Add additional shortcuts for ontology construction

pyproject.toml

@@ -71,7 +71,7 @@ dependencies = [
     "cachier",
     "pystow>=0.7.0",
     "bioversions>=0.8.44",
-    "bioregistry>=0.12.27",
+    "bioregistry>=0.12.30",
     "bioontologies>=0.7.2",
     "ssslm>=0.0.13",
     "zenodo-client>=0.3.6",

src/pyobo/struct/struct.py

@@ -939,10 +939,21 @@ def _iterate_property_pairs(self) -> Iterable[Annotation]:
                 license_literal = OBOLiteral.string(license_spdx_id)
             yield Annotation(v.has_license, license_literal)
 
-        # Description
         if description := bioregistry.get_description(self.ontology):
             description = obo_escape_slim(description.strip())
             yield Annotation(v.has_description, OBOLiteral.string(description.strip()))
+        if homepage := bioregistry.get_homepage(self.ontology):
+            yield Annotation(v.has_homepage, OBOLiteral.uri(homepage))
+        if repository := bioregistry.get_repository(self.ontology):
+            yield Annotation(v.has_repository, OBOLiteral.uri(repository))
+        if logo := bioregistry.get_logo(self.ontology):
+            yield Annotation(v.has_logo, OBOLiteral.uri(logo))
+        if mailing_list := bioregistry.get_mailing_list(self.ontology):
+            yield Annotation(v.has_mailing_list, OBOLiteral.string(mailing_list))
+        if maintainer_orcid := bioregistry.get_contact_orcid(self.ontology):
+            yield Annotation(
+                v.has_maintainer, Reference(prefix="orcid", identifier=maintainer_orcid)
+            )
 
         # Root terms
         for root_term in self.root_terms or []:
@@ -2281,6 +2292,7 @@ class AdHocOntologyBase(Obo):
 
 def build_ontology(
     prefix: str,
+    *,
     terms: list[Term] | None = None,
     synonym_typedefs: list[SynonymTypeDef] | None = None,
     typedefs: list[TypeDef] | None = None,
@@ -2291,12 +2303,58 @@ def build_ontology(
     subsetdefs: list[tuple[Reference, str]] | None = None,
     properties: list[Annotation] | None = None,
     imports: list[str] | None = None,
+    description: str | None = None,
+    homepage: str | None = None,
+    mailing_list: str | None = None,
+    logo: str | None = None,
+    repository: str | None,
 ) -> Obo:
     """Build an ontology from parts."""
     resource = bioregistry.get_resource(prefix, strict=True)
     if name is None:
         name = resource.get_name()
     # TODO auto-populate license and other properties
+
+    if properties is None:
+        properties = []
+    if typedefs is None:
+        typedefs = []
+
+    if description:
+        from .typedef import has_description
+
+        properties.append(Annotation.string(has_description.reference, description))
+        if has_description not in typedefs:
+            typedefs.append(has_description)  # TODO get proper typedef
+
+    if homepage:
+        from .typedef import has_homepage
+
+        properties.append(Annotation.uri(has_homepage.reference, homepage))
+        if has_homepage not in typedefs:
+            typedefs.append(has_homepage)
+
+    if logo:
+        from .typedef import has_depiction
+
+        properties.append(Annotation.uri(has_depiction.reference, logo))
+        if has_depiction not in typedefs:
+            typedefs.append(has_depiction)
+
+    if mailing_list:
+        from .typedef import has_mailing_list
+
+        properties.append(Annotation.string(has_mailing_list.reference, mailing_list))
+        if has_mailing_list not in typedefs:
+            typedefs.append(has_mailing_list)
+
+    if repository:
+        from .typedef import has_repository
+
+        properties.append(Annotation.uri(has_repository.reference, repository))
+        if has_repository not in typedefs:
+            typedefs.append(has_repository)
+
     return make_ad_hoc_ontology(
         _ontology=prefix,
         _name=name,

src/pyobo/struct/struct_utils.py

@@ -63,6 +63,16 @@ def float(cls, predicate: Reference, value: float) -> Self:
         """Return a literal property for a float."""
         return cls(predicate, OBOLiteral.float(value))
 
+    @classmethod
+    def uri(cls, predicate: Reference, uri: str) -> Self:
+        """Return a literal property for a URI."""
+        return cls(predicate, OBOLiteral.uri(uri))
+
+    @classmethod
+    def string(cls, predicate: Reference, value: str, *, language: str | None = None) -> Self:
+        """Return a literal property for a float."""
+        return cls(predicate, OBOLiteral.string(value, language=language))
+
     @staticmethod
     def _sort_key(x: Annotation):
         return x.predicate, _reference_or_literal_key(x.value)

src/pyobo/struct/typedef.py

@@ -31,6 +31,7 @@
     "has_gene_product",
     "has_homepage",
     "has_inchi",
+    "has_mailbox",
     "has_mature",
     "has_member",
     "has_part",
@@ -266,13 +267,11 @@
 
 has_inchi = TypeDef(reference=v.has_inchi, is_metadata_tag=True).append_xref(v.debio_has_inchi)
 
-has_homepage = TypeDef(
-    reference=Reference(prefix="foaf", identifier="homepage", name="homepage"), is_metadata_tag=True
-)
-has_depiction = TypeDef(
-    reference=Reference(prefix="foaf", identifier="depicted_by", name="depicted by"),
-    is_metadata_tag=True,
-)
+has_homepage = TypeDef(reference=v.has_homepage, is_metadata_tag=True)
+has_depiction = TypeDef(reference=v.has_depiction, is_metadata_tag=True)
+has_mailbox = TypeDef(reference=v.has_mailbox, is_metadata_tag=True)
+has_mailing_list = TypeDef(reference=v.has_mailing_list, is_metadata_tag=True)
+has_repository = TypeDef(reference=v.has_repository, is_metadata_tag=True)
 
 has_category = TypeDef(
     reference=Reference(prefix="biolink", identifier="category", name="has category"),

src/pyobo/struct/vocabulary.py

@@ -90,6 +90,14 @@ def _c(c: curies.Reference) -> Reference:
 has_license = _c(_v.has_license)
 has_title = _c(_v.has_title)
 
