Multi species importer ontologies

Chris Mungall edited this page Aug 12, 2014 · 3 revisions

Multi-species importer ontologies

Authors and contributors:

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

Please read inter-anatomy-ontology-bridge-ontologies before this one.

Problem

Ontologies such as ZFA, MA and FMA all contain structures with labels such as 'vertebra' or 'lung' (the latter is not in the ZFA, as zebrafish do not have lungs). How do we connect between these classes and the subsuming Uberon structure?

Multi-species importers and bridge modules

The importer strategy uses recursive OWL import chains to connect multiple species anatomy ontologies with Uberon at the desired level of taxonomic granularity. An importer/collector module for a taxon imports the relevant species-specific anatomy ontologies, together with bridging axioms that connect the species anatomy class with its generic uberon subsumer. These may be subclass axioms, equivalence axioms, or taxonomic equivalence axioms. In addition, each bridge file adds 'obo foundry unique label' properties which 're-label' existing classes, such that FMA:lung has the unique label 'adult human lung'.

This is illustrated via Figure 3 from the uberon paper:

Figure 3

Figure legend: Import chain of taxonomically arranged Uberon modules. Each combined module at different taxonomic levels imports the relevant native ontologies as well as bridge files that specify the logical definitions. The number of equivalent class (EC) or SubClass (SC) axioms in each bridge file are shown, illustrating the contributions of each ontology to the total infrastructure.

(Note the ontology landscape continues to change since this paper was published, but even if the individual ontologies change, the principle is the same)

Advantages

  • retains all logical and non-logical axioms of source ontology; reasoning 'just works'

  • allows incorporation at desired level of granularity

Disadvantages

  • resulting import chain is very large

  • resulting ontology is highly latticed and difficult to navigate

  • differences between a species class and the uberon parent is often trivial or non-existent, resulting in duplicated portions of the hierarchy.

  • Many tools not configured to show 'obo foundry unique label', which means that for example collected-metazoa.owl will display 10 or so classes with the rdfs:label of 'brain'

  • obo foundry unique label is only generated for primary label, not existing synonyms.

  • Difficult to use with obo-format, as obo-format tools do not handle imports well