sssom

What it is and what it does

SSSOM is a Python library and CLI for working with SSSOM, a standard format for sharing ontology mappings. It reads and writes mapping tables in TSV format, parses them into a mapping set dataframe object that bundles a pandas DataFrame, a curies.Converter for URI handling, and mapping metadata. The library can export mappings to JSON, OWL, and RDF formats, making it a bridge between tabular mapping data and semantic web representations.

The package is designed for ontology curators, bioinformaticians, and knowledge engineers who need to manage, validate, and transform ontology mappings at scale. It integrates with LinkML for schema validation and RDFlib for semantic output, and provides a command-line interface alongside its Python API. The library is actively maintained and part of the broader Mapping Commons ecosystem.

Use it for:

• Parse and manipulate SSSOM TSV files from mapping repositories to extract and analyze ontology mappings programmatically.
• Convert ontology mappings from TSV to OWL or RDF/Turtle format for use in semantic web applications and triple stores.
• Validate mapping tables against the SSSOM schema and enrich them with metadata using the pandas DataFrame interface.
• Build mapping pipelines that read, filter, and export mappings in multiple formats for downstream ontology alignment tools.
• Integrate ontology mappings into knowledge graphs by exporting to RDF and loading into graph databases.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Parse, validate, and convert SSSOM (Simple Standard for Sharing Ontology Mappings) files between TSV, JSON, OWL, and RDF formats, with built-in support for ontology mapping metadata and curation.

Yes. The package is actively maintained, has low install friction, carries no known vulnerabilities, and is MIT-licensed. Install it if you work with ontology mappings in SSSOM format or need to convert between mapping representations. Note that JSON and RDF export formats are still evolving—pin a version if stability is critical for your workflow.

Install

sssom on PyPI

pip install sssom

uv add sssom

poetry add sssom

Installing sssom

Before you install

Low friction installation with a pure-Python wheel and active maintenance—last release 83 days ago. Requires Python 3.10 or later and pulls in 12 runtime dependencies including linkml, pandas, rdflib, and sparqlwrapper; no compiled dependencies.

License in practice

MIT license permits unrestricted use, modification, and distribution in both open-source and commercial projects with minimal obligations.

Quickstart

import sssom

url = "https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_eye_impc.sssom.tsv"
msdf = sssom.parse_tsv(url)
sssom.write_json(msdf, "output.json")

Requires Python 3.10 or later; JSON and RDF export formats are not yet finalized and may change in future releases.

Verify before relying

• Stability and completeness of JSON and RDF export formats—documentation warns these are not yet finalized.
• Performance characteristics with large mapping sets or complex ontologies.
• Specific SSSOM specification version(s) supported by this release.

Package facts

Evidence: sssom-0.4.21-py3-none-any.whl

Tags

More Information Analysis packages