CLI Commands

Full auto-generated reference for every sssom subcommand.

sssom

Run the SSSOM CLI.

Usage:

sssom [OPTIONS] COMMAND [ARGS]...

Options:

Name	Type	Description	Default
-v, --verbose	integer range (0 and above)	N/A	0
-q, --quiet	text	N/A	Sentinel.UNSET
--version	boolean	Show the version and exit.	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom annotate

Annotate metadata of a mapping set.

Usage:

sssom annotate [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--replace-multivalued	boolean	Multivalued slots should be replaced or not.	False
--sssom_version	text	N/A	Sentinel.UNSET
--curie_map	text	N/A	Sentinel.UNSET
--mappings	text	N/A	Sentinel.UNSET
--mapping_set_id	text	N/A	Sentinel.UNSET
--mapping_set_version	text	N/A	Sentinel.UNSET
--mapping_set_source	text	N/A	Sentinel.UNSET
--mapping_set_title	text	N/A	Sentinel.UNSET
--mapping_set_description	text	N/A	Sentinel.UNSET
--mapping_set_confidence	text	N/A	Sentinel.UNSET
--creator_id	text	N/A	Sentinel.UNSET
--creator_label	text	N/A	Sentinel.UNSET
--license	text	N/A	Sentinel.UNSET
--subject_type	text	N/A	Sentinel.UNSET
--subject_source	text	N/A	Sentinel.UNSET
--subject_source_version	text	N/A	Sentinel.UNSET
--object_type	text	N/A	Sentinel.UNSET
--object_source	text	N/A	Sentinel.UNSET
--object_source_version	text	N/A	Sentinel.UNSET
--predicate_type	text	N/A	Sentinel.UNSET
--mapping_provider	text	N/A	Sentinel.UNSET
--cardinality_scope	text	N/A	Sentinel.UNSET
--mapping_tool	text	N/A	Sentinel.UNSET
--mapping_tool_id	text	N/A	Sentinel.UNSET
--mapping_tool_version	text	N/A	Sentinel.UNSET
--mapping_date	text	N/A	Sentinel.UNSET
--publication_date	text	N/A	Sentinel.UNSET
--subject_match_field	text	N/A	Sentinel.UNSET
--object_match_field	text	N/A	Sentinel.UNSET
--subject_preprocessing	text	N/A	Sentinel.UNSET
--object_preprocessing	text	N/A	Sentinel.UNSET
--similarity_measure	text	N/A	Sentinel.UNSET
--curation_rule	text	N/A	Sentinel.UNSET
--curation_rule_text	text	N/A	Sentinel.UNSET
--see_also	text	N/A	Sentinel.UNSET
--issue_tracker	text	N/A	Sentinel.UNSET
--other	text	N/A	Sentinel.UNSET
--comment	text	N/A	Sentinel.UNSET
--extension_definitions	text	N/A	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom cliquesummary

Calculate summaries for each clique in a SSSOM file.

Usage:

sssom cliquesummary [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-m, --metadata	path	The path to a file containing the sssom metadata (including prefix_map) to be used.	Sentinel.UNSET
-s, --statsfile	text	N/A	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom convert

Convert a file.

Usage:

sssom convert [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-O, --output-format	choice (tsv | owl | ontoportal_json | fhir_json | json | rdf | ttl | xml | turtle | nt)	Desired output format.	Sentinel.UNSET
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
--condense / --no-condense	boolean	Automatically condense slots upon writing.	True
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom correlations

Calculate correlations.

Usage:

sssom correlations [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-t, --transpose	boolean	N/A	False
-f, --fields	text	Fields.	('subject_category', 'object_category')
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom crosstab

Write sssom summary cross-tabulated by categories.

Usage:

sssom crosstab [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-t, --transpose	boolean	N/A	False
-f, --fields	text	Fields.	('subject_category', 'object_category')
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom dedupe

Remove lower confidence duplicate lines from an SSSOM file.

Usage:

sssom dedupe [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom diff

Compare two SSSOM files.

The output is a new SSSOM file with the union of all mappings, and injected comments indicating uniqueness to set1 or set2.

Usage:

sssom diff [OPTIONS] INPUTS...

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom dosql

Each of the N inputs is assigned a table name df1, df2, ..., dfN

Alternatively, the filenames can be used as table names - these are first stemmed E.g. ~/dir/my.sssom.tsv becomes a table called 'my'

Examples:

$ sssom dosql -Q "SELECT * FROM df1 WHERE confidence>0.5 ORDER BY confidence" my.sssom.tsv

$ sssom dosql -Q "SELECT file1.*,file2.object_id AS ext_object_id, file2.object_label AS ext_object_label FROM file1 INNER JOIN file2 WHERE file1.object_id = file2.subject_id" FROM file1.sssom.tsv file2.sssom.tsv

Usage:

sssom dosql [OPTIONS] [INPUTS]...

Options:

Name	Type	Description	Default
-Q, --query	text	SQL query. Use "df" as table name.	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom filter

Filter a dataframe by dynamically generating queries based on user input.

e.g. sssom filter --subject_id x:% --subject_id y:% --object_id y:% --object_id z:% tests/data/basic.tsv

yields the query:

"SELECT * FROM df WHERE (subject_id LIKE 'x:%' OR subject_id LIKE 'y:%') AND (object_id LIKE 'y:%' OR object_id LIKE 'z:%') " and displays the output.

:param input: DataFrame to be queried over. :param output: Output location. :param kwargs: Filter options provided by user which generate queries (e.g.: --subject_id x:%).

Usage:

sssom filter [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--record_id	text	N/A	Sentinel.UNSET
--subject_id	text	N/A	Sentinel.UNSET
--subject_label	text	N/A	Sentinel.UNSET
--subject_category	text	N/A	Sentinel.UNSET
--predicate_id	text	N/A	Sentinel.UNSET
--predicate_label	text	N/A	Sentinel.UNSET
--predicate_modifier	text	N/A	Sentinel.UNSET
--object_id	text	N/A	Sentinel.UNSET
--object_label	text	N/A	Sentinel.UNSET
--object_category	text	N/A	Sentinel.UNSET
--mapping_justification	text	N/A	Sentinel.UNSET
--author_id	text	N/A	Sentinel.UNSET
--author_label	text	N/A	Sentinel.UNSET
--reviewer_id	text	N/A	Sentinel.UNSET
--reviewer_label	text	N/A	Sentinel.UNSET
--creator_id	text	N/A	Sentinel.UNSET
--creator_label	text	N/A	Sentinel.UNSET
--license	text	N/A	Sentinel.UNSET
--subject_type	text	N/A	Sentinel.UNSET
--subject_source	text	N/A	Sentinel.UNSET
--subject_source_version	text	N/A	Sentinel.UNSET
--object_type	text	N/A	Sentinel.UNSET
--object_source	text	N/A	Sentinel.UNSET
--object_source_version	text	N/A	Sentinel.UNSET
--predicate_type	text	N/A	Sentinel.UNSET
--mapping_provider	text	N/A	Sentinel.UNSET
--mapping_source	text	N/A	Sentinel.UNSET
--mapping_cardinality	text	N/A	Sentinel.UNSET
--cardinality_scope	text	N/A	Sentinel.UNSET
--mapping_tool	text	N/A	Sentinel.UNSET
--mapping_tool_id	text	N/A	Sentinel.UNSET
--mapping_tool_version	text	N/A	Sentinel.UNSET
--mapping_date	text	N/A	Sentinel.UNSET
--publication_date	text	N/A	Sentinel.UNSET
--review_date	text	N/A	Sentinel.UNSET
--confidence	text	N/A	Sentinel.UNSET
--reviewer_agreement	text	N/A	Sentinel.UNSET
--curation_rule	text	N/A	Sentinel.UNSET
--curation_rule_text	text	N/A	Sentinel.UNSET
--subject_match_field	text	N/A	Sentinel.UNSET
--object_match_field	text	N/A	Sentinel.UNSET
--match_string	text	N/A	Sentinel.UNSET
--subject_preprocessing	text	N/A	Sentinel.UNSET
--object_preprocessing	text	N/A	Sentinel.UNSET
--similarity_score	text	N/A	Sentinel.UNSET
--similarity_measure	text	N/A	Sentinel.UNSET
--see_also	text	N/A	Sentinel.UNSET
--issue_tracker_item	text	N/A	Sentinel.UNSET
--other	text	N/A	Sentinel.UNSET
--comment	text	N/A	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom help

Echoes help for subcommands.

