401,42 +13835,6 @@ "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000075", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000117", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000118", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000121", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000132", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000136", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000138", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000139", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000181", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000039", "lbl" : "has measurement unit label", @@ -14841,38 +14239,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021011", - "lbl" : "legally revokes", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021012", - "lbl" : "obsolete_legally transfers", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/OBIB_0000732", "lbl" : "owns", @@ -16283,30 +15649,14 @@ "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x has participant y if and only if x realizes some active role that inheres in y" + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'heart development' has active participant some Shh protein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This may be obsoleted and replaced by the original 'has agent' relation" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" @@ -27667,10 +27017,6 @@ "id" : "http://www.w3.org/2002/07/owl#Thing" } ], "edges" : [ { - "sub" : "http://purl.obolibary.org/obo/IAO_0021001", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" @@ -28962,14 +28308,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020021", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020021", - "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020022" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020022", "pred" : "is_a", @@ -28982,142 +28320,22 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020024", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020024", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020025", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020026", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021000", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0021009" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021007" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021002", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021004", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021005", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021006", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021010", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021013", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021014", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021015", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021016", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021017", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021018", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021019", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021020", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021021", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021022", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021023", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021030", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021031", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021032", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021033", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021300", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", "pred" : "is_a", @@ -29410,18 +28628,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000024", "pred" : "is_a", @@ -29474,10 +28684,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -31012,14 +30218,6 @@ "sub" : "http://purl.obolibrary.org/obo/UO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", "pred" : "type", @@ -32776,14 +31974,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000055", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "subPropertyOf", @@ -32852,14 +32042,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020013", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021011", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021012", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "subPropertyOf", @@ -32888,10 +32070,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000009", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000021", "pred" : "subPropertyOf", @@ -33080,10 +32258,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002218", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", @@ -33733,23 +32907,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020024", - "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000054", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020023" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0021001", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0021009" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000293", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0021007" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000310" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000030", "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ], @@ -34009,10 +33166,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/IAO_0020013", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0021011", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0021009" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0021008" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] diff --git a/omrse-full.obo b/omrse-full.obo index 1ab26dd..a2d1d0a 100644 --- a/omrse-full.obo +++ b/omrse-full.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omrse/releases/2024-08-14/omrse-full.owl +data-version: omrse/releases/2024-11-25/omrse-full.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -50,7 +50,7 @@ property_value: dc:creator "Swetha Garimalla" xsd:string property_value: dc:creator "William Hogan" xsd:string property_value: dc:description "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." xsd:string property_value: dc:title "Ontology for Modeling and Representation of Social Entities" xsd:string -property_value: owl:versionInfo "2024-08-14" xsd:string +property_value: owl:versionInfo "2024-11-25" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] @@ -3284,8 +3284,6 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA id: IAO:0020021 name: identity document def: "A document that denotes some identity and is concretized by the bearer of some credential role." [] -is_a: IAO:0000310 ! document -relationship: IAO:0000136 IAO:0020022 ! is about documented identity property_value: IAO:0000117 "Amanda Hicks" xsd:string [Term] @@ -3309,79 +3307,15 @@ id: IAO:0020024 name: credential role def: "A role that inheres in a concretization of an identity document and is realized by an authentication process." [] is_a: BFO:0000023 ! role -relationship: BFO:0000054 IAO:0020023 ! realized in authentication property_value: IAO:0000117 "Amanda Hicks" xsd:string -[Term] -id: IAO:0020025 -name: obsolete obligor role -def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "obligor role" xsd:string -property_value: IAO:0000112 "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true -replaced_by: duty holder role (IAO:210016) - -[Term] -id: IAO:0020026 -name: obsolete obligee role -def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "obligee role" xsd:string -property_value: IAO:0000112 "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true -replaced_by: claimant role (IAO:0021013) - -[Term] -id: IAO:0020027 -name: owner role -def: "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." [] -is_a: OMRSE:00002072 ! role in human social processes -property_value: IAO:0000112 "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "https://github.com/d-acts/d-acts/issues/29" xsd:string -property_value: IAO:0000119 "OBIB/ICO community" xsd:string - -[Term] -id: IAO:0021000 -name: obsolete_claim -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - [Term] id: IAO:0021001 name: deontic document act -name: obsolete_deontic document act def: "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." [] is_a: IAO:0021009 ! deontic declaration -is_a: oboInOwl:ObsoleteClass -intersection_of: IAO:0021009 ! deontic declaration -intersection_of: OBI:0000293 IAO:0021007 ! has_specified_input document act input document -intersection_of: OBI:0000299 IAO:0000310 ! has_specified_output document -relationship: OBI:0000293 IAO:0021007 ! has_specified_input document act input document -relationship: OBI:0000299 IAO:0000310 ! has_specified_output document -property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string -property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021002 -name: obsolete_document act -def: "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." [] -is_a: oboInOwl:ObsoleteClass property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true -replaced_by: IAO:0021001 [Term] id: IAO:0021003 @@ -3392,51 +3326,6 @@ is_a: OBI:0000011 ! planned process property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021004 -name: obsolete_socio-legal generically dependent continuant -def: "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - -[Term] -id: IAO:0021005 -name: obsolete_deontic declaration -def: "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "deontic declaration" xsd:string -property_value: IAO:0000112 "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "declaration" xsd:string -property_value: IAO:0000118 "status function declaration" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021006 -name: obsolete obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - -[Term] -id: IAO:0021007 -name: document act input document -def: "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." [] -is_a: IAO:0000310 ! document -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0021008 -name: deontic role -def: "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Neil Otte" xsd:string - [Term] id: IAO:0021009 name: deontic declaration @@ -3444,126 +3333,6 @@ def: "A social act that creates or revokes a deontic role." [] is_a: IAO:0021003 ! social act property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021010 -name: obsolete_obligation -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021013 -name: claimant role -def: "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A." [] -comment: Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. \nhttps://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child. -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021014 -name: obsolete_declaration executive role -def: "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021015 -name: obsolete_document template creator role -def: "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." [] -comment: not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants. -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021016 -name: duty holder role -def: "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021017 -name: obsolete_claimant role -def: "The role of a human being or an aggregate of human beings concretizing a claim." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021018 -name: obsolete_obligator role -def: "The role of a human being or an aggregate of human beings concretizing an obligation." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021019 -name: privilege holder role -def: "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021020 -name: obsolete_declaration target -def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021021 -name: document act template creator role -def: "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000112 "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0021022 -name: deontic declaration performer role -def: "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "declaration performer role" xsd:string - -[Term] -id: IAO:0021023 -name: power role -def: "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021030 -name: obsoleted_document act target -def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - [Term] id: IAO:0021031 name: document act performer role @@ -3572,41 +3341,6 @@ is_a: BFO:0000023 ! role property_value: IAO:0000112 "a judge's role of signing a court order" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021032 -name: obsolete_obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021033 -name: obsolete_obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021102 -name: standing declaration -def: "A social act that postulates a socio-legal fact for a specified group of people or organizations." [] -is_a: IAO:0021003 ! social act -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "enactment" xsd:string - -[Term] -id: IAO:0021300 -name: obsolete obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "John Judkins" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - [Term] id: IAO:8000000 name: ontology module @@ -3853,7 +3587,6 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl id: OBI:0000245 name: organization def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] -def: "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string @@ -4166,20 +3899,15 @@ property_value: IAO:0000117 "Amanda Hicks" xsd:string [Term] id: OMRSE:00000022 name: aggregate of objectual organisms -name: collection of organisms def: "An object aggregate of objectual organisms." [] -def: "An object aggregate of organisms." [] comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class. is_a: BFO:0000027 ! object aggregate -relationship: OMRSE:00000020 OBI:0100026 ! obsolete is-aggregate-of organism [Term] id: OMRSE:00000023 name: collection of humans def: "An object aggregate all of whose components are human beings." [] -comment: An object aggregate all of whose components are human beings. is_a: OMRSE:00000022 ! aggregate of objectual organisms -relationship: OMRSE:00000020 NCBITaxon:9606 ! obsolete is-aggregate-of Homo sapiens relationship: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens [Term] @@ -4264,15 +3992,11 @@ is_obsolete: true [Term] id: OMRSE:00000033 name: aggregate of organizations -def: "An aggregate of organizations that have some feature in common, but is not itself an organization." [] def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" [] comment: It is often convenient to group organizations together that otherwise might not even interact with one another. is_a: BFO:0000040 ! material entity -relationship: OMRSE:00000020 OBI:0000245 ! obsolete is-aggregate-of organization relationship: RO:0002351 OBI:0000245 ! has member organization -property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl" xsd:string [Term] id: OMRSE:00000034 @@ -4968,7 +4692,7 @@ is_a: BFO:0000034 ! function id: OMRSE:00000126 name: patient discharge def: "A deontic document act that concludes an inpatient encounter." [] -is_a: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act relationship: RO:0002229 OGMS:0000100 ! ends inpatient encounter property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000118 "discharge process" xsd:string @@ -5507,7 +5231,7 @@ property_value: IAO:0000117 "S. Clint Dowland" xsd:string id: OMRSE:00000201 name: admission process def: "A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter." [] -is_a: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act relationship: RO:0002083 OMRSE:00000126 ! before patient discharge relationship: RO:0002223 OGMS:0000100 ! starts inpatient encounter property_value: IAO:0000117 "Amanda Hicks" xsd:string @@ -6478,8 +6202,8 @@ id: OMRSE:00002037 name: awarding an academic degree def: "A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree." [] comment: Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam). -is_a: IAO:0021001 ! obsolete_deontic document act -intersection_of: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act +intersection_of: IAO:0021001 ! deontic document act intersection_of: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree relationship: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree property_value: IAO:0000111 "awarding of an academic degree" xsd:string @@ -6874,7 +6598,6 @@ is_a: OMRSE:00000048 ! material entity role relationship: RO:0000052 BFO:0000040 {all_only="true"} ! characteristic of material entity property_value: dc:contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" xsd:string [Term] id: OOSTT:00000074 @@ -7024,22 +6747,6 @@ is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl -[Term] -id: obligee_role -name: obsolete obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true - -[Term] -id: obligor_role -name: obsolete obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true - [Typedef] id: BFO:0000050 name: part of @@ -7101,7 +6808,6 @@ property_value: IAO:0000112 "this fragility is realized in this shattering" xsd: property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000017 ! realizable entity @@ -7388,28 +7094,6 @@ def: "p1 is designated by p2, if p2 is an information content entity that repres property_value: IAO:0000117 "Mathias Brochhausen" xsd:string is_asymmetric: true -[Typedef] -id: IAO:0021011 -name: legally revokes -def: "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -domain: IAO:0021009 ! deontic declaration -range: IAO:0021008 ! deontic role -is_functional: true -is_a: RO:0000057 ! has_participant -is_asymmetric: true - -[Typedef] -id: IAO:0021012 -name: obsolete_legally transfers -def: "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_functional: true -is_a: oboInOwl:ObsoleteProperty -is_obsolete: true -is_asymmetric: true - [Typedef] id: OBI:0000293 name: has_specified_input @@ -7525,7 +7209,6 @@ replaced_by: OBIB:0000735 [Typedef] id: OMRSE:00000020 -name: is-aggregate-of name: obsolete is-aggregate-of comment: We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.\n property_value: IAO:0000231 "BFO relation takes precedence." xsd:string @@ -8159,19 +7842,10 @@ replaced_by: RO:0002608 [Typedef] id: RO:0002218 -name: has active participant name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -subset: ro-eco -property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -is_a: RO:0000057 ! has_participant is_obsolete: true replaced_by: RO:0002500 diff --git a/omrse-full.owl b/omrse-full.owl index 52bd92f..a592b68 100644 --- a/omrse-full.owl +++ b/omrse-full.owl @@ -20,7 +20,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:language-individuals="http://purl.obolibrary.org/obo/omrse/language-individuals/"> - + Barry Smith Chris Stoeckert Daniel Welch @@ -42,7 +42,7 @@ Ontology for Modeling and Representation of Social Entities https://creativecommons.org/licenses/by/4.0/ This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt - 2024-08-14 + 2024-11-25 @@ -1445,7 +1445,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1455,7 +1454,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigator role is realized in this investigation is realized by realized_in - http://purl.obolibrary.org/obo/ro.owl [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process @@ -1467,7 +1465,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes @@ -1567,60 +1564,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1994,39 +1937,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - - - d socio-legally revokes s if s participates in d and at the end of d s no longer exists. -It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question. - Mathias Brochhausen - legally revokes - - - - - - - - - - - - d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical. - Mathias Brochhausen - - obsolete_legally transfers - true - - - - @@ -2201,11 +2111,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. - is-aggregate-of obsolete is-aggregate-of true @@ -3209,19 +3117,10 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - 'heart development' has active participant some Shh protein - OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall has agent - http://purl.obolibrary.org/obo/ro.owl - - has active participant obsolete has active participant true @@ -4899,20 +4798,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. - Mathias Brochhausen - - obsolete_deontic document act - true - - - - @@ -10950,83 +10835,6 @@ When there is no such string, it is almost always because the entities take the - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A document that denotes some identity and is concretized by the bearer of some credential role. Amanda Hicks identity document @@ -11038,28 +10846,6 @@ When there is no such string, it is almost always because the entities take the - - - - - - - - - - - - - - - - - - - - - - A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents. Amanda Hicks is an aggregate of ICEs also an ICE? yes @@ -11073,34 +10859,6 @@ Is part_of the appropriate relation to use for data items and documented identit - - - - - - - - - - - - - - - - - - - - - - - - - - - - I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database. Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit). @@ -11113,54 +10871,7 @@ Is part_of the appropriate relation to use for data items and documented identit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role that inheres in a concretization of an identity document and is realized by an authentication process. Amanda Hicks credential role @@ -11168,465 +10879,48 @@ Is part_of the appropriate relation to use for data items and documented identit - + - - - obligor role - Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla. - A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. + + + my filling in an immigration form, a judge's signing and stamping a court order + A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. Mathias Brochhausen - Sarah Bost - duty holder role (IAO:210016) - obsolete obligor role - true + deontic document act - + - - - obligee role - Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money. - A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. + + + Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom + A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. Mathias Brochhausen - Sarah Bost - claimant role (IAO:0021013) - obsolete obligee role - true + The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). +Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. +Thanks to W.R. Hogan for finding the Reinach quote. + social act - + - - - Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script - A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role. + + + A social act that creates or revokes a deontic role. Mathias Brochhausen - OBIB/ICO community - https://github.com/d-acts/d-acts/issues/29 - owner role + deontic declaration - - - - - - obsolete_claim - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. - Mathias Brochhausen - deontic document act - - - - - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document. - Mathias Brochhausen - - - obsolete_document act - true - - - - - - - - - Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom - A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. - Mathias Brochhausen - The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). -Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. -Thanks to W.R. Hogan for finding the Reinach quote. - social act - - - - - - - - - the claim of a piece of land, the obligation to pay rent to the owner of a rental property - Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities. - Mathias Brochhausen - obsolete_socio-legal generically dependent continuant - true - - - - - - - - - deontic declaration - my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract. - A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document. - Mathias Brochhausen - declaration - status function declaration - - obsolete_deontic declaration - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Mathias Brochhausen - obsolete obligee role - true - - - - - - - - - A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification). - Mathias Brochhausen - document act input document - - - - - - - - - A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave. - Mathias Brochhausen - Neil Otte - deontic role - - - - - - - - - - - - - - - - - - - - - - - A social act that creates or revokes a deontic role. - Mathias Brochhausen - deontic declaration - - - - - - - - - - obsolete_obligation - true - - - - - - - - - A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. -https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child. - claimant role - - - - - - - - - The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration. - Mathias Brochhausen - - obsolete_declaration executive role - true - - - - - - - - - the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline - The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant. - Mathias Brochhausen - - not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants. - obsolete_document template creator role - true - - - - - - - - - A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - duty holder role - - - - - - - - - The role of a human being or an aggregate of human beings concretizing a claim. - Mathias Brochhausen - - obsolete_claimant role - true - - - - - - - - - The role of a human being or an aggregate of human beings concretizing an obligation. - Mathias Brochhausen - - obsolete_obligator role - true - - - - - - - - - A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - privilege holder role - - - - - - - - - me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act - The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. - Mathias Brochhausen - - obsolete_declaration target - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified - A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act. - Mathias Brochhausen - document act template creator role - - - - - - - - - A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration. - Mathias Brochhausen - declaration performer role - deontic declaration performer role - - - - - - - - - A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - power role - - - - - - - - - The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. - Mathias Brochhausen - obsoleted_document act target - true - - - - - + - - - - - - - - - - - - - - - - - - - - - - - a judge's role of signing a court order A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act. Mathias Brochhausen @@ -11635,57 +10929,6 @@ https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the clai - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - - obsolete_obligee role - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - - obsolete_obligor role - true - - - - - - - - - A social act that postulates a socio-legal fact for a specified group of people or organizations. - Mathias Brochhausen - enactment - standing declaration - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - John Judkins - Mathias Brochhausen - obsolete obligor role - true - - - - @@ -12104,7 +11347,6 @@ objectives is a planned process. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch @@ -12689,19 +11931,7 @@ edited date: 30 SEPT 2015 - - - - - - - - - - - - @@ -12716,10 +11946,8 @@ edited date: 30 SEPT 2015 An object aggregate of objectual organisms. - An object aggregate of organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. aggregate of objectual organisms - collection of organisms @@ -12727,19 +11955,7 @@ edited date: 30 SEPT 2015 - - - - - - - - - - - - @@ -12747,7 +11963,6 @@ edited date: 30 SEPT 2015 An object aggregate all of whose components are human beings. - An object aggregate all of whose components are human beings. collection of humans @@ -12903,31 +12118,16 @@ Ditto for its current descendants. - - - - - - - - - - - - - An aggregate of organizations that have some feature in common, but is not itself an organization. An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common - William R. Hogan William R. Hogan Amanda Hicks - http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations @@ -13471,7 +12671,7 @@ Note: this definition was taken over from "geopolitical organization". - + @@ -13482,14 +12682,14 @@ Note: this definition was taken over from "geopolitical organization". Mathias Brochhausen facility - + - + 09/09/2017 @@ -18595,7 +17795,6 @@ It indicates that a person has completed only early childhood education and noth A role that inheres in some entity that is realized in a social act. Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -18754,9 +17953,6 @@ It indicates that a person has completed only early childhood education and noth - - - quality pressure @@ -18831,30 +18027,6 @@ It indicates that a person has completed only early childhood education and noth - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - obsolete obligee role - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - obsolete obligor role - true - - - - diff --git a/omrse.json b/omrse.json index a21940e..a612a99 100644 --- a/omrse.json +++ b/omrse.json @@ -67,31 +67,11 @@ "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-14" + "val" : "2024-11-25" } ], - "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-08-14/omrse.json" + "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-11-25/omrse.json" }, "nodes" : [ { - "id" : "http://purl.obolibary.org/obo/IAO_0021001", - "lbl" : "obsolete_deontic document act", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my filling in an immigration form, a judge's signing and stamping a court order" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "lbl" : "software development", "type" : "CLASS", @@ -7280,91 +7260,6 @@ "val" : "Amanda Hicks" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020025", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obligor role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "duty holder role (IAO:210016)" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020026", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "obligee role" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "claimant role (IAO:0021013)" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0020027", - "lbl" : "owner role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "OBIB/ICO community" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://github.com/d-acts/d-acts/issues/29" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021000", - "lbl" : "obsolete_claim", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021001", "lbl" : "deontic document act", @@ -7381,29 +7276,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021002", - "lbl" : "obsolete_document act", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my filling in an immigration form, a judge's signing and stamping a court order" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", - "val" : "http://purl.obolibary.org/obo/IAO_0021001" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021003", "lbl" : "social act", @@ -7421,95 +7293,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021004", - "lbl" : "obsolete_socio-legal generically dependent continuant", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021005", - "lbl" : "obsolete_deontic declaration", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "deontic declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "status function declaration" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021006", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021007", - "lbl" : "document act input document", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021008", - "lbl" : "deontic role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Neil Otte" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021009", "lbl" : "deontic declaration", @@ -7523,244 +7306,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021010", - "lbl" : "obsolete_obligation", - "type" : "CLASS", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021013", - "lbl" : "claimant role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A." - }, - "comments" : [ "Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. \nhttps://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021014", - "lbl" : "obsolete_declaration executive role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021015", - "lbl" : "obsolete_document template creator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." - }, - "comments" : [ "not that the \"template\" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021016", - "lbl" : "duty holder role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021017", - "lbl" : "obsolete_claimant role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings concretizing a claim." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021018", - "lbl" : "obsolete_obligator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The role of a human being or an aggregate of human beings concretizing an obligation." