Improve typedefs in sources

src/pyobo/sources/mirbase.py

@@ -136,6 +136,8 @@ def _process_definitions_lines(
             xref_prefix, xref_identifier, xref_label = map(str.strip, line.split(";"))
             xref_prefix = xref_prefix.lower()
             xref_prefix = xref_mapping.get(xref_prefix, xref_prefix)
+            if xref_prefix == "pictar":
+                continue
             xrefs.append(
                 Reference(prefix=xref_prefix, identifier=xref_identifier, name=xref_label or None)
             )

src/pyobo/sources/mirbase_family.py

@@ -26,6 +26,7 @@ class MiRBaseFamilyGetter(Obo):
 
     ontology = PREFIX
     bioversions_key = "mirbase"
+    typedefs = [has_member]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""

src/pyobo/sources/pombase.py

@@ -29,7 +29,7 @@ class PomBaseGetter(Obo):
     """An ontology representation of PomBase's fission yeast gene nomenclature."""
 
     ontology = bioversions_key = PREFIX
-    typedefs = [from_species, has_gene_product]
+    typedefs = [from_species, has_gene_product, orthologous]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""

src/pyobo/struct/typedef.py

@@ -264,14 +264,21 @@ def get_reference_tuple(relation: RelationHint) -> Tuple[str, str]:
     reference=Reference(prefix="debio", identifier="0000006", name="has salt"),
 )
 
-example_of_usage = Reference(prefix=IAO_PREFIX, identifier="0000112", name="example of usage")
-alternative_term = Reference(prefix=IAO_PREFIX, identifier="0000118", name="alternative term")
+term_replaced_by = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0100001", name="term replaced by"
+)
+example_of_usage = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0000112", name="example of usage"
+)
+alternative_term = TypeDef.from_triple(
+    prefix=IAO_PREFIX, identifier="0000118", name="alternative term"
+)
 has_ontology_root_term = TypeDef.from_triple(
     prefix=IAO_PREFIX, identifier="0000700", name="has ontology root term"
 )
 has_dbxref = TypeDef.from_curie("oboInOwl:hasDbXref", name="has database cross-reference")
 
-editor_note = Reference(prefix=IAO_PREFIX, identifier="0000116", name="editor note")
+editor_note = TypeDef.from_triple(prefix=IAO_PREFIX, identifier="0000116", name="editor note")
 
 is_immediately_transformed_from = TypeDef.from_triple(
     prefix=SIO_PREFIX, identifier="000658", name="is immediately transformed from"