Usage:

sssom help [OPTIONS] SUBCOMMAND

Options:

Name	Type	Description	Default
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom invert

Invert subject and object IDs such that all subjects have the prefix provided.

:param input: SSSOM TSV file. :param subject_prefix: Prefix of all subject_ids. :param merge_inverted: If True (default), add inverted dataframe to input else, just return inverted data. :param update_justification: If True (default), the justification is updated to "sempav:MappingInversion", else it is left as it is. :param inverse_map: YAML file providing the inverse mapping for predicates. :param output: SSSOM TSV file with columns sorted.

Usage:

sssom invert [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-P, --subject-prefix	text	Invert subject_id and object_id such that all subject_ids have the same prefix.	Sentinel.UNSET
--merge-inverted / --no-merge-inverted	boolean	If True (default), add inverted mappings to the input mapping set, else, just return inverted mappings as a separate mapping set.	True
--update-justification / --no-update-justification	boolean	If True (default), the justification is updated to 'sempav:MappingInversion', else it is left as it is.	True
--inverse-map	text	Path to file that contains the inverse predicate dictionary.	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom merge

Merge multiple MappingSetDataFrames into one.

Usage:

sssom merge [OPTIONS] [INPUTS]...

Options:

Name	Type	Description	Default
-R, --reconcile	boolean	If true, the deduplicate (i.e., remove redundant lower confidence mappings) and reconcile (if msdf contains a higher confidence negative mapping, then remove lower confidence positive one. If confidence is the same, prefer HumanCurated. If both HumanCurated, prefer negative mapping)	False
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
--condense / --no-condense	boolean	Automatically condense slots upon writing.	True
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom parse

Parse a file in one of the supported formats (such as obographs) into an SSSOM TSV file.

Usage:

sssom parse [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-I, --input-format	choice (csv | tsv | obographs-json | alignment-api-xml | json | rdf)	The string denoting the input format.	Sentinel.UNSET
-m, --metadata	path	The path to a file containing the sssom metadata (including prefix_map) to be used.	Sentinel.UNSET
-C, --prefix-map-mode	choice (metadata_only | sssom_default_only | merged)	Defines whether the prefix map in the metadata should be extended or replaced with the SSSOM default prefix map.	metadata_only
-p, --clean-prefixes / --no-clean-prefixes	boolean	If True (default), prefixes the mapping set does not use are removed from its curie_map.	True
--strict-clean-prefixes / --no-strict-clean-prefixes	boolean	If True (default), --clean-prefixes fails on a used prefix that the prefix map does not declare. If False, it declares the prefix with a placeholder IRI.	True
-E, --embedded-mode / --non-embedded-mode	boolean	If False, the resultant SSSOM file will be saved in the 'filename'.tsv provided by -o/--output option AND the metadata gets saved in the 'filename'.yml.	True
-F, --mapping-predicate-filter	text	A list of predicates or a file path containing the list of predicates to be considered.	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
--condense / --no-condense	boolean	Automatically condense slots upon writing.	True
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom partition

Partition an SSSOM into one file for each strongly connected component.

Usage:

sssom partition [OPTIONS] [INPUTS]...

Options:

Name	Type	Description	Default
-d, --output-directory	path	Output directory path.	/home/runner/work/sssom-py/sssom-py
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom ptable

Convert an SSSOM file to a ptable for kboom/boomer <https://github.com/INCATools/boomer>_.

Usage:

sssom ptable [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-W, --inverse-factor	text	Inverse factor.	Sentinel.UNSET
--default-confidence	float range (between 0 and 1)	Default confidence to be assigned if absent.	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom reconcile-prefixes

Reconcile prefix_map based on provided YAML file.

Usage:

sssom reconcile-prefixes [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-p, --reconcile-prefix-file	text	Provide YAML file with prefix reconciliation information.	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom remove

Remove mappings from an input mapping.

