Examples¶
There are two modes for using KGX:
Using KGX as a module
Using KGX CLI
Using KGX as a module¶
KGX provides a variety of functionality that can be achieved by your script by importing KGX as a module and calling the relevant classes/methods as needed.
Examples on how to use the KGX as a module can be found in examples folder. Some additional insights on usage may also be obtained by examination of the tests folder.
Using KGX CLI¶
The KGX CLI is a way of accessing KGX’s functionality directly from the command line.
Currently, the CLI supports the following operations:
graph-summary¶
Summarizes a graph and generate a YAML report regarding the composition of node and edge types in the graph.
kgx graph-summary --input-format tsv \
--output graph_stats.yaml \
--report-type kgx-map \
--error-log graph_stats.err \
tests/resources/graph_nodes.tsv tests/resources/graph_edges.tsv
An alternate summary of a graph generates a TRAPI 1.*-compliant meta knowledge graph (“content metadata”) JSON report:
kgx graph-summary --input-format tsv \
--output content_metadata.json \
--report-type meta-knowledge-graph \
--error-log graph_stats.err \
tests/resources/graph_nodes.tsv tests/resources/graph_edges.tsv
Some basic validation is done during graph-summary operation, with detected errors reported on the --error_log (default: stderr). For more complete graph validation, the validate command (below) may be used.
validate¶
Validate a graph for Biolink Model compliance and generate a report for nodes and edges that are not compliant (if any).
kgx validate --input-format tsv \
tests/resources/test_nodes.tsv tests/resources/test_edges.tsv
neo4j-download¶
Download a (sub)graph from a local or remote Neo4j instance.
kgx neo4j-download --uri http://localhost:7474 \
--username neo4j \
--password admin \
--output neo_graph_download \
--output-format tsv
neo4j-upload¶
Upload a (sub)graph to a clean local or remote Neo4j instance.
Note: This operation expects the Neo4j instance to be empty. This operation does not support updating an existing Neo4j graph. Writing to an existing graph may lead to side effects.
kgx neo4j-upload --uri http://localhost:7474 \
--username neo4j \
--password admin \
--input-format tsv \
tests/resources/test_nodes.tsv tests/resources/test_edges.tsv
transform¶
Transform a graph from one serialization to another (including a knowledge source InfoRes rewrite).
kgx transform --input-format tsv \
--output test_graph.json \
--output-format json \
--knowledge-sources aggregator_knowledge_source "string,string database" \
--knowledge-sources aggregator_knowledge_source "go,gene ontology" \
tests/resources/graph_nodes.tsv tests/resources/graph_edges.tsv
Alternatively, you can also perform transformation driven by a YAML.
A sample of the merge configuration can be found here.
kgx transform --transform-config transform.yaml