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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,171 @@ | ||
| try: | ||
| from tqdm import tqdm | ||
| TQDM_AVAILABLE = True | ||
| except ImportError: | ||
| TQDM_AVAILABLE = False | ||
|
|
||
| from Common.biolink_constants import PREDICATE, QUALIFIED_PREDICATE, SUBJECT_DERIVATIVE_QUALIFIER, SUBJECT_FORM_OR_VARIANT_QUALIFIER, SUBJECT_PART_QUALIFIER, \ | ||
| SUBJECT_DIRECTION_QUALIFIER, SUBJECT_ASPECT_QUALIFIER, OBJECT_DERIVATIVE_QUALIFIER, OBJECT_FORM_OR_VARIANT_QUALIFIER, \ | ||
| OBJECT_PART_QUALIFIER, OBJECT_DIRECTION_QUALIFIER, OBJECT_ASPECT_QUALIFIER, CAUSAL_MECHANISM_QUALIFIER, \ | ||
| ANATOMICAL_CONTEXT_QUALIFIER, SPECIES_CONTEXT_QUALIFIER | ||
| from Common.biolink_utils import get_biolink_model_toolkit | ||
| from Common.utils import quick_jsonl_file_iterator | ||
| from Common.kgx_file_writer import KGXFileWriter | ||
|
|
||
| ### The goal of this script is to collapse the qualifiers, which are in edge properties, into a single statement, then replace the | ||
| ### existing predicate label with the collapsed qualifier statement. | ||
|
|
||
| ### Call the biolink model toolkit to get the list of all qualifiers. This may change, but the way qualifiers are handled is currently hard-coded in this script. | ||
| bmt = get_biolink_model_toolkit() | ||
|
|
||
| def write_edge_no_q(edge, predicate, qualifiers): | ||
| tmp_edge = edge.copy() | ||
| tmp_edge[PREDICATE] = f"{predicate}" | ||
| for qualifier in qualifiers.keys(): | ||
| tmp_edge.pop(qualifier, None) | ||
| return tmp_edge | ||
|
|
||
| def aspect_qualifier_semantic_adjustment(aspect_qualifier): | ||
| # TODO check if other aspect qualifiers besides molecular interaction need to be treated differently. | ||
| if aspect_qualifier.split('_')[-1] == 'interaction': | ||
| aspect_conversion = aspect_qualifier + "_with" | ||
| else: | ||
| aspect_conversion = aspect_qualifier + "_of" | ||
| return aspect_conversion | ||
|
|
||
| def form_or_variant_qualifier_semantic_adjustment(form_or_variant_qualifier): | ||
| # TODO check if other form_or_variant_qualifier qualifiers besides molecular interaction need to be treated differently. | ||
| form_or_variant_conversion = form_or_variant_qualifier + "_of" | ||
| return form_or_variant_conversion | ||
|
|
||
| def causal_mechanism_qualifier_semantic_adjustment(causal_mechanism_qualifier): | ||
| # TODO check if other causal_mechanism qualifiers besides molecular interaction need to be treated differently. | ||
| causal_mechanism_qualifier = "via_"+ causal_mechanism_qualifier | ||
| return causal_mechanism_qualifier | ||
|
|
||
| def species_context_qualifier_semantic_adjustment(species_context_qualifier): | ||
| species_context_qualifier = "in_"+ species_context_qualifier | ||
| return species_context_qualifier | ||
|
|
||
| def anatomical_context_qualifier_semantic_adjustment(anatomical_context_qualifier, species_context_qualifier=False): | ||
| if species_context_qualifier == False: | ||
| anatomical_context_qualifier = "in_"+ anatomical_context_qualifier | ||
| return anatomical_context_qualifier | ||
|
|
||
| def generate_collapsed_qualifiers_kg(infile, edges_file_path): | ||
|
|
||
| with KGXFileWriter(edges_output_file_path=edges_file_path) as kgx_file_writer: | ||
| for edge in tqdm(quick_jsonl_file_iterator(infile)) if TQDM_AVAILABLE else quick_jsonl_file_iterator(infile): | ||
|
|
||
| try: | ||
| edge_predicate = edge['predicate'] | ||
| except KeyError: | ||
| print(f"Collapsed Qualifiers Graph Failed - missing predicate on edge: {edge}") | ||
| break | ||
|
|
||
| qualifiers = {key:value for key, value in edge.items() if bmt.is_qualifier(key)} | ||
| # Count the number of qualifiers and print a warning if number of qualifiers we handle in the next section doesn't match number of qualifiers detected. | ||
| # This will help warn us if new qualifiers are added in the future while giving us the option to still run the script as is. | ||
| qualifier_count = len(qualifiers.keys()) | ||
| counted_qualifiers = 0 | ||
|
|
||
| # The following section crafts a new collapsed qualifier statement to replace the edge predicate, but needs to do some semantic adjustment. | ||
| # This is where to edit if the biolink model ever changes and handles qualifiers differently. | ||
| # Take guidance from: https://biolink.github.io/biolink-model/reading-a-qualifier-based-statement/ | ||
| # Example jsonl edge used here: {"subject":"UNII:7PK6VC94OU","predicate":"biolink:affects","object":"NCBIGene:6531","primary_knowledge_source":"infores:ctd","description":"decreases activity of","NCBITaxon":"9606","publications":["PMID:30776375"],"knowledge_level":"knowledge_assertion","agent_type":"manual_agent","subject_direction_qualifier":"increased","subject_aspect_qualifier":"abundance","subject_form_or_variant_qualifier":"mutant_form","subject_derivative_qualifier":"transcript","subject_part_qualifier":"polyA_tail","object_aspect_qualifier":"activity","object_direction_qualifier":"upregulated","object_form_or_variant_qualifier":"wildtype_form","object_derivative_qualifier":"protein","object_part_qualifier":"catalytic_site","causal_mechanism_qualifier":"phosyphorylation","species_context_qualifier":"human","anatomical_context_qualifier":"liver","qualified_predicate":"biolink:causes"} | ||