+has_homepage = Reference(prefix="foaf", identifier="homepage", name="has homepage")
+has_logo = Reference(prefix="foaf", identifier="logo", name="has logo")
+has_mailbox = Reference(prefix="foaf", identifier="mbox", name="has mailbox")
+has_depiction = Reference(prefix="foaf", identifier="depicted_by", name="depicted by")
+has_repository = Reference(prefix="doap", identifier="repository", name="has repository")
+has_mailing_list = Reference(prefix="doap", identifier="mailing-list", name="has mailing list")
+has_maintainer = Reference(prefix="doap", identifier="maintainer", name="has maintainer")
+
 has_part = Reference(prefix=BFO_PREFIX, identifier="0000051", name="has part")
 part_of = Reference(prefix=BFO_PREFIX, identifier="0000050", name="part of")
 orthologous = Reference(

src/pyobo/utils/misc.py

@@ -15,8 +15,11 @@
 VERSION_REWRITES = {
     "$Date: 2009/11/15 10:54:12 $": "2009-11-15",  # for owl
     "http://www.w3.org/2006/time#2016": "2016",  # for time
+    "https://purl.org/ontology/modalia#1.0.0": "1.0.0",  # for dalia
+}
+STATIC_VERSION_REWRITES = {
+    "orth": "2",
 }
-STATIC_VERSION_REWRITES = {"orth": "2"}
 VERSION_PREFIXES = [
     "http://www.orpha.net/version",
     "https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_",

tests/test_obo_reader/test_reader.py

@@ -27,6 +27,8 @@
     "for synonyms fails on the open squiggly bracket {"
 )
 
+ADNAN_MALIK = Reference(prefix="orcid", identifier="0000-0001-8123-5351")
+
 
 class TestUtils(unittest.TestCase):
     """Test utilities for the reader."""
@@ -1361,5 +1363,9 @@ def test_get_references(self) -> None:
             std1.prefix: {std1},
             "dcterms": {v.has_description, v.has_license, v.has_title},
             v.has_dbxref.prefix: {v.has_exact_synonym},
+            # these get automatically added
+            "doap": {v.has_maintainer, v.has_repository},
+            "foaf": {v.has_homepage, v.has_logo},
+            "orcid": {ADNAN_MALIK},
         }
         self.assertEqual(expected_references, ontology._get_references())

tests/test_struct/test_obo/test_struct_obo.py

@@ -160,9 +160,16 @@ def test_18_properties_bioregistry(self) -> None:
             """\
             format-version: 1.4
             idspace: dcterms http://purl.org/dc/terms/ "Dublin Core Metadata Initiative Terms"
+            idspace: doap http://usefulinc.com/ns/doap# "Description of a Project"
+            idspace: foaf http://xmlns.com/foaf/0.1/ "Friend of a Friend"
+            idspace: orcid https://orcid.org/ "Open Researcher and Contributor"
             ontology: go
             property_value: dcterms:license "CC-BY-4.0" xsd:string
             property_value: dcterms:description "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism." xsd:string
+            property_value: foaf:homepage "http\\://geneontology.org/" xsd:anyURI
+            property_value: doap:repository "https\\://github.com/geneontology/go-ontology" xsd:anyURI
+            property_value: foaf:logo "https\\://obofoundry.org/images/go_logo.png" xsd:anyURI
+            property_value: doap:maintainer orcid:0000-0001-6787-2901
             """,
             ontology,
         )

tests/test_struct/test_ofn/test_obo_to_ofn.py

@@ -48,11 +48,14 @@ def test_simple_conversion(self) -> None:
         self.assertEqual(
             dedent("""\
                 Prefix(dcterms:=<http://purl.org/dc/terms/>)
+                Prefix(doap:=<http://usefulinc.com/ns/doap#>)
+                Prefix(foaf:=<http://xmlns.com/foaf/0.1/>)
                 Prefix(GO:=<http://purl.obolibrary.org/obo/GO_>)
                 Prefix(IAO:=<http://purl.obolibrary.org/obo/IAO_>)
                 Prefix(obo:=<http://purl.obolibrary.org/obo/>)
                 Prefix(oboInOwl:=<http://www.geneontology.org/formats/oboInOwl#>)
                 Prefix(OMO:=<http://purl.obolibrary.org/obo/OMO_>)
+                Prefix(orcid:=<https://orcid.org/>)
                 Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
                 Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
                 Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)
@@ -62,6 +65,10 @@ def test_simple_conversion(self) -> None:
                 Annotation(dcterms:title "Gene Ontology"^^xsd:string)
                 Annotation(dcterms:license "CC-BY-4.0"^^xsd:string)
                 Annotation(dcterms:description "The Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism."^^xsd:string)
+                Annotation(foaf:homepage "http://geneontology.org/"^^xsd:anyURI)
+                Annotation(doap:repository "https://github.com/geneontology/go-ontology"^^xsd:anyURI)
+                Annotation(foaf:logo "https://obofoundry.org/images/go_logo.png"^^xsd:anyURI)
+                Annotation(doap:maintainer orcid:0000-0001-6787-2901)
                 Annotation(IAO:0000700 GO:1234567)
                 Annotation(owl:versionInfo "30"^^xsd:string)
                 Annotation(oboInOwl:auto-generated-by "PyOBO"^^xsd:string)