JBMS Paper: The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology

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JBMS Paper: The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology image

Our paper on the Poriferan Ontology (PORO) has been published in JBMS.

Why a separate ontology?

We made the decision to create a distinct federated ontology for sponges in part because there is so little overlap between sponge anatomy and the rest of Uberon. Uberon represents many bilaterian classes such as organ , mesoderm , brain , nervous system , compound organ and so on, but these are not found in sponges.

Managing the ontology as a separate unit makes it easier for the domain experts to make changes as required. At the same time, the ontology is federated, and ultra-generic uberon classes are used where appropriate. Future versions of the composite and collected versions of Uberon will include PORO as modular units.

Cardinality

One modeling difference from Uberon is the frequent use of OWL cardinality constraints. E.g.

'triaxone’ EquivalentTo 
 spicule and (has_component exactly 3 ‘ray axis’) and (has_component exactly 6 ‘ray’)

This necessitates the use of a DL reasoner like HermiT for managing PORO.

Reference

Thacker, R.W. et al (2014). Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Journal of Biomedical Semantics, 5(34), 21. doi:10.1186/2041-1480-5-34 http://www.jbiomedsem.com/content/5/1/34

September 23, 2014 |

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