The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant

Abstract

Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is used to describe plant anatomy and morphology in publications and genomic databases for different species. The same terms are sometimes applied to different plant structures in different taxonomic groups. Conversely, similar structures are named by their species-specific terms. To address this problem, we created the Plant Structure Ontology (PSO), the first generic ontological representation of anatomy and morphology of a flowering plant. The PSO is intended for a broad plant research community, including bench scientists, curators in genomic databases, and bioinformaticians. The initial releases of the PSO integrated existing ontologies for Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa); more recent versions of the ontology encompass terms relevant to Fabaceae, Solanaceae, additional cereal crops, and poplar (Populus spp.). Databases such as The Arabidopsis Information Resource, Nottingham Arabidopsis Stock Centre, Gramene, MaizeGDB, and SOL Genomics Network are using the PSO to describe expression patterns of genes and phenotypes of mutants and natural variants and are regularly contributing new annotations to the Plant Ontology database. The PSO is also used in specialized public databases, such as BRENDA, GENEVESTIGATOR, NASCArrays, and others. Over 10,000 gene annotations and phenotype descriptions from participating databases can be queried and retrieved using the Plant Ontology browser. The PSO, as well as contributed gene associations, can be obtained at www.plantontology.org.

Figure 1.

A, A screen shot of the ontology browser; top nodes of the PSO. Clicking on the [+] or [−] sign in front of a term vertically expands or collapses the ontology tree, respectively. B, Expanded sporophyte node. A mouse click on a term itself opens a term detail page (data not shown). Numbers in parentheses next to the term name indicate the number of the annotations for unique object types associated with a term (including annotations to all children terms). Legends for relationship-type icons are shown on the right. Term detail pages for the PSO term sporophyte at TAIR (C) and Gramene (D) databases. Each database has hyperlinks back to the PSO, allowing for quick access to the POC browser and database. At species-specific databases, additional annotations to the term sporophyte can be found.

Figure 2.

Analysis of the ontology and annotations in the PSO. A, Distribution of all PSO terms (white) and leaf terms (gray) as a function of longest path depth from the root. B, The number and distribution of direct annotations as a function of longest path depth from the root.

Figure 3.

A, Annotations to the term leaf vein (PO:0020138) in the POC database. Hyperlinks in the Source column take the user to the gene page in the database where the annotation was created. Encircled is a hyperlink to TAIR database for the annotation of Arabidopsis YSL1 gene. B, Gene detail page at TAIR for the YSL1 gene, where additional information about the YSL1 gene can be retrieved. C, TAIR annotation detail page for YSL1 gene, where all annotations to the PO and GO are listed with the evidence code and evidence description for each annotation entry.