Skip to content

Simple Standard for Sharing Ontological Mappings (SSSOM)

SSSOM banner

The Simple Standard for Sharing Ontological Mappings (SSSOM) is a community-driven standard designed to facilitate the exchange and integration of semantic entity mappings. As data interoperability becomes increasingly crucial across various domains, SSSOM provides a standardized format to share mappings, enabling researchers and developers to more easily connect and utilize diverse datasets. By establishing a common framework, SSSOM enhances the consistency, quality, and discoverability of mappings, thereby supporting more effective data integration and analysis.

  • Standardization: SSSOM provides a unified format for representing semantic, or ontological, mappings, making it easier for different systems and organizations to exchange mapping data consistently.
  • Interoperability: By using SSSOM, data from diverse sources can be integrated more seamlessly, allowing for improved data analysis and research across various fields, including biology, healthcare, and information technology.

Beyond defining the standard itself, the SSSOM Core Team and the SSSOM community also develop reference tools and software libraries for working with the standard.

SSSOM at a glance: Model and Exchange Format

Basic model

The data model of SSSOM is centered around two fundamental concepts: mappings and mapping sets.

A SSSOM mapping is a statement that there is a correspondence between two semantic entities. It comprises two components:

  1. The core mapping (or raw mapping), which is a triple <subject, predicate, object> that represents the correspondence itself between a subject entity, for example a class in an ontology, and an object entity, for example an identifier in some database, via a semantic mapping predicate, for example skos:exactMatch.
  2. Metadata that provide supplementary pieces of information about the core mapping. This notably includes information about the provenance of the statement (for example, who authored the statement), the confidence with which the mappings holds, and its justification (a reason that supports the fidelity of the mapping between the subject and the object, such as expert review, or exact lexical matching on the entities' primary names).

A SSSOM mapping set is a collection of SSSOM mappings. Mapping sets can also be associated with metadata, such as license statements, or a description.

The SSSOM/TSV format

The main format proposed by the SSSOM standard to exchange mapping sets is the SSSOM/TSV format. Here is a basic example of a file in that format:

#curie_map:
#  FOODON: http://purl.obolibrary.org/obo/FOODON_
#  KF_FOOD: https://kewl-foodie.inc/food/
#  orcid: https://orcid.org/
#mapping_set_id: https://w3id.org/sssom/tutorial/example1.sssom.tsv
#mapping_set_description: Manually curated alignment of KEWL FOODIE INC internal food and nutrition database with Food Ontology (FOODON). Intended to be used for ontological analysis and grouping of KEWL FOODIE INC related data.
#license: https://creativecommons.org/licenses/by/4.0/
#mapping_date: 2022-05-02
subject_id  subject_label   predicate_id    object_id   object_label    mapping_justification   author_id   confidence  comment
KF_FOOD:F001    apple   skos:exactMatch FOODON:00002473 apple (whole)   semapv:ManualMappingCuration    orcid:0000-0002-7356-1779   0.95    "We could map to FOODON:03310788 instead to cover sliced apples, but only ""whole"" apple types exist."
KF_FOOD:F002    gala    skos:exactMatch FOODON:00003348 Gala apple (whole)  semapv:ManualMappingCuration    orcid:0000-0002-7356-1779   1   
KF_FOOD:F003    pink    skos:exactMatch FOODON:00004186 Pink apple (whole)  semapv:ManualMappingCuration    orcid:0000-0002-7356-1779   0.9 "We could map to FOODON:00004187 instead which more specifically refers to ""raw"" Pink apples. Decided against to be consistent with other mapping choices."
KF_FOOD:F004    braeburn    skos:broadMatch FOODON:00002473 apple (whole)   semapv:ManualMappingCuration    orcid:0000-0002-7356-1779   1

General

Publications

Related software

  • sssom-py (reference implementation of the standard, a toolkit and API for processing mappings, written in Python)
  • SSSOM-Java (an implementation of the SSSOM standard for the Java language)

The SSSOM Core Team

Contact

The preferred way to contact the SSSOM team is through the issue tracker (for problems with SSSOM) or the GitHub discussion forums (for general questions).

You can find any of the members of the SSSOM core team on GitHub. Their GitHub profiles usually also provide email addresses.

You can also reach us in the OBO Foundry Slack, in the #sssom channel.

Steering committee

The Steering committee is a self-appointed group of SSSOM contributors, whose aim is to drive the evolution of the standard and coordinate community contributions.

Documentation/specification editors

Contributors

Acknowledgements