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000226" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021019", - "lbl" : "privilege holder role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021020", - "lbl" : "obsolete_declaration target", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021021", - "lbl" : "document act template creator role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021022", - "lbl" : "deontic declaration performer role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "declaration performer role" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021023", - "lbl" : "power role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "J. Neil Otte" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://plato.stanford.edu/entries/rights/" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021030", - "lbl" : "obsoleted_document act target", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021031", "lbl" : "document act performer role", @@ -7777,73 +7322,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021032", - "lbl" : "obsolete_obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021033", - "lbl" : "obsolete_obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021102", - "lbl" : "standing declaration", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A social act that postulates a socio-legal fact for a specified group of people or organizations." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enactment" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021300", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "John Judkins" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", @@ -8385,7 +7863,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." + "val" : "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", @@ -8940,11 +8418,11 @@ } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "lbl" : "collection of organisms", + "lbl" : "aggregate of objectual organisms", "type" : "CLASS", "meta" : { "definition" : { - "val" : "An object aggregate of organisms." + "val" : "An object aggregate of objectual organisms." }, "comments" : [ "Any arbitrary collection of organisms. They need not be of the same taxonomic class. " ] } @@ -8955,8 +8433,7 @@ "meta" : { "definition" : { "val" : "An object aggregate all of whose components are human beings." - }, - "comments" : [ "An object aggregate all of whose components are human beings." ] + } } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000024", @@ -9088,14 +8565,8 @@ }, "comments" : [ "It is often convenient to group organizations together that otherwise might not even interact with one another. " ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "William R. Hogan" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan\nAmanda Hicks" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl" } ] } }, { @@ -13795,9 +13266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" @@ -14002,10 +13470,7 @@ "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485219" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", - "val" : "_:genid2147485220" + "val" : "_:genid2147485116" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" @@ -14105,34 +13570,6 @@ "val" : "http://purl.obolibrary.org/obo/uo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", - "lbl" : "obsolete obligee role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - } ], - "deprecated" : true - } - }, { - "id" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", - "lbl" : "obsolete obligor role", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Sarah Bost" - } ], - "deprecated" : true - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass", "type" : "CLASS" @@ -14272,9 +13709,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "realized_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" @@ -14401,42 +13835,6 @@ "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000075", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000117", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000118", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000121", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000132", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000136", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000138", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000139", - "type" : "PROPERTY", - "propertyType" : "OBJECT" - }, { - "id" : "http://purl.obolibrary.org/obo/BFO_0000181", - "type" : "PROPERTY", - "propertyType" : "OBJECT" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000039", "lbl" : "has measurement unit label", @@ -14841,38 +14239,6 @@ "val" : "Mathias Brochhausen" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021011", - "lbl" : "legally revokes", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/IAO_0021012", - "lbl" : "obsolete_legally transfers", - "type" : "PROPERTY", - "propertyType" : "OBJECT", - "meta" : { - "definition" : { - "val" : "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Mathias Brochhausen" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", - "val" : "http://purl.obolibrary.org/obo/IAO_0000103" - } ], - "deprecated" : true - } }, { "id" : "http://purl.obolibrary.org/obo/OBIB_0000732", "lbl" : "owns", @@ -16283,30 +15649,14 @@ "propertyType" : "OBJECT", "meta" : { "definition" : { - "val" : "x has participant y if and only if x realizes some active role that inheres in y" + "val" : "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'heart development' has active participant some Shh protein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", - "val" : "This may be obsoleted and replaced by the original 'has agent' relation" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", - "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" @@ -27667,10 +27017,6 @@ "id" : "http://www.w3.org/2002/07/owl#Thing" } ], "edges" : [ { - "sub" : "http://purl.obolibary.org/obo/IAO_0021001", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { "sub" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" @@ -28962,14 +28308,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020020", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/IAO_0020000" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020021", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020021", - "pred" : "http://purl.obolibrary.org/obo/IAO_0000136", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020022" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0020022", "pred" : "is_a", @@ -28982,142 +28320,22 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020024", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020024", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000054", - "obj" : "http://purl.obolibrary.org/obo/IAO_0020023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020025", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020026", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0020027", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/OMRSE_00002072" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021000", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0021009" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000293", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021007" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021001", - "pred" : "http://purl.obolibrary.org/obo/OBI_0000299", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021002", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OBI_0000011" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021004", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021005", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021006", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021007", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0000310" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021008", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021010", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021013", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021014", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021015", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021016", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021017", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021018", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021019", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021020", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021021", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021022", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021023", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021008" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021030", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0021031", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000023" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021032", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021033", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021102", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/IAO_0021003" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021300", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_8000000", "pred" : "is_a", @@ -29410,18 +28628,10 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000027" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000022", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/OBI_0100026" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/OMRSE_00000022" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000023", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000024", "pred" : "is_a", @@ -29474,10 +28684,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/BFO_0000040" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", - "pred" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "obj" : "http://purl.obolibrary.org/obo/OBI_0000245" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000033", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -31012,14 +30218,6 @@ "sub" : "http://purl.obolibrary.org/obo/UO_0000003", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/IAO_0000003" - }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligee_role", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" - }, { - "sub" : "http://purl.obolibrary.org/obo/iao/d-acts.owl#obligor_role", - "pred" : "is_a", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteClass" }, { "sub" : "http://purl.obolibrary.org/obo/IAO_0000002", "pred" : "type", @@ -32776,14 +31974,6 @@ "sub" : "http://purl.obolibrary.org/obo/BFO_0000051", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002131" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000054", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/BFO_0000055", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/BFO_0000062", "pred" : "subPropertyOf", @@ -32852,14 +32042,6 @@ "sub" : "http://purl.obolibrary.org/obo/IAO_0020013", "pred" : "subPropertyOf", "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021011", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/IAO_0021012", - "pred" : "subPropertyOf", - "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OBIB_0000732", "pred" : "subPropertyOf", @@ -32888,10 +32070,6 @@ "sub" : "http://purl.obolibrary.org/obo/OMIABIS_0000009", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000020", - "pred" : "subPropertyOf", - "obj" : "http://www.w3.org/2002/07/owl#topObjectProperty" }, { "sub" : "http://purl.obolibrary.org/obo/OMRSE_00000021", "pred" : "subPropertyOf", @@ -33080,10 +32258,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0002217", "pred" : "subPropertyOf", "obj" : "http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty" - }, { - "sub" : "http://purl.obolibrary.org/obo/RO_0002218", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/RO_0000057" }, { "sub" : "http://purl.obolibrary.org/obo/RO_0002223", "pred" : "subPropertyOf", @@ -33733,23 +32907,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020000" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0020024", - "genusIds" : [ "http://purl.obolibrary.org/obo/BFO_0000023" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000054", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0020023" - } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/IAO_0021001", - "genusIds" : [ "http://purl.obolibrary.org/obo/IAO_0021009" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000293", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0021007" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/OBI_0000299", - "fillerId" : "http://purl.obolibrary.org/obo/IAO_0000310" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/OMRSE_00000030", "genusIds" : [ "http://purl.obolibrary.org/obo/OMRSE_00000011" ], @@ -34009,10 +33166,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/IAO_0020013", "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0020000" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/IAO_0021011", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0021009" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/IAO_0021008" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/OBI_0000293", "domainClassIds" : [ "http://purl.obolibrary.org/obo/OBI_0000011" ] diff --git a/omrse.obo b/omrse.obo index 4390e37..a2d1d0a 100644 --- a/omrse.obo +++ b/omrse.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: omrse/releases/2024-08-14/omrse-full.owl +data-version: omrse/releases/2024-11-25/omrse-full.owl subsetdef: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_gp2term "" subsetdef: http://purl.obolibrary.org/obo/valid_for_go_ontology "" @@ -50,7 +50,7 @@ property_value: dc:creator "Swetha Garimalla" xsd:string property_value: dc:creator "William Hogan" xsd:string property_value: dc:description "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." xsd:string property_value: dc:title "Ontology for Modeling and Representation of Social Entities" xsd:string -property_value: owl:versionInfo "2024-08-14" xsd:string +property_value: owl:versionInfo "2024-11-25" xsd:string property_value: terms:license "https://creativecommons.org/licenses/by/4.0/" xsd:string [Term] @@ -3284,8 +3284,6 @@ property_value: IAO:0000233 "https://github.com/information-artifact-ontology/IA id: IAO:0020021 name: identity document def: "A document that denotes some identity and is concretized by the bearer of some credential role." [] -is_a: IAO:0000310 ! document -relationship: IAO:0000136 IAO:0020022 ! is about documented identity property_value: IAO:0000117 "Amanda Hicks" xsd:string [Term] @@ -3309,79 +3307,15 @@ id: IAO:0020024 name: credential role def: "A role that inheres in a concretization of an identity document and is realized by an authentication process." [] is_a: BFO:0000023 ! role -relationship: BFO:0000054 IAO:0020023 ! realized in authentication property_value: IAO:0000117 "Amanda Hicks" xsd:string -[Term] -id: IAO:0020025 -name: obsolete obligor role -def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "obligor role" xsd:string -property_value: IAO:0000112 "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true -replaced_by: duty holder role (IAO:210016) - -[Term] -id: IAO:0020026 -name: obsolete obligee role -def: "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "obligee role" xsd:string -property_value: IAO:0000112 "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true -replaced_by: claimant role (IAO:0021013) - -[Term] -id: IAO:0020027 -name: owner role -def: "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." [] -is_a: OMRSE:00002072 ! role in human social processes -property_value: IAO:0000112 "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "https://github.com/d-acts/d-acts/issues/29" xsd:string -property_value: IAO:0000119 "OBIB/ICO community" xsd:string - -[Term] -id: IAO:0021000 -name: obsolete_claim -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - [Term] id: IAO:0021001 name: deontic document act -name: obsolete_deontic document act def: "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." [] is_a: IAO:0021009 ! deontic declaration -is_a: oboInOwl:ObsoleteClass -intersection_of: IAO:0021009 ! deontic declaration -intersection_of: OBI:0000293 IAO:0021007 ! has_specified_input document act input document -intersection_of: OBI:0000299 IAO:0000310 ! has_specified_output document -relationship: OBI:0000293 IAO:0021007 ! has_specified_input document act input document -relationship: OBI:0000299 IAO:0000310 ! has_specified_output document -property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string -property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021002 -name: obsolete_document act -def: "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." [] -is_a: oboInOwl:ObsoleteClass property_value: IAO:0000112 "my filling in an immigration form, a judge's signing and stamping a court order" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true -replaced_by: IAO:0021001 [Term] id: IAO:0021003 @@ -3392,51 +3326,6 @@ is_a: OBI:0000011 ! planned process property_value: IAO:0000112 "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021004 -name: obsolete_socio-legal generically dependent continuant -def: "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - -[Term] -id: IAO:0021005 -name: obsolete_deontic declaration -def: "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000111 "deontic declaration" xsd:string -property_value: IAO:0000112 "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "declaration" xsd:string -property_value: IAO:0000118 "status function declaration" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021006 -name: obsolete obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - -[Term] -id: IAO:0021007 -name: document act input document -def: "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." [] -is_a: IAO:0000310 ! document -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0021008 -name: deontic role -def: "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000117 "Neil Otte" xsd:string - [Term] id: IAO:0021009 name: deontic declaration @@ -3444,126 +3333,6 @@ def: "A social act that creates or revokes a deontic role." [] is_a: IAO:0021003 ! social act property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021010 -name: obsolete_obligation -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021013 -name: claimant role -def: "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A." [] -comment: Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. \nhttps://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child. -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021014 -name: obsolete_declaration executive role -def: "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021015 -name: obsolete_document template creator role -def: "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." [] -comment: not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants. -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021016 -name: duty holder role -def: "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021017 -name: obsolete_claimant role -def: "The role of a human being or an aggregate of human beings concretizing a claim." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021018 -name: obsolete_obligator role -def: "The role of a human being or an aggregate of human beings concretizing an obligation." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000226 -is_obsolete: true - -[Term] -id: IAO:0021019 -name: privilege holder role -def: "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021020 -name: obsolete_declaration target -def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000112 "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021021 -name: document act template creator role -def: "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000112 "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string - -[Term] -id: IAO:0021022 -name: deontic declaration performer role -def: "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." [] -is_a: BFO:0000023 ! role -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "declaration performer role" xsd:string - -[Term] -id: IAO:0021023 -name: power role -def: "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role." [] -is_a: IAO:0021008 ! deontic role -property_value: IAO:0000117 "J. Neil Otte" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000119 "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." xsd:string -property_value: IAO:0000119 "https://plato.stanford.edu/entries/rights/" xsd:string - -[Term] -id: IAO:0021030 -name: obsoleted_document act target -def: "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - [Term] id: IAO:0021031 name: document act performer role @@ -3572,41 +3341,6 @@ is_a: BFO:0000023 ! role property_value: IAO:0000112 "a judge's role of signing a court order" xsd:string property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -[Term] -id: IAO:0021032 -name: obsolete_obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021033 -name: obsolete_obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_obsolete: true - -[Term] -id: IAO:0021102 -name: standing declaration -def: "A social act that postulates a socio-legal fact for a specified group of people or organizations." [] -is_a: IAO:0021003 ! social act -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000118 "enactment" xsd:string - -[Term] -id: IAO:0021300 -name: obsolete obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "John Judkins" xsd:string -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -is_obsolete: true - [Term] id: IAO:8000000 name: ontology module @@ -3853,7 +3587,6 @@ property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl id: OBI:0000245 name: organization def: "An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] -def: "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string @@ -4166,20 +3899,15 @@ property_value: IAO:0000117 "Amanda Hicks" xsd:string [Term] id: OMRSE:00000022 name: aggregate of objectual organisms -name: collection of organisms def: "An object aggregate of objectual organisms." [] -def: "An object aggregate of organisms." [] comment: Any arbitrary collection of organisms. They need not be of the same taxonomic class. is_a: BFO:0000027 ! object aggregate -relationship: OMRSE:00000020 OBI:0100026 ! obsolete is-aggregate-of organism [Term] id: OMRSE:00000023 name: collection of humans def: "An object aggregate all of whose components are human beings." [] -comment: An object aggregate all of whose components are human beings. -is_a: OMRSE:00000022 ! collection of organisms -relationship: OMRSE:00000020 NCBITaxon:9606 ! obsolete is-aggregate-of Homo sapiens +is_a: OMRSE:00000022 ! aggregate of objectual organisms relationship: RO:0002351 NCBITaxon:9606 {all_only="true"} ! has member Homo sapiens [Term] @@ -4264,15 +3992,11 @@ is_obsolete: true [Term] id: OMRSE:00000033 name: aggregate of organizations -def: "An aggregate of organizations that have some feature in common, but is not itself an organization." [] def: "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common" [] comment: It is often convenient to group organizations together that otherwise might not even interact with one another. is_a: BFO:0000040 ! material entity -relationship: OMRSE:00000020 OBI:0000245 ! obsolete is-aggregate-of organization relationship: RO:0002351 OBI:0000245 ! has member organization -property_value: IAO:0000117 "William R. Hogan" xsd:string property_value: IAO:0000117 "William R. Hogan\nAmanda Hicks" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl" xsd:string [Term] id: OMRSE:00000034 @@ -4968,7 +4692,7 @@ is_a: BFO:0000034 ! function id: OMRSE:00000126 name: patient discharge def: "A deontic document act that concludes an inpatient encounter." [] -is_a: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act relationship: RO:0002229 OGMS:0000100 ! ends inpatient encounter property_value: IAO:0000117 "Amanda Hicks" xsd:string property_value: IAO:0000118 "discharge process" xsd:string @@ -5507,7 +5231,7 @@ property_value: IAO:0000117 "S. Clint Dowland" xsd:string id: OMRSE:00000201 name: admission process def: "A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter." [] -is_a: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act relationship: RO:0002083 OMRSE:00000126 ! before patient discharge relationship: RO:0002223 OGMS:0000100 ! starts inpatient encounter property_value: IAO:0000117 "Amanda Hicks" xsd:string @@ -6478,8 +6202,8 @@ id: OMRSE:00002037 name: awarding an academic degree def: "A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree." [] comment: Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam). -is_a: IAO:0021001 ! obsolete_deontic document act -intersection_of: IAO:0021001 ! obsolete_deontic document act +is_a: IAO:0021001 ! deontic document act +intersection_of: IAO:0021001 ! deontic document act intersection_of: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree relationship: OBI:0000299 OOSTT:00000074 ! has_specified_output academic degree property_value: IAO:0000111 "awarding of an academic degree" xsd:string @@ -6874,7 +6598,6 @@ is_a: OMRSE:00000048 ! material entity role relationship: RO:0000052 BFO:0000040 {all_only="true"} ! characteristic of material entity property_value: dc:contributor "Mathias Brochhausen" xsd:string property_value: IAO:0000117 "Matthew Diller" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" xsd:string [Term] id: OOSTT:00000074 @@ -6989,7 +6712,7 @@ id: PCO:0000020 name: family def: "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." [] comment: Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry. -is_a: OMRSE:00000022 ! collection of organisms +is_a: OMRSE:00000022 ! aggregate of objectual organisms property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Needs axioms for family relationships." xsd:string property_value: IAO:0000119 "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173" xsd:string @@ -7024,22 +6747,6 @@ is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl -[Term] -id: obligee_role -name: obsolete obligee role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true - -[Term] -id: obligor_role -name: obsolete obligor role -def: "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." [] -is_a: oboInOwl:ObsoleteClass -property_value: IAO:0000117 "Sarah Bost" xsd:string -is_obsolete: true - [Typedef] id: BFO:0000050 name: part of @@ -7101,7 +6808,6 @@ property_value: IAO:0000112 "this fragility is realized in this shattering" xsd: property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl domain: BFO:0000017 ! realizable entity @@ -7388,28 +7094,6 @@ def: "p1 is designated by p2, if p2 is an information content entity that repres property_value: IAO:0000117 "Mathias Brochhausen" xsd:string is_asymmetric: true -[Typedef] -id: IAO:0021011 -name: legally revokes -def: "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -domain: IAO:0021009 ! deontic declaration -range: IAO:0021008 ! deontic role -is_functional: true -is_a: RO:0000057 ! has_participant -is_asymmetric: true - -[Typedef] -id: IAO:0021012 -name: obsolete_legally transfers -def: "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." [] -property_value: IAO:0000117 "Mathias Brochhausen" xsd:string -property_value: IAO:0000231 IAO:0000103 -is_functional: true -is_a: oboInOwl:ObsoleteProperty -is_obsolete: true -is_asymmetric: true - [Typedef] id: OBI:0000293 name: has_specified_input @@ -7525,7 +7209,6 @@ replaced_by: OBIB:0000735 [Typedef] id: OMRSE:00000020 -name: is-aggregate-of name: obsolete is-aggregate-of comment: We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation.\n property_value: IAO:0000231 "BFO relation takes precedence." xsd:string @@ -8159,19 +7842,10 @@ replaced_by: RO:0002608 [Typedef] id: RO:0002218 -name: has active participant name: obsolete has active participant def: "OBSOLETE x has participant y if and only if x realizes some active role that inheres in y" [] -def: "x has participant y if and only if x realizes some active role that inheres in y" [] -subset: ro-eco -property_value: IAO:0000112 "'heart development' has active participant some Shh protein" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000116 "This may be obsoleted and replaced by the original 'has agent' relation" xsd:string -property_value: IAO:0000117 "Chris Mungall" xsd:string property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: IAO:0000118 "has agent" xsd:string -property_value: IAO:0000412 "http://purl.obolibrary.org/obo/ro.owl" xsd:string -is_a: RO:0000057 ! has_participant is_obsolete: true replaced_by: RO:0002500 diff --git a/omrse.owl b/omrse.owl index 3a39ce1..ad3648e 100644 --- a/omrse.owl +++ b/omrse.owl @@ -20,7 +20,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:language-individuals="http://purl.obolibrary.org/obo/omrse/language-individuals/"> - + Barry Smith Chris Stoeckert Daniel Welch @@ -42,7 +42,7 @@ Ontology for Modeling and Representation of Social Entities https://creativecommons.org/licenses/by/4.0/ This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's "meaningful use" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt - 2024-08-14 + 2024-11-25 @@ -1445,7 +1445,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - @@ -1455,7 +1454,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. this investigator role is realized in this investigation is realized by realized_in - http://purl.obolibrary.org/obo/ro.owl [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process @@ -1467,7 +1465,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - realizes @@ -1567,60 +1564,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1994,39 +1937,6 @@ Werner suggests a solution based on "Magnitudes" a proposal for which - - - - - - - - - - d socio-legally revokes s if s participates in d and at the end of d s no longer exists. -It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question. - Mathias Brochhausen - legally revokes - - - - - - - - - - - - d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical. - Mathias Brochhausen - - obsolete_legally transfers - true - - - - @@ -2201,11 +2111,9 @@ https://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_ - BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. - is-aggregate-of obsolete is-aggregate-of true @@ -3209,19 +3117,10 @@ We expect BFO 2.0 to have this relation as well, and we will obsolete this prope - - 'heart development' has active participant some Shh protein - OBSOLETE x has participant y if and only if x realizes some active role that inheres in y - x has participant y if and only if x realizes some active role that inheres in y - This may be obsoleted and replaced by the original 'has agent' relation - Chris Mungall has agent - http://purl.obolibrary.org/obo/ro.owl - - has active participant obsolete has active participant true @@ -4899,20 +4798,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. - Mathias Brochhausen - - obsolete_deontic document act - true - - - - @@ -10950,83 +10835,6 @@ When there is no such string, it is almost always because the entities take the - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A document that denotes some identity and is concretized by the bearer of some credential role. Amanda Hicks identity document @@ -11038,28 +10846,6 @@ When there is no such string, it is almost always because the entities take the - - - - - - - - - - - - - - - - - - - - - - A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents. Amanda Hicks is an aggregate of ICEs also an ICE? yes @@ -11073,34 +10859,6 @@ Is part_of the appropriate relation to use for data items and documented identit - - - - - - - - - - - - - - - - - - - - - - - - - - - - I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database. Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit). @@ -11113,54 +10871,7 @@ Is part_of the appropriate relation to use for data items and documented identit - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A role that inheres in a concretization of an identity document and is realized by an authentication process. Amanda Hicks credential role @@ -11168,465 +10879,48 @@ Is part_of the appropriate relation to use for data items and documented identit - + - - - obligor role - Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla. - A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. + + + my filling in an immigration form, a judge's signing and stamping a court order + A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. Mathias Brochhausen - Sarah Bost - duty holder role (IAO:210016) - obsolete obligor role - true + deontic document act - + - - - obligee role - Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money. - A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. + + + Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom + A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. Mathias Brochhausen - Sarah Bost - claimant role (IAO:0021013) - obsolete obligee role - true + The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). +Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. +Thanks to W.R. Hogan for finding the Reinach quote. + social act - + - - - Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script - A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role. + + + A social act that creates or revokes a deontic role. Mathias Brochhausen - OBIB/ICO community - https://github.com/d-acts/d-acts/issues/29 - owner role + deontic declaration - - - - - - obsolete_claim - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document. - Mathias Brochhausen - deontic document act - - - - - - - - - my filling in an immigration form, a judge's signing and stamping a court order - A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document. - Mathias Brochhausen - - - obsolete_document act - true - - - - - - - - - Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom - A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived. - Mathias Brochhausen - The phrase "in need of being perceived" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: "The command is according to its essence in need of being heard (vernehmungsbedürtig". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target." (A. Reinach: The Apriori Foundations of the Civil Law." Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012). -Reinach clearly does not imply that a command that does not fulfill its prupose would not be a command. -Thanks to W.R. Hogan for finding the Reinach quote. - social act - - - - - - - - - the claim of a piece of land, the obligation to pay rent to the owner of a rental property - Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities. - Mathias Brochhausen - obsolete_socio-legal generically dependent continuant - true - - - - - - - - - deontic declaration - my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract. - A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document. - Mathias Brochhausen - declaration - status function declaration - - obsolete_deontic declaration - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Mathias Brochhausen - obsolete obligee role - true - - - - - - - - - A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification). - Mathias Brochhausen - document act input document - - - - - - - - - A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave. - Mathias Brochhausen - Neil Otte - deontic role - - - - - - - - - - - - - - - - - - - - - - - A social act that creates or revokes a deontic role. - Mathias Brochhausen - deontic declaration - - - - - - - - - - obsolete_obligation - true - - - - - - - - - A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. -https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child. - claimant role - - - - - - - - - The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration. - Mathias Brochhausen - - obsolete_declaration executive role - true - - - - - - - - - the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline - The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant. - Mathias Brochhausen - - not that the "template" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants. - obsolete_document template creator role - true - - - - - - - - - A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - duty holder role - - - - - - - - - The role of a human being or an aggregate of human beings concretizing a claim. - Mathias Brochhausen - - obsolete_claimant role - true - - - - - - - - - The role of a human being or an aggregate of human beings concretizing an obligation. - Mathias Brochhausen - - obsolete_obligator role - true - - - - - - - - - A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - privilege holder role - - - - - - - - - me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act - The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. - Mathias Brochhausen - - obsolete_declaration target - true - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified - A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act. - Mathias Brochhausen - document act template creator role - - - - - - - - - A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration. - Mathias Brochhausen - declaration performer role - deontic declaration performer role - - - - - - - - - A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role. - J. Neil Otte - Mathias Brochhausen - Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919. - https://plato.stanford.edu/entries/rights/ - power role - - - - - - - - - The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act. - Mathias Brochhausen - obsoleted_document act target - true - - - - - + - - - - - - - - - - - - - - - - - - - - - - - a judge's role of signing a court order A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act. Mathias Brochhausen @@ -11635,57 +10929,6 @@ https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the clai - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - - obsolete_obligee role - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - - obsolete_obligor role - true - - - - - - - - - A social act that postulates a socio-legal fact for a specified group of people or organizations. - Mathias Brochhausen - enactment - standing declaration - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - John Judkins - Mathias Brochhausen - obsolete obligor role - true - - - - @@ -12104,7 +11347,6 @@ objectives is a planned process. PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch @@ -12689,19 +11931,7 @@ edited date: 30 SEPT 2015 - - - - - - - - - - - - @@ -12716,10 +11946,8 @@ edited date: 30 SEPT 2015 An object aggregate of objectual organisms. - An object aggregate of organisms. Any arbitrary collection of organisms. They need not be of the same taxonomic class. aggregate of objectual organisms - collection of organisms @@ -12727,19 +11955,7 @@ edited date: 30 SEPT 2015 - - - - - - - - - - - - @@ -12747,7 +11963,6 @@ edited date: 30 SEPT 2015 An object aggregate all of whose components are human beings. - An object aggregate all of whose components are human beings. collection of humans @@ -12903,31 +12118,16 @@ Ditto for its current descendants. - - - - - - - - - - - - - An aggregate of organizations that have some feature in common, but is not itself an organization. An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common - William R. Hogan William R. Hogan Amanda Hicks - http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl It is often convenient to group organizations together that otherwise might not even interact with one another. aggregate of organizations @@ -13471,7 +12671,7 @@ Note: this definition was taken over from "geopolitical organization". - + @@ -13482,14 +12682,14 @@ Note: this definition was taken over from "geopolitical organization". Mathias Brochhausen facility - + - + 09/09/2017 @@ -18595,7 +17795,6 @@ It indicates that a person has completed only early childhood education and noth A role that inheres in some entity that is realized in a social act. Matthew Diller - http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl Mathias Brochhausen Previous definition: A role played by an entity in human social processes. role in human social processes @@ -18754,9 +17953,6 @@ It indicates that a person has completed only early childhood education and noth - - - quality pressure @@ -18831,30 +18027,6 @@ It indicates that a person has completed only early childhood education and noth - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - obsolete obligee role - true - - - - - - - - - A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements. - Sarah Bost - obsolete obligor role - true - - - - diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 078b681..51edf3e 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -16,7 +16,7 @@ # 3. [Update repo to latest ODK](update_repo) # Fingerprint of the configuration file when this Makefile was last generated -CONFIG_HASH= 6d7fdabc7e6d622e63f340c8f29791bf031e15c86faa2df55199cd04a497bc9f +CONFIG_HASH= e982da79af6e23c70c7eacfef4b1468d45fe5e4f48d15d34bbff904800ec1fb4 # ---------------------------------------- @@ -382,10 +382,8 @@ $(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt $(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) merge -i $< \ - query --update ../sparql/preprocess-module.ru \ - remove --base-iri $(OBOBASE)"/$(shell echo $* | tr a-z A-Z)_" --axioms external --preserve-structure false --trim false \ - remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) -T $(IMPORTDIR)/$*_terms_combined.txt --select complement \ + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ $(ANNOTATE_CONVERT_FILE); fi @@ -442,8 +440,12 @@ $(IMPORTDIR)/pno_import.owl: $(MIRRORDIR)/pno.owl $(IMPORTDIR)/pno_terms_combine ## Module for ontology: d-acts $(IMPORTDIR)/d-acts_import.owl: $(MIRRORDIR)/d-acts.owl $(IMPORTDIR)/d-acts_terms_combined.txt - if [ $(IMP) = true ]; then $(ROBOT) merge -i $< query --update ../sparql/preprocess-module.ru --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ - $(ANNOTATE_CONVERT_FILE); fi + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/d-acts_terms_combined.txt --copy-ontology-annotations true --force true --method BOT \ + remove --base-iri http://purl.obolibrary.org/obo/IAO_ --axioms external --preserve-structure false --trim false \ + remove $(patsubst %, --term %, $(ANNOTATION_PROPERTIES)) --term rdfs:label --term IAO:0000115 -T $(IMPORTDIR)/d-acts_terms_combined.txt --select complement \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi .PHONY: refresh-imports diff --git a/src/ontology/imports/d-acts_import.owl b/src/ontology/imports/d-acts_import.owl index 7e9c712..dc90f71 100644 --- a/src/ontology/imports/d-acts_import.owl +++ b/src/ontology/imports/d-acts_import.owl @@ -7,424 +7,38 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-08-09") + +Annotation(owl:versionInfo "2024-11-25") -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) 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-Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(Class()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(ObjectProperty()) -Declaration(DataProperty()) -Declaration(DataProperty()) -Declaration(DataProperty()) -Declaration(DataProperty()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(NamedIndividual()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -433,96 +47,26 @@ Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty(rdfs:comment)) -Declaration(AnnotationProperty(rdfs:isDefinedBy)) -Declaration(AnnotationProperty(rdfs:label)) -Declaration(AnnotationProperty(rdfs:seeAlso)) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) -Declaration(AnnotationProperty()) ############################ # Annotation Properties ############################ -# Annotation Property: (BFO OWL specification label) - -AnnotationAssertion( "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification."@en) -AnnotationAssertion( "Really of interest to developers only"@en) -AnnotationAssertion(rdfs:label "BFO OWL specification label"@en) -SubAnnotationPropertyOf( rdfs:label) - -# Annotation Property: (BFO CLIF specification label) - -AnnotationAssertion( "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2"@en) -AnnotationAssertion( "Person:Alan Ruttenberg") -AnnotationAssertion( "Really of interest to developers only"@en) -AnnotationAssertion(rdfs:label "BFO CLIF specification label"@en) -SubAnnotationPropertyOf( rdfs:label) - # Annotation Property: (editor preferred term) AnnotationAssertion( "editor preferred term"@en) -AnnotationAssertion( ) AnnotationAssertion( "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)"@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor preferred label"@en) AnnotationAssertion(rdfs:label "editor preferred term"@en) AnnotationAssertion(rdfs:label "editor preferred term") @@ -530,21 +74,11 @@ AnnotationAssertion(rdfs:label "edi # Annotation Property: (example of usage) AnnotationAssertion( "example of usage"@en) -AnnotationAssertion( ) AnnotationAssertion( "A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "example of usage"@en) -# Annotation Property: (in branch) - -AnnotationAssertion( "in branch"@en) -AnnotationAssertion( "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet."@en) -AnnotationAssertion( "GROUP:OBI"@en) -AnnotationAssertion( "OBI_0000277"@en) -AnnotationAssertion(rdfs:label "in branch"@en) - # Annotation Property: (has curation status) AnnotationAssertion( "has curation status"@en) @@ -556,7 +90,6 @@ AnnotationAssertion(rdfs:label "has # Annotation Property: (definition) AnnotationAssertion( "definition"@en) -AnnotationAssertion( ) AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) AnnotationAssertion( "2012-04-05: Barry Smith @@ -580,7 +113,6 @@ Personally, I am more comfortable weakening definition to documentation, with in We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition"@en) AnnotationAssertion(rdfs:label "definition") AnnotationAssertion(rdfs:label "textual definition") @@ -588,22 +120,18 @@ AnnotationAssertion(rdfs:label "tex # Annotation Property: (editor note) AnnotationAssertion( "editor note"@en) -AnnotationAssertion( ) AnnotationAssertion( "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "editor note"@en) # Annotation Property: (definition editor) AnnotationAssertion( "term editor"@en) -AnnotationAssertion( ) AnnotationAssertion( "Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people"@en) AnnotationAssertion( "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition editor"@en) AnnotationAssertion(rdfs:label "term editor"@en) AnnotationAssertion(rdfs:label "definition editor") @@ -611,7 +139,6 @@ AnnotationAssertion(rdfs:label "def # Annotation Property: (alternative label) AnnotationAssertion( "alternative label"@en) -AnnotationAssertion( ) AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "OBO Operations committee") @@ -622,12 +149,10 @@ AnnotationAssertion(rdfs:label "alt # Annotation Property: (definition source) AnnotationAssertion( "definition source"@en) -AnnotationAssertion( ) AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) AnnotationAssertion( "PERSON:Daniel Schober"@en) AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "definition source"@en) # Annotation Property: (has obsolescence reason) @@ -641,471 +166,44 @@ AnnotationAssertion(rdfs:label "has # Annotation Property: (curator note) AnnotationAssertion( "curator note"@en) -AnnotationAssertion( ) AnnotationAssertion( "An administrative note of use for a curator but of no use for a user"@en) AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "curator note"@en) -# Annotation Property: (term tracker item) - -AnnotationAssertion( "term tracker item"@en) -AnnotationAssertion( "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An IRI or similar locator for a request or discussion of an ontology term."@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:comment "The 'tracker item' can associate a tracker with a specific ontology term."@en) -AnnotationAssertion(rdfs:label "term tracker item"@en) - -# Annotation Property: (ontology term requester) - -AnnotationAssertion( "ontology term requester"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition."@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:comment "The 'term requester' can credit the person, organization or project who request the ontology term.") -AnnotationAssertion(rdfs:label "ontology term requester"@en) - -# Annotation Property: (is denotator type) - -AnnotationAssertion( "is denotator type"@en) -AnnotationAssertion( "Relates an class defined in an ontology, to the type of it's denotator"@en) -AnnotationAssertion( "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "is denotator type"@en) - # Annotation Property: (imported from) AnnotationAssertion( "imported from"@en) -AnnotationAssertion( ) AnnotationAssertion( "For external terms/classes, the ontology from which the term was imported"@en) AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) AnnotationAssertion( "PERSON:Melanie Courtot"@en) AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "imported from"@en) -# Annotation Property: (expand expression to) - -AnnotationAssertion( "expand expression to"@en) -AnnotationAssertion( "ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" -"@en) -AnnotationAssertion( "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones"@en) -AnnotationAssertion( "Chris Mungall"@en) -AnnotationAssertion(rdfs:label "expand expression to"@en) - -# Annotation Property: (expand assertion to) - -AnnotationAssertion( "expand assertion to"@en) -AnnotationAssertion( "ObjectProperty: RO??? -Label: spatially disjoint from -Annotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\" -"@en) -AnnotationAssertion( "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom."@en) -AnnotationAssertion( "Chris Mungall"@en) -AnnotationAssertion(rdfs:label "expand assertion to"@en) - -# Annotation Property: (first order logic expression) - -AnnotationAssertion( "first order logic expression"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "first order logic expression"@en) - -# Annotation Property: (antisymmetric property) - -AnnotationAssertion( "antisymmetric property"@en) -AnnotationAssertion( "part_of antisymmetric property xsd:true"@en) -AnnotationAssertion( "Use boolean value xsd:true to indicate that the property is an antisymmetric property"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "antisymmetric property"@en) -SubAnnotationPropertyOf( ) - -# Annotation Property: (OBO foundry unique label) - -AnnotationAssertion( "OBO foundry unique label"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An alternative name for a class or property which is unique across the OBO Foundry."@en) -AnnotationAssertion( "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Bjoern Peters"@en) -AnnotationAssertion( "PERSON:Chris Mungall"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "GROUP:OBO Foundry "@en) -AnnotationAssertion(rdfs:label "OBO foundry unique label"@en) - -# Annotation Property: (has ID digit count) - -AnnotationAssertion( "has ID digit count"@en) -AnnotationAssertion( "Ontology: - Annotations: - 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" - 'has ID digit count' : 7, - rdfs:label \"RO id policy\" - 'has ID policy for': \"RO\""@en) -AnnotationAssertion( "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has ID digit count"@en) - -# Annotation Property: (has ID range allocated to) - -AnnotationAssertion( "has ID range allocated"@en) -AnnotationAssertion( "Datatype: idrange:1 -Annotations: 'has ID range allocated to': \"Chris Mungall\" -EquivalentTo: xsd:integer[> 2151 , <= 2300] -"@en) -AnnotationAssertion( "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has ID range allocated to"@en) - -# Annotation Property: (has ID policy for) - -AnnotationAssertion( "has ID policy for"@en) -AnnotationAssertion( "Ontology: - Annotations: - 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" - 'has ID digit count' : 7, - rdfs:label \"RO id policy\" - 'has ID policy for': \"RO\""@en) -AnnotationAssertion( "Relating an ontology used to record id policy to the ontology namespace whose policy it manages"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has ID policy for"@en) - -# Annotation Property: (has ID prefix) - -AnnotationAssertion( "has ID prefix"@en) -AnnotationAssertion( "Ontology: - Annotations: - 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\" - 'has ID digit count' : 7, - rdfs:label \"RO id policy\" - 'has ID policy for': \"RO\""@en) -AnnotationAssertion( "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created."@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has ID prefix"@en) - # Annotation Property: (elucidation) AnnotationAssertion( "elucidation"@en) AnnotationAssertion( "person:Alan Ruttenberg"@en) AnnotationAssertion( "Person:Barry Smith"@en) AnnotationAssertion( "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms"@en) -AnnotationAssertion(rdfs:isDefinedBy ) AnnotationAssertion(rdfs:label "elucidation"@en) -# Annotation Property: (has associated axiom(nl)) - -AnnotationAssertion( "has associated axiom(nl)"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "An axiom associated with a term expressed using natural language"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "has associated axiom(nl)"@en) - -# Annotation Property: (has associated axiom(fol)) - -AnnotationAssertion( "has associated axiom(fol)"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "An axiom expressed in first order logic using CLIF syntax"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "has associated axiom(fol)"@en) - -# Annotation Property: (is allocated id range) - -AnnotationAssertion( "is allocated id range"@en) -AnnotationAssertion( "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\""@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) -AnnotationAssertion(rdfs:label "is allocated id range"@en) - -# Annotation Property: (retired from use as of) - -AnnotationAssertion( "retired from use as of"@en) -AnnotationAssertion( "relates a class of CRID to the date after which further instances should not be made, according to the central authority") -AnnotationAssertion( "In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "retired from use as of") - -# Annotation Property: (has ontology root term) - -AnnotationAssertion( "has ontology root term"@en) -AnnotationAssertion( "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root."@en) -AnnotationAssertion( "Nicolas Matentzoglu"@en) -AnnotationAssertion(rdfs:label "has ontology root term"@en) - -# Annotation Property: (may be identical to) - -AnnotationAssertion( "may be identical to"@en) -AnnotationAssertion( "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged."@en) -AnnotationAssertion( "David Osumi-Sutherland"@en) -AnnotationAssertion( "#40"@en) -AnnotationAssertion( "VFB"@en) -AnnotationAssertion(rdfs:comment "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance."@en) -AnnotationAssertion(rdfs:label "may be identical to"@en) - -# Annotation Property: (scheduled for obsoletion on or after) - -AnnotationAssertion( "scheduled for obsoletion on or after"@en) -AnnotationAssertion( "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date."@en) -AnnotationAssertion( "Chris Mungall, Jie Zheng"@en) -AnnotationAssertion( "https://github.com/geneontology/go-ontology/issues/15532"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/32"@en) -AnnotationAssertion( "GO ontology"@en) -AnnotationAssertion(rdfs:label "scheduled for obsoletion on or after"@en) -AnnotationPropertyRange( xsd:dateTime) - -# Annotation Property: (has axiom label) - -AnnotationAssertion( "has axiom id"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "has axiom label"@en) - -# Annotation Property: (IUI) - -AnnotationAssertion( "instance unique identifier"@en) -AnnotationAssertion(rdfs:comment "An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system."@en) -AnnotationAssertion(rdfs:label "IUI") - # Annotation Property: (term replaced by) AnnotationAssertion( "term replaced by"@en) -AnnotationAssertion( ) AnnotationAssertion( "Use on obsolete terms, relating the term to another term that can be used as a substitute"@en) AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion( "Person:Alan Ruttenberg"@en) AnnotationAssertion(rdfs:comment "Add as annotation triples in the granting ontology"@en) AnnotationAssertion(rdfs:label "term replaced by"@en) -# Annotation Property: (logical characteristic of object property) - -AnnotationAssertion( "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL.") -AnnotationAssertion( "OBO Operations call") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "logical characteristic of object property") - -# Annotation Property: (defined by construct) - -AnnotationAssertion( "'part disjoint with' 'defined by construct' \"\"\" - PREFIX owl: - PREFIX : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation.") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "defined by construct") - -# Annotation Property: (temporal interpretation) - -AnnotationAssertion( "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.") -AnnotationAssertion(rdfs:label "temporal interpretation"@en) - -# Annotation Property: () - -SubAnnotationPropertyOf( ) - -# Annotation Property: (has broad synonym) - -AnnotationAssertion( "An alternative label for a class or property which has a more general meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -AnnotationAssertion(rdfs:label "has broad synonym"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/18") -SubAnnotationPropertyOf( ) - -# Annotation Property: (has exact synonym) - -AnnotationAssertion( "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -AnnotationAssertion(rdfs:label "has exact synonym"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/20") -SubAnnotationPropertyOf( ) - -# Annotation Property: (has narrow synonym) - -AnnotationAssertion( "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") -AnnotationAssertion(rdfs:label "has narrow synonym"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/19") -SubAnnotationPropertyOf( ) - -# Annotation Property: (has related synonym) - -AnnotationAssertion( "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.") -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") -AnnotationAssertion(rdfs:label "has related synonym"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/ontology-metadata/issues/21") -SubAnnotationPropertyOf( ) - -# Annotation Property: rdfs:label (label) - -AnnotationAssertion(rdfs:label rdfs:label "label") - ############################ # Object Properties ############################ -# Object Property: (part of) - -AnnotationAssertion( "is part of"@en) -AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) -AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a part and its whole"@en) -AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) - -A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) -AnnotationAssertion( "part_of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "part of"@en) -AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (has part) - -AnnotationAssertion( "has part"@en) -AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) -AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) -AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) -AnnotationAssertion( "a core relation that holds between a whole and its part"@en) -AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) -AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) - -A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) -AnnotationAssertion( "has_part"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has part"@en) -TransitiveObjectProperty() - -# Object Property: (realized in) - -AnnotationAssertion( "realized in"@en) -AnnotationAssertion( "this disease is realized in this disease course"@en) -AnnotationAssertion( "this fragility is realized in this shattering"@en) -AnnotationAssertion( "this investigator role is realized in this investigation"@en) -AnnotationAssertion( "is realized by"@en) -AnnotationAssertion( "realized_in"@en) -AnnotationAssertion( "http://purl.obolibrary.org/obo/ro.owl") -AnnotationAssertion( "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "realized in"@en) -SubObjectPropertyOf( owl:topObjectProperty) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (realizes) - -AnnotationAssertion( "realizes"@en) -AnnotationAssertion( "this disease course realizes this disease"@en) -AnnotationAssertion( "this investigation realizes this investigator role"@en) -AnnotationAssertion( "this shattering realizes this fragility"@en) -AnnotationAssertion( "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "realizes"@en) -SubObjectPropertyOf( owl:topObjectProperty) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (occurs in) - -AnnotationAssertion( "occurs in"@en) -AnnotationAssertion( "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion( "occurs_in"@en) -AnnotationAssertion( "unfolds in"@en) -AnnotationAssertion( "unfolds_in"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "occurs in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (contains process) - -AnnotationAssertion( "site of"@en) -AnnotationAssertion( "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t"@en) -AnnotationAssertion(rdfs:comment "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "contains process"@en) - -# Object Property: (has measurement unit label) - -AnnotationAssertion(rdfs:label "has measurement unit label"@en) -SubObjectPropertyOf( ) -FunctionalObjectProperty() -ObjectPropertyRange( ) - -# Object Property: (obsolete_specifically denotes) - -AnnotationAssertion( "The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink. - -Here the ink + paper is the independent continuant and the carrier is the pattern in the ink. - -c = pattern in the ink -b = paper + ink -r = friend") -AnnotationAssertion( ) -AnnotationAssertion( "c specifically denotes r =def -r is a portion of reality -& c is a particular quality -& c depends specifically on some independent continuant b -& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. - -Marked means there is a changed or additional quality of the bearer - the quality is the information carrier. - -Case 1 -Memory trace as mark created when reading some description of some friend. The trace can denote. - -Case 2 -Pattern of ink arrayed on paper as mark when writing down a friend's name - -Case 3 -Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.") -AnnotationAssertion( "8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense") -AnnotationAssertion( "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_specifically denotes") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) - # Object Property: (is about) AnnotationAssertion( "This document is about information artifacts and their representations"@en) -AnnotationAssertion( ) AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. @@ -1117,26 +215,6 @@ AnnotationAssertion( "is about"@en) ObjectPropertyDomain( ) -# Object Property: (mentions) - -AnnotationAssertion( ) -AnnotationAssertion( "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E"@en) -AnnotationAssertion( "7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)"@en) -AnnotationAssertion( "7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation \"mentions\" in it's (logical) definition"@en) -AnnotationAssertion( "PERSON: Jonathan Rees"@en) -AnnotationAssertion( "Person: Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "mentions"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (mentioned by) - -AnnotationAssertion( "Inverse of the relation 'mentions'"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "2022-01-28T07:20:08Z"^^xsd:dateTime) -AnnotationAssertion(rdfs:label "mentioned by"@en) - # Object Property: (denotes) AnnotationAssertion( "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named."@en) @@ -1151,3873 +229,202 @@ AnnotationAssertion( ""@en) AnnotationAssertion(rdfs:label "denotes"@en) SubObjectPropertyOf( ) -InverseObjectProperties( ) ObjectPropertyDomain( ) -ObjectPropertyRange( ) -# Object Property: (obsolete_materially denotes) -AnnotationAssertion( "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_materially denotes") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) -# Object Property: (is quality measurement of) - -AnnotationAssertion( "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q"@en) -AnnotationAssertion( "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later"@en) -AnnotationAssertion( "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] +############################ +# Classes +############################ -This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. +# Class: (conditional specification) -Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details. --- -From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] +AnnotationAssertion( "conditional specification"@en) +AnnotationAssertion( "A directive information entity that specifies what should happen if the trigger condition is fulfilled."