Merge pull request #676 from biolink/go-site-2246-gorule-0000001-rnac…

…-rna-types-are-getting-mangled

Go site 2246 gorule 0000001 rnac rna types are getting mangled

ontobio/io/assocparser.py

@@ -351,6 +351,7 @@ class Report(object):
     VIOLATES_GO_RULE = "Violates GO Rule"
     RULE_PASS = "Passes GO Rule"
     INVALID_REFERENCES = "Only one reference per ID space allowed"
+    INVALID_SUBJECT_TYPE = "Invalid subject type"
 
     def __init__(self, group="unknown", dataset="unknown", config=None):
         self.messages = []

ontobio/io/gafparser.py

@@ -385,6 +385,9 @@ def to_association(gaf_line: List[str], report=None, group="unknown", dataset="u
     DB_OBJECT_SYMBOL = 2
     TAXON_INDEX = 12
     REFERENCE_INDEX = 5
+    DEFAULT_SUBJECT_TYPE = 'gene_product'
+    STR_DEFAULT_SUBJECT_TYPE_CURIE = str(association.map_gp_type_label_to_curie(DEFAULT_SUBJECT_TYPE))
+
     if gaf_line[DB_INDEX] == "":
         report.error(source_line, Report.INVALID_IDSPACE, "EMPTY", "col1 is empty", taxon=gaf_line[TAXON_INDEX], rule=1)
         return assocparser.ParseResult(source_line, [], True, report=report)
@@ -417,7 +420,14 @@ def to_association(gaf_line: List[str], report=None, group="unknown", dataset="u
 
     interacting_taxon = parsed_taxons_result.parsed[1] if len(parsed_taxons_result.parsed) == 2 else None
     subject_curie = association.Curie(gaf_line[0], gaf_line[1])
+    type_label = gaf_line[11]
     subject = association.Subject(subject_curie, gaf_line[2], [gaf_line[9]], gaf_line[10].split("|"), [association.map_gp_type_label_to_curie(gaf_line[11])], taxon)
+    # Output warnig, if system is defaulting to gene_product
+    if DEFAULT_SUBJECT_TYPE != type_label and len(subject.type) == 1 and STR_DEFAULT_SUBJECT_TYPE_CURIE == str(subject.type[0]):
+        report.warning(source_line, Report.INVALID_SUBJECT_TYPE, type_label, "defaulting to 'gene_product'", taxon=gaf_line[TAXON_INDEX], rule=1)
+    if association.map_gp_type_label_to_repair_curie(type_label) is not None:
+        report.warning(source_line, Report.INVALID_SUBJECT_TYPE, type_label, "has been repaired", taxon=gaf_line[TAXON_INDEX], rule=1)
+
     gpi_entity = bio_entities.get(subject_curie)
     if gpi_entity is not None and subject != gpi_entity:
         subject = gpi_entity

ontobio/model/association.py

@@ -209,20 +209,24 @@ 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"),
     "snRNA": Curie.from_str("SO:0000274"),
     "ncRNA": Curie.from_str("SO:0000655"),
     "rRNA": Curie.from_str("SO:0000252"),
     "mRNA": Curie.from_str("SO:0000234"),
-    "lnc_RNA": Curie.from_str("SO:0001877"),
     "lincRNA": Curie.from_str("SO:0001463"),
+    "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"),
     "primary_transcript": Curie.from_str("SO:0000185"),
     "ribozyme": Curie.from_str("SO:0000374"),
@@ -234,12 +238,14 @@ def fullname_field(self, max=None) -> str:
     "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"),    
     "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"),    
     "transposable_element_gene": Curie.from_str("SO:0000111"),
     "gene_segment": Curie.from_str("SO:3000000"),
     "genetic_marker": Curie.from_str("SO:0001645"),
@@ -257,7 +263,14 @@ def fullname_field(self, max=None) -> str:
     "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")
+    "tRNA_gene": Curie.from_str("SO:0001272"),
+    "vault_RNA": Curie.from_str("SO:0000404"),
+    "Y_RNA": Curie.from_str("SO:0000405")    
+})
+
+# ===============================================================================
+__repair_entity_type_to_curie_mapping = bidict.bidict({
+    "lnc_RNA": Curie.from_str("SO:0001877")
 })
 
 def map_gp_type_label_to_curie(type_label: str) -> Curie:
@@ -267,9 +280,13 @@ def map_gp_type_label_to_curie(type_label: str) -> Curie:
 
