Graph generation

Commands

To generate the default graph (with all edges of all qualifies) in the current directory, use:

openbiolink generate

For a list of arguments, use:

openbiolink generate --help

File description

TSV

Default File Name	Description	Columns
ALL_nodes.csv	All nodes present in the graph	Node Id, Node type
edges.csv	All true positive edges	Node 1 ID, Edge type, Node 2 ID, Quality score, Source
edges_list.csv	List of edge types present in edges.csv	Edge type
nodes.csv	All nodes present in edges.csv	Node ID, Node type
nodes_list.csv	List of node types present in nodes.csv	Node type
TN_edges.csv	All true negative edges	Node 1 ID, Edge type, Node 2 ID, Quality score, Source
TN_edges_list.csv	List of edge types present in TN_edges.csv	Edge type
TN_nodes.csv	All nodes present in TN_edges.csv	Node ID, Node type
TN_nodes_list.csv	List of node types present in TN_nodes.csv	Node type
ids_no_mapping.tsv	ID’s of nodes that could not be mapped to other ontology systems	Node ID, Node type
tn_ids_no_mapping.tsv	ID’s of nodes that could not be mapped to other ontology systems	Node ID, Node type
stats.txt	Statistics about edges.csv and nodes.csv	(See column headers of file)
tn_stats.txt	Statistics about TN_edges.csv and TN_nodes.csv	(See column headers of file)

Biological Expression Language (BEL)

The Biological Expression Language (BEL) is a domain specific language that enables the expression of biological relationships in a machine-readable format. It is supported by the PyBEL software ecosystem.

BEL can be exported with:

openbiolink generate --output-format BEL

Default File Name	Description
positive.bel.gz	All true positive edges in BEL Script format (gzipped) for usage in PyBEL or other BEL-aware applications)
positive.bel.nodelink.json.gz	All true positive edges in Nodelink JSON format (gzipped) for direct usage with PyBEL
negative.bel.gz	All true negative edges in BEL Script format (gzipped)
negative.bel.nodelink.json.gz	All true negative edges in Nodelink JSON format (gzipped)

Example opening BEL Script using pybel.from_bel_script() :

import gzip
from pybel import from_bel_script
with gzip.open('positive.bel.gz') as file:
    graph = from_bel_script(file)

Example opening Nodelink JSON using pybel.from_nodelink_gz() :

from pybel import from_nodelink_gz
graph = from_nodelink_gz('positive.bel.nodelink.json.gz')

There’s an externally hosted copy of OpenBioLink here that contains the exports as BEL.

CURIE’s

All node ID’s in the graph are encoded as CURIE’s, meaning entities can be easily looked up online by concatenating https://identifiers.org/ with the ID, f.e.:

CURIE	Identifiers.org
GO:0006915	https://identifiers.org/GO:0006915
REACTOME:R-HSA-201451	https://identifiers.org/REACTOME:R-HSA-201451

Detailed information of how the Identifiers are resolved can be found here https://registry.identifiers.org/