For #2246

biolink · Jun 11, 2024 · fe46253 · fe46253
1 parent 1bb6f9c
commit fe46253
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Showing 2 changed files with 32 additions and 15 deletions.
diff --git a/ontobio/model/association.py b/ontobio/model/association.py
@@ -209,45 +209,63 @@ def fullname_field(self, max=None) -> str:
 
 # ===============================================================================
 __default_entity_type_to_curie_mapping = bidict.bidict({
+    "autocatalytically_spliced_intron": Curie.from_str("SO:0000588"),
     "protein_coding_gene": Curie.from_str("SO:0001217"),
-    "protein": Curie.from_str("PR:000000001"),
-    "gene_product": Curie.from_str("CHEBI:33695"),
-    "autocatalytically_spliced_intron": Curie.from_str("SO:0000588"),    
     "snRNA": Curie.from_str("SO:0000274"),
     "ncRNA": Curie.from_str("SO:0000655"),
     "rRNA": Curie.from_str("SO:0000252"),
     "mRNA": Curie.from_str("SO:0000234"),
-    "pre_miRNA": Curie.from_str("SO:0001244"),
     "lincRNA": Curie.from_str("SO:0001463"),
-    "lncRNA": Curie.from_str("SO:0001877"),    
+    "lncRNA": Curie.from_str("SO:0001877"),     
     "tRNA": Curie.from_str("SO:0000253"),
     "snoRNA": Curie.from_str("SO:0000275"),
     "miRNA": Curie.from_str("SO:0000276"),
+    "RNA": Curie.from_str("SO:0000356"),
     "scRNA": Curie.from_str("SO:0000013"),
     "piRNA": Curie.from_str("SO:0001035"),
     "pre_miRNA": Curie.from_str("SO:0001244"),    
     "tmRNA": Curie.from_str("SO:0000584"),
     "scaRNA": Curie.from_str("SO:0002095"),
-    "siRNA": Curie.from_str("SO:0000646"),         
-    "SRP_RNA": Curie.from_str("SO:0000590"),    
+    "siRNA": Curie.from_str("SO:0000646"),        
+    "SRP_RNA": Curie.from_str("SO:0000590"),
+    "primary_transcript": Curie.from_str("SO:0000185"),
     "ribozyme": Curie.from_str("SO:0000374"),
     "telomerase_RNA": Curie.from_str("SO:0000390"),
     "RNase_P_RNA": Curie.from_str("SO:0000386"),
     "antisense_RNA": Curie.from_str("SO:0000644"),
     "RNase_MRP_RNA": Curie.from_str("SO:0000385"),
     "guide_RNA": Curie.from_str("SO:0000602"),
-    "vault_RNA": Curie.from_str("SO:0000404"),
-    "Y_RNA": Curie.from_str("SO:0000405"),         
     "hammerhead_ribozyme": Curie.from_str("SO:0000380"),
+    "protein": Curie.from_str("PR:000000001"),
     "pseudogene": Curie.from_str("SO:0000336"),
     "pseudogenic_transcript": Curie.from_str("SO:0000516"),    
-    "protein_complex": Curie.from_str("GO:0032991"),    
+    "gene": Curie.from_str("SO:0000704"),
+    "biological region": Curie.from_str("SO:0001411"),
+    "protein_complex": Curie.from_str("GO:0032991"),
+    "transcript": Curie.from_str("SO:0000673"),
+    "gene_product": Curie.from_str("CHEBI:33695"),
     "antisense_lncRNA": Curie.from_str("SO:0001904"),
-    "antisense_lncRNA_gene": Curie.from_str("SO:0002182"),  
+    "antisense_lncRNA_gene": Curie.from_str("SO:0002182"),    
+    "transposable_element_gene": Curie.from_str("SO:0000111"),
     "gene_segment": Curie.from_str("SO:3000000"),
     "genetic_marker": Curie.from_str("SO:0001645"),
-    "biological region": Curie.from_str("SO:0001411"),
-    "transposable_element_gene": Curie.from_str("SO:0000111")
+    "lincRNA_gene": Curie.from_str("SO:0001641"),
+    "lncRNA_gene": Curie.from_str("SO:0002127"),
+    "miRNA_gene": Curie.from_str("SO:0001265"),
+    "ncRNA_gene": Curie.from_str("SO:0001263"),
+    "RNase_MRP_RNA_gene": Curie.from_str("SO:0001640"),
+    "RNase_P_RNA_gene": Curie.from_str("SO:0001639"),
+    "rRNA_gene": Curie.from_str("SO:0001637"),
+    "scRNA_gene": Curie.from_str("SO:0001266"),
+    "sense_intronic_ncRNA_gene": Curie.from_str("SO:0002184"),
+    "sense_overlap_ncRNA_gene": Curie.from_str("SO:0002183"),
+    "snoRNA_gene": Curie.from_str("SO:0001267"),
+    "snRNA_gene": Curie.from_str("SO:0001268"),
+    "SRP_RNA_gene": Curie.from_str("SO:0001269"),
+    "telomerase_RNA_gene": Curie.from_str("SO:0001643"),
+    "tRNA_gene": Curie.from_str("SO:0001272"),
+    "vault_RNA": Curie.from_str("SO:0000404"),
+    "Y_RNA": Curie.from_str("SO:0000405")    
 })
 
 # ===============================================================================

diff --git a/tests/test_gafparser.py b/tests/test_gafparser.py
@@ -611,8 +611,7 @@ def test_gaf_gpi_bridge():
     association = gafparser.to_association(gaf, qualifier_parser=assocparser.Qualifier2_2()).associations[0]
     bridge = gafgpibridge
     entity = bridge.convert_association(association)
-    #gene gets updated to gene_product!!!!
-    assert entity.get("type") == ["gene_product"]
+    assert entity.get("type") == ["gene"]
 
 
 if __name__ == "__main__":