The parent and child term organization in the whole-plant GSO. The solid curved lines joining the terms represent IS_A relationship and the dotted curved lines suggest a PART_OF relationship between the child and the parent terms. A term may or may not have a child term. In this example, germination IS_A vegetative stage and flowering IS_A reproductive stage. Similarly vegetative stage, reproductive stage, senescence, and dormancy are subtypes (IS_A) of whole-plant growth stage. Root emergence and shoot emergence are PART_OF the seedling growth stage. The seedling growth stage and imbibition are PART_OF germination. In this image not all the children terms are shown for every parent term in the GSO.

The GSO as seen on the ontology browser available at http://www.plantontology.org/amigo/go.cgi. A, For browsing, simply click on the [+] icon before the term name plant growth and developmental stages, and then on the [+] next to whole-plant growth stages (GSO). This will expand the tree by opening the children terms. The PO ID is the term's accession number, and the number followed by the term name is the total number of associations that have been curated to the genes for a given term. This number will change depending on the gene product filter a user may have chosen. Users can also get a pie chart showing the distribution of data associations to a term's children term. In this image, the general level (top level) terms in the GSO are “A_Vegetative growth,” “B_Reproductive growth,” “C_Senescence,” and “D_Dormancy.” The substages of “A_Vegetative growth” are “0_Germination,” “1_Main Shoot Growth,” and “2_Formation of Axillary Shoot,” while the substages of “B_Reproductive growth” are “3_Inflorescence Visible,” “4_Flowering,” “5_Fruit Formation,” and “6_Ripening.” Neither “C_Senescence” nor “D_Dormancy” currently has substages beneath them. The alphanumeric prefixes serve to make the substages appear in the order in which they occur during the plant's life cycle. If the temporal order is not defined consistently in all plants, the terms may not have these prefixes. The prefixes are usually abbreviations of the term name; for example, LP is for leaf production, SE is for stem elongation. The numerical portion uses double digits starting with 01, 02, and so on. Each of the substages may have more specific stages beneath it. When a term is retired or superseded, it is considered Obsolete. Such terms are moved to a location in the hierarchy underneath a term named “obsolete_growth_and_developmental_stage.” B, A detailed view of the substage PO:0007133, “Leaf production” and its children. Children terms up to 20 leaves visible were added to accommodate the growth stage requirements of the maize plant.

Corresponding growth stages in different plants and advantages of using broad and granular terms for annotations. In this example one can say flowering occurs in plant A at the six-leaf visible stage, in plant B at the nine-leaf visible stage, and in plant C at the11-leaf visible stage. Plants A to C represent either different germplasm accessions/cultivars of the same species or accessions/cultivars from different species. This nomenclature allows the researcher to record when a gene is expressed or a phenotype is observed by following the gradual progression of the plant's life cycle. For example, if a gene is expressed at the six-leaf or the fifth-internode stage, the meaning is now clear, while in the past, the information had to be recorded as the fifth leaf from the top of the plant. Such annotation required that one wait until the plant completed its life cycle to count the number of leaves from the top, or that one make an assumption how many leaves there would be in the plant/population used in the study. Note: the number of nodes and the number of leaves is always less than the number of internodes by one. The arrow pointing upwards suggests that the numbers are counted in that direction in ascending order starting with 1 and going up to n, where n can be any number depending on the plant.

An example of a GSO search using the ontology browser and search Web interface. A, Ontology search results for 0 germination by using the exact match and terms filter. To start searching, visit the www.plantontology.org Web site and click on the “Search and Browse Plant Ontology” link on the page menu. An ontology browser page opens that has a search option on the left-hand side. Type the term name of interest, such as “germination” for a generic search or “0 germination” for an exact match. Select the term filter and submit query. Click on the term name to visit the term detail page or browse the lineage of this term in the ontology by clicking the tree icon next to the check box. B, The term detail page provides information on the term name, accession/ID, synonyms, definition, comments, and associations to genes. C, The list of genes associated to the term are listed in the bottom half of the term detail page. A default list gives all the genes with every type of evidence code and source. The evidence type, species, and source filters can be used to generate the list as desired. The list provides the gene symbol, name, source, evidence, and a citation. The gene symbol links to the gene detail page and the source links to the original record in the contributor's database (e.g. TAIR/Gramene), the evidence code links to its details and the reference links to the original citation referred to by the contributor for inferring the ontology association to the gene. D, The gene detail page provides information on the symbol, name, synonym, source, a list of all the terms in the GSO and PSO, evidence, and the citations. This view suggests where and when a gene is expressed and/or an associated phenotype is observed.

Summary of the Arabidopsis and rice gene annotations to the GSO. A, Growth stage-specific gene annotations from Arabidopsis and rice. The stages prefixed with A to D are the top most categories of the growth stages, namely vegetative, reproductive, senescence, and dormancy. The stages prefixed with 0 to 2 are vegetative substages, and those with 3 to 6 are reproductive substages. All stages means all the GSO terms. B, A list of selected Arabidopsis and rice genes annotated to five specific growth stage terms, suggesting the current state of annotations and not the actual growth stage-specific profile. A similar list can be generated to get growth stage-specific gene expression profiles for a given species. In columns 2 and 3, the numbers (written in bold) appearing before the parentheses are the total number of gene annotations; species-specific genes are written in italics.

Genes participating in the flowering time pathway. This image illustrates the flowering time pathway genes from Arabidopsis, GI, CO and FT, and rice, OsGI, Se1 (Hd1), and Hd3a. In the PO database, the annotation for these genes is provided by three databases, the National Arabidopsis Stock Centre, TAIR (for Arabidopsis), and Gramene (for rice). The curators have used terms (Table III) from the whole GSO and PSO to suggest when and where in a plant these genes were expressed or their phenotype was observed. Based on the experiment types (evidence codes) and citation evidences, the databases recorded information about the mutant/gene/gene product to the GSO and the PSO terms. Compared to the short-day length promotion of flowering in rice, flowering is promoted by long-day exposure in Arabidopsis. When rice is exposed to long days, it leads to a down regulation of the Hd3a gene by Se1 (Hd1), leading to a delayed transition of the vegetative shoot apical meristem to the reproductive inflorescence meristem. In other words, the growth stage inflorescence visible (sensu Poaceae), which is synonymous with heading stage, is delayed. The double-headed arrows suggest that the Arabidopsis and rice genes are orthologous. The colored boxes around the genes represent the databases that provided the gene annotations. In the PO database, the putative orthology of these genes cannot currently be determined or displayed, but it can be inferred by visiting either the Gramene or the TAIR database.