closurizer

Details

GitHub	monarch-initiative/closurizer
Language	Python
Description	Add closure expansion fields to kgx files following the Golr pattern

Dependencies

External Dependencies

Package	Version
python	^3.8
click	^8
SQLAlchemy	^1.4.37
duckdb	^0.9.1

Documentation

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