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.

Figure 1.

An overview of the Planteome ontology and data annotation browser. (A) The drill-down browser allows users to explore the ontology hierarchy and the associated annotation data. Gray circles next to the ontology term names show the number of bioentities annotated to that ontology term either directly or accumulated indirectly from its children terms guided by the ontology tree and the term–term relationship types (B) Bioentities can be filtered by type and source taxon by selecting the red (exclude from search) or green (restrict search to) boxes on the left hand side. (C) Term information window appears if one clicks on an ontology term and displays the alphanumeric identifier, term name, definition, ontology source, synonyms and alternate IDs (if any). (D) The term detail page can be accessed by clicking on the term name in the popup window, with additional information and links to direct and indirect annotations. (E) A full list of all the bioentities associated with the selected term can be opened by selecting the ‘Retrieve Bioentities’ link in the popup box. (F) Free text search box. (G) Faceted search menu.

Figure 2.

Faceted Searches for (A) Ontology terms, (B) Bioentities or (C) Annotations. Results can be filtered using the drop down menus on the left hand sides of each view.

Figure 3.

A view of a model under development in Planteome Noctua. Planteome Noctua (http://noctua.planteome.org/) is a web-based tool for collaborative curation and gene annotation supported by published literature or empirical data. Individuals from the reference ontologies are linked to one another through relationships and these assertions are supported by an evidence code from the Evidence and Conclusion Ontology. Once the model is complete, the information is saved and can be exported as a formatted file which can be processed to add the information to the database.

Figure 4.

A view of the ontology hierarchy around Trait Ontology term plant height (TO:0000207). Crop Ontology (CO) terms for plant height from the lentil, wheat, rice and cassava ontologies are mapped to the Trait Ontology term for data integration.