@en) +AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) +AnnotationAssertion( "OBI branch derived"@en) +AnnotationAssertion( "OBI_0000349"@en) +AnnotationAssertion(rdfs:label "conditional specification"@en) +SubClassOf( ) -unit of measure is a quality, e.g. the length of a ruler. +# Class: (objective specification) -[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] +AnnotationAssertion( "objective specification"@en) +AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) +AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) +AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) +AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) +AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Barry Smith"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Jennifer Fostel"@en) +AnnotationAssertion( "goal specification"@en) +AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) +AnnotationAssertion( "OBI_0000217"@en) +AnnotationAssertion(rdfs:label "objective specification"@en) +SubClassOf( ) -[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] +# Class: (action specification) -a represents b means either a denotes b or a describes +AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) +AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion(rdfs:label "action specification"@en) +SubClassOf( ) -describe: -a describes b means a is about b and a allows an inference of at least one quality of b +# Class: (data item) -We have had a long discussion about denotes versus describes."@en) -AnnotationAssertion( "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith -a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality."@en) -AnnotationAssertion( "From the second meeting on IAO: +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) -An attempt at defining assay using Barry's \"reliability\" wording +# Class: (symbol) -assay: -process and has_input some material entity -and has_output some information content entity -and which is such that instances of this process type reliably generate -outputs that describes the input."@en) -AnnotationAssertion( "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. +AnnotationAssertion( "symbol"@en) +AnnotationAssertion( "a serial number such as \"12324X\""@en) +AnnotationAssertion( "a stop sign"@en) +AnnotationAssertion( "a written proper name such as \"OBI\""@en) +AnnotationAssertion( "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en) +AnnotationAssertion( "20091104, MC: this needs work and will most probably change"@en) +AnnotationAssertion( "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)."@en) +AnnotationAssertion( "PERSON: James A. Overton"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "based on Oxford English Dictionary"@en) +AnnotationAssertion(rdfs:label "symbol"@en) +SubClassOf( ) -Werner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "is quality measurement of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +# Class: (information content entity) -# Object Property: (obsolete_describes) +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_describes") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) -# Object Property: (obsolete_represents) +# Class: (directive information entity) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_represents") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) +AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) +AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) +AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) +AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion(rdfs:label "directive information entity"@en) +SubClassOf( ) -# Object Property: (denoted by) +# Class: (data set) -AnnotationAssertion( "inverse of the relation 'denotes'"@en) -AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "denoted by"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +AnnotationAssertion( "data set"@en) +AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) +AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) +AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) +AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") +AnnotationAssertion( "person:Allyson Lister"@en) +AnnotationAssertion( "person:Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000042"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "data set"@en) +SubClassOf( ) -# Object Property: (has coordinate unit label) +# Class: (plan specification) -AnnotationAssertion(rdfs:comment "relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point"@en) -AnnotationAssertion(rdfs:label "has coordinate unit label"@en) -SubObjectPropertyOf( ) -FunctionalObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +AnnotationAssertion( "plan specification"@en) +AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) +AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) +AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) +AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) +AnnotationAssertion( "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231."@en) +AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Clint Dowland"@en) +AnnotationAssertion( "OBI Plan and Planned Process branch"@en) +AnnotationAssertion( "OBI_0000344"@en) +AnnotationAssertion(rdfs:comment "2/3/2009 Comment from OBI review. -# Object Property: (is duration of) +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. -AnnotationAssertion( ) -AnnotationAssertion( "relates a process to a time-measurement-datum that represents the duration of the process"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "is duration of"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +Request that IAO either clarify these or change definitions not to use them"@en) +AnnotationAssertion(rdfs:label "plan specification"@en) +SubClassOf( ) -# Object Property: (is quality measured as) +# Class: (document) -AnnotationAssertion( ) -AnnotationAssertion( "inverse of the relation of is quality measurement of"@en) -AnnotationAssertion( "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "is quality measured as"@en) +AnnotationAssertion( "document"@en) +AnnotationAssertion( "A journal article, patent application, laboratory notebook, or a book"@en) +AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion(rdfs:label "document"@en) +SubClassOf( ) -# Object Property: (is quality specification of) +# Class: (time measurement datum) -AnnotationAssertion( ) -AnnotationAssertion( "A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality."@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Bjoern Peters"@en) -AnnotationAssertion(rdfs:label "is quality specification of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) +AnnotationAssertion( "A scalar measurement datum that is the result of measuring a temporal interval"@en) +AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "time measurement datum"@en) +SubClassOf( ) -# Object Property: (quality is specified as) +# Class: (documenting) -AnnotationAssertion( ) -AnnotationAssertion( "inverse of the relation of is quality specification of"@en) -AnnotationAssertion( "2009/10/19 Alan Ruttenberg. Named 'junk' relation useful in restrictions, but not a real instance relationship"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Bjoern Peters"@en) -AnnotationAssertion(rdfs:label "quality is specified as"@en) +AnnotationAssertion( "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en) +AnnotationAssertion( "A planned process in which a document is created or added to by including the specified input in it."@en) +AnnotationAssertion( "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape"@en) +AnnotationAssertion( "Bjoern Peters"@en) +AnnotationAssertion( "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) +AnnotationAssertion(rdfs:label "documenting"@en) +SubClassOf( ) -# Object Property: (has time stamp) +# Class: (centrally registered identifier) -AnnotationAssertion( ) -AnnotationAssertion( "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has time stamp"@en) -SubObjectPropertyOf( ) -FunctionalObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) +AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) +AnnotationAssertion( "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs."@en) +AnnotationAssertion( "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')."@en) +AnnotationAssertion( "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation."@en) +AnnotationAssertion( "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "PERSON: Bjoern Peters"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion( "CRID") +AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) +AnnotationAssertion(rdfs:label "centrally registered identifier"@en) +SubClassOf( ) -# Object Property: (has measurement datum) +# Class: (identity document) -AnnotationAssertion( ) -AnnotationAssertion( "relates a time stamped measurement datum to the measurement datum that was measured"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "has measurement datum"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) +AnnotationAssertion( "A document that denotes some identity and is concretized by the bearer of some credential role."@en) +AnnotationAssertion( "Amanda Hicks") +AnnotationAssertion(rdfs:label "identity document"@en) -# Object Property: (obsolete_designates) - -AnnotationAssertion( "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.."@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "obsolete_designates"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) - -# Object Property: (is_borrowed_reference_to) - -AnnotationAssertion( "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "is_borrowed_reference_to"@en) -SubObjectPropertyOf( owl:topObjectProperty) -AsymmetricObjectProperty() -IrreflexiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (is_fixing_reference_to) - -AnnotationAssertion( "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "is_fixing_reference_to"@en) -AsymmetricObjectProperty() -IrreflexiveObjectProperty() - -# Object Property: (is designated by) - -AnnotationAssertion( "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "is designated by"@en) -AsymmetricObjectProperty() -IrreflexiveObjectProperty() - -# Object Property: (legally revokes) - -AnnotationAssertion( "d socio-legally revokes s if s participates in d and at the end of d s no longer exists. -It is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "legally revokes"@en) -SubObjectPropertyOf( ) -FunctionalObjectProperty() -AsymmetricObjectProperty() -IrreflexiveObjectProperty() -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (obsolete_legally transfers) - -AnnotationAssertion( "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_legally transfers"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubObjectPropertyOf( ) -FunctionalObjectProperty() -AsymmetricObjectProperty() -IrreflexiveObjectProperty() - -# Object Property: (has_specified_input) - -AnnotationAssertion( "has_specified_input"@en) -AnnotationAssertion( "has_specified_input") -AnnotationAssertion( "see is_input_of example_of_usage"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The inverse property of is_specified_input_of"@en) -AnnotationAssertion( "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.") -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bjoern Peters") -AnnotationAssertion( "PERSON: Larry Hunter") -AnnotationAssertion( "PERSON: Melanie Coutot") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has_specified_input"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) - -# Object Property: (is_specified_input_of) - -AnnotationAssertion(rdfs:label "is_specified_input_of"@en) - -# Object Property: (has_specified_output) - -AnnotationAssertion( "has_specified_output"@en) -AnnotationAssertion( "has_specified_output") -AnnotationAssertion( ) -AnnotationAssertion( "The inverse property of is_specified_output_of"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bjoern Peters") -AnnotationAssertion( "PERSON: Larry Hunter") -AnnotationAssertion( "PERSON: Melanie Courtot") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has_specified_output"@en) -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) -SubObjectPropertyOf( owl:topObjectProperty) -ObjectPropertyDomain( ) - -# Object Property: (is_specified_output_of) - -AnnotationAssertion( "is_specified_output_of"@en) -AnnotationAssertion( "is_specified_output_of") -AnnotationAssertion( ) -AnnotationAssertion( "A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Bjoern Peters") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "is_specified_output_of"@en) -AnnotationAssertion(rdfs:label "is_specified_output_of") -EquivalentObjectProperties( ObjectInverseOf()) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - -# Object Property: (is-aggregate-of) - -AnnotationAssertion( "BFO relation takes precedence."@en) -AnnotationAssertion(rdfs:comment "We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. -"@en) -AnnotationAssertion(rdfs:label "is-aggregate-of") -SubObjectPropertyOf( owl:topObjectProperty) - -# Object Property: (characteristic of) - -AnnotationAssertion( "inheres in"@en) -AnnotationAssertion( "this fragility is a characteristic of this vase"@en) -AnnotationAssertion( "this red color is a characteristic of this apple"@en) -AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) -AnnotationAssertion( "inheres_in"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") -AnnotationAssertion(rdfs:label "characteristic of"@en) -InverseObjectProperties( ) -FunctionalObjectProperty() - -# Object Property: (bearer_of) - -AnnotationAssertion( "bearer of"@en) -AnnotationAssertion( "this apple is bearer of this red color"@en) -AnnotationAssertion( "this vase is bearer of this fragility"@en) -AnnotationAssertion( "Inverse of characteristic_of"@en) -AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) -AnnotationAssertion( "bearer_of"@en) -AnnotationAssertion( "is bearer of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "bearer_of"@en) -AnnotationAssertion(rdfs:label "has characteristic"@en) -InverseFunctionalObjectProperty() -ObjectPropertyRange( ) - -# Object Property: (participates in) - -AnnotationAssertion( "participates in"@en) -AnnotationAssertion( "this blood clot participates in this blood coagulation"@en) -AnnotationAssertion( "this input material (or this output material) participates in this process"@en) -AnnotationAssertion( "this investigator participates in this investigation"@en) -AnnotationAssertion( "a relation between a continuant and a process, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "participates_in"@en) -AnnotationAssertion(rdfs:label "participates in"@en) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has_participant) - -AnnotationAssertion( "has participant"@en) -AnnotationAssertion( "this blood coagulation has participant this blood clot"@en) -AnnotationAssertion( "this investigation has participant this investigator"@en) -AnnotationAssertion( "this process has participant this input material (or this output material)"@en) -AnnotationAssertion( "a relation between a process and a continuant, in which the continuant is somehow involved in the process"@en) -AnnotationAssertion( "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time."@en) -AnnotationAssertion( "has_participant"@en) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:has_participant") -AnnotationAssertion(rdfs:label "has participant"@en) -AnnotationAssertion(rdfs:label "has_participant") -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (is concretized as) - -AnnotationAssertion( "is concretized as"@en) -AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) -AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) -AnnotationAssertion( "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label "is concretized as"@en) -SubObjectPropertyOf( owl:topObjectProperty) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (concretizes) - -AnnotationAssertion( "concretizes"@en) -AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) -AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) -AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) -AnnotationAssertion( "http://purl.obolibrary.org/obo/obi.owl") -AnnotationAssertion(rdfs:label "concretizes"@en) -SubObjectPropertyOf( owl:topObjectProperty) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (function of) - -AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) -AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "function_of"@en) -AnnotationAssertion( "is function of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "function of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) - -# Object Property: (quality of) - -AnnotationAssertion( "this red color is a quality of this apple"@en) -AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) -AnnotationAssertion( "is quality of"@en) -AnnotationAssertion( "quality_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "quality of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (role of) - -AnnotationAssertion( "this investigator role is a role of this person"@en) -AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "is role of"@en) -AnnotationAssertion( "role_of"@en) -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "role of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has function) - -AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) -AnnotationAssertion( "has_function"@en) -AnnotationAssertion(rdfs:label "has function"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has quality) - -AnnotationAssertion( "this apple has quality this red color"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) -AnnotationAssertion( "has_quality"@en) -AnnotationAssertion(rdfs:label "has quality"@en) -SubObjectPropertyOf( ) -ObjectPropertyRange( ) - -# Object Property: (has role) - -AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) -AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) -AnnotationAssertion( "has_role"@en) -AnnotationAssertion(rdfs:label "has role"@en) -SubObjectPropertyOf( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has disposition) - -AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) -AnnotationAssertion(rdfs:label "has disposition"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (disposition of) - -AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") -AnnotationAssertion(rdfs:label "disposition of"@en) -SubObjectPropertyOf( ) - -# Object Property: (derives from) - -AnnotationAssertion( "this cell derives from this parent cell (cell division)"@en) -AnnotationAssertion( "this nucleus derives from this parent nucleus (nuclear division)"@en) -AnnotationAssertion( ) -AnnotationAssertion( "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) -AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'."@en) -AnnotationAssertion( "derives_from"@en) -AnnotationAssertion(rdfs:label "derives from"@en) -InverseObjectProperties( ) - -# Object Property: (derives into) - -AnnotationAssertion( "this parent cell derives into this cell (cell division)"@en) -AnnotationAssertion( "this parent nucleus derives into this nucleus (nuclear division)"@en) -AnnotationAssertion( ) -AnnotationAssertion( "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity"@en) -AnnotationAssertion( "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'."@en) -AnnotationAssertion( "derives_into"@en) -AnnotationAssertion(rdfs:label "derives into"@en) - -# Object Property: (location of) - -AnnotationAssertion( "is location of"@en) -AnnotationAssertion( "my head is the location of my brain"@en) -AnnotationAssertion( "this cage is the location of this rat"@en) -AnnotationAssertion( "a relation between two independent continuants, the location and the target, in which the target is entirely within the location"@en) -AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "location_of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "location of"@en) -InverseObjectProperties( ) -TransitiveObjectProperty() - -# Object Property: (located in) - -AnnotationAssertion( "located in"@en) -AnnotationAssertion( "my brain is located in my head"@en) -AnnotationAssertion( "this rat is located in this cage"@en) -AnnotationAssertion( "a relation between two independent continuants, the target and the location, in which the target is entirely within the location"@en) -AnnotationAssertion( "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus"@en) -AnnotationAssertion( "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) -AnnotationAssertion( "located_in"@en) -AnnotationAssertion( ) -AnnotationAssertion( "http://www.obofoundry.org/ro/#OBO_REL:located_in") -AnnotationAssertion(rdfs:label "located in"@en) -TransitiveObjectProperty() -ObjectPropertyDomain(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) -ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) -ObjectPropertyRange(Annotation( "This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation.") ) -ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) - -# Object Property: (2D boundary of) - -AnnotationAssertion( "the surface of my skin is a 2D boundary of my body"@en) -AnnotationAssertion( "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity"@en) -AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) -AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) -AnnotationAssertion( "2D_boundary_of"@en) -AnnotationAssertion( "boundary of"@en) -AnnotationAssertion( "is 2D boundary of"@en) -AnnotationAssertion( "is boundary of"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "2D boundary of"@en) -InverseObjectProperties( ) - -# Object Property: (has 2D boundary) - -AnnotationAssertion( "my body has 2D boundary the surface of my skin"@en) -AnnotationAssertion( "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en) -AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) -AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) -AnnotationAssertion( "has boundary"@en) -AnnotationAssertion( "has_2D_boundary"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has 2D boundary"@en) -ObjectPropertyDomain( ) -ObjectPropertyRange( ) - -# Object Property: (has active participant) - -AnnotationAssertion( "'heart development' has active participant some Shh protein") -AnnotationAssertion( ) -AnnotationAssertion( "x has participant y if and only if x realizes some active role that inheres in y") -AnnotationAssertion( "This may be obsoleted and replaced by the original 'has agent' relation") -AnnotationAssertion( "Chris Mungall") -AnnotationAssertion( "has agent") -AnnotationAssertion( "http://purl.obolibrary.org/obo/ro.owl") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has active participant"@en) -SubObjectPropertyOf( ) - -# Object Property: (member of) - -AnnotationAssertion( "An organism that is a member of a population of organisms") -AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") -AnnotationAssertion( "is member of") -AnnotationAssertion( "member part of") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "member of"@en) -SubObjectPropertyOf( ) -InverseObjectProperties( ) - -# Object Property: (has member) - -AnnotationAssertion( "has member is a mereological relation between a collection and an item.") -AnnotationAssertion( "SIO") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "has member"@en) -SubObjectPropertyOf( ) -IrreflexiveObjectProperty() - -# Object Property: (DEPRECATED inheres in) - -AnnotationAssertion(rdfs:comment "DEPRECATED This relation is similar to but different in important respects to the characteristic-of relation. See comments on that relation for more information.") -AnnotationAssertion(rdfs:label "DEPRECATED inheres in"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - -# Object Property: (DEPRECATED bearer of) - -AnnotationAssertion(rdfs:label "DEPRECATED bearer of"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - - -############################ -# Data Properties -############################ - -# Data Property: (has measurement value) - -AnnotationAssertion(rdfs:label "has measurement value"@en) -FunctionalDataProperty() -DataPropertyDomain( ) -DataPropertyRange( xsd:double) - -# Data Property: (has x coordinate value) - -AnnotationAssertion(rdfs:label "has x coordinate value"@en) -FunctionalDataProperty() -DataPropertyDomain( ) -DataPropertyRange( xsd:float) - -# Data Property: (has z coordinate value) - -AnnotationAssertion(rdfs:label "has z coordinate value"@en) -FunctionalDataProperty() -DataPropertyDomain( ) -DataPropertyRange( xsd:float) - -# Data Property: (has y coordinate value) - -AnnotationAssertion(rdfs:label "has y coordinate value"@en) -FunctionalDataProperty() -DataPropertyDomain( ) -DataPropertyRange( xsd:float) - - - -############################ -# Classes -############################ - -# Class: (obsolete_deontic document act) - -AnnotationAssertion( "my filling in an immigration form, a judge's signing and stamping a court order"@en) -AnnotationAssertion( "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_deontic document act"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (software development) - -AnnotationAssertion( "A planned process that has specified output a software product and that involves the creation of source code."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "William R. Hogan"@en) -AnnotationAssertion( "http://en.wikipedia.org/wiki/Software_development") -AnnotationAssertion( "A planned process resulting in a software product involving the creation of source code."@en) -AnnotationAssertion(rdfs:label "software development"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectUnionOf( )))) -SubClassOf( ) - -# Class: (count) - -AnnotationAssertion( "A measurement datum that is the output of counting."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "A measurement datum that is the output of counting."@en) -AnnotationAssertion(rdfs:label "count"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (counting) - -AnnotationAssertion( "The planned process of finding the number of elements in a finite set of objects."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "http://en.wikipedia.org/wiki/Counting") -AnnotationAssertion( "The planned process of finding the number of elements in a finite set of objects."@en) -AnnotationAssertion(rdfs:label "counting"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (source code repository) - -AnnotationAssertion( "software source code version control repository"@en) -AnnotationAssertion( "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc."@en) -AnnotationAssertion( "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment "Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based"@en) -AnnotationAssertion(rdfs:label "source code repository"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) - -# Class: (compiling software) - -AnnotationAssertion( "process of compiling software"@en) -AnnotationAssertion( "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions."@en) -AnnotationAssertion( "William R. Hogan"@en) -AnnotationAssertion(rdfs:comment "It's compiling \"software\" (scare quotes) and not \"source code\" because you can compile Java bytecode to machine code, and Java bytecode is not technically \"source code\". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.)."@en) -AnnotationAssertion(rdfs:comment "Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code."@en) -AnnotationAssertion(rdfs:label "compiling software"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectUnionOf( )) ObjectSomeValuesFrom( ))) - -# Class: (dataset creating) - -AnnotationAssertion( "creating a data set"@en) -AnnotationAssertion( "A planned process that has a data set as its specified output."@en) -AnnotationAssertion( "William R. Hogan"@en) -AnnotationAssertion( "data set creation"@en) -AnnotationAssertion( "dataset creation"@en) -AnnotationAssertion(rdfs:label "dataset creating"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (entity) - -AnnotationAssertion( "entity") -AnnotationAssertion( "Entity") -AnnotationAssertion( "Julius Caesar"@en) -AnnotationAssertion( "Verdi’s Requiem"@en) -AnnotationAssertion( "the Second World War"@en) -AnnotationAssertion( "your body mass index"@en) -AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) -AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "entity"@en) -SubClassOf( owl:Thing) - -# Class: (continuant) - -AnnotationAssertion( "continuant") -AnnotationAssertion( "Continuant") -AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) -AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) -AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) -AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) -AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) -AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) -AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "continuant"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (occurrent) - -AnnotationAssertion( "occurrent") -AnnotationAssertion( "Occurrent") -AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) -AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) -AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) -AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") -AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) -AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) -AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "occurrent"@en) -SubClassOf( ) -DisjointClasses( ObjectSomeValuesFrom( )) - -# Class: (independent continuant) - -AnnotationAssertion( "ic") -AnnotationAssertion( "IndependentContinuant") -AnnotationAssertion( "a chair"@en) -AnnotationAssertion( "a heart"@en) -AnnotationAssertion( "a leg"@en) -AnnotationAssertion( "a molecule"@en) -AnnotationAssertion( "a spatial region"@en) -AnnotationAssertion( "an atom"@en) -AnnotationAssertion( "an orchestra."@en) -AnnotationAssertion( "an organism"@en) -AnnotationAssertion( "the bottom right portion of a human torso"@en) -AnnotationAssertion( "the interior of your mouth"@en) -AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) -AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) -AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") -AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") -AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "independent continuant"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (spatial region) - -AnnotationAssertion( "s-region") -AnnotationAssertion( "SpatialRegion") -AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional."@en) -AnnotationAssertion(Annotation( ) "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])"@en) -AnnotationAssertion(Annotation( ) "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "spatial region"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (temporal region) - -AnnotationAssertion( "t-region") -AnnotationAssertion( "TemporalRegion") -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional"@en) -AnnotationAssertion(Annotation( ) "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])"@en) -AnnotationAssertion(Annotation( ) "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])"@en) -AnnotationAssertion(Annotation( ) "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ") -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "temporal region"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (two-dimensional spatial region) - -AnnotationAssertion( "2d-s-region") -AnnotationAssertion( "TwoDimensionalSpatialRegion") -AnnotationAssertion( "an infinitely thin plane in space."@en) -AnnotationAssertion( "the surface of a sphere-shaped part of space"@en) -AnnotationAssertion(Annotation( ) "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "two-dimensional spatial region"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (spatiotemporal region) - -AnnotationAssertion( "st-region") -AnnotationAssertion( "SpatiotemporalRegion") -AnnotationAssertion( "the spatiotemporal region occupied by a human life"@en) -AnnotationAssertion( "the spatiotemporal region occupied by a process of cellular meiosis."@en) -AnnotationAssertion( "the spatiotemporal region occupied by the development of a cancer tumor"@en) -AnnotationAssertion(Annotation( ) "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])"@en) -AnnotationAssertion(Annotation( ) "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])"@en) -AnnotationAssertion(Annotation( ) "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])"@en) -AnnotationAssertion(Annotation( ) "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])"@en) -AnnotationAssertion( "Every spatiotemporal region occupies_spatiotemporal_region itself."@en) -AnnotationAssertion(Annotation( ) "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] ") -AnnotationAssertion(Annotation( ) "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] ") -AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "spatiotemporal region"@en) -SubClassOf( ) - -# Class: (process) - -AnnotationAssertion( "process") -AnnotationAssertion( "Process") -AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) -AnnotationAssertion( "a process of meiosis"@en) -AnnotationAssertion( "a process of sleeping"@en) -AnnotationAssertion( "the course of a disease"@en) -AnnotationAssertion( "the flight of a bird"@en) -AnnotationAssertion( "the life of an organism"@en) -AnnotationAssertion( "your process of aging."