Meeting report: advancing practical applications of biodiversity ontologies View Full Text


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Article Info

DATE

2014-12-08

AUTHORS

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

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. More... »

PAGES

17-17

References to SciGraph publications

  • 2004-12-20. Using ontologies to describe mouse phenotypes in GENOME BIOLOGY
  • 2014-07-29. The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web in BMC BIOINFORMATICS
  • 2011-04-07. The genomic standards consortium: bringing standards to life for microbial ecology in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-12-11. The environment ontology: contextualising biological and biomedical entities in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2013-10-18. The Drosophila anatomy ontology in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2013-10-08. Developing a semantically rich ontology for the biobank-administration domain in JOURNAL OF BIOMEDICAL SEMANTICS
  • 2013-08-09. The Vertebrate Trait Ontology: a controlled vocabulary for the annotation of trait data across species in JOURNAL OF BIOMEDICAL SEMANTICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/1944-3277-9-17

    DOI

    http://dx.doi.org/10.1186/1944-3277-9-17

    DIMENSIONS

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