Merge branch 'main' of github.com:wilkinsonlab/FLAIR-GG into main

SemanticModel/CSV/germplasm.csv

@@ -1,3 +1,3 @@
-bgvid,uniqid,org_name,collection_comment,accession_number,national_catalogue_code,WFO_idenfifier,lista_patron_identifier,WFO_vernacular_name,WFO_scientific_name,WFO_scientific_name_authorship,lista_patron_vernacular_name,lista_patron_scientific_name,lista_patron_scientific_name_authorship,WFO_determination_status,lista_patron_determination_status,lespre_endangerment_category,iucn_endangerment_category
+bgvid,uniqid,org_name,collection_comment,accession_number,national_catalogue_code,WFO_idenfifier,chosen_taxonomy_identifier,WFO_vernacular_name,WFO_scientific_name,WFO_scientific_name_authorship,chosen_taxonomy_vernacular_name,chosen_taxonomy_scientific_name,chosen_taxonomy_scientific_name_authorship,WFO_determination_status,chosen_taxonomy_determination_status,chosen_taxonomy_reference,chosen_taxonomy_reference_url,lespre_endangerment_category,iucn_endangerment_category
 bgv123,1234567,UPM BGV,"amazing collection",1234567,ES1234,
 

SemanticModel/YARRRML/germplasm_model.py

@@ -22,11 +22,11 @@
     ["this:$(uniqid)#Germplasm", "sio:SIO_000671", "this:$(uniqid)#Accession_number", "iri"],
     ["this:$(uniqid)#Germplasm", "sio:SIO_000671", "this:$(uniqid)#National_catalogue_code", "iri"],
     ["this:$(uniqid)#Germplasm", "prov:wasUsedBy", "this:$(uniqid)#Plant_determination_process_WFO", "iri"],
-    ["this:$(uniqid)#Germplasm", "prov:wasUsedBy", "this:$(uniqid)#Plant_determination_process_lista_patron", "iri"],
+    ["this:$(uniqid)#Germplasm", "prov:wasUsedBy", "this:$(uniqid)#Plant_determination_process_chosen_taxonomy", "iri"],
     ["this:$(uniqid)#Germplasm", "sio:SIO_000231", "this:$(uniqid)#Plant_determination_process_WFO", "iri"],
-    ["this:$(uniqid)#Germplasm", "sio:SIO_000231", "this:$(uniqid)#Plant_determination_process_lista_patron", "iri"],
+    ["this:$(uniqid)#Germplasm", "sio:SIO_000231", "this:$(uniqid)#Plant_determination_process_chosen_taxonomy", "iri"],
     ["this:$(uniqid)#Plant_determination_process_WFO", "sio:SIO_000229", "this:$(uniqid)#Plant_identification_WFO", "iri"],
-    ["this:$(uniqid)#Plant_determination_process_lista_patron", "sio:SIO_000229", "this:$(uniqid)#Plant_identification_lista_patron", "iri"],
+    ["this:$(uniqid)#Plant_determination_process_chosen_taxonomy", "sio:SIO_000229", "this:$(uniqid)#Plant_identification_chosen_taxonomy", "iri"],
     ["this:$(uniqid)#Germplasm", "prov:wasUsedBy", "this:$(uniqid)#Endangerment_assesment_process_LESPRE", "iri"],
     ["this:$(uniqid)#Germplasm", "sio:SIO_000231", "this:$(uniqid)#Endangerment_assesment_process_IUCN", "iri"],
     ["this:$(uniqid)#Germplasm", "prov:wasUsedBy", "this:$(uniqid)#Endangerment_assesment_process_LESPRE", "iri"],
@@ -56,33 +56,44 @@
 
     ["this:$(uniqid)#Plant_determination_process_WFO", "rdf:type", "prov:activity", "iri"],
     ["this:$(uniqid)#Plant_determination_process_WFO", "rdf:type", "sio:SIO_000006", "iri"],
-    ["this:$(uniqid)#Plant_determination_process_lista_patron", "rdf:type", "prov:activity", "iri"],
-    ["this:$(uniqid)#Plant_determination_process_lista_patron", "rdf:type", "sio:SIO_000006", "iri"],
+    ["this:$(uniqid)#Plant_determination_process_chosen_taxonomy", "rdf:type", "prov:activity", "iri"],
+    ["this:$(uniqid)#Plant_determination_process_chosen_taxonomy", "rdf:type", "sio:SIO_000006", "iri"],
 
     ["this:$(uniqid)#Plant_identification_WFO", "dwc:vernacularName", "$(WFO_vernacular_name)", "iri"],
     ["this:$(uniqid)#Plant_identification_WFO", "rdf:type", "dwc:Taxon", "iri"],
-    ["this:$(uniqid)#Plant_identification_WFO", "dwc:sientificName", "$(WFO_scientific_name)", "iri"],
+    ["this:$(uniqid)#Plant_identification_WFO", "dwc:sientificName", "this:$(uniqid)#WFO_scientific_name", "iri"],
     ["this:$(uniqid)#Plant_identification_WFO", "dwc:sientificNameAuthorship", "$(WFO_scientific_name_authorship)", "iri"],
 
