working with onthologies

toardb/utils/TOARII_ontology.py

@@ -5,45 +5,120 @@ class TOAR_Ontology
 """
 
 import rdflib
-from rdflib.namespace import RDF, RDFS
-
-g = rdflib.Graph()
-result = g.parse("TOAR-II-Ontology_2020-11-24.owl",format='json-ld')
-#print("graph has %s statements." % len(g))
+from rdflib import URIRef, Literal
+from rdflib.namespace import RDF, RDFS, SKOS
 
 class TOAR_Ontology:
     """
-    some information
+    A class to represent the TOAR onthology.
+
+    ...
+
+    Attributes
+    ----------
+    filename : str
+        filename of file containing onthology (in json-ld-Format)
+
+    graph : Graph
+        onthology graph
+
+    Methods
+    -------
+    get_class(title):
+        find the onthology class for the given title
+
+    def show_class_definition(ont_class):
+        show information on given ontology class
+
+    show_entries(ont_class):
+        show information on given ontology class
+
+    def add_entry(self, ont_class, idcount, label, definition):
+        add entry to given ontology class
+
+    def check_entry(entry, ont_class):
+        check whether entry is a valid value of the ontology
+
+    print(format=""):
+        Prints the onthology in the given format
+
+    def save(self, filename):
+        save the onthology in json-ld format to the given file
     """
 
-    def get_class(title):
+    def __init__(self, filename):
+        """
+        initialize the onthology
+        """
+        self.filename = filename
+        g = rdflib.Graph()
+        self.graph = g.parse("TOAR-II-Ontology_2020-11-24.owl",format='json-ld')
+
+    def get_class(self, title):
         """
-        find the right class for the given title
+        find the onthology class for the given title
         """
-        for s, p, o in g.triples( (None,  RDF.type, rdflib.URIRef("http://www.w3.org/2002/07/owl#Class") ) ):
-            value = g.value(subject=s,predicate=RDFS.label)
+        for s, p, o in self.graph.triples( (None,  RDF.type, rdflib.URIRef("http://www.w3.org/2002/07/owl#Class") ) ):
+            value = self.graph.value(subject=s,predicate=RDFS.label)
+            print(f"value: {value}, title: {title}")
             if value and value.strip() == title.strip():
                 ont_class = s
         return ont_class
 
-    def show_entries(ont_class):
+    def show_class_definition(self, ont_class):
         """
         show information on given ontology class
         """
-        print(f"show information on '{ont_class}'")
-        for s, p, o in g.triples( (None,  RDF.type, ont_class ) ):
-            print("%s is %s"%(s, g.value(subject=s,predicate=RDFS.label)))
+        for s, p, o in self.graph.triples( (ont_class,  SKOS.definition, None) ):
+            print(f"definition of {ont_class}: {o}")
 
-    def check_entry(entry, ont_class):
+    def show_entries(self, ont_class):
+        """
+        show information on given ontology class
+        """
+        for s, p, o in self.graph.triples( (None,  RDF.type, ont_class ) ):
+            label=self.graph.value(subject=s,predicate=RDFS.label)
+            print(f"{s} is {label}")
+            for s, p, o in self.graph.triples( (s,  SKOS.definition, None) ):
+                print(f"definition of {label}: {o}")
+
+    def add_entry(self, ont_class, idcount, label, definition):
+        """
+        add entry to given ontology class
+        """
+        print(f"add entry to '{ont_class}'")
+        s=URIRef(f"http://www.fz-juelich.de/ontologies/2020/ToarOntotology#OWLNamedIndividual_{idcount:06d}")
+        p=URIRef("http://www.w3.org/1999/02/22-rdf-syntax-ns#type")
+        o=URIRef(ont_class)
+        self.graph.add((s,p,o))
+        o=URIRef("http://www.w3.org/2002/07/owl#NamedIndividual")
+        self.graph.add((s,p,o))
+        self.graph.add((s,RDFS.label,Literal(label,lang="en")))
+        self.graph.add((s,SKOS.definition,Literal(definition)))
+
+    def check_entry(self, entry, ont_class):
         """
         check whether entry is a valid value of the ontology
         """
         found=False
-        for s, p, o in g.triples( (None,  RDF.type, ont_class ) ):
-            if g.value(subject=s,predicate=RDFS.label).strip() == entry:
+        for s, p, o in self.graph.triples( (None,  RDF.type, ont_class ) ):
+            if self.graph.value(subject=s,predicate=RDFS.label).strip() == entry:
                 found=True
         return found
 
+    def print(self, format='json-ld'):
+        """
+        print the onthology in the given format
+        """
+        print(self.graph.serialize(format=format).decode("utf-8"))
+
+    def save(self, filename):
+        """
+        save the onthology in json-ld format to the given file
+        """
+        outfile = open(filename,'w')
+        outfile.write(self.graph.serialize(format='json-ld').decode("utf-8"))
+
 #       #check_entry would have been nicer, if something like this worked:
 #       subj2 = rdflib.URIRef("http://www.fz-juelich.de/ontologies/2020/ToarOntotology#OWLNamedIndividual_000141")
 #       pred2 = RDFS.label

toardb/utils/onto_example.py

+import TOARII_ontology
+help(TOARII_ontology)
+onto=TOARII_ontology.TOAR_Ontology('TOAR-II-Ontology_2020-11-24.owl')
+help(onto)
+onto.print()
+onto.print(format="turtle")
+onto.print(format='application/rdf+xml')
+dlclass=onto.get_class('Station Dominant Landcover Type')
+onto.show_class_definition(dlclass)
+onto.show_entries(dlclass)
+onto.check_entry('Croplands',dlclass)
+onto.check_entry('Craplands',dlclass)
+czclass=onto.get_class('Climatic Zone')
+onto.show_class_definition(czclass)
+onto.show_entries(czclass)
+onto.check_entry('PolarMoist',czclass)
+onto.check_entry('PolarWet',czclass)
+onto=TOARII_ontology.TOAR_Ontology('TOAR-Ontology-TimeZone-CountryCode.owl')
+dlclass=onto.get_class('Station Dominant Landcover Type')
+onto.show_class_definition(dlclass)
+onto.show_entries(dlclass)
+ccclass=onto.get_class('Country Code')
+ccclass=onto.get_class('Country Code')
+onto.show_class_definition(ccclass)
+onto.show_entries(ccclass)
+#highest index of NamedInvidual is 194
+#==> start counting from here
+onto.add_entry(ccclass,195,"GB","United Kingdom of Great Britain and Northern Ireland")
+onto.show_entries(ccclass)
+onto.save('TOAR-II-Ontology_2021-01-26.owl')