setup BFO2020

materialdigital · Jan 28, 2025 · d2ca66a · d2ca66a
1 parent 36aeaac
commit d2ca66a
Show file tree

Hide file tree

Showing 24 changed files with 1,990 additions and 1,222 deletions.
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -10,7 +10,7 @@
 # More information: https://github.com/INCATools/ontology-development-kit/
 
 # Fingerprint of the configuration file when this Makefile was last generated
-CONFIG_HASH=                99359b0f9276f5e48fd795ed93903e222b1b3693a8993c86306f5497e1ed5c1c
+CONFIG_HASH=                e7c37ef1f14696386f69b0405f6936b8b271f5595c68397e99e6dbbe8597bdcd
 
 
 # ----------------------------------------
@@ -160,7 +160,7 @@ all_main: $(MAIN_FILES)
 # ----------------------------------------
 
 
-IMPORTS =  bfo ro iao obi chebi
+IMPORTS =  bfo iao obi chebi
 
 IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS))
 IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl)
@@ -464,14 +464,6 @@ mirror-bfo: | $(TMPDIR)
 	$(ROBOT) convert -I https://raw.githubusercontent.com/BFO-ontology/BFO-2020/release-2024-01-29/src/owl/bfo-core.ttl -o $(TMPDIR)/$@.owl
 
 
-## ONTOLOGY: ro
-.PHONY: mirror-ro
-.PRECIOUS: $(MIRRORDIR)/ro.owl
-mirror-ro: | $(TMPDIR)
-	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: iao
 .PHONY: mirror-iao
 .PRECIOUS: $(MIRRORDIR)/iao.owl

diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml
@@ -7,10 +7,10 @@
   <uri name="https://w3id.org/pmd/co/pmdco/components/pmdco-shared.owl" uri="components/pmdco-shared.owl"/>
   <uri name="https://w3id.org/pmd/co/pmdco/components/pmdco-axioms-shared.owl" uri="components/pmdco-axioms-shared.owl"/>
 
-  <uri name="https://w3id.org/pmd/co/pmdco/imports/ro_import.owl" uri="imports/ro_import.owl"/>
+  <!--uri name="https://w3id.org/pmd/co/pmdco/imports/ro_import.owl" uri="imports/ro_import.owl"/ -->
   <uri name="https://w3id.org/pmd/co/pmdco/imports/iao_import.owl" uri="imports/iao_import.owl"/>
   <uri name="https://w3id.org/pmd/co/pmdco/imports/obi_import.owl" uri="imports/obi_import.owl"/>
-  <uri name="https://w3id.org/pmd/co/pmdco/imports/bfo_import.owl" uri="imports/bfo_import.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl" uri="imports/bfo_import.owl"/>
   <uri name="https://w3id.org/pmd/co/pmdco/imports/chebi_import.owl" uri="imports/chebi_import.owl"/>
 
   <uri name="https://w3id.org/pmd/co/qualities" uri="components/pmdco-qualities.owl"/>

diff --git a/src/ontology/components/catalog-v001.xml b/src/ontology/components/catalog-v001.xml
@@ -2,10 +2,10 @@
 <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
 <group id="Folder Repository, directory=, recursive=false, Auto-Update=false, version=2" prefer="public" xml:base="">
 
-  <uri name="https://w3id.org/pmd/co/pmdco/imports/ro_import.owl" uri="../imports/ro_import.owl"/>
+  <!--uri name="https://w3id.org/pmd/co/pmdco/imports/ro_import.owl" uri="../imports/ro_import.owl"/-->
   <uri name="https://w3id.org/pmd/co/pmdco/imports/iao_import.owl" uri="../imports/iao_import.owl"/>
   <uri name="https://w3id.org/pmd/co/pmdco/imports/obi_import.owl" uri="../imports/obi_import.owl"/>
-  <uri name="https://w3id.org/pmd/co/pmdco/imports/bfo_import.owl" uri="../imports/bfo_import.owl"/>
+  <uri name="http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl" uri="../imports/bfo_import.owl"/>
   <uri name="https://w3id.org/pmd/co/pmdco/imports/chebi_import.owl" uri="../imports/chebi_import.owl"/>
 
   <uri name="https://w3id.org/pmd/co/components/imports-edit" uri="imports-edit.owl"/>

diff --git a/src/ontology/components/imports-edit.owl b/src/ontology/components/imports-edit.owl
@@ -10,10 +10,9 @@ Prefix(dcterms:=<http://purl.org/dc/terms/>)
 
