docs: add example ontology import NFDI MatWerk

Author: SimonStier

examples/ontology_import_mwo.py

@@ -0,0 +1,250 @@
+import os
+
+from osw.auth import CredentialManager
+from osw.core import model
+from osw.express import OswExpress
+from osw.ontology import ImportConfig, OntologyImporter, ParserSettings
+
+# Use credentials from file. if none are found, the user will be prompted to enter them
+cm = CredentialManager(
+    cred_filepath=os.path.join(
+        os.path.dirname(os.path.abspath(__file__)), "accounts.pwd.yaml"
+    )
+)
+# Create the OSW object
+# Set a local password in you user settings when using SSO login (e.g. ORCID)
+osw_obj = OswExpress(domain="demo.open-semantic-lab.org", cred_mngr=cm)
+# Load the required schemas / data classes
+DEPENDENCIES = {
+    # "OwlClass": "Category:OSW725a3cf5458f4daea86615fcbd0029f8",
+    "OwlIndividual": "Category:OSW6b9ef2784a934b8ab96523366e23e906",
+    "OwlOntology": "Category:OSW662db0a2ad0946148422245f84e82f64",
+    "EmmoClass": "Category:OSW57beed5e1294434ba77bb6516e461456",
+    "Item": "Category:Item",
+    "ObjectProperty": "Category:ObjectProperty",
+    "DataProperty": "Category:DataProperty",
+    "AnnotationProperty": "Category:AnnotationProperty",
+}
+osw_obj.install_dependencies(DEPENDENCIES, mode="append")  # , policy="if-missing")
+
+ontology_name = "MWO"
+
+# Define ontology metadata
+mwo = model.OwlOntology(
+    name="MWO",
+    label=[model.Label(text="MWO", lang="en")],
+    iri="http://purls.helmholtz-metadaten.de/mwo",
+    prefix="http://purls.helmholtz-metadaten.de/mwo/",
+    prefix_name="mwo",
+    see_also=["https://ise-fizkarlsruhe.github.io/mwo"],
+)
+pmdco = model.OwlOntology(
+    name="PMDco",
+    label=[model.Label(text="PMDco", lang="en")],
+    iri="https://w3id.org/pmd/co",
+    prefix="https://w3id.org/pmd/co/",
+    prefix_name="pmdco",
+    see_also=["https://w3id.org/pmd/co"],
+)
+nfdi = model.OwlOntology(
+    name="NFDI",
+    label=[model.Label(text="NFDI Ontology", lang="en")],
+    iri="https://nfdi.fiz-karlsruhe.de/ontology",
+    prefix="https://nfdi.fiz-karlsruhe.de/ontology/",
+    prefix_name="nfdicore",
+    see_also=["https://nfdi.fiz-karlsruhe.de/ontology"],
+)
+owl = model.OwlOntology(
+    name="OWL",
+    label=[model.Label(text="Web Ontology Language", lang="en")],
+    iri="http://www.w3.org/2002/07/owl",
+    prefix="http://www.w3.org/2002/07/owl#",
+    prefix_name="owl",
+    see_also=["http://www.w3.org/2002/07/owl"],
+)
+schema = model.OwlOntology(
+    name="Schema.org",
+    label=[model.Label(text="Schema.org", lang="en")],
+    iri="http://schema.org/",
+    prefix="http://schema.org/",
+    prefix_name="schema",
+    see_also=["http://schema.org/"],
+)
+skos = model.OwlOntology(
+    name="SKOS",
+    label=[model.Label(text="Simple Knowledge Organization System", lang="en")],
+    iri="http://www.w3.org/2004/02/skos/core",
+    prefix="http://www.w3.org/2004/02/skos/core#",
+    prefix_name="skos",
+    see_also=["http://www.w3.org/2004/02/skos/core"],
+)
+foaf = model.OwlOntology(
+    name="FOAF",
+    label=[model.Label(text="Friend of a Friend", lang="en")],
+    iri="http://xmlns.com/foaf/0.1/",
+    prefix="http://xmlns.com/foaf/0.1/",
+    prefix_name="foaf",
+    see_also=["http://xmlns.com/foaf/0.1/"],
+)
+dc = model.OwlOntology(
+    name="DC",
+    label=[model.Label(text="Dublin Core", lang="en")],
+    iri="http://purl.org/dc/elements/1.1",
+    prefix="http://purl.org/dc/elements/1.1/",
+    prefix_name="dc",
+    see_also=["http://purl.org/dc"],
+)
+bibo = model.OwlOntology(
+    name="BIBO",
+    label=[model.Label(text="The Bibliographic Ontology", lang="en")],
+    iri="http://purl.org/ontology/bibo/",
+    prefix="http://purl.org/ontology/bibo/",
+    prefix_name="bibo",
+    see_also=["http://purl.org/ontology/bibo/"],
+)
+vann = model.OwlOntology(
+    name="VANN",
+    label=[model.Label(text="Vocabulary Annotation", lang="en")],
+    iri="http://purl.org/vocab/vann/",
+    prefix="http://purl.org/vocab/vann/",
+    prefix_name="vann",
+    see_also=["http://purl.org/vocab/vann/"],
+)
+adms = model.OwlOntology(
+    name="ADMS",
+    label=[model.Label(text="ADMS Ontology", lang="en")],
+    iri="http://www.w3.org/ns/adms",