-    ["this:$(uniqid)#Plant_identification_lista_patron", "dwc:vernacularName", "$(lista_patron_vernacular_name)", "iri"],
-    ["this:$(uniqid)#Plant_identification_lista_patron", "rdf:type", "dwc:Taxon", "iri"],
-    ["this:$(uniqid)#Plant_identification_lista_patron", "dwc:sientificName", "$(lista_patron_scientific_name)", "iri"],
-    ["this:$(uniqid)#Plant_identification_lista_patron", "dwc:sientificNameAuthorship", "$(lista_patron_scientific_name_authorship)", "iri"],
+    ["this:$(uniqid)#WFO_scientific_name", "rdf:type", "dwc:scientificName", "iri"],
+    ["this:$(uniqid)#WFO_scientific_name", "sio:SIO_000300", "$(WFO_scientific_name)", "xsd:string"],
+    ["this:$(uniqid)#WFO_scientific_name", "dwc:nameAccordingTo", "WFO (2024): World Flora Online. Published on the Internet;http://www.worldfloraonline.org", "xsd:string"],
+    ["this:$(uniqid)#WFO_scientific_name", "dwc:nameAccordingToID", "https://www.worldfloraonline.org/", "iri"],
 
-    ["this:$(uniqid)#Plant_identification_lista_patron", "sio:SIO_000671", "this:$(uniqid)#Lista_patron_identifier", "iri"],
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "dwc:vernacularName", "$(chosen_taxonomy_vernacular_name)", "iri"],
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "rdf:type", "dwc:Taxon", "iri"],
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "dwc:sientificName", "this:$(uniqid)#Chosen_taxonomy_scientific_name", "iri"],
+
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "dwc:sientificNameAuthorship", "$(chosen_taxonomy_scientific_name_authorship)", "iri"],
+
+    ["this:$(uniqid)#Chosen_taxonomy_scientific_name", "rdf:type", "dwc:scientificName", "iri"],
+    ["this:$(uniqid)#Chosen_taxonomy_scientific_name", "sio:SIO_000300", "$(chosen_taxonomy_scientific_name)", "xsd:string"],
+    ["this:$(uniqid)#Chosen_taxonomy_scientific_name", "dwc:nameAccordingTo", "$(chosen_taxonomy_reference)", "xsd:string"],
+    ["this:$(uniqid)#Chosen_taxonomy_scientific_name", "dwc:nameAccordingToID", "$(chosen_taxonomy_reference_url)", "iri"],
+
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "sio:SIO_000671", "this:$(uniqid)#chosen_taxonomy_identifier", "iri"],
     ["this:$(uniqid)#Plant_identification_WFO", "sio:SIO_000671", "this:$(uniqid)#WFO_identifier", "iri"],
 
-    ["this:$(uniqid)#Lista_patron_identifier", "rdf:type", "sio:SIO_000115", "iri"],
+    ["this:$(uniqid)#chosen_taxonomy_identifier", "rdf:type", "sio:SIO_000115", "iri"],
     ["this:$(uniqid)#WFO_identifier", "rdf:type", "sio:SIO_000115", "iri"],
-    ["this:$(uniqid)#Lista_patron_identifier", "sio:SIO_000300", "$(lista_patron_identifier)", "xsd:string"],
+    ["this:$(uniqid)#chosen_taxonomy_identifier", "sio:SIO_000300", "$(chosen_taxonomy_identifier)", "xsd:string"],
     ["this:$(uniqid)#WFO_identifier", "sio:SIO_000300", "$(WFO_identifier)", "xsd:string"],
 
-    ["this:$(uniqid)#Plant_identification_lista_patron", "sio:SIO_000008", "this:$(uniqid)#Determination_status_lista_patron", "iri"],
+    ["this:$(uniqid)#Plant_identification_chosen_taxonomy", "sio:SIO_000008", "this:$(uniqid)#Determination_status_chosen_taxonomy", "iri"],
     ["this:$(uniqid)#Plant_identification_WFO", "sio:SIO_000008", "this:$(uniqid)#Determination_status_WFO", "iri"],
 
-    ["this:$(uniqid)#Determination_status_lista_patron", "rdf:type", "fao:determination_status", "iri"],
+    ["this:$(uniqid)#Determination_status_chosen_taxonomy", "rdf:type", "fao:determination_status", "iri"],
     ["this:$(uniqid)#Determination_status_WFO", "rdf:type", "fao:determination_status", "iri"],
-    ["this:$(uniqid)#Determination_status_lista_patron", "sio:SIO_000300", "$(lista_patron_determination_status)", "xsd:string"],
+    ["this:$(uniqid)#Determination_status_chosen_taxonomy", "sio:SIO_000300", "$(chosen_taxonomy_determination_status)", "xsd:string"],
     ["this:$(uniqid)#Determination_status_WFO", "sio:SIO_000300", "$(WFO_determination_status)", "xsd:string"],
 
     ["this:$(uniqid)#Endangerment_assesment_process_LESPRE", "rdf:type", "sio:SIO_000006", "iri"],