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	None
--version	boolean	Show the version and exit.	False
--help	boolean	Show this message and exit.	False

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	None
--curie_map	text	N/A	None
--mappings	text	N/A	None
--mapping_set_id	text	N/A	None
--mapping_set_version	text	N/A	None
--mapping_set_source	text	N/A	None
--mapping_set_title	text	N/A	None
--mapping_set_description	text	N/A	None
--mapping_set_confidence	text	N/A	None
--creator_id	text	N/A	None
--creator_label	text	N/A	None
--license	text	N/A	None
--subject_type	text	N/A	None
--subject_source	text	N/A	None
--subject_source_version	text	N/A	None
--object_type	text	N/A	None
--object_source	text	N/A	None
--object_source_version	text	N/A	None
--predicate_type	text	N/A	None
--mapping_provider	text	N/A	None
--cardinality_scope	text	N/A	None
--mapping_tool	text	N/A	None
--mapping_tool_id	text	N/A	None
--mapping_tool_version	text	N/A	None
--mapping_date	text	N/A	None
--publication_date	text	N/A	None
--subject_match_field	text	N/A	None
--object_match_field	text	N/A	None
--subject_preprocessing	text	N/A	None
--object_preprocessing	text	N/A	None
--similarity_measure	text	N/A	None
--curation_rule	text	N/A	None
--curation_rule_text	text	N/A	None
--see_also	text	N/A	None
--issue_tracker	text	N/A	None
--other	text	N/A	None
--comment	text	N/A	None
--extension_definitions	text	N/A	None
--help	boolean	Show this message and exit.	False

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.	None
-s, --statsfile	text	N/A	None
--help	boolean	Show this message and exit.	False

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 | turtle | ttl | xml | nt)	Desired output format.	None
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
--condense / --no-condense	boolean	Automatically condense slots upon writing.	True
--help	boolean	Show this message and exit.	False

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')
--help	boolean	Show this message and exit.	False

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')
--help	boolean	Show this message and exit.	False

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'>
--help	boolean	Show this message and exit.	False

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'>
--help	boolean	Show this message and exit.	False

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.	None
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--help	boolean	Show this message and exit.	False

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	None
--subject_id	text	N/A	None
--subject_label	text	N/A	None
--subject_category	text	N/A	None
--predicate_id	text	N/A	None
--predicate_label	text	N/A	None
--predicate_modifier	text	N/A	None
--object_id	text	N/A	None
--object_label	text	N/A	None
--object_category	text	N/A	None
--mapping_justification	text	N/A	None
--author_id	text	N/A	None
--author_label	text	N/A	None
--reviewer_id	text	N/A	None
--reviewer_label	text	N/A	None
--creator_id	text	N/A	None
--creator_label	text	N/A	None
--license	text	N/A	None
--subject_type	text	N/A	None
--subject_source	text	N/A	None
--subject_source_version	text	N/A	None
--object_type	text	N/A	None
--object_source	text	N/A	None
--object_source_version	text	N/A	None
--predicate_type	text	N/A	None
--mapping_provider	text	N/A	None
--mapping_source	text	N/A	None
--mapping_cardinality	text	N/A	None
--cardinality_scope	text	N/A	None
--mapping_tool	text	N/A	None
--mapping_tool_id	text	N/A	None
--mapping_tool_version	text	N/A	None
--mapping_date	text	N/A	None
--publication_date	text	N/A	None
--review_date	text	N/A	None
--confidence	text	N/A	None
--reviewer_agreement	text	N/A	None
--curation_rule	text	N/A	None
--curation_rule_text	text	N/A	None
--subject_match_field	text	N/A	None
--object_match_field	text	N/A	None
--match_string	text	N/A	None
--subject_preprocessing	text	N/A	None
--object_preprocessing	text	N/A	None
--similarity_score	text	N/A	None
--similarity_measure	text	N/A	None
--see_also	text	N/A	None
--issue_tracker_item	text	N/A	None
--other	text	N/A	None
--comment	text	N/A	None
--help	boolean	Show this message and exit.	False

sssom help

Echoes help for subcommands.

Usage:

sssom help [OPTIONS] SUBCOMMAND

Options:

Name	Type	Description	Default
--help	boolean	Show this message and exit.	False

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.	None
--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.	None
--help	boolean	Show this message and exit.	False

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
--help	boolean	Show this message and exit.	False

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.	None
-m, --metadata	path	The path to a file containing the sssom metadata (including prefix_map) to be used.	None
-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), records with unknown prefixes are removed from the SSSOM file.	True
--strict-clean-prefixes / --no-strict-clean-prefixes	boolean	If True (default), clean_prefixes(strict = True).	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.	None
-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
--help	boolean	Show this message and exit.	False

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
--help	boolean	Show this message and exit.	False

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.	None
--default-confidence	float range (between 0 and 1)	Default confidence to be assigned if absent.	None
--help	boolean	Show this message and exit.	False

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.	None
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--help	boolean	Show this message and exit.	False

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.	None
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--help	boolean	Show this message and exit.	False

sssom rewire

Example:

$ sssom rewire -I xml -i tests/data/cob.owl -m tests/data/cob-to-external.tsv --precedence PR

Usage:

sssom rewire [OPTIONS] INPUT

Options:

Name	Type	Description	Default
-m, --mapping-file	text	Path to SSSOM file.	None
-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.	None
-o, --output	filename	Path of SSSOM output file.	<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>
--help	boolean	Show this message and exit.	False

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
--help	boolean	Show this message and exit.	False

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
--help	boolean	Show this message and exit.	False

sssom sparql

Run a SPARQL query.

Usage:

sssom sparql [OPTIONS]

Options:

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

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	None
--help	boolean	Show this message and exit.	False

sssom validate

Produce an error report for an SSSOM file.

Usage:

sssom validate [OPTIONS] INPUT

Options:

Name	Type	Description	Default
--validation-types, -V	choice (JsonSchema | Shacl | Sparql | PrefixMapCompleteness | StrictCurieFormat)	N/A	[<SchemaValidationType.JsonSchema: 'JsonSchema'>, <SchemaValidationType.PrefixMapCompleteness: 'PrefixMapCompleteness'>, <SchemaValidationType.StrictCurieFormat: 'StrictCurieFormat'>]
--propagate / --no-propagate	boolean	Automatically propagate condensed slots upon parsing.	True
--help	boolean	Show this message and exit.	False