CLI Reference

sssom-py provides the sssom command line tool with commands for all common mapping operations.

Global options

sssom [OPTIONS] COMMAND [ARGS]...

Option	Description
-v, --verbose	Increase verbosity (use -vv for debug).
-q, --quiet	Suppress all output except errors.
--version	Show the version and exit.

Commands at a glance

Command	Description
convert	Convert a file between formats (TSV, OWL, RDF, JSON).
parse	Parse a file in any supported format into SSSOM TSV.
validate	Produce an error report for an SSSOM file.
diff	Compare two SSSOM files.
merge	Merge multiple SSSOM files into one.
filter	Filter mappings by dynamic column queries.
sort	Sort rows and columns canonically.
split	Split a file by prefixes.
dedupe	Remove lower-confidence duplicate mappings.
annotate	Annotate mapping set metadata.
dosql	Run SQL queries over SSSOM files.
invert	Swap subject and object IDs.
remove	Remove mappings present in another file.
partition	Partition into strongly connected components.
cliquesummary	Summarise each clique in a file.
sparql	Run a SPARQL query against an endpoint.
crosstab	Cross-tabulate mappings by categories.
correlations	Calculate correlations between mapping categories.
ptable	Convert to ptable format for boomer.
rewire	Rewire an ontology using mappings.
reconcile-prefixes	Reconcile prefixes using a YAML config.
serve-rdf	Serve mappings as an RDF SPARQL endpoint.

See the full command reference for detailed options and examples.