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Monarch Closurizer

Closurizer adds expansion fields to kgx files following the Golr pattern

Usage

As a module

from closurizer.closurizer import add_closure

add_closure(node_file=f"my-kg_nodes.tsv",
            edge_file=f"my-kg_edges.tsv",
            kg_archive=f"my-kg.tar.gz",
            closure_file="my-relations-non-redundant.tsv",
            path="output/",
            output_file=f"my-kg-denornalized_edges.tsv",
            fields=["subject", "object"])

Example

Closurizer will produce a denormalized edge file including subject namespace and category along with ID and label closures

subject_category subject_closure subject_closure_label subject_namespace subject predicate object object_namespace object_closure_label object_closure object_category
biolink:Gene HGNC HGNC:4851 biolink:gene_associated_with_condition MONDO:0007739 MONDO Huntington disease and related disorders, movement disorder MONDO:0000167, MONDO:0005395 biolink:Disease

Example source KG

Nodes:

category id name in_taxon
biolink:Gene HGNC:4851 HTT NCBITaxon:9606
biolink:Disease MONDO:0007739 Huntington disease

Edges:

subject predicate object
HGNC:4851 biolink:gene_associated_with_condition MONDO:0007739

and a Relation Graph closure tsv file with:

subject predicate object
MONDO:0007739 rdfs:subClassOf MONDO:0000167
MONDO:0007739 rdfs:subClassOf MONDO:0005395