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

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.

[1]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[2]  J. Görlach,et al.  Growth Stage–Based Phenotypic Analysis of Arabidopsis , 2001, The Plant Cell Online.

[3]  Christian E. V. Storm,et al.  Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. , 2001, Journal of molecular biology.

[4]  L. Stein,et al.  Gramene: Development and Integration of Trait and Gene Ontologies for Rice , 2002, Comparative and functional genomics.

[5]  John M. Hancock,et al.  Using ontologies to describe mouse phenotypes , 2004, Genome Biology.

[6]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[7]  L. Stein,et al.  Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages , 2005, Comparative and functional genomics.

[8]  L. Stein,et al.  Whole-Plant Growth Stage Ontology for Angiosperms and Its Application in Plant Biology1[OA] , 2006, Plant Physiology.

[9]  L. Stein,et al.  The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant1[W][OA] , 2006, Plant Physiology.

[10]  M. Ashburner,et al.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration , 2007, Nature Biotechnology.

[11]  Lincoln Stein,et al.  The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations , 2008, Nucleic Acids Res..

[12]  Judith A. Blake,et al.  Gene Ontology annotations: what they mean and where they come from , 2008, BMC Bioinformatics.

[13]  Liya Ren,et al.  Gramene QTL database: development, content and applications , 2009, Database J. Biol. Databases Curation.

[14]  Dennis Shasha,et al.  miRò: a miRNA knowledge base , 2009, Database J. Biol. Databases Curation.

[15]  Chris Mungall,et al.  AmiGO: online access to ontology and annotation data , 2008, Bioinform..

[16]  Kriston L. McGary,et al.  Systematic discovery of nonobvious human disease models through orthologous phenotypes , 2010, Proceedings of the National Academy of Sciences.

[17]  Ojs Jki.  The extended BBCH-scale , 2010 .

[18]  Ambuj K. Singh,et al.  Bisque: a platform for bioimage analysis and management , 2009, Bioinform..

[19]  Henry D. Priest,et al.  The genome of woodland strawberry (Fragaria vesca) , 2011, Nature Genetics.

[20]  Barry Smith,et al.  Ontologies as integrative tools for plant science. , 2012, American journal of botany.

[21]  Graham McLaren,et al.  Towards a Reference Plant Trait Ontology for Modeling Knowledge of Plant Traits and Phenotypes , 2012, KEOD.

[22]  Scott Federhen,et al.  The NCBI Taxonomy database , 2011, Nucleic Acids Res..

[23]  Arllet M. Portugal,et al.  Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice , 2012, Front. Physio..

[24]  Barry Smith,et al.  The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses , 2012, Plant & cell physiology.

[25]  Richard D. Hayes,et al.  The genome of Eucalyptus grandis , 2014, Nature.

[26]  Sinisa Todorovic,et al.  AISO: Annotation of Image Segments with Ontologies , 2014, Journal of Biomedical Semantics.

[27]  Rachael P. Huntley,et al.  Standardized description of scientific evidence using the Evidence Ontology (ECO) , 2014, Database J. Biol. Databases Curation.

[28]  Eva Huala,et al.  An ontology approach to comparative phenomics in plants , 2015, Plant Methods.

[29]  Pankaj Jaiswal,et al.  Annotating Germplasm to Planteome Reference Ontologies , 2016, ICBO/BioCreative.

[30]  Amit Gupta,et al.  A Web Application for Extracting Key Domain Information for Scientific Publications Using Ontology , 2016, ICBO/BioCreative.

[31]  Christoph Steinbeck,et al.  ChEBI in 2016: Improved services and an expanding collection of metabolites , 2015, Nucleic Acids Res..

[32]  P. Jaiswal,et al.  The Plant Ontology: A Tool for Plant Genomics. , 2016, Methods in molecular biology.

[33]  Chris Mungall,et al.  Comparison of Ontology Mapping Techniques to Map Plant Trait Ontologies , 2016, ICBO/BioCreative.

[34]  Anushya Muruganujan,et al.  PANTHER version 11: expanded annotation data from Gene Ontology and Reactome pathways, and data analysis tool enhancements , 2016, Nucleic Acids Res..

[35]  The Gene Ontology Consortium,et al.  Expansion of the Gene Ontology knowledgebase and resources , 2016, Nucleic Acids Res..

[36]  The Gene Ontology Consortium.  Expansion of the Gene Ontology knowledgebase and resources , 2016, Nucleic Acids Res..