The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique; Elser, Justin L.; Mungall, Chris; Sinn, Brandon T.; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan A.; Smith, Barry; Qu, Botong; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John H.; Stevenson, Dennis W.; Arnaud, Elizabeth; Jaiswal, Pankaj

doi:10.1093/nar/gkx1152

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

Journal Article · Thu Nov 23 00:00:00 EST 2017 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkx1152· OSTI ID:1625561

Cooper, Laurel ^[1]; Meier, Austin ^[2]; Laporte, Marie-Angélique ^[3]; Elser, Justin L. ^[2]; Mungall, Chris ^[4]; Sinn, Brandon T. ^[5]; Cavaliere, Dario ^[5]; Carbon, Seth ^[6]; Dunn, Nathan A. ^[6]; Smith, Barry ^[7]; Qu, Botong ^[8]; Preece, Justin ^[2]; Zhang, Eugene ^[9]; Todorovic, Sinisa ^[9]; Gkoutos, Georgios ^[10]; Doonan, John H. ^[11]; Stevenson, Dennis W. ^[5]; Arnaud, Elizabeth ^[3]; ^[2]

Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology; DOE/OSTI
Oregon State Univ., Corvallis, OR (United States). Dept. of Botany and Plant Pathology
Bioversity International, Parc Scientifique Agropolis II, Montpellier (France)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
New York Botanical Garden, Bronx, NY (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
Univ. at Buffalo, NY (United States). Dept. of Philosophy
Oregon State Univ., Corvallis, OR (United States). School of Electrical Engineering and Computer Science
Oregon State Univ., Corvallis, OR (United States). School of Electrical Engineering and Computer Science
Univ. of Birmingham (United Kingdom), Institute of Cancer and Genomic Sciences
Aberystwyth Univ., Aberystwyth (United Kingdom). National Plant Phenomics Centre, Institute of Biological, Environmental, and Rural Sciences

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.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625561

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 46; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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