Metal phases

src/ontology/Makefile

@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for pmdco
 # Generated using ontology-development-kit
-# ODK Version: v1.6
+# ODK Version: "Unknown"
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use pmdco.Makefile instead
 
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                8700addd8a55cdb81c70f5b3a4657df5fbc2acb4a7669ff60df63a9beafbbf7a
+CONFIG_HASH=                54072dc574a377048daa0be07494524ef16b0e62e4cbf5483bb9f4e1401d0586
 
 
 # ----------------------------------------
@@ -42,14 +42,15 @@ UPDATEREPODIR=              target
 SPARQLDIR =                 ../sparql
 EXTENDED_PREFIX_MAP=        $(TMPDIR)/obo.epm.json
 COMPONENTSDIR =             components
+ODK_RESOURCES_DIR ?=        /tools/resources
 ROBOT_PROFILE =             profile.txt
 REPORT_FAIL_ON =            ERROR
 REPORT_LABEL =              -l true
 REPORT_PROFILE_OPTS =       --profile $(ROBOT_PROFILE)
 OBO_FORMAT_OPTIONS =        --clean-obo "strict drop-untranslatable-axioms"
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by 
 SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.6
+ODK_VERSION_MAKEFILE =      "Unknown"
 RELAX_OPTIONS =             --include-subclass-of true
 REDUCE_OPTIONS =            --include-subproperties true
 
@@ -58,11 +59,12 @@ OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')
 VERSION=                    $(TODAY)
 ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION)
 ANNOTATE_CONVERT_FILE =     annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@
-OTHER_SRC =                 $(COMPONENTSDIR)/imports-edit.owl $(COMPONENTSDIR)/pmdco-shared.owl $(COMPONENTSDIR)/pmdco-axioms-shared.owl $(COMPONENTSDIR)/pmdco-qualities.owl $(COMPONENTSDIR)/pmdco-materials.owl $(COMPONENTSDIR)/pmdco-manufacturing.owl $(COMPONENTSDIR)/pmdco-devices.owl $(COMPONENTSDIR)/pmdco-datatransformation.owl $(COMPONENTSDIR)/pmdco-characterization.owl $(COMPONENTSDIR)/materials-listing.owl 
+OTHER_SRC =                 $(COMPONENTSDIR)/imports-edit.owl $(COMPONENTSDIR)/pmdco-shared.owl $(COMPONENTSDIR)/pmdco-axioms-shared.owl $(COMPONENTSDIR)/pmdco-qualities.owl $(COMPONENTSDIR)/pmdco-materials.owl $(COMPONENTSDIR)/pmdco-manufacturing.owl $(COMPONENTSDIR)/pmdco-devices.owl $(COMPONENTSDIR)/pmdco-datatransformation.owl $(COMPONENTSDIR)/pmdco-characterization.owl $(COMPONENTSDIR)/pmdco-microstructure.owl $(COMPONENTSDIR)/materials-listing.owl 
 ONTOLOGYTERMS =             $(TMPDIR)/ontologyterms.txt
 EDIT_PREPROCESSED =         $(TMPDIR)/$(ONT)-preprocess.owl
 
 
+
 FORMATS = $(sort  owl ttl owl)
 FORMATS_INCL_TSV = $(sort $(FORMATS) tsv)
 RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple $(ONT)-minimal )
@@ -126,12 +128,12 @@ reason_test: $(EDIT_PREPROCESSED)
 .PHONY: odkversion
 odkversion:
 	@echo "ODK Makefile $(ODK_VERSION_MAKEFILE)"
-	@odk-info --tools
+	@odk-helper info --tools
 .PHONY: config_check
 config_check:
 	@if [ "$$(tr -d '\r' < $(ONT)-odk.yaml | sha256sum | cut -c1-64)" = "$(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
+		echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'sh run.sh update_repo'." ; fi
 
 
 $(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR):
@@ -149,23 +151,20 @@ export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/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)) \
+all_robot_plugins: $(foreach plugin,$(notdir $(wildcard $(ODK_RESOURCES_DIR)/robot/plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
 		   $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \
-		   custom_robot_plugins extra_robot_plugins  \
+		   custom_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 $@ ;  \
+	elif [ -f $(ODK_RESOURCES_DIR)/robot/plugins/$*.jar ]; then \
+		cp $(ODK_RESOURCES_DIR)/robot/plugins/$*.jar $@ ;  \
 	fi
 
