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

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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.

Related collections

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Mansi Srivastava, Oleg Simakov, Jarrod Chapman … (2010)

Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse 'toolkit' of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.

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Is Open Access

Uberon, an integrative multi-species anatomy ontology

Christopher Mungall, Carlo Torniai, Georgios Gkoutos … (2012)

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org

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Author and article information

Contributors

Robert W Thacker: thacker@uab.edu

Maria Cristina Díaz: taxochica@gmail.com

Adeline Kerner: kerner@mnhn.fr

Régine Vignes-Lebbe: regine.vignes_lebbe@upmc.fr

Erik Segerdell: segerdel@ohsu.edu

Melissa A Haendel: haendel@ohsu.edu

Christopher J Mungall: cjmungall@lbl.gov

Journal

Journal ID (nlm-ta): J Biomed Semantics

Journal ID (iso-abbrev): J Biomed Semantics

Title: Journal of Biomedical Semantics

Publisher: BioMed Central (London )

ISSN (Electronic): 2041-1480

Publication date (Electronic): 8 September 2014

Publication date PMC-release: 8 September 2014

Publication date Collection: 2014

Volume: 5

Issue: 1

Electronic Location Identifier: 39

Affiliations

[ ]Department of Biology, University of Alabama at Birmingham, Birmingham, USA

[ ]Museo Margarita, Boca de Rio, 6304 Venezuela

[ ]CR2P, UMR 7207 CNRS-MNHN-UPMC, Département Histoire de la Terre, Muséum National d’Histoire Naturelle, Bâtiment de Géologie, CP48, 57 rue Cuvier, 75005 Paris, France

[ ]Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, USA

[ ]Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA

Article

Publisher ID: 186

DOI: 10.1186/2041-1480-5-39

PMC ID: 4177528

SO-VID: ba8d416f-2009-4f1b-8a14-6c4d91f0801c

License:

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.