From 162084311953adabcb068c0a1af33fa348d7d3e4 Mon Sep 17 00:00:00 2001 From: Justin Reese Date: Wed, 10 Jun 2020 19:30:16 -0700 Subject: [PATCH] Correctly type drugs and nucleic acids in IntAct ingest --- kg_covid_19/transform_utils/intact/intact.py | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/kg_covid_19/transform_utils/intact/intact.py b/kg_covid_19/transform_utils/intact/intact.py index 394e3b73..48d62bd3 100644 --- a/kg_covid_19/transform_utils/intact/intact.py +++ b/kg_covid_19/transform_utils/intact/intact.py @@ -33,12 +33,18 @@ def __init__(self, input_dir: str = None, output_dir: str = None) -> None: source_name = "intact" super().__init__(source_name, input_dir, output_dir) # interactor type to biolink category + bl_protein_cat = 'biolink:Protein' bl_rna_cat = 'biolink:RNA' + bl_nucleic_acid = 'biolink:MolecularEntity' + bl_drug_cat = 'biolink:Drug' self.type_to_biolink_category = { - 'protein': 'biolink:Protein', + 'protein': bl_protein_cat, + 'peptide': bl_protein_cat, 'rna': bl_rna_cat, 'mrna': bl_rna_cat, - 'snrna': bl_rna_cat + 'snrna': bl_rna_cat, + 'nucleic acid': bl_nucleic_acid, + 'small molecule': bl_drug_cat } self.db_to_prefix = { 'uniprot': 'UniProtKB', @@ -255,6 +261,8 @@ def interactor_to_node(self, interactor) -> List[Union[int, list]]: interactor.getElementsByTagName('interactorType')[0].getElementsByTagName( 'shortLabel')[0].childNodes[0].data type = type.lower() + if type == 'small molecule': + pass if type in self.type_to_biolink_category: category = self.type_to_biolink_category[type] except (KeyError, IndexError, AttributeError) as e: