Merge pull request #128 from monarch-initiative/abbrevs

The symbol value from "Preferred Title; symbol" should have a synonym type of abbreviation

omim2obo/main.py

@@ -164,53 +164,68 @@ def omim2obo(use_cache: bool = False):
                 continue
 
         # - Non-deprecated
-        omim_type, pref_label, alt_labels, inc_labels = omim_type_and_titles[omim_id]
-        label = pref_label
+        # Parse titles
+        omim_type, pref_labels_str, alt_labels, inc_labels = omim_type_and_titles[omim_id]
         other_labels = []
         cleaned_inc_labels = []
         label_endswith_included_alt = False
         label_endswith_included_inc = False
+        pref_labels: List[str] = [x.strip() for x in pref_labels_str.split(';')]
+        pref_title: str = pref_labels[0]
+        pref_symbols: List[str] = pref_labels[1:]
         if alt_labels:
             cleaned_alt_labels, label_endswith_included_alt = get_alt_labels(alt_labels)
             other_labels += cleaned_alt_labels
         if inc_labels:
             cleaned_inc_labels, label_endswith_included_inc = get_alt_labels(inc_labels)
             # other_labels += cleaned_inc_labels  # deactivated 7/2024 in favor of alternative for tagging 'included'
 
-        included_detected_comment = "This term has one or more labels that end with ', INCLUDED'."
-        if label_endswith_included_alt or label_endswith_included_inc:
-            graph.add((omim_uri, RDFS['comment'], Literal(included_detected_comment)))
-
-        use_abbrev_over_label = False
-        abbrev = label.split(';')[1].strip() if ';' in label else None
+        # Special cases depending on OMIM term type
+        is_gene = omim_type == OmimType.GENE or omim_type == OmimType.HAS_AFFECTED_FEATURE
         if omim_type == OmimType.HERITABLE_PHENOTYPIC_MARKER:  # %
             graph.add((omim_uri, BIOLINK['category'], BIOLINK['Disease']))
-        elif omim_type == OmimType.GENE or omim_type == OmimType.HAS_AFFECTED_FEATURE:  # * or +
-            use_abbrev_over_label = True
+        elif is_gene:  # * or +
             graph.add((omim_uri, RDFS.subClassOf, SO['0000704']))  # gene
             graph.add((omim_uri, MONDO.exclusionReason, MONDO.nonDisease))
             graph.add((omim_uri, BIOLINK['category'], BIOLINK['Gene']))
         elif omim_type == OmimType.PHENOTYPE:
             graph.add((omim_uri, BIOLINK['category'], BIOLINK['Disease']))  # phenotype ~= disease
         elif omim_type == OmimType.SUSPECTED:
             graph.add((omim_uri, MONDO.exclusionReason, MONDO.excludeTrait))
-        else:
-            pass
 
-        if use_abbrev_over_label and abbrev:
-            graph.add((omim_uri, RDFS.label, Literal(abbrev)))
+        # Alternative rdfs:label for genes
+        if is_gene and pref_symbols:
+            gene_label_err = 'Warning: Only 1 symbol picked for label for gene term, but there were 2 to choose' \
+                 f'from. Unsure which is best. Picking the first.\nhttps://omim.org/entry/{omim_id} - {pref_symbols}'
+            if len(pref_symbols) > 1:
+                LOG.warning(gene_label_err)  # todo: decide the best way to handle these situations
+            graph.add((omim_uri, RDFS.label, Literal(pref_symbols[0])))
         else:
-            graph.add((omim_uri, RDFS.label, Literal(label_cleaner.clean(label))))
-
-        exact_labels = [s.strip() for s in label.split(';')]
-        # the last string is an abbreviation. Add OWL reification. See issue #2
-        if len(exact_labels) > 1:
-            abbr = exact_labels.pop()
-            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(abbr)))
-        for exact_label in exact_labels:
-            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(exact_label, abbrev))))
-        for label in other_labels:
-            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(label, abbrev))))
+            graph.add((omim_uri, RDFS.label, Literal(label_cleaner.clean(pref_title))))
+
+        # todo: .clean()/.cleanup_label() 2nd param `explicit_abbrev` should be List[str] instead of str. And below,
+        #  should pass all symbols/abbrevs from each of preferred, alt, included each time it is called. If no symbols
+        #  for given term, should pass empty list. See: https://github.com/monarch-initiative/omim/issues/129
+        abbrev: Union[str, None] = None if not pref_symbols else pref_symbols[0]
+
+        # Add synonyms
+        graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(pref_title, abbrev))))
+        for alt_label in other_labels:
+            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(label_cleaner.clean(alt_label, abbrev))))
+        for abbreviation in pref_symbols:
+            graph.add((omim_uri, oboInOwl.hasExactSynonym, Literal(abbreviation)))
+            # Reify on abbreviations. See: https://github.com/monarch-initiative/omim/issues/2
+            axiom = BNode()
+            graph.add((axiom, RDF.type, OWL.Axiom))
+            graph.add((axiom, OWL.annotatedSource, omim_uri))
+            graph.add((axiom, OWL.annotatedProperty, oboInOwl.hasExactSynonym))
+            graph.add((axiom, OWL.annotatedTarget, Literal(abbreviation)))
+            graph.add((axiom, OBOINOWL.hasSynonymType, MONDONS.abbreviation))
+
+        # Add 'included' entry properties
+        included_detected_comment = "This term has one or more labels that end with ', INCLUDED'."
+        if label_endswith_included_alt or label_endswith_included_inc:
+            graph.add((omim_uri, RDFS['comment'], Literal(included_detected_comment)))
         for included_label in cleaned_inc_labels:
             graph.add((omim_uri, URIRef(INCLUDED_URI), Literal(label_cleaner.clean(included_label, abbrev))))
 

omim2obo/parsers/omim_entry_parser.py

@@ -165,6 +165,7 @@ def _detect_abbreviations(
     return replacements
 
 
+# todo: explicit_abbrev: Change to List[str]. See: https://github.com/monarch-initiative/omim/issues/129
 def cleanup_label(
         label: str,
         explicit_abbrev: str = None,