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Nucleic Acids Res. 2018 Jan 4;46(D1):D1168-D1180. doi: 10.1093/nar/gkx1152.

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

Author information

1
Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
2
Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.
3
Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
4
New York Botanical Garden, Bronx, NY 10458-5126, USA.
5
Department of Philosophy, University at Buffalo, Buffalo, NY 14260, USA.
6
School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR 97331, USA.
7
Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
8
National Plant Phenomics Centre, Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3DA, UK.

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.

PMID:
29186578
PMCID:
PMC5753347
DOI:
10.1093/nar/gkx1152
[Indexed for MEDLINE]
Free PMC Article

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