|
|
||
| qualifier_statement = "" | ||
|
|
||
| # Add on subject direction and aspect qualifiers first. eg. "increased_abundance_of_" | ||
| if SUBJECT_DIRECTION_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= qualifiers[SUBJECT_DIRECTION_QUALIFIER] | ||
| qualifier_statement+= "_" | ||
| if SUBJECT_ASPECT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= aspect_qualifier_semantic_adjustment(qualifiers[SUBJECT_ASPECT_QUALIFIER]) | ||
| qualifier_statement+= "_" | ||
| # Add on subject form_or_variant qualifiers. eg. "increased_abundance_of_mutant_form_of_<subject_node>" | ||
| if SUBJECT_FORM_OR_VARIANT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= form_or_variant_qualifier_semantic_adjustment(qualifiers[SUBJECT_FORM_OR_VARIANT_QUALIFIER]) | ||
| qualifier_statement+= "_" | ||
| # Add placeholder slot for subject node. eg. "increased_abundance_of_mutant_form_of_<subject_node>" | ||
| qualifier_statement+= "<subject_node>_" | ||
| # Add on subject derivative and part qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail" | ||
| if SUBJECT_DERIVATIVE_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= qualifiers[SUBJECT_DERIVATIVE_QUALIFIER] | ||
| qualifier_statement+= "_" | ||
| if SUBJECT_PART_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= qualifiers[SUBJECT_PART_QUALIFIER] | ||
| qualifier_statement+= "_" | ||
|
|
||
| # Add the qualified predicate. eg. "increased_abundance_of_mutant_form_of_<subject_node>_transcript_poly_A_tail_causes" | ||
| if QUALIFIED_PREDICATE in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= qualifiers[QUALIFIED_PREDICATE].replace("biolink:","") | ||
| qualifier_statement+= "_" | ||
|
|
||
| # Add on object direction and aspect qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of" | ||
| if OBJECT_DIRECTION_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= qualifiers[OBJECT_DIRECTION_QUALIFIER] | ||
| qualifier_statement+= "_" | ||
| if OBJECT_ASPECT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= aspect_qualifier_semantic_adjustment(qualifiers[OBJECT_ASPECT_QUALIFIER]) | ||
| qualifier_statement+= "_" | ||
| # Add on object form_or_variant qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of" | ||
| if OBJECT_FORM_OR_VARIANT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= form_or_variant_qualifier_semantic_adjustment(qualifiers[OBJECT_FORM_OR_VARIANT_QUALIFIER]) | ||
| qualifier_statement+= "_" | ||
| # Add placeholder slot for object node. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>" | ||
| qualifier_statement+= "<object_node>" | ||
|
|
||
| # Add on object derivative and part qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site" | ||
| # Need to start putting "_" before each qualifier as any given one could be the last in the statement. | ||
| if OBJECT_DERIVATIVE_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= "_" | ||
| qualifier_statement+= qualifiers[OBJECT_DERIVATIVE_QUALIFIER] | ||
| if OBJECT_PART_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= "_" | ||
| qualifier_statement+= qualifiers[OBJECT_PART_QUALIFIER] | ||
|
|
||
| # Add on mechanism qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation" | ||
| if CAUSAL_MECHANISM_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= "_" | ||
| qualifier_statement+= causal_mechanism_qualifier_semantic_adjustment(qualifiers[CAUSAL_MECHANISM_QUALIFIER]) | ||
|
|
||
| # Add on species qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation_in_human" | ||
| if SPECIES_CONTEXT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= "_" | ||
| qualifier_statement+= species_context_qualifier_semantic_adjustment(qualifiers[SPECIES_CONTEXT_QUALIFIER]) | ||
|
|
||
| # Add on anatomical context qualifiers. eg. "increased_abundance_of_mutant_form_of<subject_node>_transcript_poly_A_tail_causes_upregulated_activity_of_mutant_form_of_<object_node>_protein_catalytic_site_via_phosphorylation_in_human_liver" | ||
| if ANATOMICAL_CONTEXT_QUALIFIER in qualifiers.keys(): | ||
| counted_qualifiers+= 1 | ||
| qualifier_statement+= "_" | ||
| if SPECIES_CONTEXT_QUALIFIER in qualifiers.keys(): | ||
| species_qualifier = True | ||
| else: | ||
| species_qualifier = False | ||
| qualifier_statement+= anatomical_context_qualifier_semantic_adjustment(qualifiers[ANATOMICAL_CONTEXT_QUALIFIER], species_qualifier) | ||
|
|
||
| if counted_qualifiers < qualifier_count: | ||
| print(f"Qualifiers on edge: {edge} are not all being handled correctly. Please revise collapse_qualifiers.py to handle all qualifiers.") | ||
|
|
||
| # Either rewrite the original edge if no qualifier collapsing happened, or rewrite with new predicate from qualifier_statement. | ||
| edges_to_write = [] | ||
| if qualifier_statement != "": | ||
| edges_to_write.append(write_edge_no_q(edge, qualifier_statement, qualifiers)) | ||
| else: | ||
| edges_to_write.append(edge) | ||
|
|
||
| kgx_file_writer.write_normalized_edges(edges_to_write) |
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