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Simple Standard for Sharing Ontological Mappings (SSSOM)

SSSOM banner

SSSOM is the Simple Standard for Sharing Ontological Mappings. It comprises three distinct components that are intended to be used together to facilitate the exchange of semantic mappings:

  1. a machine-readable and extensible vocabulary to describe metadata of mappings;
  2. a data model to represent mappings and their associated metadata;
  3. several file formats to represent sets of mappings on disk and on the network.

Beyond defining the standard itself, the SSSOM Core Team also aims to implement open and community-driven collaborative workflows designed to evolve the standard continuously to address changing requirements and mapping practices, and to provide reference tools and software libraries for working with the standard.

SSSOM at a glance

Basic concepts

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 of some sort 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 pertaining to the provenance of the statement (for example, who emitted the statement, in other words who decided that the subject and the object should be mapped) and its justification (why should the subject and the object be mapped).

A SSSOM mapping set is a collection of SSSOM mappings, with its own metadata.

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 Toolkit (reference implementation of the standard, in Python)

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.

Documentation/specification editors

Contributors

Acknowledgements

Funding

Phenomics First

Parts of this work were funded by Phenomics First (NIH / NHGRI #1RM1HG010860-01):

  • design of the specification;
  • integration of sssom-py into Mondo;
  • development of the sssom-py command-line interface.

Bosch Gift to LBNL

Parts of this work were funded by a gift from Bosch to the Lawrence Berkely National Laboratories (LBNL):

  • sssom-py:
    • IO functionality,
    • file format converters,
    • testing framework,
    • deployment on the Python Package Index;
  • SSSOM documentation (this document).

Significant contributions

  • The Link Model Language (LinkML) project (used to define the data model).
  • Harvard Medical School (through significant contributions of Charlie Hoyt, including refactoring of sssom-py, release and quality control infrastructure).