@en) -AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) -AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) -AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "process"@en) -SubClassOf( ) - -# Class: (disposition) - -AnnotationAssertion( "disposition") -AnnotationAssertion( "Disposition") -AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) -AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) -AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) -AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) -AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) -AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) -AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "disposition"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (realizable entity) - -AnnotationAssertion( "realizable") -AnnotationAssertion( "RealizableEntity") -AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) -AnnotationAssertion( "the disposition of your blood to coagulate"@en) -AnnotationAssertion( "the function of your reproductive organs"@en) -AnnotationAssertion( "the role of being a doctor"@en) -AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) -AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) -AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) -AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "realizable entity"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (zero-dimensional spatial region) - -AnnotationAssertion( "0d-s-region") -AnnotationAssertion( "ZeroDimensionalSpatialRegion") -AnnotationAssertion(Annotation( ) "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "zero-dimensional spatial region"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (quality) - -AnnotationAssertion( "quality") -AnnotationAssertion( "Quality") -AnnotationAssertion( "the ambient temperature of this portion of air"@en) -AnnotationAssertion( "the color of a tomato"@en) -AnnotationAssertion( "the length of the circumference of your waist"@en) -AnnotationAssertion( "the mass of this piece of gold."@en) -AnnotationAssertion( "the shape of your nose"@en) -AnnotationAssertion( "the shape of your nostril"@en) -AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) -AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "quality"@en) -SubClassOf( ) - -# Class: (specifically dependent continuant) - -AnnotationAssertion( "sdc") -AnnotationAssertion( "SpecificallyDependentContinuant") -AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) -AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) -AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) -AnnotationAssertion( "the disposition of this fish to decay"@en) -AnnotationAssertion( "the function of this heart: to pump blood"@en) -AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) -AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) -AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) -AnnotationAssertion( "the role of being a doctor"@en) -AnnotationAssertion( "the shape of this hole."@en) -AnnotationAssertion( "the smell of this portion of mozzarella"@en) -AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) -AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (role) - -AnnotationAssertion( "role") -AnnotationAssertion( "Role") -AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) -AnnotationAssertion( "the priest role"@en) -AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) -AnnotationAssertion( "the role of a building in serving as a military target"@en) -AnnotationAssertion( "the role of a stone in marking a property boundary"@en) -AnnotationAssertion( "the role of subject in a clinical trial"@en) -AnnotationAssertion( "the student role"@en) -AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) -AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) -AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "role"@en) -SubClassOf( ) - -# Class: (fiat object part) - -AnnotationAssertion( "fiat-object-part") -AnnotationAssertion( "FiatObjectPart") -AnnotationAssertion( "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29"@en) -AnnotationAssertion( "the FMA:regional parts of an intact human body."@en) -AnnotationAssertion( "the Western hemisphere of the Earth"@en) -AnnotationAssertion( "the division of the brain into regions"@en) -AnnotationAssertion( "the division of the planet into hemispheres"@en) -AnnotationAssertion( "the dorsal and ventral surfaces of the body"@en) -AnnotationAssertion( "the upper and lower lobes of the left lung"@en) -AnnotationAssertion( "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions"@en) -AnnotationAssertion(Annotation( ) "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "fiat object part"@en) -SubClassOf( ) - -# Class: (one-dimensional spatial region) - -AnnotationAssertion( "1d-s-region") -AnnotationAssertion( "OneDimensionalSpatialRegion") -AnnotationAssertion( "an edge of a cube-shaped portion of space."@en) -AnnotationAssertion(Annotation( ) "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "one-dimensional spatial region"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (object aggregate) - -AnnotationAssertion( "object-aggregate") -AnnotationAssertion( "ObjectAggregate") -AnnotationAssertion( "a collection of cells in a blood biobank."@en) -AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) -AnnotationAssertion( "a symphony orchestra"@en) -AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) -AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) -AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) -AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) -AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) -AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) -AnnotationAssertion( "the aggregate of blood cells in your body"@en) -AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) -AnnotationAssertion( "the restaurants in Palo Alto"@en) -AnnotationAssertion( "your collection of Meissen ceramic plates."@en) -AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) -AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") -AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") -AnnotationAssertion(Annotation( ) "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.") -AnnotationAssertion(Annotation( ) "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "object aggregate"@en) -SubClassOf( ) - -# Class: (three-dimensional spatial region) - -AnnotationAssertion( "3d-s-region") -AnnotationAssertion( "ThreeDimensionalSpatialRegion") -AnnotationAssertion( "a cube-shaped region of space"@en) -AnnotationAssertion( "a sphere-shaped region of space,"@en) -AnnotationAssertion(Annotation( ) "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "three-dimensional spatial region"@en) -SubClassOf( ) - -# Class: (site) - -AnnotationAssertion( "site") -AnnotationAssertion( "Site") -AnnotationAssertion( "Manhattan Canyon)"@en) -AnnotationAssertion( "a hole in the interior of a portion of cheese"@en) -AnnotationAssertion( "a rabbit hole"@en) -AnnotationAssertion( "an air traffic control region defined in the airspace above an airport"@en) -AnnotationAssertion( "the Grand Canyon"@en) -AnnotationAssertion( "the Piazza San Marco"@en) -AnnotationAssertion( "the cockpit of an aircraft"@en) -AnnotationAssertion( "the hold of a ship"@en) -AnnotationAssertion( "the interior of a kangaroo pouch"@en) -AnnotationAssertion( "the interior of the trunk of your car"@en) -AnnotationAssertion( "the interior of your bedroom"@en) -AnnotationAssertion( "the interior of your office"@en) -AnnotationAssertion( "the interior of your refrigerator"@en) -AnnotationAssertion( "the lumen of your gut"@en) -AnnotationAssertion( "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en) -AnnotationAssertion(Annotation( ) "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "site"@en) -SubClassOf( ) - -# Class: (object) - -AnnotationAssertion( "object") -AnnotationAssertion( "Object") -AnnotationAssertion( "atom"@en) -AnnotationAssertion( "cell"@en) -AnnotationAssertion( "cells and organisms"@en) -AnnotationAssertion( "engineered artifacts"@en) -AnnotationAssertion( "grain of sand"@en) -AnnotationAssertion( "molecule"@en) -AnnotationAssertion( "organelle"@en) -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "planet"@en) -AnnotationAssertion( "solid portions of matter"@en) -AnnotationAssertion( "star"@en) -AnnotationAssertion( "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting."@en) -AnnotationAssertion( "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)."@en) -AnnotationAssertion( "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47"@en) -AnnotationAssertion( "BFO 2 Reference: an object is a maximal causally unified material entity"@en) -AnnotationAssertion( "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74"@en) -AnnotationAssertion(Annotation( ) "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "object"@en) -SubClassOf( ) - -# Class: (generically dependent continuant) - -AnnotationAssertion( "gdc") -AnnotationAssertion( "GenericallyDependentContinuant") -AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) -AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) -AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) -AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) -AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "generically dependent continuant"@en) -SubClassOf( ) - -# Class: (function) - -AnnotationAssertion( "function") -AnnotationAssertion( "Function") -AnnotationAssertion( "the function of a hammer to drive in nails"@en) -AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) -AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) -AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) -AnnotationAssertion(Annotation( ) "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "function"@en) -SubClassOf( ) - -# Class: (process boundary) - -AnnotationAssertion( "p-boundary") -AnnotationAssertion( "ProcessBoundary") -AnnotationAssertion( "the boundary between the 2nd and 3rd year of your life."@en) -AnnotationAssertion(Annotation( ) "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])"@en) -AnnotationAssertion(Annotation( ) "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] ") -AnnotationAssertion(Annotation( ) "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "process boundary"@en) -SubClassOf( ) - -# Class: (one-dimensional temporal region) - -AnnotationAssertion( "1d-t-region") -AnnotationAssertion( "OneDimensionalTemporalRegion") -AnnotationAssertion( "the temporal region during which a process occurs."@en) -AnnotationAssertion( "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)."@en) -AnnotationAssertion(Annotation( ) "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "one-dimensional temporal region"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (material entity) - -AnnotationAssertion( "material") -AnnotationAssertion( "MaterialEntity") -AnnotationAssertion( "a flame"@en) -AnnotationAssertion( "a forest fire"@en) -AnnotationAssertion( "a human being"@en) -AnnotationAssertion( "a hurricane"@en) -AnnotationAssertion( "a photon"@en) -AnnotationAssertion( "a puff of smoke"@en) -AnnotationAssertion( "a sea wave"@en) -AnnotationAssertion( "a tornado"@en) -AnnotationAssertion( "an aggregate of human beings."@en) -AnnotationAssertion( "an energy wave"@en) -AnnotationAssertion( "an epidemic"@en) -AnnotationAssertion( "the undetached arm of a human being"@en) -AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) -AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) -AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) -AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) -AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) -AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) -AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") -AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "material entity"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (continuant fiat boundary) - -AnnotationAssertion( "cf-boundary") -AnnotationAssertion( "ContinuantFiatBoundary") -AnnotationAssertion(Annotation( ) "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])"@en) -AnnotationAssertion( "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions."@en) -AnnotationAssertion( "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29"@en) -AnnotationAssertion(Annotation( ) "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions."@en) -AnnotationAssertion( "Every continuant fiat boundary is located at some spatial region at every time at which it exists"@en) -AnnotationAssertion(Annotation( ) "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "continuant fiat boundary"@en) -SubClassOf( ) - -# Class: (immaterial entity) - -AnnotationAssertion( "immaterial") -AnnotationAssertion( "ImmaterialEntity") -AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "immaterial entity"@en) -SubClassOf( ) - -# Class: (one-dimensional continuant fiat boundary) - -AnnotationAssertion( "1d-cf-boundary") -AnnotationAssertion( "OneDimensionalContinuantFiatBoundary") -AnnotationAssertion( "The Equator"@en) -AnnotationAssertion( "all geopolitical boundaries"@en) -AnnotationAssertion( "all lines of latitude and longitude"@en) -AnnotationAssertion( "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin."@en) -AnnotationAssertion( "the median sulcus of your tongue"@en) -AnnotationAssertion(Annotation( ) "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])"@en) -AnnotationAssertion(Annotation( ) "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "one-dimensional continuant fiat boundary"@en) -SubClassOf( ) -DisjointClasses( ) -DisjointClasses( ) - -# Class: (process profile) - -AnnotationAssertion( "process-profile") -AnnotationAssertion( "ProcessProfile") -AnnotationAssertion( "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels"@en) -AnnotationAssertion( "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance."@en) -AnnotationAssertion( "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on."@en) -AnnotationAssertion(Annotation( ) "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])"@en) -AnnotationAssertion(Annotation( ) "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])"@en) -AnnotationAssertion(Annotation( ) "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] ") -AnnotationAssertion(Annotation( ) "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "process profile"@en) -SubClassOf( ) -DisjointClasses( ) - -# Class: (relational quality) - -AnnotationAssertion( "r-quality") -AnnotationAssertion( "RelationalQuality") -AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) -AnnotationAssertion( "a marriage bond, an instance of requited love, an obligation between one person and another."@en) -AnnotationAssertion(Annotation( ) "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])"@en) -AnnotationAssertion(Annotation( ) "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "relational quality"@en) -SubClassOf( ) - -# Class: (two-dimensional continuant fiat boundary) - -AnnotationAssertion( "2d-cf-boundary") -AnnotationAssertion( "TwoDimensionalContinuantFiatBoundary") -AnnotationAssertion(Annotation( ) "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])"@en) -AnnotationAssertion(Annotation( ) "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "two-dimensional continuant fiat boundary"@en) -SubClassOf( ) - -# Class: (zero-dimensional continuant fiat boundary) - -AnnotationAssertion( "0d-cf-boundary") -AnnotationAssertion( "ZeroDimensionalContinuantFiatBoundary") -AnnotationAssertion( "the geographic North Pole"@en) -AnnotationAssertion( "the point of origin of some spatial coordinate system."@en) -AnnotationAssertion( "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet"@en) -AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "requested by Melanie Courtot") Annotation(rdfs:seeAlso ) "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona."@en) -AnnotationAssertion(Annotation( ) "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])"@en) -AnnotationAssertion(Annotation( ) "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "zero-dimensional continuant fiat boundary"@en) -SubClassOf( ) - -# Class: (zero-dimensional temporal region) - -AnnotationAssertion( "0d-t-region") -AnnotationAssertion( "ZeroDimensionalTemporalRegion") -AnnotationAssertion( "a temporal region that is occupied by a process boundary"@en) -AnnotationAssertion( "right now"@en) -AnnotationAssertion( "the moment at which a child is born"@en) -AnnotationAssertion( "the moment at which a finger is detached in an industrial accident"@en) -AnnotationAssertion( "the moment of death."@en) -AnnotationAssertion( "temporal instant."@en) -AnnotationAssertion(Annotation( ) "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])"@en) -AnnotationAssertion(Annotation( ) "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] ") -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "zero-dimensional temporal region"@en) -SubClassOf( ) - -# Class: (history) - -AnnotationAssertion( "history") -AnnotationAssertion( "History") -AnnotationAssertion(Annotation( ) "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])"@en) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "history"@en) -SubClassOf( ) - -# Class: (Anatomical cluster) - -AnnotationAssertion(rdfs:label "Anatomical cluster"@en) -SubClassOf( ) - -# Class: (vocal fold) - -AnnotationAssertion(rdfs:label "vocal fold"@en) -SubClassOf( ) - -# Class: (Subdivision of larynx) - -AnnotationAssertion(rdfs:label "Subdivision of larynx"@en) -SubClassOf( ) - -# Class: (Heterogeneous cluster) - -AnnotationAssertion(rdfs:label "Heterogeneous cluster"@en) -SubClassOf( ) - -# Class: (Anatomical structure) - -AnnotationAssertion(rdfs:label "Anatomical structure"@en) -SubClassOf( ) - -# Class: (Material anatomical entity) - -AnnotationAssertion(rdfs:label "Material anatomical entity"@en) -SubClassOf( ) - -# Class: (conditional specification) - -AnnotationAssertion( "conditional specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A directive information entity that specifies what should happen if the trigger condition is fulfilled."@en) -AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) -AnnotationAssertion( "OBI branch derived"@en) -AnnotationAssertion( "OBI_0000349"@en) -AnnotationAssertion(rdfs:label "conditional specification"@en) -SubClassOf( ) - -# Class: (measurement unit label) - -AnnotationAssertion( "measurement unit label"@en) -AnnotationAssertion( "Examples of measurement unit labels are liters, inches, weight per volume."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) -AnnotationAssertion( "2009-03-16: provenance: a term measurement unit was -proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and -Cristian Cocos, and subsequently moved to IAO where the objective for -which the original term was defined was satisfied with the definition -of this, different, term."@en) -AnnotationAssertion( "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "measurement unit label"@en) -SubClassOf( ) - -# Class: (objective specification) - -AnnotationAssertion( "objective specification"@en) -AnnotationAssertion( "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved."@en) -AnnotationAssertion( "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\""@en) -AnnotationAssertion( "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that."@en) -AnnotationAssertion( "Answers the question, why did you do this experiment?"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Barry Smith"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Jennifer Fostel"@en) -AnnotationAssertion( "goal specification"@en) -AnnotationAssertion( "OBI Plan and Planned Process/Roles Branch"@en) -AnnotationAssertion( "OBI_0000217"@en) -AnnotationAssertion(rdfs:label "objective specification"@en) -SubClassOf( ) - -# Class: (narrative object) - -AnnotationAssertion( "narrative object"@en) -AnnotationAssertion( "Examples of narrative objects are reports, journal articles, and patents submission."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A narrative object is an information content entity that is a set of propositions."@en) -AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion"@en) -AnnotationAssertion( "agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000013"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "narrative object"@en) -SubClassOf( ) - -# Class: (action specification) - -AnnotationAssertion( "Pour the contents of flask 1 into flask 2"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A directive information entity that describes an action the bearer will take."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "OBI Plan and Planned Process branch"@en) -AnnotationAssertion(rdfs:label "action specification"@en) -SubClassOf( ) - -# Class: (obsolete_artifact) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_artifact") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (datum label) - -AnnotationAssertion( "datum label"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) -AnnotationAssertion( "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) -AnnotationAssertion( "GROUP: IAO"@en) -AnnotationAssertion( "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. -") -AnnotationAssertion(rdfs:label "datum label"@en) -SubClassOf( ) - -# Class: (software) - -AnnotationAssertion( "software"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Software is a plan specification composed of a series of instructions that can be -interpreted by or directly executed by a processing unit."@en) -AnnotationAssertion( "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "GROUP: OBI"@en) -AnnotationAssertion(rdfs:label "software"@en) -SubClassOf( ) - -# Class: (obsolete2_digital entity) - -AnnotationAssertion( "obsolete_digital entity"@en) -AnnotationAssertion( "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical."@en) -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 - -Superclass was 'digitial quality'"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000261") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_digital entity"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (journal article) - -AnnotationAssertion( "journal article"@en) -AnnotationAssertion( "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A report that is published in a journal."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000159"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "journal article"@en) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectAllValuesFrom( )) - -# Class: (information carrier) - -AnnotationAssertion( "information carrier"@en) -AnnotationAssertion( "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A quality of an information bearer that imparts the information content"@en) -AnnotationAssertion( "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en) -AnnotationAssertion( "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.") -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) -AnnotationAssertion(rdfs:label "information carrier"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -SubClassOf( ) - -# Class: (model number) - -AnnotationAssertion( "model number"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots."@en) -AnnotationAssertion( "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers"@en) -AnnotationAssertion( "Person: Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "model number"@en) -SubClassOf( ) - -# Class: (obsolete_material_entity) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_material_entity") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete2_binary digital entity) - -AnnotationAssertion( "binary digital entity"@en) -AnnotationAssertion( "MS Word document, ZIP file, DICOM file, JPEG file"@en) -AnnotationAssertion( "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters."@en) -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -Superclass was 'digital entity'"@en) -AnnotationAssertion( "digital_entity"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000244") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_binary digital entity"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete_unit of measure) - -AnnotationAssertion( "The length of a ruler.") -AnnotationAssertion( "a unit of measure is the quality of some material entity compared to which another quality is some multiple of.") -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_unit of measure") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (programming language) - -AnnotationAssertion( "programming language"@en) -AnnotationAssertion( "R, Perl, Java"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it."@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000058"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "programming language"@en) -SubClassOf( ) - -# Class: (data item) - -AnnotationAssertion( "data item"@en) -AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) -AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) -AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) -AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) -AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some -information-like stuff that might be put into a computer and that is -meant, by someone, to denote and/or to be interpreted by some -process... I would include lists, tables, sentences... I think I might -defer to Barry, or to Brian Cantwell Smith - -JAR: A data item is an approximately justified approximately true approximate belief"@en) -AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "PERSON: Jonathan Rees"@en) -AnnotationAssertion( "data"@en) -AnnotationAssertion(rdfs:label "data item"@en) -SubClassOf( ) - -# Class: (symbol) - -AnnotationAssertion( "symbol"@en) -AnnotationAssertion( "a serial number such as \"12324X\""@en) -AnnotationAssertion( "a stop sign"@en) -AnnotationAssertion( "a written proper name such as \"OBI\""@en) -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity."@en) -AnnotationAssertion( "20091104, MC: this needs work and will most probably change"@en) -AnnotationAssertion( "2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154)."@en) -AnnotationAssertion( "PERSON: James A. Overton"@en) -AnnotationAssertion( "PERSON: Jonathan Rees"@en) -AnnotationAssertion( "based on Oxford English Dictionary"@en) -AnnotationAssertion(rdfs:label "symbol"@en) -SubClassOf( ) - -# Class: (numeral) - -AnnotationAssertion( "numeral"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A symbol that denotes a number."@en) -AnnotationAssertion( "PERSON: Jonathan Rees"@en) -AnnotationAssertion(rdfs:label "numeral"@en) -SubClassOf( ) - -# Class: (information content entity) - -AnnotationAssertion( "information content entity"@en) -AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) -AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) -AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). - -Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000142"@en) -AnnotationAssertion(rdfs:label "information content entity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (integer numeral) - -AnnotationAssertion( "integer numeral"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A numeral that denotes an integer"@en) -AnnotationAssertion( "PERSON: Jonathan Rees"@en) -AnnotationAssertion(rdfs:label "integer numeral"@en) -SubClassOf( ) - -# Class: (scalar measurement datum) - -AnnotationAssertion( "10 feet. 3 ml."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label."@en) -AnnotationAssertion( "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in -this case we explicitly refer to the singular form"@en) -AnnotationAssertion( "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "scalar measurement datum"@en) -SubClassOf( ) -SubClassOf( ObjectMinCardinality(1 )) -SubClassOf( DataMinCardinality(1 )) - -# Class: (directive information entity) - -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity whose concretizations indicate to their bearer how to realize them in a process."@en) -AnnotationAssertion( "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) -AnnotationAssertion( "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it."@en) -AnnotationAssertion( "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO"@en) -AnnotationAssertion( "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion(rdfs:label "directive information entity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (time trigger) - -AnnotationAssertion( "time trigger"@en) -AnnotationAssertion( ) -AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) -AnnotationAssertion(rdfs:label "time trigger"@en) -SubClassOf( ) - -# Class: (obsolete_study interpretation) - -AnnotationAssertion( "obsolete_study interpretation"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses"@en) -AnnotationAssertion( "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead."@en) -AnnotationAssertion( "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"") -AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") -AnnotationAssertion( "Lawrence Hunter"@en) -AnnotationAssertion( "PERSON: Jennifer Fostel"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg") -AnnotationAssertion( "PERSON: Melanie Courtot") -AnnotationAssertion( "conclusion") -AnnotationAssertion( "OBI_0000005") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_study interpretation"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (dot plot) - -AnnotationAssertion( "dot plot"@en) -AnnotationAssertion( "Dot plot of SSC-H and FSC-H."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions."@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000123"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "dot plot"@en) -SubClassOf( ) - -# Class: (graph) - -AnnotationAssertion( "graph"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "OBI_0000240"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "graph"@en) -SubClassOf( ) - -# Class: (obsolete2_text based digital entity) - -AnnotationAssertion( "text based digital entity"@en) -AnnotationAssertion( "XML file, C++ source code file"@en) -AnnotationAssertion( "A text based digital entity is a digital entity that is encoded so that it only contains text characters."@en) -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital document'"@en) -AnnotationAssertion( "digital_entity"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000132") -AnnotationAssertion( "group:OBI") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_text based digital entity"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (rule) - -AnnotationAssertion( "rule"@en) -AnnotationAssertion( "example to be added"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A rule is an executable which guides, defines, restricts actions."@en) -AnnotationAssertion( "MSI"@en) -AnnotationAssertion( "PRS"@en) -AnnotationAssertion( "OBI_0500021"@en) -AnnotationAssertion( "PRS"@en) -AnnotationAssertion(rdfs:label "rule"@en) -SubClassOf( ) - -# Class: (contour plot) - -AnnotationAssertion( "contour plot"@en) -AnnotationAssertion( "Contour plot of SSC-H, FSC-H, and FL1-H."@en) -AnnotationAssertion( ) -AnnotationAssertion( "generically_dependent_continuants"@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000246"@en) -AnnotationAssertion( "group:Flow Cytometry community"@en) -AnnotationAssertion(rdfs:label "contour plot"@en) -SubClassOf( ) - -# Class: (obsolete2_report figure) - -AnnotationAssertion( "report figure"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements"@en) -AnnotationAssertion( "I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report"@en) -AnnotationAssertion( "Replaced by defined version of figure"@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000027") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_report figure"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (algorithm) - -AnnotationAssertion( "algorithm"@en) -AnnotationAssertion( "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata."@en) -AnnotationAssertion( "Philippe Rocca-Serra"@en) -AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) -AnnotationAssertion( "OBI_0000270"@en) -AnnotationAssertion( "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)"@en) -AnnotationAssertion(rdfs:label "algorithm"@en) -SubClassOf( ) - -# Class: (software interpreter) - -AnnotationAssertion( "software interpreter"@en) -AnnotationAssertion( "R program, Perl interpreter, Java virtual machine"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A software interpreter is a software application that executes some specified input software."@en) -AnnotationAssertion( "Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter"@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000199"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "software interpreter"@en) -SubClassOf( ) - -# Class: (curation status specification) - -AnnotationAssertion( "curation status specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) -AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) -AnnotationAssertion( "PERSON:Bill Bug"@en) -AnnotationAssertion( "GROUP:OBI:"@en) -AnnotationAssertion( "OBI_0000266"@en) -AnnotationAssertion(rdfs:label "curation status specification"@en) -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (density plot) - -AnnotationAssertion( "density plot"@en) -AnnotationAssertion( "Density plot of SSC-H and FSC-H."