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 E. Gallery; J. Jacob Parnell; David Osumi-Sutherland; Robert J. Robbins; Philippe Rocca-Serra; John Wieczorek; Jie Zheng

doi:10.1186/1944-3277-9-17

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 E. Gallery, J. Jacob Parnell, David Osumi-Sutherland, Robert J. Robbins, Philippe Rocca-Serra, John Wieczorek, Jie Zheng

Research output: Contribution to journal › Article › peer-review

12 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 16^th 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 language	English (US)
Article number	17
Journal	Standards in Genomic Sciences
Volume	9
Issue number	1
DOIs	https://doi.org/10.1186/1944-3277-9-17
State	Published - Dec 8 2014

Keywords

Biodiversity
Community
Darwin Core
Microbial ecology
OWL
Ontology
Population
RDF
Sequencing

ASJC Scopus subject areas

Genetics

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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), Article 17. https://doi.org/10.1186/1944-3277-9-17

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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, OWL, Ontology, 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 E.} and Parnell, {J. Jacob} and David Osumi-Sutherland and Robbins, {Robert J.} and Philippe Rocca-Serra and John Wieczorek and Jie Zheng",

note = "Funding Information: Funding was provided by EAGER: An Interoperable Information Infrastructure for Biodiversity Research (NSF-IIS-1255035), by RCN4GSC: A Research Coordination Network for the Genomic Standards Consortium (NSF-DBI-0840989), by Collaborative Research: BiSciCol Tracker: Towards a tagging and tracking infrastructure for biodiversity science collections (NSF-DBI: 0956371, 0956350, 0956426), and by the Phenotype Ontology Research Coordination Network (NSF-DEB-0956049). Logistical support and meeting space was provided by the iPlant Collaborative (NSF-DBI-0735191) and by the Genomic Publisher Copyright: {\textcopyright} 2014 Walls et al.; licensee BioMed Central Ltd.",

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doi = "10.1186/1944-3277-9-17",

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AU - Buntzman, Adam

AU - Buttigieg, Pier Luigi

AU - Davies, Neil

AU - Denslow, Michael W.

AU - Gallery, Rachel E.

AU - Parnell, J. Jacob

AU - Osumi-Sutherland, David

AU - Robbins, Robert J.

AU - Rocca-Serra, Philippe

AU - Wieczorek, John

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PY - 2014/12/8

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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.

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KW - Community

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KW - Microbial ecology

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KW - Population

KW - RDF

KW - Sequencing

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Meeting report: Advancing practical applications of biodiversity ontologies

Abstract

Keywords

ASJC Scopus subject areas

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