 # Specific rules for supplementary plugins defined in configuration
@@ -225,6 +224,11 @@ RELEASED_MAPPING_FILES = $(foreach p, $(RELEASED_MAPPINGS), $(MAPPINGDIR)/$(p).s
 .PHONY: all_mappings
 all_mappings: $(MAPPING_FILES)
 
+# ----------------------------------------
+# Bridge assets
+# ----------------------------------------
+
+BRIDGE_FILES =
 
 # ----------------------------------------
 # QC Reports & Utilities
@@ -279,13 +283,8 @@ $(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR)
 $(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR)
 	$(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --print 5 -o $@
 
-check_for_robot_updates:	
-	@cut -f2 "/tools/templates/src/ontology/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
+check_for_robot_updates:
+	@odk-helper check-robot-profile
 
 # ----------------------------------------
 # Release assets
@@ -296,11 +295,13 @@ ASSETS = \
   $(MAIN_FILES) \
   $(REPORT_FILES) \
   $(SUBSET_FILES) \
-  $(MAPPING_FILES)
+  $(MAPPING_FILES) \
+  $(BRIDGE_FILES)
 
 RELEASE_ASSETS = \
   $(MAIN_FILES) \
-  $(SUBSET_FILES)
+  $(SUBSET_FILES)\
+  $(BRIDGE_FILES)
 
 .PHONY: all_assets
 all_assets: $(ASSETS) check_rdfxml_assets
@@ -311,7 +312,7 @@ show_assets:
 	du -sh $(ASSETS)
 
 check_rdfxml_%: %
-	@check-rdfxml  $<
+	@odk-helper check-rdfxml $<
 
 .PHONY: check_rdfxml_assets
 check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl)
@@ -548,6 +549,7 @@ recreate-components:
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-devices.owl \
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-datatransformation.owl \
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-characterization.owl \
+		--assume-new=$(TMPDIR)/stamp-component-pmdco-microstructure.owl \
 		--assume-new=$(TMPDIR)/stamp-component-materials-listing.owl \
 		COMP=true IMP=false MIR=true PAT=true all_components
 
@@ -562,6 +564,7 @@ no-mirror-recreate-components:
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-devices.owl \
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-datatransformation.owl \
 		--assume-new=$(TMPDIR)/stamp-component-pmdco-characterization.owl \
+		--assume-new=$(TMPDIR)/stamp-component-pmdco-microstructure.owl \
 		--assume-new=$(TMPDIR)/stamp-component-materials-listing.owl \
 		COMP=true IMP=false MIR=false PAT=true all_components
 
@@ -824,7 +827,7 @@ validate-all-tsv: $(ALL_TSV_FILES)
 # can use to pull the (currently inofficial) OBO EPM into the workspace.
 # Users are instructed to refer to the EPM only through the variable $(EXTENDED_PREFIX_MAP) as 
 # its location might change in a feature version of ODK.
-$(EXTENDED_PREFIX_MAP): /tools/obo.epm.json
+$(EXTENDED_PREFIX_MAP): $(ODK_RESOURCES_DIR)/obo.epm.json
 	cp $< $@
 
 

src/ontology/catalog-v001.xml

@@ -20,6 +20,7 @@
     <uri name="https://w3id.org/pmd/co/components/pmdco-devices.owl" uri="components/pmdco-devices.owl" />
     <uri name="https://w3id.org/pmd/co/components/pmdco-datatransformation.owl" uri="components/pmdco-datatransformation.owl" />
     <uri name="https://w3id.org/pmd/co/components/pmdco-characterization.owl" uri="components/pmdco-characterization.owl" />
+    <uri name="https://w3id.org/pmd/co/components/pmdco-microstructure.owl" uri="components/pmdco-microstructure.owl" />
     <uri name="https://w3id.org/pmd/co/components/materials-listing.owl" uri="components/materials-listing.owl" />
   </group>
 </catalog>

src/ontology/components/catalog-v001.xml

@@ -21,7 +21,8 @@
   <uri name="https://w3id.org/pmd/co/components/devices.owl" uri="pmdco-devices.owl"/>
   <uri name="https://w3id.org/pmd/co/components/datatransformation.owl" uri="pmdco-datatransformation.owl"/>
   <uri name="https://w3id.org/pmd/co/components/characterization.owl" uri="pmdco-characterization.owl"/>
-
+  <uri name="https://w3id.org/pmd/co/components/pmdco-microstructure.owl" uri="pmdco-microstructure.owl" />
+
 