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel."@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000179"@en) -AnnotationAssertion( "group:Flow Cytometry community"@en) -AnnotationAssertion(rdfs:label "density plot"@en) -SubClassOf( ) - -# Class: (report) - -AnnotationAssertion( "report"@en) -AnnotationAssertion( "Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)."@en) -AnnotationAssertion( "2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence \"Topic of the report is on -something that has completed.\" Should it be restricted to those things -that are completed? For example, a progress report is (usually) about -something that definitely has *not* been completed, or may include -(only) projections. I think the definition would not suffer if the -whole sentence is deleted."@en) -AnnotationAssertion( "2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so."@en) -AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) -AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion"@en) -AnnotationAssertion( "disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "GROUP: OBI"@en) -AnnotationAssertion( "OBI_0000099"@en) -AnnotationAssertion(rdfs:label "report"@en) -SubClassOf( ) - -# Class: (obsolete_report element) - -AnnotationAssertion( "report element"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)."@en) -AnnotationAssertion( "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text"@en) -AnnotationAssertion( "2009-03-16: needs some more work (clarify relations).") -AnnotationAssertion( "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.") -AnnotationAssertion( "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI.") -AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion") -AnnotationAssertion( "Replaced by textual entity and figure") -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Allyson Lister"@en) -AnnotationAssertion( "PERSON: Melanie Courtot") -AnnotationAssertion( "GROUP:OBI"@en) -AnnotationAssertion( "OBI_0000001") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_report element"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete2_binary executable) - -AnnotationAssertion( "binary executable"@en) -AnnotationAssertion( "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)"@en) -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digital entity'"@en) -AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000222") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_binary executable"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (source code module) - -AnnotationAssertion( "source code module"@en) -AnnotationAssertion( "The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A source code module is a directive information entity that specifies, using a programming language, some algorithm."@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000039"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "source code module"@en) -SubClassOf( ) - -# Class: (obsolete_report table) - -AnnotationAssertion( "report table"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content"@en) -AnnotationAssertion( "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion") -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000265") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_report table"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (data format specification) - -AnnotationAssertion( "data format specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A data format specification is the information content borne by the document published defining the specification. -Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file"@en) -AnnotationAssertion( "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes -information. Example: The ISO document specifying what encompasses an -XML document; The instructions in a XSD file\""@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PlanAndPlannedProcess Branch"@en) -AnnotationAssertion( "OBI branch derived"@en) -AnnotationAssertion( "OBI_0000187"@en) -AnnotationAssertion(rdfs:label "data format specification"@en) -SubClassOf( ) - -# Class: (data set) - -AnnotationAssertion( "data set"@en) -AnnotationAssertion( "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets."@en) -AnnotationAssertion( "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type"@en) -AnnotationAssertion( "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction.") -AnnotationAssertion( "person:Allyson Lister"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000042"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "data set"@en) -SubClassOf( ) - -# Class: (image) - -AnnotationAssertion( "image"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface."@en) -AnnotationAssertion( "person:Alan Ruttenberg"@en) -AnnotationAssertion( "person:Allyson"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000030"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "image"@en) -SubClassOf( ) - -# Class: (data about an ontology part) - -AnnotationAssertion( "data about an ontology part"@en) -AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "data about an ontology part"@en) -SubClassOf( ) - -# Class: (plan specification) - -AnnotationAssertion( "plan specification"@en) -AnnotationAssertion( "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified."@en) -AnnotationAssertion( "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term."@en) -AnnotationAssertion( "2014-03-31: A plan specification can have other parts, such as conditional specifications."@en) -AnnotationAssertion( "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231."@en) -AnnotationAssertion( "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "Clint Dowland"@en) -AnnotationAssertion( "OBI Plan and Planned Process branch"@en) -AnnotationAssertion( "OBI_0000344"@en) -AnnotationAssertion(rdfs:comment "2/3/2009 Comment from OBI review. - -Action specification not well enough specified. -Conditional specification not well enough specified. -Question whether all plan specifications have objective specifications. - -Request that IAO either clarify these or change definitions not to use them"@en) -AnnotationAssertion(rdfs:label "plan specification"@en) -AnnotationAssertion(rdfs:seeAlso "https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (obsolete2_digital document) - -AnnotationAssertion( "digital document"@en) -AnnotationAssertion( "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file."@en) -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4 -superclass was 'digial entity'"@en) -AnnotationAssertion( "person:Jennifer Fostel"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion( "OBI_0000195") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete2_digital document"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (measurement datum) - -AnnotationAssertion( "measurement datum"@en) -AnnotationAssertion( "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device."@en) -AnnotationAssertion( "2/2/2009 is_specified_output of some assay?"@en) -AnnotationAssertion( "person:Chris Stoeckert"@en) -AnnotationAssertion( "OBI_0000305"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "measurement datum"@en) -SubClassOf( ) - -# Class: (obsolete_identifier) - -AnnotationAssertion( ) -AnnotationAssertion( "_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. - -Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group \"identifiying\" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_identifier") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (version number) - -AnnotationAssertion( "version number"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name."@en) -AnnotationAssertion( "Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version"@en) -AnnotationAssertion( "GROUP: IAO"@en) -AnnotationAssertion(rdfs:label "version number"@en) -SubClassOf( ) - -# Class: (serial number) - -AnnotationAssertion( "serial number"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots."@en) -AnnotationAssertion( "Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)"@en) -AnnotationAssertion( "GROUP: IAO"@en) -AnnotationAssertion(rdfs:label "serial number"@en) -SubClassOf( ) - -# Class: (lot number) - -AnnotationAssertion( "lot number"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots."@en) -AnnotationAssertion( "GROUP: IAO"@en) -AnnotationAssertion( "batch number"@en) -AnnotationAssertion(rdfs:label "lot number"@en) -SubClassOf( ) - -# Class: (setting datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A settings datum is a datum that denotes some configuration of an instrument."@en) -AnnotationAssertion( "2/3/2009 Feedback from OBI - -This should be a \"setting specification\". There is a question of whether it is information about a realizable or not. - -Pro other specification are about realizables. -Cons sometimes specifies a quality which is not a realizable."@en) -AnnotationAssertion( "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum."@en) -AnnotationAssertion(rdfs:label "setting datum"@en) -SubClassOf( ) - -# Class: (obsolete_digital quality) - -AnnotationAssertion( "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4") -AnnotationAssertion( "Need to rework digital entity. Digital quality was suggested by Barry.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_digital quality") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (conclusion textual entity) - -AnnotationAssertion( "conclusion textual entity"@en) -AnnotationAssertion( "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers."@en) -AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) -AnnotationAssertion( "2009/10/23 Alan Ruttenberg: We need to work on the definition still"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "conclusion textual entity"@en) -SubClassOf( ) - -# Class: (material information bearer) - -AnnotationAssertion( "material information bearer"@en) -AnnotationAssertion( "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier."@en) -AnnotationAssertion( "a brain"@en) -AnnotationAssertion( "a hard drive"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity in which a concretization of an information content entity inheres."@en) -AnnotationAssertion( "GROUP: IAO"@en) -AnnotationAssertion(rdfs:label "material information bearer"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) -SubClassOf( ) - -# Class: (histogram) - -AnnotationAssertion( "histogram"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A histogram is a report graph which is a statistical description of a -distribution in terms of occurrence frequencies of different event classes."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "GROUP:OBI"@en) -AnnotationAssertion(rdfs:label "histogram"@en) -SubClassOf( ) - -# Class: (heatmap) - -AnnotationAssertion( "heatmap"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A heatmap is a report graph which is a graphical representation of data -where the values taken by a variable(s) are shown as colors in a -two-dimensional map."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "GROUP:OBI"@en) -AnnotationAssertion(rdfs:label "heatmap"@en) -SubClassOf( ) - -# Class: (Venn diagram) - -AnnotationAssertion( "Venn diagram"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A Venn diagram is a report graph showing all hypothetically possible -logical relations between a finite collection of sets."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Venn_diagram"@en) -AnnotationAssertion(rdfs:label "Venn diagram"@en) -SubClassOf( ) - -# Class: (obsolete_survival curve) - -AnnotationAssertion( "obsolete_survival curve"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "WEB: http://www.graphpad.com/www/book/survive.htm"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_survival curve"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (dendrogram) - -AnnotationAssertion( "dendrogram"@en) -AnnotationAssertion( "Dendrograms are often used in computational biology to -illustrate the clustering of genes."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A dendrogram is a report graph which is a tree diagram -frequently used to illustrate the arrangement of the clusters produced by a -clustering algorithm."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Dendrogram"@en) -AnnotationAssertion(rdfs:label "dendrogram"@en) -SubClassOf( ) - -# Class: (scatter plot) - -AnnotationAssertion( "scatter plot"@en) -AnnotationAssertion( "Comparison of gene expression values in two samples can be displayed in a scatter plot"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:James Malone"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "scattergraph"@en) -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Scatterplot"@en) -AnnotationAssertion(rdfs:label "scatter plot"@en) -SubClassOf( ) - -# Class: (photograph) - -AnnotationAssertion( ) -AnnotationAssertion( "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Joanne Luciano"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "WEB: http://en.wiktionary.org/wiki/photograph"@en) -AnnotationAssertion(rdfs:label "photograph"@en) -SubClassOf( ) - -# Class: (photographic print) - -AnnotationAssertion( "photographic print"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A photographic print is a material entity upon which a photograph generically depends."@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "photographic print"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) -SubClassOf( ) - -# Class: (obsolescence reason specification) - -AnnotationAssertion( "obsolescence reason specification"@en) -AnnotationAssertion( ) -AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) -AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (textual entity) - -AnnotationAssertion( "textual entity"@en) -AnnotationAssertion( "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en) -AnnotationAssertion( "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en) -AnnotationAssertion( "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "text"@en) -AnnotationAssertion(rdfs:label "textual entity"@en) -SubClassOf( ) - -# Class: (citation) - -AnnotationAssertion( "citation"@en) -AnnotationAssertion( "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity intended to identify a particular publication."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "citation"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author identification) - -AnnotationAssertion( "author identification"@en) -AnnotationAssertion( "L. Hunter"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity intended to identify a particular author"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "author identification"@en) -SubClassOf( ) - -# Class: (institutional identification) - -AnnotationAssertion( "institutional identification"@en) -AnnotationAssertion( "University of Colorado Denver School of Medicine"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity intended to identify a particular institution"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "institutional identification"@en) -SubClassOf( ) - -# Class: (caption) - -AnnotationAssertion( "caption"@en) -AnnotationAssertion( "Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that describes a figure"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "caption"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (document title) - -AnnotationAssertion( "document title"@en) -AnnotationAssertion( "Textual characteristics of traditional and Open Access scientific journals are similar"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that names a document"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "document title"@en) -SubClassOf( ) - -# Class: (table) - -AnnotationAssertion( "table"@en) -AnnotationAssertion( "| T F ---+----- -T | T F -F | F F"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "table"@en) -SubClassOf( ) - -# Class: (table of abbreviations) - -AnnotationAssertion( "table of abbreviations"@en) -AnnotationAssertion( "IAO information artifact ontology -OBI ontology of biomedical investiations -GO gene ontology"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A table where the constituent texts are abbreviations and their expansions"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "table of abbreviations"@en) -SubClassOf( ) - -# Class: (figure) - -AnnotationAssertion( "figure"@en) -AnnotationAssertion( "Any picture, diagram or table"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "figure"@en) -SubClassOf( ) - -# Class: (diagram) - -AnnotationAssertion( "diagram"@en) -AnnotationAssertion( "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A figure that expresses one or more propositions"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "diagram"@en) -SubClassOf( ) - -# Class: (document) - -AnnotationAssertion( "document"@en) -AnnotationAssertion( "A journal article, patent application, laboratory notebook, or a book"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A collection of information content entities intended to be understood together as a whole"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "document"@en) -SubClassOf( ) - -# Class: (publication) - -AnnotationAssertion( "publication"@en) -AnnotationAssertion( "journal article, newspaper story, book, etc."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document that is the output of a publishing process."@en) -AnnotationAssertion( "PERSON: Chris Stoeckert"@en) -AnnotationAssertion( "PERSON: Jie Zheng"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "published document"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "Revisit the term in Octorber 2020. Improve the defintion."@en) -AnnotationAssertion(rdfs:label "publication"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) -SubClassOf( ) - -# Class: (publication about an investigation) - -AnnotationAssertion( "publication about an investigation"@en) -AnnotationAssertion( "Most scientific journal articles"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A publication that is about an investigation"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "scientific publication"@en) -AnnotationAssertion(rdfs:label "publication about an investigation"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (patent) - -AnnotationAssertion( "patent"@en) -AnnotationAssertion( "US Patent 6,449,603"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document that has been accepted by a patent authority"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "patent"@en) -SubClassOf( ) - -# Class: (document part) - -AnnotationAssertion( "document part"@en) -AnnotationAssertion( "An abstract, introduction, method or results section."@en) -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity that is part of a document."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "document part"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (abstract) - -AnnotationAssertion( "abstract"@en) -AnnotationAssertion( "The profusion of high-throughput instruments and the explosion of new results in the scientific literature, particularly in molecular biomedicine, is both a blessing and a curse to the bench researcher. Even knowledgeable and experienced scientists can benefit from computational tools that help navigate this vast and rapidly evolving terrain. In this paper, we describe a novel computational approach to this challenge, a knowledge-based system that combines reading, reasoning and reporting methods to facilitate analysis of experimental data. Reading methods extract information from external resources, either by parsing structured data or biomedical language processing to extract information from unstructured data, and track knowledge provenance. Reasoning methods enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. Reasoning is also used to combine all sources into a knowledge network that represents the integration of all sorts of relationships between a pair of genes, and to calculate a combined reliability score. Reporting methods combine the knowledge network with a congruent network constructed from experimental data and visualize the combined network in a tool that facilitates the knowledge-based analysis of that data."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "precis"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "abstract"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (introduction to a publication about an investigation) - -AnnotationAssertion( "introduction to a publication about an investigation"@en) -AnnotationAssertion( "Section labelled 'introduction' of a typical scientific journal article"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "background"@en) -AnnotationAssertion( "introduction"@en) -AnnotationAssertion( "overview"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "introduction to a publication about an investigation"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (methods section) - -AnnotationAssertion( "methods section"@en) -AnnotationAssertion( "The section labelled 'Methods' or 'Materials and Methods' in a typical scientific journal article."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a publication about an investigation that is about the study design of the investigation"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "experimental"@en) -AnnotationAssertion( "experimental methods"@en) -AnnotationAssertion( "experimental procedures"@en) -AnnotationAssertion( "experimental section"@en) -AnnotationAssertion( "method"@en) -AnnotationAssertion( "methodology"@en) -AnnotationAssertion( "methods"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "methods section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (results section) - -AnnotationAssertion( "results section"@en) -AnnotationAssertion( "The section labelled 'results' in a typical scientific journal article"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a publication about an investigation that is about a study design execution"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "results"@en) -AnnotationAssertion(rdfs:label "results section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (discussion section of a publication about an investigation) - -AnnotationAssertion( "discussion section of a publication about an investigation"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a publication about an investigation that is about the study interpretation of the investigation"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "discussion"@en) -AnnotationAssertion( "discussion section"@en) -AnnotationAssertion( "discussions"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "discussion section of a publication about an investigation"@en) -SubClassOf( ) - -# Class: (references section) - -AnnotationAssertion( "references section"@en) -AnnotationAssertion( "The list of citations found at the end of a scientific publication, grant proposal or patent application, sometimes called \"literature cited\" or \"bibliography\""@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a document that has citations as parts"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "literature cited"@en) -AnnotationAssertion( "reference"@en) -AnnotationAssertion( "reference list"@en) -AnnotationAssertion( "references"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "references section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author list) - -AnnotationAssertion( "author list"@en) -AnnotationAssertion( "Lawrence Hunter and Kevin Brettonel Cohen"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a document that enumerates the authors of the document"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "author list"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (institution list) - -AnnotationAssertion( "institution list"@en) -AnnotationAssertion( "The University of Colorado Denver School of Medicine and the University of Colorado Boulder."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a document that has parts that are institution identifications associated with the authors of the document"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "institution list"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author contributions section) - -AnnotationAssertion( "author contributions section"@en) -AnnotationAssertion( "LH conceived of the hypothesis, designed the study and contributed to the writing of the manuscript. KBC executed the experiments, analyzed the data, and contributed to the writing of the manuscript."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a publication that is about the specific contributions of each author"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "author contributions"@en) -AnnotationAssertion( "authors' contribution"@en) -AnnotationAssertion( "authors' contributions"@en) -AnnotationAssertion( "authors' roles"@en) -AnnotationAssertion( "contributions by the authors"@en) -AnnotationAssertion( "contributorship"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "author contributions section"@en) -SubClassOf( ) - -# Class: (acknowledgements section) - -AnnotationAssertion( "acknowledgements section"@en) -AnnotationAssertion( "The authors wish to thank Alan Ruttenberg for his constructive comments about an earlier draft of this manuscript"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Part of a publication that is about the contributions of people or institutions other than the authors."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "acknowledgement"@en) -AnnotationAssertion( "acknowledgements"@en) -AnnotationAssertion( "acknowledgment"@en) -AnnotationAssertion( "acknowledgments"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "acknowledgements section"@en) -SubClassOf( ) - -# Class: (footnote) - -AnnotationAssertion( "footnote"@en) -AnnotationAssertion( "The referent in the text is usually indicated by a special typographic character such as * or a superscripted number, which is also used to indicate the footnote that refers to that text."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "endnote"@en) -AnnotationAssertion( "footnotes"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "footnote"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (supplementary material to a document) - -AnnotationAssertion( "supplementary material to a document"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A part of a document that is segregated from the rest of the document due to its size"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion( "additional file"@en) -AnnotationAssertion( "additional files"@en) -AnnotationAssertion( "additional information"@en) -AnnotationAssertion( "appendix"@en) -AnnotationAssertion( "electronic supplementary material"@en) -AnnotationAssertion( "electronic supplementary materials"@en) -AnnotationAssertion( "supplemental data"@en) -AnnotationAssertion( "supplemental information"@en) -AnnotationAssertion( "supplemental material"@en) -AnnotationAssertion( "supplementary data"@en) -AnnotationAssertion( "supplementary files"@en) -AnnotationAssertion( "supplementary information"@en) -AnnotationAssertion( "supplementary material"@en) -AnnotationAssertion( "supplementary materials"@en) -AnnotationAssertion( "supporting information"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "supplementary material to a document"@en) -SubClassOf( ) - -# Class: (table of contents) - -AnnotationAssertion( "table of contents"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred)."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "table of contents"@en) -SubClassOf( ) - -# Class: (table of figures) - -AnnotationAssertion( "table of figures"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred)."@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "table of figures"@en) -SubClassOf( ) - -# Class: (running title) - -AnnotationAssertion( "running title"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A shorter version of a document title"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "running title"@en) -SubClassOf( ) - -# Class: (copyright section) - -AnnotationAssertion( "copyright section"@en) -AnnotationAssertion( "This work is licensed under a Creative Commons Attribution-Share Alike 3.0 United States License."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document part that describes legal restrictions on making or distributing copies of the document"@en) -AnnotationAssertion( "PERSON: Lawrence Hunter"@en) -AnnotationAssertion(rdfs:label "copyright section"@en) -SubClassOf( ) - -# Class: (cartesian spatial coordinate datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude"@en) -AnnotationAssertion( "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "AR notes: We need to discuss whether it should include site.") -AnnotationAssertion(rdfs:label "cartesian spatial coordinate datum"@en) -AnnotationAssertion(rdfs:seeAlso "http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectExactCardinality(1 )) - -# Class: (one dimensional cartesian spatial coordinate datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "one dimensional cartesian spatial coordinate datum"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) -SubClassOf( DataExactCardinality(1 )) - -# Class: (two dimensional cartesian spatial coordinate datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "two dimensional cartesian spatial coordinate datum"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) -SubClassOf( DataExactCardinality(1 )) -SubClassOf( DataExactCardinality(1 )) - -# Class: (three dimensional cartesian spatial coordinate datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "three dimensional cartesian spatial coordinate datum"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) -SubClassOf( DataExactCardinality(1 )) -SubClassOf( DataExactCardinality(1 )) -SubClassOf( DataExactCardinality(1 )) - -# Class: (length measurement datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A scalar measurement datum that is the result of measurement of length quality"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "length measurement datum"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (denotator type) - -AnnotationAssertion( "denotator type"@en) -AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) -AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) -AnnotationAssertion(rdfs:label "denotator type"@en) -EquivalentClasses( ObjectOneOf( )) -SubClassOf( ) - -# Class: (mass measurement datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A scalar measurement datum that is the result of measurement of mass quality"@en) -AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "mass measurement datum"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectAllValuesFrom( ) ObjectAllValuesFrom( ))) - -# Class: (hypothesis textual entity) - -AnnotationAssertion( "hypothesis textual entity"@en) -AnnotationAssertion( "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that expresses an assertion that is intended to be tested."@en) -AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "hypothesis textual entity"@en) -SubClassOf( ) - -# Class: (time measurement datum) - -AnnotationAssertion( ) -AnnotationAssertion( "A scalar measurement datum that is the result of measuring a temporal interval"@en) -AnnotationAssertion( "2009/09/28 Alan Ruttenberg. Fucoidan-use-case"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "time measurement datum"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectAllValuesFrom( ) ObjectAllValuesFrom( ))) - -# Class: (postal address) - -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that is used as directive to deliver something to a person, or organization") -AnnotationAssertion( "2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue https://github.com/information-artifact-ontology/IAO/issues/59") -AnnotationAssertion(rdfs:label "postal address"@en) -SubClassOf( ) - -# Class: (email address) - -AnnotationAssertion( "email address"@en) -AnnotationAssertion( ) -AnnotationAssertion( "Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Chris Stoeckart"@en) -AnnotationAssertion(rdfs:label "email address"@en) -SubClassOf( ) - -# Class: (author role) - -AnnotationAssertion( "author role"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion(rdfs:label "author role"@en) -SubClassOf( ) - -# Class: (data item extraction from journal article) - -AnnotationAssertion( ) -AnnotationAssertion( "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing") -AnnotationAssertion( "Person:Alan Ruttenberg") -AnnotationAssertion(rdfs:label "data item extraction from journal article") -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (publishing process) - -AnnotationAssertion( ) -AnnotationAssertion( "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free."