     This is a measure to upgrade the pseudo-labels into proper Curies. Present here are
     the existing set of labels in current use, and how they should be mapped into CURIEs.
+    Repair Sequence Ontology (SO) labels if possible
     """
     # normalized_label = type_label.translate()
     global __default_entity_type_to_curie_mapping
+    global __repair_entity_type_to_curie_mapping
+    if type_label not in __default_entity_type_to_curie_mapping and type_label in __repair_entity_type_to_curie_mapping:
+        return __repair_entity_type_to_curie_mapping.get(type_label)
     return __default_entity_type_to_curie_mapping.get(type_label, __default_entity_type_to_curie_mapping["gene_product"])
 
 def gp_type_label_to_curie(type: Curie) -> str:
@@ -279,6 +296,10 @@ def gp_type_label_to_curie(type: Curie) -> str:
     global __default_entity_type_to_curie_mapping
     return __default_entity_type_to_curie_mapping.inverse.get(type, "gene_product")
 
+def map_gp_type_label_to_repair_curie(type_label: str) -> Curie:
+    global __repair_entity_type_to_curie_mapping
+    return __repair_entity_type_to_curie_mapping.get(type_label)
+
 @dataclass(unsafe_hash=True)
 class Term:
     """

tests/test_gafparser.py

@@ -471,7 +471,36 @@ def test_obsolete_replair_of_withfrom():
     assoc_result = p.parse_line(obsolete_no_replacement_line)
     assert assoc_result.associations == []
     assert p.report.to_report_json()["messages"]["gorule-0000020"][0]["obj"] == "GO:0016458"
+
+
+def test_invalid_db_type():
+    #gene_product gets mapped to gene_product
+    line = ["UniProtKB", "P0AFI2", "parC", "", "GO:0003916", "PMID:1334483", "IDA", "", "F", "", "", "gene_product", "taxon:83333", "20081208", "EcoliWiki"]
+    parsed = gafparser.to_association(line)
+    assoc = parsed.associations[0]
+    assert assoc.subject.type == [association.map_gp_type_label_to_curie('gene_product')]
 
+    #protein gets mapped to protein
+    line = ["UniProtKB", "P0AFI2", "parC", "", "GO:0003916", "PMID:1334483", "IDA", "", "F", "", "", "protein", "taxon:83333", "20081208", "EcoliWiki"]
+    parsed = gafparser.to_association(line)
+    assoc = parsed.associations[0]
+    assert assoc.subject.type == [association.map_gp_type_label_to_curie('protein')]
+
+    #Unhandled types get mapped to 'gene_product'
+    line = ["UniProtKB", "P0AFI2", "parC", "", "GO:0003916", "PMID:1334483", "IDA", "", "F", "", "", "invalid_gene_product", "taxon:83333", "20081208", "EcoliWiki"]
+    parsed = gafparser.to_association(line)
+    assoc = parsed.associations[0]
+    assert assoc.subject.type == [association.map_gp_type_label_to_curie('gene_product')]
+    assert parsed.report.to_report_json()["messages"]["gorule-0000001"][0]["type"] == parsed.report.INVALID_SUBJECT_TYPE
+
+    #'lnc_RNA' gets repaired to 'lncRNA'
+    line = ["UniProtKB", "P0AFI2", "parC", "", "GO:0003916", "PMID:1334483", "IDA", "", "F", "", "", "lnc_RNA", "taxon:83333", "20081208", "EcoliWiki"]
+    parsed = gafparser.to_association(line)
+    assoc = parsed.associations[0]
+    assert assoc.subject.type == [association.map_gp_type_label_to_curie('lncRNA')]                
+    assert parsed.report.to_report_json()["messages"]["gorule-0000001"][0]["type"] == parsed.report.INVALID_SUBJECT_TYPE
+
+
 
 def test_subject_extensions_bad_curie():
     """