Command Line Interface

sssom_pydantic automatically installs the command sssom_pydantic. See sssom_pydantic --help for usage details.

sssom_pydantic

CLI for sssom_pydantic.

Usage

sssom_pydantic [OPTIONS] COMMAND [ARGS]...

bridge

Write OWL bridge axioms in Functional OWL (OFN).

Usage

sssom_pydantic bridge [OPTIONS]

Options

-i, --input <input>: Path to a local file or URL to a remote file. If not given, will get input from STDIN

-o, --output <output>: Path to a local file to output. If not given, will write to STDOUT

--cutoff <cutoff>: Minimum confidence cutoff. Mappings w/o confidence are assumed to have 1.0 confidence

-a, --mapping-annotations: If set, propagates annotations from mappings into bridge

-d, --declarations: If set, adds declarations (and labels, when available)

format

Lint a SSSOM TSV file.

Usage

sssom_pydantic format [OPTIONS] PATH

Options

--standardize: Standardize against Bioregistry preferred CURIE prefixes and (RDF) URI prefixes

--relabel: Re-label all subjects and objects using PyOBO

--drop-duplicates

Arguments

PATH: Required argument

merge

Merge SSSOM documents.

Usage

sssom_pydantic merge [OPTIONS]

Options

-i, --input <input>: Path to a local file or URL to a remote file. If not given, will get input from STDIN

-o, --output <output>: Path to a local file to output. If not given, will write to STDOUT

--mapping-set-id <mapping_set_id>: The ID for the merged mapping set

--merge-manual

--standardize: Standardize against Bioregistry preferred CURIE prefixes and (RDF) URI prefixes

subset

Implement the filter workflow for a given prefix.

This workflow removes negative mappings, unsure mappings, and non-exact mappings.

Usage

sssom_pydantic subset [OPTIONS]

Options

-p, --prefix <prefix>: Required The prefix that becomes the subjects of all mappings. If used in combination with –standardize, will get automatically standardized.

--target-prefix <target_prefix>: The prefix that becomes the object of all mappings. If used in combination with –standardize, will get automatically standardized.

-i, --input <input>: Path to a local file or URL to a remote file. If not given, will get input from STDIN

-o, --output <output>: Path to a local file to output. If not given, will write to STDOUT

--justification-policy

When inverting mappings, should the justification be derived to semapv:MappingInversion and reference be made back to the original mapping, or should the original jusitication be retained?

Options:: retain | derive

--standardize: Standardize against Bioregistry preferred CURIE prefixes and (RDF) URI prefixes

web

Run the web app (with SQL backend).

Usage

sssom_pydantic web [OPTIONS]

Options

--add-examples: Add example SSSOM records.

--tab

--host <host>

Default:: '0.0.0.0'

--port <port>

Default:: 8876

Here’s an end-to-end workflow for merging several SSSOM documents together, filtering to an appropriate subset, and generating an OWL bridge.

$ sssom_pydantic subset \
    --input https://w3id.org/biopragmatics/biomappings/sssom/biomappings.sssom.tsv \
    --prefix CHMO \
    --target-prefix FIX \
    --standardize \
    --output biomappings-chmo-fix.sssom.tsv
$ sssom_pydantic subset \
    --input https://github.com/nfdi-de/section-metadata-wg-onto/raw/refs/heads/main/sssom/data/positive.sssom.tsv \
    --prefix CHMO \
    --target-prefix FIX \
    --standardize \
    --output nfdi-chmo-fix.sssom.tsv
$ sssom_pydantic merge \
   --input https://github.com/NFDI4Chem/rsc-cmo/raw/0e53ad96495576890c217ebdddac7fadc2e9e0b1/src/mappings/fix-mappings.sssom.tsv \
   --input nfdi-chmo-fix.sssom.tsv \
   --input biomappings-chmo-fix.sssom.tsv \
   --standardize \
   --merge-manual \
   --mapping-set-id https://example.org/chmo-fix.sssom.tsv \
   | sssom_pydantic bridge \
    --output chmo-fix-bridge.ofn