Merge branch 'main' into Zack-83-patch-2

NFDI4Chem · Nov 11, 2024 · bef4fc5 · bef4fc5
2 parents 85c9f71 + 5209a26
commit bef4fc5
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Showing 34 changed files with 5,910 additions and 10,049 deletions.
diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml
@@ -19,7 +19,7 @@ jobs:
   ontology_qc:
     # The type of runner that the job will run on
     runs-on: ubuntu-latest
-    container: obolibrary/odkfull:v1.5
+    container: obolibrary/odkfull:v1.5.2
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:

diff --git a/docs/images/VIBSO_Raman_Tbox.png b/docs/images/VIBSO_Raman_Tbox.png
diff --git a/docs/images/VIBSO_T-Box_graph_views.drawio b/docs/images/VIBSO_T-Box_graph_views.drawio
diff --git a/docs/images/VIBSO_T-Box_graph_views.drawio.html b/docs/images/VIBSO_T-Box_graph_views.drawio.html
diff --git a/docs/images/VIBSO_TBox_graph_views.html b/docs/images/VIBSO_TBox_graph_views.html
diff --git a/src/ontology/Makefile b/src/ontology/Makefile
@@ -1,7 +1,7 @@
 # ----------------------------------------
 # Makefile for vibso
 # Generated using ontology-development-kit
-# ODK Version: v1.5
+# ODK Version: v1.5.2
 # ----------------------------------------
 # IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use vibso.Makefile instead
 
@@ -45,8 +45,8 @@ REPORT_LABEL =              -l true
 REPORT_PROFILE_OPTS =       
 OBO_FORMAT_OPTIONS =        
 SPARQL_VALIDATION_CHECKS =  owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties 
-SPARQL_EXPORTS =            basic-report edges xrefs obsoletes synonyms 
-ODK_VERSION_MAKEFILE =      v1.5
+SPARQL_EXPORTS =            basic-report class-count-by-prefix edges xrefs obsoletes synonyms 
+ODK_VERSION_MAKEFILE =      v1.5.2
 
 TODAY ?=                    $(shell date +%Y-%m-%d)
 OBODATE ?=                  $(shell date +'%d:%m:%Y %H:%M')

diff --git a/src/ontology/components/vibso_classes.owl b/src/ontology/components/vibso_classes.owl
diff --git a/src/ontology/components/vibso_examples.owl b/src/ontology/components/vibso_examples.owl
@@ -24,11 +24,11 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_examples.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2024-02-01/components/vibso_examples.owl>
+<http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/components/vibso_examples.owl>
 Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_examples.tsv' template.")
 
+Declaration(Class(obo:CHMO_0000656))
 Declaration(Class(obo:CHMO_0001235))
-Declaration(Class(obo:CHMO_0002515))
 Declaration(Class(obo:IAO_0000027))
 Declaration(Class(obo:OBI_0000441))
 Declaration(Class(obo:OBI_0000747))
@@ -44,8 +44,8 @@ Declaration(ObjectProperty(obo:OBI_0000299))
 Declaration(ObjectProperty(obo:OBI_0000417))
 Declaration(ObjectProperty(obo:OBI_0001927))
 Declaration(ObjectProperty(obo:OBI_0001938))
+Declaration(ObjectProperty(obo:RO_0000058))
 Declaration(ObjectProperty(obo:RO_0000080))
-Declaration(ObjectProperty(obo:RO_0002566))
 Declaration(ObjectProperty(obo:STATO_0000102))
 Declaration(DataProperty(obo:OBI_0002135))
 Declaration(NamedIndividual(obo:UO_0000018))
@@ -85,7 +85,7 @@ ClassAssertion(obo:CHMO_0001235 ex:_Raman_Spectrometer_1)
 
 AnnotationAssertion(dcterms:description ex:_Raman_Spectroscopy_1 "The Raman spectroscopy in which _Sample_1 is being assayed according to _Raman_Spectroscopy_Method_1 in order to achieve _Raman_Spectrum_Objective_1."@en)
 AnnotationAssertion(rdfs:label ex:_Raman_Spectroscopy_1 "_Raman_Spectroscopy_1"@en)
-ClassAssertion(obo:CHMO_0002515 ex:_Raman_Spectroscopy_1)
+ClassAssertion(obo:CHMO_0000656 ex:_Raman_Spectroscopy_1)
 ObjectPropertyAssertion(obo:OBI_0000293 ex:_Raman_Spectroscopy_1 ex:_Raman_Spectrometer_1)
 ObjectPropertyAssertion(obo:OBI_0000293 ex:_Raman_Spectroscopy_1 ex:_Sample_1)
 ObjectPropertyAssertion(obo:OBI_0000293 ex:_Raman_Spectroscopy_1 ex:_Wavelength_Setting_Info_1)
@@ -128,7 +128,7 @@ AnnotationAssertion(dcterms:description ex:_Wavelength_Setting_Info_1 "The infor
 AnnotationAssertion(rdfs:label ex:_Wavelength_Setting_Info_1 "_Wavelength_Setting_Info_1"@en)
 ClassAssertion(obo:VIBSO_0000013 ex:_Wavelength_Setting_Info_1)
 ObjectPropertyAssertion(obo:OBI_0001938 ex:_Wavelength_Setting_Info_1 ex:_Wavelength_Value_Specification_1)
-ObjectPropertyAssertion(obo:RO_0002566 ex:_Wavelength_Setting_Info_1 ex:_Laser_Wavelength_1)
+ObjectPropertyAssertion(obo:RO_0000058 ex:_Wavelength_Setting_Info_1 ex:_Laser_Wavelength_1)
 
 # Individual: ex:_Wavelength_Value_Specification_1 (_Wavelength_Value_Specification_1)
 

diff --git a/src/ontology/components/vibso_examples.ttl b/src/ontology/components/vibso_examples.ttl
@@ -24,7 +24,7 @@
 @base <http://purl.obolibrary.org/obo/vibso/components/vibso_examples.owl> .
 