@en) -AnnotationAssertion( "Person: Jie Zheng"@en) -AnnotationAssertion( "https://en.wikipedia.org/wiki/Publishing") -AnnotationAssertion( ) -AnnotationAssertion( "VEuPathDB"@en) -AnnotationAssertion(rdfs:label "publishing process"@en) -SubClassOf( ) - -# Class: (document in preparation for publication) - -AnnotationAssertion( ) -AnnotationAssertion( "A document that is in preparation for submission to be published."@en) -AnnotationAssertion( "PERSON: Jie Zheng"@en) -AnnotationAssertion( "EFO_0001795 in preparation"@en) -AnnotationAssertion( ) -AnnotationAssertion( "VEuPathDB"@en) -AnnotationAssertion(rdfs:label "document in preparation for publication"@en) -SubClassOf( ) - -# Class: (documenting) - -AnnotationAssertion( "Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A planned process in which a document is created or added to by including the specified input in it."@en) -AnnotationAssertion( "6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape"@en) -AnnotationAssertion( "Bjoern Peters"@en) -AnnotationAssertion( "wikipedia http://en.wikipedia.org/wiki/Documenting"@en) -AnnotationAssertion(rdfs:label "documenting"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (line graph) - -AnnotationAssertion( "line graph"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A line graph is a type of graph created by connecting a series of data -points together with a line."@en) -AnnotationAssertion( "PERSON:Chris Stoeckert"@en) -AnnotationAssertion( "PERSON:Melanie Courtot"@en) -AnnotationAssertion( "line chart"@en) -AnnotationAssertion( "GROUP:OBI"@en) -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Line_chart"@en) -AnnotationAssertion(rdfs:label "line graph"@en) -SubClassOf( ) - -# Class: (assigning a centrally registered identifier) - -AnnotationAssertion( "A new pubmed ID being created for a journal article, and the associated pubmed record containing information to the journal article. A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity"@en) -AnnotationAssertion( "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry."@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion( "Person:Bjoern Peters"@en) -AnnotationAssertion( "Person:Melanie Courtot"@en) -AnnotationAssertion( "assigning a CRID") -AnnotationAssertion(rdfs:label "assigning a centrally registered identifier"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (associating information with a centrally registered identifier in its registry) - -AnnotationAssertion( "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. ") -AnnotationAssertion( ) -AnnotationAssertion( "A planned process in which a CRID registry associates an information content entity with a CRID symbol"@en) -AnnotationAssertion( "PERSON:Alan Ruttenberg"@en) -AnnotationAssertion( "associating information with a CRID in the CRID registry") -AnnotationAssertion(rdfs:label "associating information with a centrally registered identifier in its registry"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (obsolete_establishing a CRID registry) - -AnnotationAssertion( "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID.") -AnnotationAssertion( "MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_establishing a CRID registry") -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (centrally registered identifier symbol) - -AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) -AnnotationAssertion( ) -AnnotationAssertion( "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bill Hogan"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "CRID symbol") -AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) -AnnotationAssertion(rdfs:label "centrally registered identifier symbol"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (centrally registered identifier) - -AnnotationAssertion( "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed."@en) -AnnotationAssertion( ) -AnnotationAssertion( "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs."@en) -AnnotationAssertion( "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')."@en) -AnnotationAssertion( "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation."@en) -AnnotationAssertion( "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bill Hogan"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "CRID") -AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) -AnnotationAssertion(rdfs:label "centrally registered identifier"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))) - -# Class: (centrally registered identifier registry) - -AnnotationAssertion( "PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. "@en) -AnnotationAssertion( ) -AnnotationAssertion( "A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bill Hogan"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "CRID registry") -AnnotationAssertion( "Original proposal from Bjoern, discussions at IAO calls"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion(rdfs:label "centrally registered identifier registry"@en) -SubClassOf( ) - -# Class: (looking up a centrally registered identifier) - -AnnotationAssertion( "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. ") -AnnotationAssertion( ) -AnnotationAssertion( "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol"@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Bill Hogan"@en) -AnnotationAssertion( "PERSON: Bjoern Peters"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "looking up a CRID") -AnnotationAssertion(rdfs:label "looking up a centrally registered identifier"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (time stamped measurement datum) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "time stamped measurement datum"@en) -SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) - -# Class: (time sampled measurement data set) - -AnnotationAssertion( "pmid:20604925 - time-lapse live cell microscopy"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "experimental time series"@en) -AnnotationAssertion(rdfs:label "time sampled measurement data set"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (written name) - -AnnotationAssertion( "written name"@en) -AnnotationAssertion( "\"Bill Clinton\""@en) -AnnotationAssertion( "\"The Eiffel Tower\""@en) -AnnotationAssertion( "\"United States of America\""@en) -AnnotationAssertion( ) -AnnotationAssertion( "A textual entity that denotes a particular in reality."@en) -AnnotationAssertion( "PERSON: Bill Hogan"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/114"@en) -AnnotationAssertion( "The qualifier \"written\" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so \"All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT\" would be a name."@en) -AnnotationAssertion(rdfs:label "written name"@en) -SubClassOf( ) - -# Class: (software method) - -AnnotationAssertion( ) -AnnotationAssertion( "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task."@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "PERSON: Michel Dumontier"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) -AnnotationAssertion(rdfs:label "software method"@en) -SubClassOf( ) - -# Class: (software module) - -AnnotationAssertion( ) -AnnotationAssertion( "A software module is software composed of a collection of software methods."@en) -AnnotationAssertion( "PERSON: Melanei Courtot"@en) -AnnotationAssertion( "PERSON: Michel Dumontier"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) -AnnotationAssertion(rdfs:label "software module"@en) -SubClassOf( ) - -# Class: (software library) - -AnnotationAssertion( ) -AnnotationAssertion( "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application."@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "PERSON: Michel Dumontier"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) -AnnotationAssertion(rdfs:label "software library"@en) -SubClassOf( ) - -# Class: (software application) - -AnnotationAssertion( ) -AnnotationAssertion( "A software application is software that can be directly executed by some processing unit."@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "PERSON: Michel Dumontier"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) -AnnotationAssertion(rdfs:label "software application"@en) -SubClassOf( ) - -# Class: (software script) - -AnnotationAssertion( ) -AnnotationAssertion( "A software script is software whose instructions can be executed using a software interpreter."@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( "PERSON: Michel Dumontier"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/80"@en) -AnnotationAssertion(rdfs:label "software script"@en) -SubClassOf( ) - -# Class: (abbreviation textual entity) - -AnnotationAssertion( "abbreviation textual entity"@en) -AnnotationAssertion( "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/): - -BAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect."@en) -AnnotationAssertion( "A textual entity listing abbreviations and their expansions that are used in a document."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "abbreviation textual entity"@en) -SubClassOf( ) - -# Class: (abbreviations section) - -AnnotationAssertion( "abbreviations section"@en) -AnnotationAssertion( "The section labelled 'abbreviations' in a typical scientific journal article."@en) -AnnotationAssertion( "A part of a document where abbreviations and their long-forms used within the document are listed."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "abbreviation and acronyms"@en) -AnnotationAssertion( "abbreviation list"@en) -AnnotationAssertion( "abbreviations"@en) -AnnotationAssertion( "abbreviations and acronyms"@en) -AnnotationAssertion( "abbreviations list"@en) -AnnotationAssertion( "abbreviations used"@en) -AnnotationAssertion( "definitions for abbreviations"@en) -AnnotationAssertion( "list of abbreviations"@en) -AnnotationAssertion( "list of abbreviations used"@en) -AnnotationAssertion( "non-standard abbreviations"@en) -AnnotationAssertion( "nonstandard abbreviations"@en) -AnnotationAssertion( "nonstandard abbreviations and acronyms"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "abbreviations section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author information section) - -AnnotationAssertion( "author information section"@en) -AnnotationAssertion( "The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)"@en) -AnnotationAssertion( "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "author information"@en) -AnnotationAssertion( "authors’ information"@en) -AnnotationAssertion( "biographies"@en) -AnnotationAssertion( "contributor information"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "author information section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author information textual entity) - -AnnotationAssertion( "author information textual entity"@en) -AnnotationAssertion( "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/): - -IT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD."@en) -AnnotationAssertion( "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "author information textual entity"@en) -SubClassOf( ) - -# Class: (author summary section) - -AnnotationAssertion( "author summary section"@en) -AnnotationAssertion( "The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)"@en) -AnnotationAssertion( "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "author summary"@en) -AnnotationAssertion( "summary"@en) -AnnotationAssertion( "synopsis"@en) -AnnotationAssertion( "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "author summary section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (author summary textual entity) - -AnnotationAssertion( "author summary textual entity"@en) -AnnotationAssertion( "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/): - - -The search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX."@en) -AnnotationAssertion( "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "author summary textual entity"@en) -SubClassOf( ) - -# Class: (availability section) - -AnnotationAssertion( "availability section"@en) -AnnotationAssertion( "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)."@en) -AnnotationAssertion( "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "availability"@en) -AnnotationAssertion( "availability of data"@en) -AnnotationAssertion( "data archiving"@en) -AnnotationAssertion( "data availability"@en) -AnnotationAssertion( "data availability statement"@en) -AnnotationAssertion( "data sharing statement"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "availability section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (availability textual entity) - -AnnotationAssertion( "availability textual entity"@en) -AnnotationAssertion( "From Qi et al. BMC Bioinformatics. 2014; 15: 11. 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[Taken from 'Effects of obstructive sleep apnoea risk on postoperative respiratory complications: protocol for a hospital-based registry study' Shin et al. 2016 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735131/)] "@en) -AnnotationAssertion( "A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "conflict of interest textual entity"@en) -SubClassOf( ) - -# Class: (consent section) - -AnnotationAssertion( "consent section"@en) -AnnotationAssertion( "The section labelled 'consent' in a typical scientific journal article, e.g. Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. 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Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/): - -The NHS National Research Ethics Service had previously approved the use of these anonymised data for research purposes and this analysis did not require independent review."@en) -AnnotationAssertion( "A textual entity that documents the ethical approval of some study design."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "ethical approval textual entity"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (figures section) - -AnnotationAssertion( "figures section"@en) -AnnotationAssertion( "The section labelled 'figures' in a typical scientific journal article."@en) -AnnotationAssertion( "A part of a document that contains one or more figures."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "figures"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "figures section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (funding source declaration section) - -AnnotationAssertion( "funding source declaration section"@en) -AnnotationAssertion( "The section labelled 'funding' in a typical scientific journal article."@en) -AnnotationAssertion( "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "financial support"@en) -AnnotationAssertion( "funding"@en) -AnnotationAssertion( "funding information"@en) -AnnotationAssertion( "funding sources"@en) -AnnotationAssertion( "funding statement"@en) -AnnotationAssertion( "funding/support"@en) -AnnotationAssertion( "grants"@en) -AnnotationAssertion( "role of the funding source"@en) -AnnotationAssertion( "source of funding"@en) -AnnotationAssertion( "sources of funding"@en) -AnnotationAssertion( "study funding"@en) -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "funding source declaration section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (funding source declaration textual entity) - -AnnotationAssertion( "funding souce declaration textual entity"@en) -AnnotationAssertion( "From Stephan et al. Accid Anal Prev. 2011 May; 43(3): 1062–1067. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062852/): - -This study was supported by the International Collaborative Research Grants Scheme with joint grants from the Wellcome Trust UK (GR071587MA) and the Australian NHMRC (268055). 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Acta Pharmacol Sin. 2016 Jan; 37(1): 25–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722976/): - -In the future, several questions will need to be resolved regarding the physiological assembly of KCNQ channels and their functional implications in complex neural circuits. First, we still lack sufficiently selective inhibitors and activators among the KCNQ family members."@en) -AnnotationAssertion( "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "future directions textual entity"@en) -SubClassOf( ) - -# Class: (genome announcement section) - -AnnotationAssertion( "genome announcement section"@en) -AnnotationAssertion( "The section labelled 'genome announcement' in a typical scientific journal article, e.g. in Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/)"@en) -AnnotationAssertion( "A document part announcing the publication of a novel draft genome sequence."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "genome announcement"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "genome announcement section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (genome announcement textual entity) - -AnnotationAssertion( "genome announcement textual entity"@en) -AnnotationAssertion( "Excerpt from Kim et al. J Bacteriol. 2011 Oct; 193(19): 5537. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187466/): - -Here we report the genome sequence of Lactobacillus malefermentans KCTC 3548, which we obtained using a whole-genome shotgun strategy (4) with Roche 454 GS (FLX Titanium) pyrosequencing (257,559 reads totaling ∼89.8 Mb; ∼45-fold coverage of the genome) at the Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)."@en) -AnnotationAssertion( "A textual entity that describes the generation and public release of a novel, draft genome sequence."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "genome announcement textual entity"@en) -SubClassOf( ) - -# Class: (keyword textual entity) - -AnnotationAssertion( "keyword textual entity"@en) -AnnotationAssertion( "From: Fu and Lin. Identification of gene-oriented exon orthology between human and mouse. BMC Genomics. 2012; 13(Suppl 1): S10. 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At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred."@en) -AnnotationAssertion( "A textual entity expressing information regarding the patients used in a study."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "patients textual entity"@en) -SubClassOf( ) - -# Class: (pre-publication history section) - -AnnotationAssertion( "pre-publication history section"@en) -AnnotationAssertion( "The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)"@en) -AnnotationAssertion( "A part of the document about the publication history of a document. 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(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/): - -• Operating systems: Platform independent - -• Programming language: Matlab, R, Python - -• Other requirements: None - -• License: GNU GPL v3 - -• Any restrictions to use by non-academics: None"@en) -AnnotationAssertion( "A textual entity that expresses the requirements necessary to use a resource, e.g. software."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "requirements textual entity"@en) -SubClassOf( ) - -# Class: (statistical analysis textual entity) - -AnnotationAssertion( "statistical analysis textual entity"@en) -AnnotationAssertion( "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/): - -Data were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant."@en) -AnnotationAssertion( "A textual entity documenting statistical analysis tools and techniques employed."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "statistical analysis textual entity"@en) -SubClassOf( ) - -# Class: (statistical analysis section) - -AnnotationAssertion( "statistical analysis section"@en) -AnnotationAssertion( "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)"@en) -AnnotationAssertion( "A part of the document used to describe the statistical methodologies employed in the work presented in the document."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "statistical analysis"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "statistical analysis section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (tables section) - -AnnotationAssertion( "tables section"@en) -AnnotationAssertion( "The section labelled 'tables' in a typical scientific journal article."@en) -AnnotationAssertion( "A part of a document that contains one or more tables."@en) -AnnotationAssertion( "PERSON: Bill Baumgartner"@en) -AnnotationAssertion( "tables"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "tables section"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (postal code) - -AnnotationAssertion( "An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "postal code"@en) -SubClassOf( ) - -# Class: (Postal delivery route) - -AnnotationAssertion( "A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "Postal delivery route"@en) -SubClassOf( ) - -# Class: (zone improvement plan code) - -AnnotationAssertion( "A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "ZIP code"@en) -AnnotationAssertion(rdfs:label "zone improvement plan code"@en) -SubClassOf( ) - -# Class: (database extract, transform, and load process) - -AnnotationAssertion( "database extract, transform, and load process"@en) -AnnotationAssertion( "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output."@en) -AnnotationAssertion( "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second") -AnnotationAssertion( "PERSON:Alan Ruttenberg") -AnnotationAssertion( "ETL"@en) -AnnotationAssertion( "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:isDefinedBy ) -AnnotationAssertion(rdfs:label "database extract, transform, and load process"@en) -AnnotationAssertion( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (descriptive data section) - -AnnotationAssertion( "descriptive data section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made."@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/prisma/") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "descriptive data section"@en) -SubClassOf( ) - -# Class: (additional results section) - -AnnotationAssertion( "additional results section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A results section that reports analyses other than main results of the study (e.g. subgroups analyses, adjusted analyses, sensitivity analyses, etc.)"@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/consort/") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/prisma/") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/strobe/") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "additional results section"@en) -SubClassOf( ) - -# Class: (research participants section) - -AnnotationAssertion( "research participants section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.)."@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/consort/") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/prisma/") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/strobe-nut/") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "research participants section"@en) -SubClassOf( ) - -# Class: (measurement methods section) - -AnnotationAssertion( "measurement methods section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A methods section that describes details of data assessment methods (data measurement)."@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "https://www.equator-network.org/reporting-guidelines/strobe/") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "measurement methods section"@en) -SubClassOf( ) - -# Class: (research settings section) - -AnnotationAssertion( "research settings section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A document part that describes the physical/social/cultural conditions around a research trial."@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "https://www.ncbi.nlm.nih.gov/books/NBK262175/") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "research settings section"@en) -SubClassOf( ) - -# Class: (study bias section) - -AnnotationAssertion( "study bias section"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others."@en) -AnnotationAssertion( "PERSON: Chen Yang") -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "DOI: 10.1097/PRS.0b013e3181de24bc") -AnnotationAssertion( ) -AnnotationAssertion( "ONE ontology") -AnnotationAssertion(rdfs:label "study bias section"@en) -SubClassOf( ) - -# Class: (graphical abstract) - -AnnotationAssertion( "graphical abstract"@en) -AnnotationAssertion( ) -AnnotationAssertion( "An abstract that is pictorial summary of the main findings described in the document."@en) -AnnotationAssertion( "PERSON: Jie Zheng") -AnnotationAssertion( "PERSON: Tim Beck") -AnnotationAssertion( "visual abstract"@en) -AnnotationAssertion( "https://www.elsevier.com/authors/journal-authors/graphical-abstract") -AnnotationAssertion( ) -AnnotationAssertion( "Biomedical literature NLP project") -AnnotationAssertion(rdfs:label "graphical abstract"@en) -SubClassOf( ) - -# Class: (ORCID identifier) - -AnnotationAssertion( ) -AnnotationAssertion( "A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor.") -AnnotationAssertion( "\"You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors.\" [https://orcid.org/]") -AnnotationAssertion( "This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)") -AnnotationAssertion( "http://orcid.org/0000-0002-1595-3213") -AnnotationAssertion( "ORCID ID") -AnnotationAssertion( "ORCiD") -AnnotationAssertion( "Open Researcher and Contributor ID") -AnnotationAssertion( "Open Researcher and Contributor Identifier") -AnnotationAssertion( "https://orcid.org/") -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/259") -AnnotationAssertion(rdfs:label "ORCID identifier"@en) -SubClassOf( ) - -# Class: (identifier) - -AnnotationAssertion( "identifier"@en) -AnnotationAssertion( "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) -AnnotationAssertion( "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "proper name"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:comment "Sep 29, 2016: The current definition has been amended from the previous version: \"A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.\" to more accuratly reflect the necessary and sufficient condition on the class. (MB)"@en) -AnnotationAssertion(rdfs:label "identifier"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) -EquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectAllValuesFrom( ))) -SubClassOf( ) - -# Class: (grapheme) - -AnnotationAssertion( "alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems"@en) -AnnotationAssertion( "A grapheme is an information content entity that is a fundamental unit in a written language. "@en) -AnnotationAssertion( "An information content entity that is a fundamental unit in a written language."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "http://en.wikipedia.org/wiki/Grapheme") -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:comment "Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there."@en) -AnnotationAssertion(rdfs:label "grapheme"@en) -SubClassOf( ) - -# Class: (utterance) - -AnnotationAssertion( "An utterance is an information content entity that is a complete unit of speech in spoken language. "@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Wikipedia: http://en.wikipedia.org/wiki/Utterance") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "utterance"@en) -SubClassOf( ) - -# Class: (mechanical wave quality) - -AnnotationAssertion( "An attributive collection of qualities inhering in energy when transported through a medium in a wave."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "mechanical wave quality"@en) -SubClassOf( ) - -# Class: (writing quality) - -AnnotationAssertion( "is a quality that is the concretization of graphemes and inheres in a material object."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "writing quality"@en) -SubClassOf( ) - -# Class: (writing bearer) - -AnnotationAssertion( "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting,"@en) -AnnotationAssertion( "is a material information bearer that bears the concretization of graphemes."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "writing bearer") -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) -SubClassOf( ) - -# Class: (portion of energy) - -AnnotationAssertion(rdfs:label "portion of energy"@en) -SubClassOf( ) - -# Class: (sound energy) - -AnnotationAssertion( "Energy that is transported in a sound wave."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "sound energy"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))) -SubClassOf( ) - -# Class: (utterance energy) - -AnnotationAssertion( "Sound energy bearing the concretization of an utterance and being the output of an uttering process. "@en) -AnnotationAssertion(rdfs:label "utterance energy"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectAllValuesFrom( ))) -SubClassOf( ) - -# Class: (oscillating) - -AnnotationAssertion( "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states."@en) -AnnotationAssertion( "http://en.wikipedia.org/wiki/Oscillation") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "oscillating"@en) -SubClassOf( ) - -# Class: (identifier creating process) - -AnnotationAssertion( "A planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) -AnnotationAssertion( "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "dubbing process"@en) -AnnotationAssertion( "naming"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "identifier creating process"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (utterance process) - -AnnotationAssertion( "is a planned process of making speech sounds which may or may not have an actual language involved. "@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "http://en.wiktionary.org/wiki/utter"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "utterance process"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (personal name) - -AnnotationAssertion( "A personal name is a proper name identifying an individual person."@en) -AnnotationAssertion( "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "http://en.wikipedia.org/wiki/Personal_name") -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion(rdfs:comment "Personal names \"today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names.\" (http://en.wikipedia.org/wiki/Personal_name)"@en) -AnnotationAssertion(rdfs:comment "Personal names to not include names of fictional characters, e.g. Sherlock Holmes."@en) -AnnotationAssertion(rdfs:comment "Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)"@en) -AnnotationAssertion(rdfs:label "personal name"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectAllValuesFrom( ))) -SubClassOf( ) - -# Class: (given name) - -AnnotationAssertion( "A given name, in Western contexts often referred to as a first name, is a personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) -AnnotationAssertion( "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name"@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "first name"@en) -AnnotationAssertion( "http://en.wikipedia.org/wiki/Given_name") -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion(rdfs:label "given name"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (family name) - -AnnotationAssertion( "A family name (in Western contexts often referred to as a surname or last name) is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) -AnnotationAssertion( "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children."@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "last name"@en) -AnnotationAssertion( "surname"@en) -AnnotationAssertion( "http://en.wikipedia.org/wiki/Family_name") -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion(rdfs:label "family name"@en) -SubClassOf( ) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (code set) - -AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate core ideas of a specified domain, and where the intention of its creators is that the aggregated entities have a one-to-one correspondence with entities in reality outside the aggregate."@en) -AnnotationAssertion( "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "Justin Whorton"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "code map"@en) -AnnotationAssertion( "code system"@en) -AnnotationAssertion( "codeset"@en) -AnnotationAssertion( "coding system"@en) -AnnotationAssertion( "controlled vocabulary"@en) -AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/237"@en) -AnnotationAssertion( "Alan Ruttenberg") -AnnotationAssertion( "Clint Dowland") -AnnotationAssertion( "Matt Diller") -AnnotationAssertion( "Sarah Bost") -AnnotationAssertion( "William R. Hogan") -AnnotationAssertion(rdfs:comment "Code sets might include non-entities/things (e.g. missing thumbs)."@en) -AnnotationAssertion(rdfs:comment "Does not imply absence vs. presence of any taxonomy."@en) -AnnotationAssertion(rdfs:comment "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities."@en) -AnnotationAssertion(rdfs:comment "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation. - -When there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean)."