 
 Ontology(<https://w3id.org/pmd/co/components/imports-edit>
-Import(<https://w3id.org/pmd/co/pmdco/imports/bfo_import.owl>)
+Import(<http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl>)
 Import(<https://w3id.org/pmd/co/pmdco/imports/iao_import.owl>)
 Import(<https://w3id.org/pmd/co/pmdco/imports/obi_import.owl>)
-Import(<https://w3id.org/pmd/co/pmdco/imports/ro_import.owl>)
 
 ############################
 #   Annotation Properties
@@ -27,6 +26,8 @@ AnnotationAssertion(rdfs:label obo:IAO_0000114 "Hat Kurationsstatus"@de)
 
 
 
+AnnotationAssertion(owl:deprecated obo:BFO_0000050 "use the BFO2020 relations 'has continuant part' or 'has occurent part'")
+AnnotationAssertion(owl:deprecated obo:BFO_0000051 "use the BFO2020 relations 'has continuant part' or 'has occurent part'")
 AnnotationAssertion(obo:IAO_0000114 obo:IAO_0000117 obo:IAO_0000428)
 AnnotationAssertion(rdfs:label obo:IAO_0000117 "Begriffseditor"@de)
 AnnotationAssertion(rdfs:label obo:IAO_0000117 "Term Editor"@en)

diff --git a/src/ontology/components/imports-edit.properties b/src/ontology/components/imports-edit.properties
@@ -1,4 +1,4 @@
-#Wed Oct 23 10:30:54 CEST 2024
+#Tue Jan 28 14:50:15 CET 2025
 jdbc.password=
 jdbc.user=
 jdbc.url=

diff --git a/src/ontology/components/pmdco-axioms-shared.owl b/src/ontology/components/pmdco-axioms-shared.owl
@@ -25,7 +25,7 @@ Import(<https://w3id.org/pmd/co/qualities>)
 
 # Class: :PMD_0000852 (Metal)
 
-SubClassOf(:PMD_0000852 ObjectIntersectionOf(:PMD_0000632 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(:PMD_0020003 ObjectSomeValuesFrom(obo:RO_0000086 :PMD_0050002)))))
+SubClassOf(:PMD_0000852 ObjectIntersectionOf(:PMD_0000632 ObjectSomeValuesFrom(obo:BFO_0000051 ObjectIntersectionOf(:PMD_0020003 ObjectSomeValuesFrom(obo:BFO_0000196 :PMD_0050002)))))
 
 
 )
diff --git a/src/ontology/components/pmdco-characterization.owl b/src/ontology/components/pmdco-characterization.owl
@@ -84,14 +84,11 @@ Declaration(AnnotationProperty(skos:definition))
 Declaration(AnnotationProperty(skos:example))
 
 
+
 ############################
 #   Classes
 ############################
 
-# Class: obo:OBI_0200000 (data transformation)
-
-DisjointClasses(obo:OBI_0200000 :PMD_0001025)
-
 # Class: :PMD_0000507 (Akustische Eigenschaften Analyseverfahren)
 
 AnnotationAssertion(obo:IAO_0000117 :PMD_0000507 "PMDco Team")
@@ -309,7 +306,7 @@ AnnotationAssertion(skos:definition :PMD_0000656 "Ein Chromatographieverfahren,
 AnnotationAssertion(skos:example :PMD_0000656 "Gas chromatography is used to analyze the composition of volatile organic compounds in a polymer matrix."@en)
 SubClassOf(:PMD_0000656 :PMD_0000556)
 
-# Class: :PMD_0000658 (Gel Permeation Chromatography Process)
+# Class: :PMD_0000658 (Gel-Permeations-Chromatographie Verfahren)
 
 AnnotationAssertion(obo:IAO_0000117 :PMD_0000658 "PMDco Team")
 AnnotationAssertion(obo:IAO_0000119 :PMD_0000658 "chatgpt 4.o"@en)
@@ -440,7 +437,7 @@ AnnotationAssertion(skos:definition :PMD_0000836 "Ein Spektroskopie Verfahren, d
 AnnotationAssertion(skos:example :PMD_0000836 "Examples are e.g. time-of-flight mass spectroscopy, particle beam mass spectrometry."@en)
 SubClassOf(:PMD_0000836 :PMD_0000945)
 
-# Class: :PMD_0000849 (Mechanical Property Analyzing Process)
+# Class: :PMD_0000849 (Mechanische Eigenschaften Analyseverfahren)
 
