Multi species composite ontologies

cmungall edited this page Oct 30, 2014 · 5 revisions

Multi-species composite ontologies

Authors and contributors:

  • Chris Mungall (author)
  • Carlo Torniai (author)
  • Melissa Haendel (author)

Date: 2012

Document Type: ontology_usage_article

Abstract

There are different ways of integrating a multi-species ontology with species-specific ones. This article describes the composite/merger strategy

Please read Multi-species-importer-ontologies before this document.

Problem

The importer/collector strategy can deal with bridging multiple anatomy ontologies, but introduces complexities and redundancy.

This article describes an alternate approach in which species anatomy classes are collapsed into their subsuming Uberon class

The two composite ontologies regularly created are:

(obo-format versions are available)

Multi-species composite modules

Using this strategy a new ontology is created that contains all core uberon classes, plus leaf branches from other AOs, consisting of structures for which there is no generalized taxonomic equivalent in Uberon.

The following OBO-Edit screenshot shows how human, zebrafish and human specific classes inherit from generic classes such as somite in Uberon:

somite

(Uberon terms are green)

This approach differs from the importer strategy is that there is no ZFA or XAO class 'somite' in the merged ontology. A composite ontology solves the problem of redundancy.

Safe axiom merging

The axioms for leaf classes can be brought in safely, as the referent of the leaf classes remains species-specific.

When a non-leaf class is merged in, its axioms are translated to a taxon GCI, preserving equivalence and avoiding introduction of contradictions.

Advantages and disadvantages

Compared to the importer strategy, there is less redundancy (although there may still be multiple classes with labels like 'somite N in species S'.

Variants

A composite ontology can be used in conjunctions with ontology bridging axioms

See Also:

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