Meeting report: Advancing practical applications of biodiversity ontologies

Ramona L. Walls, Robert Guralnick, John Deck, Adam Buntzman, Pier Luigi Buttigieg, Neil Davies, Michael W. Denslow, Rachel Elizabeth Gallery, J. Jacob Parnell, David Osumi-Sutherland, Robert J. Robbins, Philippe Rocca-Serra, John Wieczorek, Jie Zheng

Research output: Contribution to journalArticle

10 Scopus citations

Abstract

We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts such as ecological niche, and developed ontology design patterns for defining collections of organisms and population-level phenotypes. The second focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO. To follow-up, a BCO hackathon was held concurrently with the 16th Genomics Standards Consortium Meeting, during which we converted additional datasets to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework, created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, and developed a workflow for converting biodiversity data among formats.

Original languageEnglish (US)
Article number17
JournalStandards in Genomic Sciences
Volume9
Issue number1
DOIs
StatePublished - Dec 8 2014

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Keywords

  • Biodiversity
  • Community
  • Darwin Core
  • Microbial ecology
  • Ontology
  • OWL
  • Population
  • RDF
  • Sequencing

ASJC Scopus subject areas

  • Genetics

Cite this

Walls, R. L., Guralnick, R., Deck, J., Buntzman, A., Buttigieg, P. L., Davies, N., Denslow, M. W., Gallery, R. E., Parnell, J. J., Osumi-Sutherland, D., Robbins, R. J., Rocca-Serra, P., Wieczorek, J., & Zheng, J. (2014). Meeting report: Advancing practical applications of biodiversity ontologies. Standards in Genomic Sciences, 9(1), [17]. https://doi.org/10.1186/1944-3277-9-17