Usage:

sssom remove [OPTIONS] INPUT

Options:

Name	Type	Description	Default
--remove-map	path	Mapping file path that needs to be removed from input.	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom rewire

Rewire an RDF graph, such as an OWL ontology, by replacing every mapped entity with its mapping partner. A graph expressed in one vocabulary is then expressed in another.

The command applies each mapping from subject to object: it replaces the mapping's subject with the mapping's object wherever the subject occurs in the graph. It uses only mappings with a chosen predicate. By default these are owl:equivalentClass and owl:equivalentProperty, and the --predicates option chooses others in their place. Only the equivalences keep the graph's meaning. A skos:broadMatch mapping, for example, puts the broader entity in every triple about the narrower one, including the triples that describe it. Negated mappings, and mappings to sssom:NoTermFound, are skipped. When no mapping is left to rewire by, the command warns, or fails with --strict.

When an entity has several candidate replacements, the command chooses the one under the predicate listed first in --predicates, so their order is the order of preference. The two default predicates are equally preferred. When candidates are equally preferred, --precedence chooses between them by the prefix of the replacement. Without --precedence, the command fails because the choice is ambiguous.

Examples:

$ sssom rewire -I xml -m tests/data/cob-to-external.tsv --precedence PR tests/data/cob.owl $ sssom rewire -m tests/data/rewire-predicates.tsv --predicates skos:exactMatch tests/data/rewire-predicates.ttl

Usage:

sssom rewire [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-m, --mapping-file	text	Path to SSSOM file.	Sentinel.UNSET
-I, --input-format	text	Ontology input format.	turtle
-O, --output-format	text	Ontology output format.	turtle
--precedence	text	List of prefixes in order of precedence.	Sentinel.UNSET
--predicates	text	Mapping predicates to rewire by, as CURIEs or IRIs, in order of preference, in place of the default ones. Repeat the option, or separate the values with commas.	Sentinel.UNSET
--strict	boolean	Fail, instead of only warning, when no mapping is left to rewire by.	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom serve-rdf

Serve the SSSOM file as an RDF SPARQL endpoint.

Usage:

sssom serve-rdf [OPTIONS] INPUT

Options:

Name	Type	Description	Default
--hydrate / --no-hydrate	boolean	Infer S-P-O simple triples from axioms. On by default.	True
--host	text	N/A	127.0.0.1
--port	integer	N/A	8000
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom sort

Sort DataFrame columns canonically.

Usage:

sssom sort [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-k, --by-columns	boolean	Sort columns of DataFrame canonically.	True
-r, --by-rows	boolean	Sort rows by DataFrame column #1 (ascending).	True
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom sparql

Run a SPARQL query.

Usage:

sssom sparql [OPTIONS]

Options:

Name	Type	Description	Default
-c, --config	filename	N/A	Sentinel.UNSET
-e, --url	text	N/A	Sentinel.UNSET
-g, --graph	text	N/A	Sentinel.UNSET
--object-labels / --no-object-labels	boolean	if set, includes object labels	None
-l, --limit	integer	N/A	Sentinel.UNSET
-P, --prefix		N/A	Sentinel.UNSET
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom split

Split input file into multiple output broken down by prefixes.

Usage:

sssom split [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-d, --output-directory	path	Output directory path.	/home/runner/work/sssom-py/sssom-py
--method	choice (disjoint-indexes | dense-indexes)	N/A	Sentinel.UNSET
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET

sssom validate

Produce an error report for an SSSOM file.

Usage:

sssom validate [OPTIONS] INPUT

Options:

Name	Type	Description	Default
--validation-types, -V	choice (SchemaValidationType.JsonSchema | SchemaValidationType.Shacl | SchemaValidationType.Sparql | SchemaValidationType.PrefixMapCompleteness | SchemaValidationType.StrictCurieFormat)	N/A	[<SchemaValidationType.JsonSchema: 'JsonSchema'>, <SchemaValidationType.PrefixMapCompleteness: 'PrefixMapCompleteness'>, <SchemaValidationType.StrictCurieFormat: 'StrictCurieFormat'>]
--report-format, -r	choice (pretty | raw)	How to show the problems. 'pretty' lists each problem once in the error message; 'raw' logs every result as LinkML reports it.	pretty
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
-h, --help	boolean	Show this message and exit.	Sentinel.UNSET