 </group>
 </catalog>

src/ontology/components/pmdco-datatransformation.owl

@@ -486,4 +486,7 @@ SubClassOf(:PMD_0025012 :PMD_0000583)
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000233> :PMD_0000128 "https://github.com/materialdigital/core-ontology/issues/418")
 AnnotationAssertion(rdfs:label :PMD_0000128 "local identifier"@en)
 AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#definition> :PMD_0000128 "name or identifier that denotes a locally defined function, variable or argument in a programming script")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> :PMD_0000128 "PERSON: Joerg Waitelonis")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> :PMD_0000128 <http://purl.obolibrary.org/obo/IAO_0000122>)
+
 )

src/ontology/components/pmdco-microstructure.owl

@@ -0,0 +1,57 @@
+Prefix(:=<https://w3id.org/pmd/co/components/pmdco-microstructure.owl/>)
+Prefix(obo:=<http://purl.obolibrary.org/obo/>)
+Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
+Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
+Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
+Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
+Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
+Prefix(skos:=<http://www.w3.org/2004/02/skos/core#>)
+Prefix(pmdco:=<https://w3id.org/pmd/co/>)
+Prefix(dcterms:=<http://purl.org/dc/terms/>)
+
+
+Ontology(<https://w3id.org/pmd/co/components/pmdco-microstructure.owl>
+Import(<https://w3id.org/pmd/co/components/pmdco-shared.owl>)
+
+Declaration(Class(pmdco:PMD_0027001))
+Declaration(Class(pmdco:PMD_0027002))
+Declaration(Class(pmdco:PMD_0027003))
+
+
+
+############################
+#   Classes
+############################
+
+# Class: pmdco:PMD_0027001 (lamella)
+
+AnnotationAssertion(rdfs:label pmdco:PMD_0027001 "lamella"@en)
+AnnotationAssertion(skos:definition pmdco:PMD_0027001 "lamella is an object that is  part of a lamellae object oggregate anf represents a thin, flat, plate-like layer or flake within microstructure of a metal"@en)
+SubClassOf(pmdco:PMD_0027001 obo:BFO_0000030)
+
+# Class: pmdco:PMD_0027002 (lamellae)
+
+AnnotationAssertion(obo:IAO_0000112 pmdco:PMD_0027002 "perlite microconstituent has part ferrite lamellae and has part cementite lamellae. Ferrite lamellae has part ferrite lamella"@en)
+AnnotationAssertion(rdfs:label pmdco:PMD_0027002 "lamellae"@en)
+AnnotationAssertion(skos:definition pmdco:PMD_0027002 "lamellae is an object aggregate that is part of some microconstituent in a metal microstructure. In this case, lamellae has a single thermodynamic phase"@en)
+AnnotationAssertion(skos:example pmdco:PMD_0027002 "ferrite lamellae in perlite microcontituent"@en)
+SubClassOf(pmdco:PMD_0027002 obo:BFO_0000027)
+SubClassOf(pmdco:PMD_0027002 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:BFO_0000051 pmdco:PMD_0027001) ObjectAllValuesFrom(obo:BFO_0000051 pmdco:PMD_0027001)))
+
+# Class: pmdco:PMD_0027003 (average lamella thickness)
+
+AnnotationAssertion(rdfs:label pmdco:PMD_0027003 "average lamella thickness"@en)
+AnnotationAssertion(skos:definition pmdco:PMD_0027003 "average lamella thickness is a quality of lamellae object aggregate which defines the average thickness across all indivudual lamella(s) of a sinlge phase in a microconstituent"@en)
+AnnotationAssertion(skos:example pmdco:PMD_0027003 "average thickness of ferrite lamellae in perlite microscontituent"@en)
+SubClassOf(pmdco:PMD_0027003 obo:BFO_0000019)
+SubClassOf(pmdco:PMD_0027003 ObjectIntersectionOf(ObjectSomeValuesFrom(obo:RO_0000080 pmdco:PMD_0027002) ObjectAllValuesFrom(obo:RO_0000080 pmdco:PMD_0027002)))
+
+
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> pmdco:PMD_0027001 "PERSON: PMDco Team")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> pmdco:PMD_0027001 <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> pmdco:PMD_0027002 "PERSON: PMDco Team")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> pmdco:PMD_0027002 <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> pmdco:PMD_0027003 "PERSON: PMDco Team")
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> pmdco:PMD_0027003 <http://purl.obolibrary.org/obo/IAO_0000122>)
+
+)