+    prefix="http://www.w3.org/ns/adms#",
+    prefix_name="adms",
+    see_also=["http://www.w3.org/ns/adms#"],
+)
+dcat = model.OwlOntology(
+    name="DCAT",
+    label=[model.Label(text="Data Catalog Vocabulary", lang="en")],
+    iri="http://www.w3.org/ns/dcat",
+    prefix="http://www.w3.org/ns/dcat#",
+    prefix_name="dcat",
+    see_also=["http://www.w3.org/ns/dcat#"],
+)
+dcterms = model.OwlOntology(
+    name="DCTerms",
+    label=[model.Label(text="Dublin Core Terms", lang="en")],
+    iri="http://purl.org/dc/terms",
+    prefix="http://purl.org/dc/terms/",
+    prefix_name="dct",
+    see_also=["http://purl.org/dc/terms"],
+)
+doap = model.OwlOntology(
+    name="DOAP",
+    label=[model.Label(text="Description of a Project", lang="en")],
+    iri="http://usefulinc.com/ns/doap",
+    prefix="http://usefulinc.com/ns/doap#",
+    prefix_name="doap",
+    see_also=["http://usefulinc.com/ns/doap"],
+)
+edam = model.OwlOntology(
+    name="EDAM",
+    label=[model.Label(text="EDAM Ontology", lang="en")],
+    iri="http://edamontology.org",
+    prefix="http://edamontology.org/",
+    prefix_name="edam",
+    see_also=["http://edamontology.org"],
+)
+edam_obo = model.OwlOntology(
+    name="EDAM-OBO",
+    label=[model.Label(text="EDAM Ontology (OBO)", lang="en")],
+    iri="http://purl.obolibrary.org/obo/edam",
+    prefix="http://purl.obolibrary.org/obo/edam#",
+    prefix_name="edamobo",
+    see_also=["http://edamontology.org"],
+)
+bfo = model.OwlOntology(
+    name="BFO",
+    label=[model.Label(text="Basic Formal Ontology", lang="en")],
+    iri="http://purl.obolibrary.org/obo/",
+    prefix="http://purl.obolibrary.org/obo/BFO_",
+    prefix_name="bfo",
+    see_also=["http://purl.obolibrary.org/obo/bfo"],
+)
+iao = model.OwlOntology(
+    name="IAO",
+    label=[model.Label(text="Information Artifact Ontology", lang="en")],
+    iri="http://purl.obolibrary.org/obo/",
+    prefix="http://purl.obolibrary.org/obo/IAO_",
+    prefix_name="iao",
+    see_also=["http://purl.obolibrary.org/obo/iao"],
+)
+omo = model.OwlOntology(
+    name="OMO",
+    label=[model.Label(text="Ontology for Media Objects", lang="en")],
+    iri="http://purl.obolibrary.org/obo/",
+    prefix="http://purl.obolibrary.org/obo/OMO_",
+    prefix_name="omo",
+    see_also=["http://purl.obolibrary.org/obo/omo"],
+)
+swo = model.OwlOntology(
+    name="SWO",
+    label=[model.Label(text="Software Ontology", lang="en")],
+    iri="http://ebi.ac.uk/swo",
+    prefix="http://ebi.ac.uk/swo/",
+    prefix_name="swo",
+    see_also=["http://ebi.ac.uk/swo/"],
+)
+obo_in_owl = model.OwlOntology(
+    name="OBOInOWL",
+    label=[model.Label(text="OBO In OWL", lang="en")],
+    iri="http://www.geneontology.org/formats/oboInOwl",
+    prefix="http://www.geneontology.org/formats/oboInOwl#",
+    prefix_name="obo_in_owl",
+    see_also=["http://www.geneontology.org/formats/oboInOwl"],
+)
+rdfs = model.OwlOntology(
+    name="RDFS",
+    label=[model.Label(text="RDF Schema", lang="en")],
+    iri="http://www.w3.org/2000/01/rdf-schema",
+    prefix="http://www.w3.org/2000/01/rdf-schema#",
+    prefix_name="rdfs",
+    see_also=["http://www.w3.org/2000/01/rdf-schema"],
+)
+
+import_config = ImportConfig(
+    ontology_name=ontology_name,
+    ontologies=[
+        mwo,
+        pmdco,
+        nfdi,
+        owl,
+        schema,
+        skos,
+        foaf,
+        dc,
+        bibo,
+        vann,
+        adms,
+        dcat,
+        dcterms,
+        doap,
+        edam,
+        edam_obo,
+        bfo,
+        obo_in_owl,
+        rdfs,
+        iao,
+        omo,
+        swo,
+    ],
+    file="https://raw.githubusercontent.com/ISE-FIZKarlsruhe/mwo/refs/heads/main/mwo.ttl",
+    base_class=model.OwlClass,
+    base_class_title="Category:OSW725a3cf5458f4daea86615fcbd0029f8",  # OwlClass
+    dump_files=True,
+    dump_path=os.path.dirname(os.path.abspath(__file__)),
+    dry_run=False,
+    change_id="84b563ec-4fd4-41da-8038-9cc4891fde85",
+)
+parser_settings = ParserSettings()
+parser_settings.ensure_array.append("elucidation")
+parser_settings.ensure_multilang.append("elucidation")
+
+# Import ontologies
+importer = OntologyImporter(osw=osw_obj, parser_settings=parser_settings)
+prefix_dict = importer.import_ontology(import_config)