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Uberon Ontology

Ontology mapping Data Integration

Uberon Case Study Infobox

  • Author: Damien Goutte-Gattat (@gouttegd)
  • Last updated: 2025-02-17
  • Mapping Type: Mapping Type
  • Status of this case study: Status

Mapping anatomical entities across anatomy ontologies.

Domain

Biology.

Purpose of the mapping

Creating a unified multi-species anatomy ontology, allowing consistent annotation of biological data.

Other purpose of the mapping

None given.

Type of mapped resources

Entities from from the species-neutral anatomy ontology Uberon and cell type ontology CL, mapped to entities from species-specific anatomy and cell type ontologies such as:

  • FlyBase’s Drosophila Anatomy Ontology (FBbt),
  • XenBase’s Xenopus Anatomy Ontology (XAO),
  • ZFIN’s Zebrafish Anatomy and Development Ontology (ZFA),
  • WormBase’s C. elegans Gross Anatomy Ontology (WBbt), etc.

Mappings between FBbt and Uberon/CL (in SSSOM/TSV format) can be found here.

Tools used for creating the mapping

Mappings are created by manual curation.

Type of mapping relations

Most mappings between Uberon/CL and the species-specific anatomy ontologies use a handful of dedicated mapping predicates specifically created to represent cross-species mappings:

  • https://w3id.org/semapv/vocab/crossSpeciesExactMatch
  • https://w3id.org/semapv/vocab/crossSpeciesBroadMatch
  • https://w3id.org/semapv/vocab/crossSpeciesNarrowMatch
  • https://w3id.org/semapv/vocab/crossSpeciesRelatedMatch

Examples (samples) of different types of mapping implementations

For an example of what we do with the mappings: the Uberon-to-FBbt ontology bridge, used to merge Uberon and FBbt together (a detailed explanation of how this bridge is derived from the Uberon/FBbt mappings is available here).