KGX CLI¶
kgx¶
Knowledge Graph Exchange CLI entrypoint.
kgx [OPTIONS] COMMAND [ARGS]...
Options
-
--version
¶
Show the version and exit.
graph-summary¶
Loads and summarizes a knowledge graph from a set of input files.
kgx graph-summary [OPTIONS] INPUTS...
Options
-
-i
,
--input-format
<input_format>
¶ The input format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’) [required]
-
-c
,
--input-compression
<input_compression>
¶ The input compression type
-
-o
,
--output
<output>
¶ [required]
-
-r
,
--report-type
<report_type>
¶ The summary report type. Must be one of (‘kgx-map’, ‘meta-knowledge-graph’)
-
-f
,
--report-format
<report_format>
¶ The input format. Can be one of (‘yaml’, ‘json’)
-
-s
,
--stream
¶
Parse input as a stream
-
-n
,
--graph-name
<graph_name>
¶ User specified name of graph being summarized (default: ‘Graph’)
-
--node-facet-properties
<node_facet_properties>
¶ A list of node properties from which to generate counts per value for those properties
-
--edge-facet-properties
<edge_facet_properties>
¶ A list of edge properties from which to generate counts per value for those properties
-
-l
,
--error-log
<error_log>
¶ File within which to report graph data parsing errors (default: “stderr”)
Arguments
-
INPUTS
¶
Required argument(s)
merge¶
Load nodes and edges from files and KGs, as defined in a config YAML, and merge them into a single graph. The merged graph can then be written to a local/remote Neo4j instance OR be serialized into a file.
kgx merge [OPTIONS]
Options
-
--merge-config
<merge_config>
¶ [required]
-
--source
<source>
¶ Source(s) from the YAML to process
-
--destination
<destination>
¶ Destination(s) from the YAML to process
-
-p
,
--processes
<processes>
¶ Number of processes to use
neo4j-download¶
Download nodes and edges from Neo4j database.
kgx neo4j-download [OPTIONS]
Options
-
-l
,
--uri
<uri>
¶ Neo4j URI to download from. For example, https://localhost:7474 [required]
-
-u
,
--username
<username>
¶ Neo4j username [required]
-
-p
,
--password
<password>
¶ Neo4j password [required]
-
-o
,
--output
<output>
¶ Output [required]
-
-f
,
--output-format
<output_format>
¶ The output format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’) [required]
-
-d
,
--output-compression
<output_compression>
¶ The output compression type
-
-s
,
--stream
¶
Parse input as a stream
-
-n
,
--node-filters
<node_filters>
¶ Filters for filtering nodes from the input graph
-
-e
,
--edge-filters
<edge_filters>
¶ Filters for filtering edges from the input graph
neo4j-upload¶
Upload a set of nodes/edges to a Neo4j database.
kgx neo4j-upload [OPTIONS] INPUTS...
Options
-
-i
,
--input-format
<input_format>
¶ The input format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’) [required]
-
-c
,
--input-compression
<input_compression>
¶ The input compression type
-
-l
,
--uri
<uri>
¶ Neo4j URI to upload to. For example, https://localhost:7474 [required]
-
-u
,
--username
<username>
¶ Neo4j username [required]
-
-p
,
--password
<password>
¶ Neo4j password [required]
-
-s
,
--stream
¶
Parse input as a stream
-
-n
,
--node-filters
<node_filters>
¶ Filters for filtering nodes from the input graph
-
-e
,
--edge-filters
<edge_filters>
¶ Filters for filtering edges from the input graph
Arguments
-
INPUTS
¶
Required argument(s)
transform¶
Transform a Knowledge Graph from one serialization form to another.
kgx transform [OPTIONS] [INPUTS]...
Options
-
-i
,
--input-format
<input_format>
¶ The input format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’)
-
-c
,
--input-compression
<input_compression>
¶ The input compression type
-
-o
,
--output
<output>
¶ Output
-
-f
,
--output-format
<output_format>
¶ The output format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’)
-
-d
,
--output-compression
<output_compression>
¶ The output compression type
-
--stream
¶
Parse input as a stream
-
-n
,
--node-filters
<node_filters>
¶ Filters for filtering nodes from the input graph
-
-e
,
--edge-filters
<edge_filters>
¶ Filters for filtering edges from the input graph
-
--transform-config
<transform_config>
¶ Transform config YAML
-
--source
<source>
¶ Source(s) from the YAML to process
-
-k
,
--knowledge-sources
<knowledge_sources>
¶ A named knowledge source with (string, boolean or tuple rewrite) specification
-
--infores-catalog
<infores_catalog>
¶ Optional dump of a CSV file of InfoRes CURIE to Knowledge Source mappings
-
-p
,
--processes
<processes>
¶ Number of processes to use
Arguments
-
INPUTS
¶
Optional argument(s)
validate¶
Run KGX validator on an input file to check for Biolink Model compliance.
kgx validate [OPTIONS] INPUTS...
Options
-
-i
,
--input-format
<input_format>
¶ The input format. Can be one of (‘tsv’, ‘csv’, ‘graph’, ‘json’, ‘jsonl’, ‘obojson’, ‘obo-json’, ‘trapi-json’, ‘neo4j’, ‘nt’, ‘owl’, ‘sssom’) [required]
-
-c
,
--input-compression
<input_compression>
¶ The input compression type
-
-o
,
--output
<output>
¶ File to write validation reports to
-
-s
,
--stream
¶
Parse input as a stream
-
-b
,
--biolink-release
<biolink_release>
¶ Biolink Model Release (SemVer) used for validation (default: latest Biolink Model Toolkit version)
Arguments
-
INPUTS
¶
Required argument(s)