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	*

Documentation

Monarch Closurizer

Closurizer adds expansion fields to kgx files following the Golr pattern

Usage

As a module

Archive input (tar.gz file):

from closurizer.closurizer import add_closure

add_closure(
    closure_file="my-relations-non-redundant.tsv",
    nodes_output_file="output/nodes-with-closures.tsv", 
    edges_output_file="output/edges-denormalized.tsv",
    kg_archive="my-kg.tar.gz",
    database_path="working-database.duckdb",  # database where processing occurs
    edge_fields=["subject", "object"]
)

Database input (existing DuckDB):

from closurizer.closurizer import add_closure

add_closure(
    closure_file="my-relations-non-redundant.tsv",
    nodes_output_file="output/nodes-with-closures.tsv",
    edges_output_file="output/edges-denormalized.tsv", 
    database_path="existing-kg.duckdb",  # existing database with nodes/edges tables
    edge_fields=["subject", "object"]
)

As a command line tool

Archive input:

closurizer --kg my-kg.tar.gz --database working.duckdb --closure relations.tsv --nodes-output nodes.tsv --edges-output edges.tsv

Database input:

closurizer --database existing.duckdb --closure relations.tsv --nodes-output nodes.tsv --edges-output edges.tsv

Note: If --kg is provided, the archive will be loaded into the specified database. If --kg is not provided, the database must already exist and contain nodes and edges tables.

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