The Planteome databasean integrated resource for reference ontologies, plant genomics and phenomics

Authors Organisations
  • Laurel Cooper(Author)
    Oregon State University
  • Austin Meier(Author)
    Oregon State University
  • Marie-Angélique Laporte(Author)
    Parc Scientifique Agropolis II
  • Justin L. Elser(Author)
    Oregon State University
  • Chris Mungall(Author)
    Lawrence Berkeley National Laboratory
  • Brandon T. Sinn(Author)
    New York Botanical Garden
  • Dario Cabaliere(Author)
    New York Botanical Garden
  • Seth Carbon(Author)
    Lawrence Berkeley National Laboratory
  • Nathan A. Dunn(Author)
    Lawrence Berkeley National Laboratory
  • Barry Smith(Author)
    University at Buffalo
  • Botong Qu(Author)
    Oregon State University
  • Justin Preece(Author)
    Oregon State University
  • Eugene Zhang(Author)
    Oregon State University
  • Sinisa Todorovic(Author)
    Oregon State University
  • Georgios Gkoutos(Author)
    University of Birmingham
  • John Doonan(Author)
  • Dennis W. Stevenson(Author)
    New York Botanical Garden
  • Elizabeth Arnaud(Author)
    Parc Scientifique Agropolis II
  • Pankaj Jaiswal(Author)
    Oregon State University
Type Article
Original languageEnglish
Article numbergkx1152
JournalNucleic Acids Research
DOI
Publication statusPublished - 23 Nov 2017
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Abstract

The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository