Add replacement info

Author: cthoyt

src/pyobo/sources/cvx.py

@@ -7,7 +7,7 @@
 
 import pandas as pd
 
-from pyobo import Obo, Term
+from pyobo import Obo, Reference, Term
 
 __all__ = [
     "CVXGetter",
@@ -28,6 +28,11 @@ def iter_terms(self, force: bool = False) -> Iterable[Term]:
         return iter_terms()
 
 
+# This got split, which it's not obvious how to deal with this
+MANUAL_OBSOLETE = {"15"}
+REPLACEMENTS = {"31": "85", "154": "86", "180": "13"}
+
+
 def iter_terms() -> Iterable[Term]:
     """Iterate over terms in CVX."""
     dd = defaultdict(set)
@@ -63,15 +68,19 @@ def iter_terms() -> Iterable[Term]:
         if cvx == "99":
             continue  # this is a placeholder
 
-        is_obsolete = pd.notna(notes) and "do not use" in notes.lower()
-        if is_obsolete:
-            # there are some records that have been obsoleted/replaced
-            continue
-        term = Term.from_triple(PREFIX, cvx, full_name)
+        is_obsolete = cvx in MANUAL_OBSOLETE or (pd.notna(notes) and "do not use" in notes.lower())
+        term = Term(
+            reference=Reference(prefix=PREFIX, identifier=cvx, name=full_name),
+            is_obsolete=is_obsolete,
+        )
         if short_name != full_name:
             term.append_synonym(short_name)
         if pd.notna(notes):
             term.append_comment(notes)
+        if is_obsolete:
+            replacement_identifier = REPLACEMENTS.get(cvx)
+            if replacement_identifier:
+                term.append_replaced_by(Reference(prefix=PREFIX, identifier=replacement_identifier))
         if pd.notna(status):
             term.append_property("status", status)
         if pd.notna(nonvaccine):

src/pyobo/struct/struct.py

@@ -53,6 +53,7 @@
     orthologous,
     part_of,
     see_also,
+    term_replaced_by,
 )
 from .utils import comma_separate, obo_escape_slim
 from ..constants import (
@@ -299,6 +300,11 @@ def append_comment(self, value: str) -> "Term":
         self.append_property(comment.curie, value)
         return self
 
+    def append_replaced_by(self, reference: ReferenceHint) -> "Term":
+        """Add a replaced by relationship."""
+        self.append_relationship(term_replaced_by, reference)
+        return self
+
     def append_parent(self, reference: ReferenceHint) -> "Term":
         """Add a parent to this entity."""
         reference = _ensure_ref(reference)