src/ontology/pmdco-edit.owl

@@ -21,6 +21,7 @@ Import(<https://w3id.org/pmd/co/components/pmdco-datatransformation.owl>)
 Import(<https://w3id.org/pmd/co/components/pmdco-devices.owl>)
 Import(<https://w3id.org/pmd/co/components/pmdco-manufacturing.owl>)
 Import(<https://w3id.org/pmd/co/components/pmdco-materials.owl>)
+Import(<https://w3id.org/pmd/co/components/pmdco-microstructure.owl>)
 Import(<https://w3id.org/pmd/co/components/pmdco-qualities.owl>)
 Import(<https://w3id.org/pmd/co/components/pmdco-shared.owl>)
 Import(<https://w3id.org/pmd/co/imports/bfo_import.owl>)
@@ -70,6 +71,7 @@ Declaration(AnnotationProperty(dcterms:title))
 Declaration(AnnotationProperty(<http://usefulinc.com/ns/doap#repository>))
 
 
+
 AnnotationAssertion(rdfs:label <https://orcid.org/0000-0001-6772-1943> "Martin Glauer")
 AnnotationAssertion(rdfs:label <https://orcid.org/0000-0001-7192-7143> "Jörg Waitelonis")
 AnnotationAssertion(rdfs:label <https://orcid.org/0000-0002-1058-3102> "Fabian Neuhaus")

src/ontology/pmdco-idranges.owl

@@ -30,82 +30,13 @@ AnnotationProperty: idsfor:
 
 AnnotationProperty: allocatedto:
 
-Datatype: idrange:1
-
-    Annotations: 
-        allocatedto: "joergwa"
-
-    EquivalentTo: 
-        xsd:integer[>= 0 , <= 9999]
-
-
-Datatype: idrange:2
-
-    Annotations: 
-        allocatedto: "bernd"
-
-    EquivalentTo: 
-        xsd:integer[>= 10000 , <= 19999]
-
 Datatype: idrange:3
 
     Annotations: 
-        allocatedto: "phillip"
-
-    EquivalentTo: 
-        xsd:integer[>= 20000 , <= 25000]
-
-Datatype: idrange:4
-
-    Annotations: 
-        allocatedto: "thomas"
-
-    EquivalentTo: 
-        xsd:integer[>= 80000 , <= 89999]
-
-
-Datatype: idrange:5
-
-    Annotations: 
-        allocatedto: "henk"
-
-    EquivalentTo: 
-        xsd:integer[>= 30000 , <= 39999]
-
-Datatype: idrange:6
-
-    Annotations: 
-        allocatedto: "lars"
-
-    EquivalentTo: 
-        xsd:integer[>= 40000 , <= 49999]
-
-
-Datatype: idrange:7
-
-    Annotations: 
-        allocatedto: "markus"
-
-    EquivalentTo: 
-        xsd:integer[>= 50000 , <= 59999]
-
-
-Datatype: idrange:8
-
-Annotations: 
-        allocatedto: "hossein"
-
-    EquivalentTo: 
-        xsd:integer[>= 60000 , <= 69999]
-
-
-Datatype: idrange:9
-
-Annotations: 
-        allocatedto: "ebrahim"
+        allocatedto: "philipp"
 
     EquivalentTo: 
-        xsd:integer[>= 70000 , <= 79999]
+        xsd:integer[>= 23000 , <= 25000]
 
 
 Datatype: idrange:10
@@ -114,24 +45,24 @@ Annotations:
         allocatedto: "kamilla"
 
     EquivalentTo: 
-        xsd:integer[>= 25001 , <= 25999]
+        xsd:integer[>= 27001 , <= 29999]
 
 
-Datatype: idrange:11
+Datatype: idrange:13
 
 Annotations: 
-        allocatedto: "thnlrd"
+        allocatedto: "Akhil"
 
     EquivalentTo: 
-        xsd:integer[>= 90000 , <= 94999]
+        xsd:integer[>= 100000 , <= 109999]
 
-Datatype: idrange:12
+Datatype: idrange:14
 
 Annotations: 
-        allocatedto: "KhashiYaar"
+        allocatedto: "Abril"
 
     EquivalentTo: 
-        xsd:integer[>= 95000 , <= 99999]
+        xsd:integer[>= 110000 , <= 119999]
 
 Datatype: idrange:999