 AnnotationAssertion(obo:IAO_0000117 :PMD_0000849 "PMDco Team")
 AnnotationAssertion(obo:IAO_0000119 :PMD_0000849 "chatgpt 4.o"@en)
@@ -480,7 +477,7 @@ AnnotationAssertion(skos:definition :PMD_0000867 "Ein Mechanische Eigenschaften
 AnnotationAssertion(skos:example :PMD_0000867 "Nanoindentation of thin films to evaluate their mechanical properties for use in microelectronic devices."@en)
 SubClassOf(:PMD_0000867 :PMD_0000849)
 
-# Class: :PMD_0000875 (Optische Mikroskopie)
+# Class: :PMD_0000875 (Optical Microscopy)
 
 AnnotationAssertion(obo:IAO_0000117 :PMD_0000875 "PMDco Team")
 AnnotationAssertion(obo:IAO_0000119 :PMD_0000875 "chatgpt 4.o"@en)
@@ -574,7 +571,7 @@ AnnotationAssertion(skos:definition :PMD_0000957 "An assay that examines the ext
 AnnotationAssertion(skos:definition :PMD_0000957 "Eine Analyse, die die äußere und innere Struktur und Morphologie von Materialien untersucht, einschließlich der Anordnung von Atomen, Kristallen, Körnern und Phasen, oft unter Verwendung von Techniken wie Mikroskopie und Beugung."@de)
 SubClassOf(:PMD_0000957 :PMD_0001025)
 
-# Class: :PMD_0000962 (Überkritische Fluidchromatographie Verfahren)
+# Class: :PMD_0000962 (Supercritical Fluid Chromatography Process)
 
 AnnotationAssertion(obo:IAO_0000117 :PMD_0000962 "PMDco Team")
 AnnotationAssertion(obo:IAO_0000119 :PMD_0000962 "chatgpt 4.o"@en)
@@ -763,7 +760,7 @@ AnnotationAssertion(rdfs:label :PMD_0001025 "Analyse"@de)
 AnnotationAssertion(rdfs:label :PMD_0001025 "assay"@en)
 AnnotationAssertion(skos:definition :PMD_0001025 "A planned process that has the objective to produce information about a material entity (the evaluant) by examining it."@en)
 AnnotationAssertion(skos:definition :PMD_0001025 "Ein geplanter Prozess, der das Ziel hat, Informationen über eine materielle Einheit (den Bewertungsgegenstand) zu gewinnen, indem er diese untersucht."@de)
-SubClassOf(:PMD_0001025 obo:OBI_0000011)
+SubClassOf(:PMD_0001025 ObjectIntersectionOf(obo:BFO_0000015 ObjectSomeValuesFrom(obo:BFO_0000055 :PMD_0000014)))
 
 
 )
diff --git a/src/ontology/components/pmdco-datatransformation.owl b/src/ontology/components/pmdco-datatransformation.owl
@@ -43,6 +43,7 @@ Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#definition>)
 Declaration(AnnotationProperty(<http://www.w3.org/2004/02/skos/core#example>))
 
 
+
 ############################
 #   Classes
 ############################
@@ -93,7 +94,7 @@ AnnotationAssertion(rdfs:label <https://w3id.org/pmd/co/PMD_0000583> "Datenverar
 AnnotationAssertion(rdfs:label <https://w3id.org/pmd/co/PMD_0000583> "Rechenprozess"@de)
 AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#definition> <https://w3id.org/pmd/co/PMD_0000583> "A planned process that involves the systematic use of computational methods and tools to perform simulations, analyses, or data transformations to achieve specific scientific or engineering goals."@en)
 AnnotationAssertion(<http://www.w3.org/2004/02/skos/core#definition> <https://w3id.org/pmd/co/PMD_0000583> "Ein geplanter Prozess, der die systematische Verwendung von rechnerischen Methoden und Werkzeugen umfasst, um Simulationen, Analysen oder Datenumwandlungen durchzuführen, um spezifische wissenschaftliche oder technische Ziele zu erreichen."@de)
-SubClassOf(<https://w3id.org/pmd/co/PMD_0000583> <http://purl.obolibrary.org/obo/OBI_0000011>)
+SubClassOf(<https://w3id.org/pmd/co/PMD_0000583> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000055> <https://w3id.org/pmd/co/PMD_0000014>)))
 
 # Class: <https://w3id.org/pmd/co/PMD_0000585> (Continuous Simulation)