The Porifera Ontology (PORO): Enhancing sponge systematics with an anatomy ontology

Robert W. Thacker, Maria C. Díaz, Adeline Kerner, Régine Vignes-Lebbe, Erik Segerdell, Melissa Haendel, Christopher J. Mungall

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Background: Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. Results: The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/.Conclusions: By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

Original languageEnglish (US)
Article number39
JournalJournal of Biomedical Semantics
Volume5
Issue number1
DOIs
StatePublished - Sep 8 2014

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Porifera
Ontology
Anatomy
Strigiformes
Neurology
Phylogeny
Nervous System
Databases

Keywords

  • Evolution
  • Morphology
  • Phylogenetics
  • Taxonomic identification

ASJC Scopus subject areas

  • Information Systems
  • Computer Science Applications
  • Computer Networks and Communications
  • Health Informatics

Cite this

Thacker, R. W., Díaz, M. C., Kerner, A., Vignes-Lebbe, R., Segerdell, E., Haendel, M., & Mungall, C. J. (2014). The Porifera Ontology (PORO): Enhancing sponge systematics with an anatomy ontology. Journal of Biomedical Semantics, 5(1), [39]. https://doi.org/10.1186/2041-1480-5-39

The Porifera Ontology (PORO) : Enhancing sponge systematics with an anatomy ontology. / Thacker, Robert W.; Díaz, Maria C.; Kerner, Adeline; Vignes-Lebbe, Régine; Segerdell, Erik; Haendel, Melissa; Mungall, Christopher J.

In: Journal of Biomedical Semantics, Vol. 5, No. 1, 39, 08.09.2014.

Research output: Contribution to journalArticle

Thacker, RW, Díaz, MC, Kerner, A, Vignes-Lebbe, R, Segerdell, E, Haendel, M & Mungall, CJ 2014, 'The Porifera Ontology (PORO): Enhancing sponge systematics with an anatomy ontology', Journal of Biomedical Semantics, vol. 5, no. 1, 39. https://doi.org/10.1186/2041-1480-5-39
Thacker, Robert W. ; Díaz, Maria C. ; Kerner, Adeline ; Vignes-Lebbe, Régine ; Segerdell, Erik ; Haendel, Melissa ; Mungall, Christopher J. / The Porifera Ontology (PORO) : Enhancing sponge systematics with an anatomy ontology. In: Journal of Biomedical Semantics. 2014 ; Vol. 5, No. 1.
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