 <http://purl.obolibrary.org/obo/vibso/components/vibso_examples.owl> rdf:type owl:Ontology ;
-                                                                      owl:versionIRI <http://purl.obolibrary.org/obo/vibso/releases/2024-02-01/components/vibso_examples.owl> ;
+                                                                      owl:versionIRI <http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/components/vibso_examples.owl> ;
                                                                       rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_examples.tsv' template." .
 
 #################################################################
@@ -71,12 +71,12 @@ obo:OBI_0001927 rdf:type owl:ObjectProperty .
 obo:OBI_0001938 rdf:type owl:ObjectProperty .
 
 
-###  http://purl.obolibrary.org/obo/RO_0000080
-obo:RO_0000080 rdf:type owl:ObjectProperty .
+###  http://purl.obolibrary.org/obo/RO_0000058
+obo:RO_0000058 rdf:type owl:ObjectProperty .
 
 
-###  http://purl.obolibrary.org/obo/RO_0002566
-obo:RO_0002566 rdf:type owl:ObjectProperty .
+###  http://purl.obolibrary.org/obo/RO_0000080
+obo:RO_0000080 rdf:type owl:ObjectProperty .
 
 
 ###  http://purl.obolibrary.org/obo/STATO_0000102
@@ -95,12 +95,12 @@ obo:OBI_0002135 rdf:type owl:DatatypeProperty .
 #    Classes
 #################################################################
 
-###  http://purl.obolibrary.org/obo/CHMO_0001235
-obo:CHMO_0001235 rdf:type owl:Class .
+###  http://purl.obolibrary.org/obo/CHMO_0000656
+obo:CHMO_0000656 rdf:type owl:Class .
 
 
-###  http://purl.obolibrary.org/obo/CHMO_0002515
-obo:CHMO_0002515 rdf:type owl:Class .
+###  http://purl.obolibrary.org/obo/CHMO_0001235
+obo:CHMO_0001235 rdf:type owl:Class .
 
 
 ###  http://purl.obolibrary.org/obo/IAO_0000027
@@ -156,7 +156,7 @@ ex:_Raman_Spectrometer_1 rdf:type owl:NamedIndividual ,
 
 ###  https://example.instances/_Raman_Spectroscopy_1
 ex:_Raman_Spectroscopy_1 rdf:type owl:NamedIndividual ,
-                                  obo:CHMO_0002515 ;
+                                  obo:CHMO_0000656 ;
                          obo:OBI_0000293 ex:_Raman_Spectrometer_1 ,
                                          ex:_Sample_1 ,
                                          ex:_Wavelength_Setting_Info_1 ;
@@ -204,7 +204,7 @@ ex:_Sample_1 rdf:type owl:NamedIndividual ,
 ex:_Wavelength_Setting_Info_1 rdf:type owl:NamedIndividual ,
                                        obo:VIBSO_0000013 ;
                               obo:OBI_0001938 ex:_Wavelength_Value_Specification_1 ;
-                              obo:RO_0002566 ex:_Laser_Wavelength_1 ;
+                              obo:RO_0000058 ex:_Laser_Wavelength_1 ;
                               dcterms:description "The information that determines the wavelength of the laser of _Raman_Spectrometer_1 which is used to excite the sample. This information gets encoded by the _Laser_Value_Specification_1."@en ;
                               rdfs:label "_Wavelength_Setting_Info_1"@en .
 
@@ -219,4 +219,4 @@ ex:_Wavelength_Value_Specification_1 rdf:type owl:NamedIndividual ,
                                      rdfs:label "_Wavelength_Value_Specification_1"@en .
 
 
-###  Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi
+###  Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi
diff --git a/src/ontology/components/vibso_object_properties.owl b/src/ontology/components/vibso_object_properties.owl
@@ -24,7 +24,7 @@ Prefix(Wikipedia:=<https://en.wikipedia.org/wiki/>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/components/vibso_object_properties.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2024-01-31/components/vibso_object_properties.owl>
+<http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/components/vibso_object_properties.owl>
 Annotation(rdfs:comment "This component is derived from the manually edited 'src/templates/vibso_object_properties.tsv' template.")
 
 

diff --git a/src/ontology/imports/bfo_import.owl b/src/ontology/imports/bfo_import.owl
@@ -7,9 +7,9 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/imports/bfo_import.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2023-12-20/imports/bfo_import.owl>
+<http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/imports/bfo_import.owl>
 Annotation(<http://purl.org/dc/elements/1.1/source> <http://purl.obolibrary.org/obo/bfo/2019-08-26/bfo.owl>)
-Annotation(owl:versionInfo "2023-12-20")
+Annotation(owl:versionInfo "2024-09-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))
 Declaration(Class(<http://purl.obolibrary.org/obo/BFO_0000002>))

diff --git a/src/ontology/imports/chebi_import.owl b/src/ontology/imports/chebi_import.owl
@@ -7,12 +7,13 @@ Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
 
 
 Ontology(<http://purl.obolibrary.org/obo/vibso/imports/chebi_import.owl>
-<http://purl.obolibrary.org/obo/vibso/releases/2023-12-20/imports/chebi_import.owl>
-Annotation(owl:versionInfo "2023-12-20")
+<http://purl.obolibrary.org/obo/vibso/releases/2024-09-23/imports/chebi_import.owl>
+Annotation(owl:versionInfo "2024-09-23")
 
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_24431>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_59999>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_60004>))
+Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000087>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000115>))
 Declaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0000231>))