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

9 Citations (Scopus)

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

Fingerprint

Biological Ontologies
Biodiversity
Population
Education
Biota
Workflow
Genomics
Language
Phenotype

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., ... 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

Meeting report : Advancing practical applications of biodiversity ontologies. / Walls, Ramona L.; Guralnick, Robert; Deck, John; Buntzman, Adam; Buttigieg, Pier Luigi; Davies, Neil; Denslow, Michael W.; Gallery, Rachel Elizabeth; Parnell, J. Jacob; Osumi-Sutherland, David; Robbins, Robert J.; Rocca-Serra, Philippe; Wieczorek, John; Zheng, Jie.

In: Standards in Genomic Sciences, Vol. 9, No. 1, 17, 08.12.2014.

Research output: Contribution to journalArticle

Walls, RL, Guralnick, R, Deck, J, Buntzman, A, Buttigieg, PL, Davies, N, Denslow, MW, Gallery, RE, Parnell, JJ, Osumi-Sutherland, D, Robbins, RJ, Rocca-Serra, P, Wieczorek, J & Zheng, J 2014, 'Meeting report: Advancing practical applications of biodiversity ontologies', Standards in Genomic Sciences, vol. 9, no. 1, 17. https://doi.org/10.1186/1944-3277-9-17
Walls RL, Guralnick R, Deck J, Buntzman A, Buttigieg PL, Davies N et al. Meeting report: Advancing practical applications of biodiversity ontologies. Standards in Genomic Sciences. 2014 Dec 8;9(1). 17. https://doi.org/10.1186/1944-3277-9-17
Walls, Ramona L. ; Guralnick, Robert ; Deck, John ; Buntzman, Adam ; Buttigieg, Pier Luigi ; Davies, Neil ; Denslow, Michael W. ; Gallery, Rachel Elizabeth ; Parnell, J. Jacob ; Osumi-Sutherland, David ; Robbins, Robert J. ; Rocca-Serra, Philippe ; Wieczorek, John ; Zheng, Jie. / Meeting report : Advancing practical applications of biodiversity ontologies. In: Standards in Genomic Sciences. 2014 ; Vol. 9, No. 1.
@article{18a00377c46947e8ba51deebb83c7bb3,
title = "Meeting report: Advancing practical applications of biodiversity ontologies",
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.",
keywords = "Biodiversity, Community, Darwin Core, Microbial ecology, Ontology, OWL, Population, RDF, Sequencing",
author = "Walls, {Ramona L.} and Robert Guralnick and John Deck and Adam Buntzman and Buttigieg, {Pier Luigi} and Neil Davies and Denslow, {Michael W.} and Gallery, {Rachel Elizabeth} and Parnell, {J. Jacob} and David Osumi-Sutherland and Robbins, {Robert J.} and Philippe Rocca-Serra and John Wieczorek and Jie Zheng",
year = "2014",
month = "12",
day = "8",
doi = "10.1186/1944-3277-9-17",
language = "English (US)",
volume = "9",
journal = "Environmental Microbiomes",
issn = "1944-3277",
publisher = "BioMed Central Ltd.",
number = "1",

}

TY - JOUR

T1 - Meeting report

T2 - Advancing practical applications of biodiversity ontologies

AU - Walls, Ramona L.

AU - Guralnick, Robert

AU - Deck, John

AU - Buntzman, Adam

AU - Buttigieg, Pier Luigi

AU - Davies, Neil

AU - Denslow, Michael W.

AU - Gallery, Rachel Elizabeth

AU - Parnell, J. Jacob

AU - Osumi-Sutherland, David

AU - Robbins, Robert J.

AU - Rocca-Serra, Philippe

AU - Wieczorek, John

AU - Zheng, Jie

PY - 2014/12/8

Y1 - 2014/12/8

N2 - 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.

AB - 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.

KW - Biodiversity

KW - Community

KW - Darwin Core

KW - Microbial ecology

KW - Ontology

KW - OWL

KW - Population

KW - RDF

KW - Sequencing

UR - http://www.scopus.com/inward/record.url?scp=84971294668&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84971294668&partnerID=8YFLogxK

U2 - 10.1186/1944-3277-9-17

DO - 10.1186/1944-3277-9-17

M3 - Article

VL - 9

JO - Environmental Microbiomes

JF - Environmental Microbiomes

SN - 1944-3277

IS - 1

M1 - 17

ER -