@en) -AnnotationAssertion(rdfs:comment "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs)."@en) -AnnotationAssertion(rdfs:comment "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets."@en) -AnnotationAssertion(rdfs:comment "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain."@en) -AnnotationAssertion(rdfs:comment "The information content entities do not denote each other."@en) -AnnotationAssertion(rdfs:label "code set"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( )) -SubClassOf( ObjectSomeValuesFrom( )) - -# Class: (identity document) - -AnnotationAssertion( "A document that denotes some identity and is concretized by the bearer of some credential role."@en) -AnnotationAssertion( "Amanda Hicks") -AnnotationAssertion(rdfs:label "identity document"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))) - -# Class: (documented identity) +# Class: (documented identity) AnnotationAssertion( "A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents."@en) AnnotationAssertion( "Amanda Hicks") @@ -5025,7 +432,6 @@ AnnotationAssertion(rdfs:comment "i Is part_of the appropriate relation to use for data items and documented identities?"@en) AnnotationAssertion(rdfs:label "documented identity"@en) SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom(ObjectInverseOf() ) ObjectAllValuesFrom( ))) # Class: (authentication) @@ -5035,77 +441,22 @@ AnnotationAssertion( "Amanda Hicks") AnnotationAssertion(rdfs:label "authentication"@en) SubClassOf( ) -SubClassOf( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectSomeValuesFrom(ObjectInverseOf() )))) # Class: (credential role) AnnotationAssertion( "A role that inheres in a concretization of an identity document and is realized by an authentication process."@en) AnnotationAssertion( "Amanda Hicks"@en) AnnotationAssertion(rdfs:label "credential role"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))) SubClassOf( ) -# Class: (obsolete obligor role) - -AnnotationAssertion( "obligor role"@en) -AnnotationAssertion( "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla."@en) -AnnotationAssertion( "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Sarah Bost") -AnnotationAssertion( "duty holder role (IAO:210016)") -AnnotationAssertion(rdfs:label "obsolete obligor role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete obligee role) - -AnnotationAssertion( "obligee role"@en) -AnnotationAssertion( "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money.") -AnnotationAssertion( "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Sarah Bost") -AnnotationAssertion( "claimant role (IAO:0021013)") -AnnotationAssertion(rdfs:label "obsolete obligee role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (owner role) - -AnnotationAssertion( "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script"@en) -AnnotationAssertion( "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "OBIB/ICO community"@en) -AnnotationAssertion( "https://github.com/d-acts/d-acts/issues/29") -AnnotationAssertion(rdfs:label "owner role"@en) -SubClassOf( ) - -# Class: (obsolete_claim) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_claim"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - # Class: (deontic document act) AnnotationAssertion( "my filling in an immigration form, a judge's signing and stamping a court order"@en) AnnotationAssertion( "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document."@en) AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion(rdfs:label "deontic document act"@en) -EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (obsolete_document act) - -AnnotationAssertion( "my filling in an immigration form, a judge's signing and stamping a court order"@en) -AnnotationAssertion( "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_document act"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - # Class: (social act) AnnotationAssertion( "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom"@en) @@ -5117,181 +468,13 @@ Thanks to W.R. Hogan for finding the Reinach quote."@en) AnnotationAssertion(rdfs:label "social act"@en) SubClassOf( ) -# Class: (obsolete_socio-legal generically dependent continuant) - -AnnotationAssertion( "the claim of a piece of land, the obligation to pay rent to the owner of a rental property"@en) -AnnotationAssertion( "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "obsolete_socio-legal generically dependent continuant"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete_deontic declaration) - -AnnotationAssertion( "deontic declaration"@en) -AnnotationAssertion( "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract."@en) -AnnotationAssertion( "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "declaration"@en) -AnnotationAssertion( "status function declaration"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_deontic declaration"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete obligee role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "obsolete obligee role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (document act input document) - -AnnotationAssertion( "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "document act input document"@en) -SubClassOf( ) - -# Class: (deontic role) - -AnnotationAssertion( "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "Neil Otte"@en) -AnnotationAssertion(rdfs:label "deontic role"@en) -SubClassOf( ) - # Class: (deontic declaration) AnnotationAssertion( "A social act that creates or revokes a deontic role.") AnnotationAssertion( "Mathias Brochhausen") AnnotationAssertion(rdfs:label "deontic declaration"@en) -EquivalentClasses( ObjectUnionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) SubClassOf( ) -# Class: (obsolete_obligation) - -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_obligation"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (claimant role) - -AnnotationAssertion( "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A."@en) -AnnotationAssertion( "J. Neil Otte") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919."@en) -AnnotationAssertion( "https://plato.stanford.edu/entries/rights/") -AnnotationAssertion(rdfs:comment "Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. -https://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child."@en) -AnnotationAssertion(rdfs:label "claimant role"@en) -SubClassOf( ) - -# Class: (obsolete_declaration executive role) - -AnnotationAssertion( "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_declaration executive role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete_document template creator role) - -AnnotationAssertion( "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline"@en) -AnnotationAssertion( "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:comment "not that the \"template\" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants."@en) -AnnotationAssertion(rdfs:label "obsolete_document template creator role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (duty holder role) - -AnnotationAssertion( "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B."@en) -AnnotationAssertion( "J. Neil Otte") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919."@en) -AnnotationAssertion( "https://plato.stanford.edu/entries/rights/") -AnnotationAssertion(rdfs:label "duty holder role"@en) -SubClassOf( ) - -# Class: (obsolete_claimant role) - -AnnotationAssertion( "The role of a human being or an aggregate of human beings concretizing a claim."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_claimant role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete_obligator role) - -AnnotationAssertion( "The role of a human being or an aggregate of human beings concretizing an obligation."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_obligator role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (privilege holder role) - -AnnotationAssertion( "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C."@en) -AnnotationAssertion( "J. Neil Otte") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919."@en) -AnnotationAssertion( "https://plato.stanford.edu/entries/rights/") -AnnotationAssertion(rdfs:label "privilege holder role"@en) -SubClassOf( ) - -# Class: (obsolete_declaration target) - -AnnotationAssertion( "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act"@en) -AnnotationAssertion( "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_declaration target"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (document act template creator role) - -AnnotationAssertion( "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified"@en) -AnnotationAssertion( "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion(rdfs:label "document act template creator role"@en) -SubClassOf( ) -SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf(ObjectUnionOf( ) ObjectAllValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))))) - -# Class: (deontic declaration performer role) - -AnnotationAssertion( "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration."@en) -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "declaration performer role"@en) -AnnotationAssertion(rdfs:label "deontic declaration performer role"@en) -SubClassOf( ) - -# Class: (power role) - -AnnotationAssertion( "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role."@en) -AnnotationAssertion( "J. Neil Otte") -AnnotationAssertion( "Mathias Brochhausen") -AnnotationAssertion( "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919."@en) -AnnotationAssertion( "https://plato.stanford.edu/entries/rights/") -AnnotationAssertion(rdfs:label "power role"@en) -SubClassOf( ) - -# Class: (obsoleted_document act target) - -AnnotationAssertion( "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act.") -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "obsoleted_document act target"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - # Class: (document act performer role) AnnotationAssertion( "a judge's role of signing a court order"@en) @@ -5299,623 +482,6 @@ AnnotationAssertion( "Mathias Brochhausen"@en) AnnotationAssertion(rdfs:label "document act performer role"@en) SubClassOf( ) -SubClassOf( ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectUnionOf( )) ObjectAllValuesFrom( ))) - -# Class: (obsolete_obligee role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Sarah Bost"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_obligee role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete_obligor role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Sarah Bost"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_obligor role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (standing declaration) - -AnnotationAssertion( "A social act that postulates a socio-legal fact for a specified group of people or organizations."@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion( "enactment"@en) -AnnotationAssertion(rdfs:label "standing declaration"@en) -SubClassOf( ) - -# Class: (obsolete obligor role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "John Judkins"@en) -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:label "obsolete obligor role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (ontology module) - -AnnotationAssertion( "ontology module"@en) -AnnotationAssertion( "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it."@en) -AnnotationAssertion( "ontology file"@en) -AnnotationAssertion( "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology."@en) -AnnotationAssertion(rdfs:label "ontology module"@en) -SubClassOf( ) - -# Class: (base ontology module) - -AnnotationAssertion( "base ontology module"@en) -AnnotationAssertion( "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies."@en) -AnnotationAssertion(rdfs:label "base ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (editors ontology module) - -AnnotationAssertion( "editors ontology module"@en) -AnnotationAssertion( "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users."@en) -AnnotationAssertion( "source ontology module"@en) -AnnotationAssertion(rdfs:label "editors ontology module"@en) -SubClassOf( ) - -# Class: (main release ontology module) - -AnnotationAssertion( "main release ontology module"@en) -AnnotationAssertion( "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools."@en) -AnnotationAssertion( "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module"@en) -AnnotationAssertion(rdfs:label "main release ontology module"@en) -SubClassOf( ) - -# Class: (bridge ontology module) - -AnnotationAssertion( "bridge ontology module"@en) -AnnotationAssertion( "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module."@en) -AnnotationAssertion(rdfs:label "bridge ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (import ontology module) - -AnnotationAssertion( "import ontology module"@en) -AnnotationAssertion( "A subset ontology module that is intended to be imported from another ontology."@en) -AnnotationAssertion( "TODO: add axioms that indicate this is the output of a module extraction process."@en) -AnnotationAssertion( "import file"@en) -AnnotationAssertion(rdfs:label "import ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (subset ontology module) - -AnnotationAssertion( "subset ontology module"@en) -AnnotationAssertion( "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms."@en) -AnnotationAssertion( "ontology slim"@en) -AnnotationAssertion( "subset ontology"@en) -AnnotationAssertion(rdfs:label "subset ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (curation subset ontology module) - -AnnotationAssertion( "curation subset ontology module"@en) -AnnotationAssertion( "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation."@en) -AnnotationAssertion(rdfs:label "curation subset ontology module"@en) -SubClassOf( ) - -# Class: (analysis subset ontology module) - -AnnotationAssertion( "analysis ontology module"@en) -AnnotationAssertion( "An ontology module that is intended for usage in analysis or discovery applications."@en) -AnnotationAssertion(rdfs:label "analysis subset ontology module"@en) -SubClassOf( ) - -# Class: (single layer subset ontology module) - -AnnotationAssertion( "single layer ontology module"@en) -AnnotationAssertion( "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint."@en) -AnnotationAssertion( "ribbon subset"@en) -AnnotationAssertion(rdfs:label "single layer subset ontology module"@en) -SubClassOf( ) - -# Class: (exclusion subset ontology module) - -AnnotationAssertion( "exclusion subset ontology module"@en) -AnnotationAssertion( "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes."@en) -AnnotationAssertion( "antislim"@en) -AnnotationAssertion(rdfs:label "exclusion subset ontology module"@en) -SubClassOf( ) - -# Class: (external import ontology module) - -AnnotationAssertion( "external import ontology module"@en) -AnnotationAssertion( "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach."@en) -AnnotationAssertion( "external import"@en) -AnnotationAssertion(rdfs:label "external import ontology module"@en) -SubClassOf( ) - -# Class: (species subset ontology module) - -AnnotationAssertion( "species subset ontology module"@en) -AnnotationAssertion( "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species."@en) -AnnotationAssertion( "taxon subset"@en) -AnnotationAssertion(rdfs:label "species subset ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (reasoned ontology module) - -AnnotationAssertion( "reasoned ontology module"@en) -AnnotationAssertion( "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available."@en) -AnnotationAssertion(rdfs:label "reasoned ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (generated ontology module) - -AnnotationAssertion( "generated ontology module"@en) -AnnotationAssertion( "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV."@en) -AnnotationAssertion( "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process"@en) -AnnotationAssertion(rdfs:label "generated ontology module"@en) -SubClassOf( ) - -# Class: (template generated ontology module) - -AnnotationAssertion( "template generated ontology module"@en) -AnnotationAssertion( "An ontology module that is automatically generated from a template specification and fillers for slots in that template."@en) -AnnotationAssertion(rdfs:label "template generated ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (taxonomic bridge ontology module) - -AnnotationAssertion( "taxonomic bridge ontology module"@en) -AnnotationAssertion(rdfs:label "taxonomic bridge ontology module"@en) -SubClassOf( ) - -# Class: (ontology module subsetted by expressivity) - -AnnotationAssertion( "ontology module subsetted by expressivity"@en) -AnnotationAssertion(rdfs:label "ontology module subsetted by expressivity"@en) -SubClassOf( ) - -# Class: (obo basic subset ontology module) - -AnnotationAssertion( "obo basic subset ontology module"@en) -AnnotationAssertion( "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools. - -Examples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses). - -An ontology is OBO Basic if and only if it has the following characteristics: -DAG -Unidirectional -No Dangling Clauses -Fully Asserted -Fully Labeled -No equivalence axioms -Singly labeled edges -No qualifier lists -No disjointness axioms -No owl-axioms header -No imports"@en) -AnnotationAssertion(rdfs:label "obo basic subset ontology module"@en) -AnnotationAssertion(rdfs:seeAlso ) -SubClassOf( ) - -# Class: (ontology module subsetted by OWL profile) - -AnnotationAssertion( "ontology module subsetted by OWL profile"@en) -AnnotationAssertion(rdfs:label "ontology module subsetted by OWL profile"@en) -SubClassOf( ) - -# Class: (EL++ ontology module) - -AnnotationAssertion( "EL++ ontology module"@en) -AnnotationAssertion(rdfs:label "EL++ ontology module"@en) -SubClassOf( ) - -# Class: (Homo sapiens) - -AnnotationAssertion( "Homo sapiens"@en) -AnnotationAssertion( "human being") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "Homo sapiens"@en) -SubClassOf( ) - -# Class: (planned process) - -AnnotationAssertion( "planned process"@en) -AnnotationAssertion( "A process that realizes a plan which is the concretization of a plan specification."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "planned process"@en) -SubClassOf( ) - -# Class: (investigation) - -AnnotationAssertion( "investigation"@en) -AnnotationAssertion( "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "investigation"@en) -SubClassOf( ) - -# Class: (organization) - -AnnotationAssertion( "organization"@en) -AnnotationAssertion( "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods."@en) -AnnotationAssertion( ) -AnnotationAssertion( "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members."@en) -AnnotationAssertion( "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: - -1) there are organization_member_roles (president, treasurer, branch -editor), with individual persons as bearers - -2) there are organization_roles (employer, owner, vendor, patent holder) - -3) an organization has a charter / rules / bylaws, which specify what roles -there are, how they should be realized, and how to modify the -charter/rules/bylaws themselves. - -It is debatable what the organization itself is (some kind of dependent -continuant or an aggregate of people). This also determines who/what the -bearer of organization_roles' are. My personal favorite is still to define -organization as a kind of 'legal entity', but thinking it through leads to -all kinds of questions that are clearly outside the scope of OBI. - -Interestingly enough, it does not seem to matter much where we place -organization itself, as long as we can subclass it (University, Corporation, -Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, -W3C, University of Oklahoma), and have it play roles. - -This leads to my proposal: We define organization through the statements 1 - -3 above, but without an 'is a' statement for now. We can leave it in its -current place in the is_a hierarchy (material entity) or move it up to -'continuant'. We leave further clarifications to BFO, and close this issue -for now."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg") -AnnotationAssertion( "PERSON: Bjoern Peters") -AnnotationAssertion( "PERSON: Philippe Rocca-Serra") -AnnotationAssertion( "PERSON: Susanna Sansone") -AnnotationAssertion( "GROUP: OBI") -AnnotationAssertion(rdfs:label "organization"@en) -SubClassOf( ) - -# Class: (study design execution) - -AnnotationAssertion( "study design execution") -AnnotationAssertion( "a planned process that carries out a study design") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "study design execution") -SubClassOf( ) - -# Class: (organism) - -AnnotationAssertion( "organism"@en) -AnnotationAssertion( "animal"@en) -AnnotationAssertion( "fungus"@en) -AnnotationAssertion( "plant"@en) -AnnotationAssertion( "virus"@en) -AnnotationAssertion( ) -AnnotationAssertion( "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en) -AnnotationAssertion( "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')") -AnnotationAssertion( "13-02-2009: -OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. -This issue is outside the scope of OBI.") -AnnotationAssertion( "GROUP: OBI Biomaterial Branch") -AnnotationAssertion( "WEB: http://en.wikipedia.org/wiki/Organism"@en) -AnnotationAssertion(rdfs:label "organism"@en) -SubClassOf( ) - -# Class: (data transformation) - -AnnotationAssertion( "data transformation"@en) -AnnotationAssertion( "A planned process that produces output data from input data."@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "data transformation"@en) -SubClassOf( ) - -# Class: (study design) - -AnnotationAssertion( "study design"@en) -AnnotationAssertion( "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "study design"@en) -SubClassOf( ) - -# Class: (collection of organisms) - -AnnotationAssertion( "An object aggregate of organisms."@en) -AnnotationAssertion(rdfs:comment "Any arbitrary collection of organisms. They need not be of the same taxonomic class. "@en) -AnnotationAssertion(rdfs:label "collection of organisms"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (collection of humans) - -AnnotationAssertion(rdfs:comment "An object aggregate all of whose components are human beings."@en) -AnnotationAssertion(rdfs:label "collection of humans"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (aggregate of organizations) - -AnnotationAssertion( "An aggregate of organizations that have some feature in common, but is not itself an organization."@en) -AnnotationAssertion( "An object aggregate that is not itself an organization and whose members are only organizations that have some feature in common"@en) -AnnotationAssertion( "William R. Hogan"@en) -AnnotationAssertion( "William R. Hogan -Amanda Hicks"@en) -AnnotationAssertion( "http://purl.obolibrary.org/obo/omrse/releases/2022-04-06/omrse.owl") -AnnotationAssertion(rdfs:comment "It is often convenient to group organizations together that otherwise might not even interact with one another. "@en) -AnnotationAssertion(rdfs:label "aggregate of organizations"@en) -EquivalentClasses( ObjectSomeValuesFrom( )) -SubClassOf( ) - -# Class: (role in human social processes) - -AnnotationAssertion( "A role that inheres in some entity that is realized in a social act."@en) -AnnotationAssertion( "Matthew Diller"@en) -AnnotationAssertion( "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl") -AnnotationAssertion( "Mathias Brochhausen"@en) -AnnotationAssertion(rdfs:comment "Previous definition: A role played by an entity in human social processes."@en) -AnnotationAssertion(rdfs:label "role in human social processes"@en) -SubClassOf( ) - -# Class: (morphology) - -AnnotationAssertion( "morphology") -AnnotationAssertion( "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "morphology") -SubClassOf( ) - -# Class: (length) - -AnnotationAssertion( "length") -AnnotationAssertion( "A 1-D extent quality which is equal to the distance between two points.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "length") -SubClassOf( ) - -# Class: (mass) - -AnnotationAssertion( "mass") -AnnotationAssertion( "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "mass") -SubClassOf( ) - -# Class: (physical quality) - -AnnotationAssertion( "physical quality") -AnnotationAssertion( "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "physical quality") -SubClassOf( ) - -# Class: (pressure) - -AnnotationAssertion( _:genid2147484144) -AnnotationAssertion( "quality") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "pressure"@en) -SubClassOf( ) - -# Class: (physical object quality) - -AnnotationAssertion( "physical object quality") -AnnotationAssertion( "A quality which inheres in a continuant.") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "physical object quality") -SubClassOf( ) - -# Class: (length unit) - -AnnotationAssertion( "length unit") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "length unit") -SubClassOf( ) - -# Class: (mass unit) - -AnnotationAssertion( "mass unit") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "mass unit") -SubClassOf( ) - -# Class: (time unit) - -AnnotationAssertion( "time unit") -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "time unit") -SubClassOf( ) - -# Class: (obsolete obligee role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Sarah Bost"@en) -AnnotationAssertion(rdfs:label "obsolete obligee role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - -# Class: (obsolete obligor role) - -AnnotationAssertion( "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements."@en) -AnnotationAssertion( "Sarah Bost"@en) -AnnotationAssertion(rdfs:label "obsolete obligor role"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) -SubClassOf( ) - - -############################ -# Named Individuals -############################ - -# Individual: (example to be eventually removed) - -AnnotationAssertion( "example to be eventually removed"@en) -AnnotationAssertion(rdfs:label "example to be eventually removed"@en) -ClassAssertion( ) - -# Individual: (failed exploratory term) - -AnnotationAssertion( "failed exploratory term"@en) -AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) -AnnotationAssertion( "Person:Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "failed exploratory term"@en) -ClassAssertion( ) -ClassAssertion(owl:Thing ) - -# Individual: (metadata complete) - -AnnotationAssertion( "metadata complete"@en) -AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) -AnnotationAssertion(rdfs:label "metadata complete"@en) -ClassAssertion( ) - -# Individual: (organizational term) - -AnnotationAssertion( "organizational term"@en) -AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) -AnnotationAssertion(rdfs:label "organizational term"@en) -ClassAssertion( ) - -# Individual: (ready for release) - -AnnotationAssertion( "ready for release"@en) -AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) -AnnotationAssertion(rdfs:label "ready for release"@en) -ClassAssertion( ) - -# Individual: (metadata incomplete) - -AnnotationAssertion( "metadata incomplete"@en) -AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) -AnnotationAssertion(rdfs:label "metadata incomplete"@en) -ClassAssertion( ) - -# Individual: (uncurated) - -AnnotationAssertion( "uncurated"@en) -AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) -AnnotationAssertion(rdfs:label "uncurated"@en) -ClassAssertion( ) - -# Individual: (pending final vetting) - -AnnotationAssertion( "pending final vetting"@en) -AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) -AnnotationAssertion(rdfs:label "pending final vetting"@en) -ClassAssertion( ) - -# Individual: (obsolete_core) - -AnnotationAssertion( "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes."@en) -AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) -AnnotationAssertion( "PERSON: Melanie Courtot"@en) -AnnotationAssertion( ) -AnnotationAssertion(rdfs:label "obsolete_core"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - -# Individual: (placeholder removed) - -AnnotationAssertion( "placeholder removed"@en) -AnnotationAssertion(rdfs:label "placeholder removed"@en) -ClassAssertion( ) -ClassAssertion(owl:Thing ) - -# Individual: (terms merged) - -AnnotationAssertion( "terms merged"@en) -AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) -AnnotationAssertion(rdfs:label "terms merged"@en) -ClassAssertion( ) - -# Individual: (term imported) - -AnnotationAssertion( "term imported"@en) -AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) -AnnotationAssertion(rdfs:label "term imported"@en) -ClassAssertion( ) - -# Individual: (term split) - -AnnotationAssertion( "term split"@en) -AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) -AnnotationAssertion(rdfs:label "term split"@en) -ClassAssertion( ) - -# Individual: (obsolete_other) - -AnnotationAssertion( "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason."@en) -AnnotationAssertion( "We expect to be able to mine these new reasons and add instances as required."@en) -AnnotationAssertion(rdfs:label "obsolete_other"@en) -AnnotationAssertion(owl:deprecated "true"^^xsd:boolean) - -# Individual: (universal) - -AnnotationAssertion( "universal"@en) -AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) -AnnotationAssertion(rdfs:label "universal"@en) -ClassAssertion( ) - -# Individual: (defined class) - -AnnotationAssertion( "defined class"@en) -AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) -AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "defined class"@en) -ClassAssertion( ) - -# Individual: (named class expression) - -AnnotationAssertion( "named class expression"@en) -AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) -AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion(rdfs:label "named class expression"@en) -ClassAssertion( ) - -# Individual: (to be replaced with external ontology term) - -AnnotationAssertion( "to be replaced with external ontology term"@en) -AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) -ClassAssertion( ) - -# Individual: (requires discussion) - -AnnotationAssertion( "requires discussion"@en) -AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) -AnnotationAssertion( "Alan Ruttenberg"@en) -AnnotationAssertion( "group:OBI"@en) -AnnotationAssertion(rdfs:label "requires discussion"@en) -ClassAssertion( ) - -# Individual: (out of scope) - -AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) -AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) -AnnotationAssertion( ) -AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") -AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") -AnnotationAssertion(rdfs:label "out of scope") -ClassAssertion( ) -DifferentIndividuals( ) -DifferentIndividuals( ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -SubObjectPropertyOf(ObjectPropertyChain( ) ) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) -DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) ) \ No newline at end of file diff --git a/src/ontology/imports/d-acts_terms.txt b/src/ontology/imports/d-acts_terms.txt index 139597f..a366e57 100644 --- a/src/ontology/imports/d-acts_terms.txt +++ b/src/ontology/imports/d-acts_terms.txt @@ -1,2 +1,8 @@ - +IAO:0020021 owl:Class +IAO:0020022 owl:Class +IAO:0020023 owl:Class +IAO:0020024 owl:Class +IAO:0021003 owl:Class +IAO:0021009 owl:Class +IAO:0021031 owl:Class diff --git a/src/ontology/imports/external_import.owl b/src/ontology/imports/external_import.owl index 7bd7cf7..6c68657 100644 --- a/src/ontology/imports/external_import.owl +++ b/src/ontology/imports/external_import.owl @@ -22,6 +22,7 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) diff --git a/src/ontology/omrse-odk.yaml b/src/ontology/omrse-odk.yaml index cac5666..d308ee0 100644 --- a/src/ontology/omrse-odk.yaml +++ b/src/ontology/omrse-odk.yaml @@ -1,6 +1,6 @@ id: omrse -title: "The Ontology of Medically Related Social Entities" -github_org: ufbmi +title: "The Ontology for Modeling and Representation of Social Entities" +github_org: mcwdsi repo: OMRSE report_fail_on: None export_formats: @@ -11,7 +11,6 @@ release_artefacts: - base - full import_group: - module_type: filter annotation_properties: - rdfs:label - IAO:0000115 @@ -19,6 +18,8 @@ import_group: - IAO:0000111 - oboInOwl:hasDbXref - rdfs:comment + exclude_iri_patterns: + - products: - id: ro module_type: slme @@ -51,7 +52,9 @@ import_group: module_type: mirror - id: d-acts mirror_from: http://purl.obolibrary.org/obo/iao/d-acts.owl - module_type: mirror + module_type: filter + base_iris: + - http://purl.obolibrary.org/obo/IAO_ - id: geo - id: mf diff --git a/src/templates/external_import.tsv b/src/templates/external_import.tsv index 19df716..38e2f08 100644 --- a/src/templates/external_import.tsv +++ b/src/templates/external_import.tsv @@ -34,6 +34,7 @@ IAO:0020023 owl:Class IAO:0020024 owl:Class IAO:0021003 owl:Class IAO:0021009 owl:Class +IAO:0021031 IAO:0100001 owl:AnnotationProperty MF:0000030 owl:Class MF:0000031 owl:Class