Content of the PSO
- The Plant Structure Ontology, a Unified Vocabulary of Anatomy and Morphology of a Flowering Plant
A term (also called a node) in the PSO is an entity that representsa component of plant structure, such as cell, tissue, organ,and organ system. Each plant structure in the PSO has a termname, a unique numerical identifier (accession no.), a definition,and a specified relationship to at least one other term. Anaccession number always starts with the PO prefix followed byseven digits (e.g. PO:0009011). Once assigned to the PO term,the accession number never changes or gets reassigned to anotherterm. Users should always cite an ontology term by its exactname and a complete accession number, including the prefix.Similar to the GO, the PSO is organized into a hierarchicalnetwork called the Directed Acyclic Graph (for definition, seehttp://www.nist.gov/dads/HTML/directAcycGraph.html). Three typesof parent-child relationships are used in the PSO to specifythe type of association between two terms: is_a, part_of, anddevelops_from (described in more detail in Jaiswal et al., 2005). The term plant structure (PO:0009011) is the highest level ofthe PSO. Each term immediately below plant structure representshigh-level structures (broadly defined entities) that containspecific classes or types, positioned in the hierarchy as theirdirect descendants, called children terms. There are five directchildren of plant structure: plant cell, tissue, organ, gametophyte,and sporophyte (Fig. 1 ). The remaining two nodes, in vitrocultured cell, tissue, and organ and whole plant, were originallyincluded in all three plant species-specific anatomical ontologiesthat preceded the PSO. Because these terms were used in annotationsby all three databases, we included them as top-level nodes.The latter node, whole plant, is conceptually inconsistent (nota botanical term) from the rest of the terms in the PSO andis intentionally left without children terms. We recommend thatthis term be used as a last option—only when precise annotationto any other term in the PSO is not possible. Sporophyte andgametophyte exist as separate terms because they represent diploidand haploid generations of the plant life cycle, respectively.The largest node, sporophyte, includes seed, root, shoot, andinfructescence as direct children nodes. The term shoot is broadlydefined as part of the sporophyte composed of the stems andleaves and includes shoot apical meristems. It has phylome,stem, and inflorescence as part_of children terms, and rhizome,shoot borne shoot, root borne shoot, stolon, and tuber as specifictypes of a shoot. The term embryo (part_of seed) consists ofa number of terms that are applicable for both eudicots andmonocots (particularly members of Poaceae). Compared to eudicots,embryo development in grasses is more advanced; a fully developedembryo has body parts, such as coleoptile, coleorhizae, andscutellum, which are nonhomologous or absent in eudicots. Becauseno plant embryo has all body parts that are designated as part_ofembryo in the PSO, we adopted a nonrestrictive part_of relationshiptype; the child must be a part_of the parent to exist in theontology. However, a parent structure does not have to be composedof all of its part_of children. For example, scutellum is necessarilypart_of embryo; that is, wherever scutellum exists, it is alwaysa part of an embryo. However, not all embryos have scutellum(only embryos in Poaceae do). The high-level term infructescencewas created to accommodate terms that describe both simple fruits,formed from a single ovary (e.g. grape [Vitis vinifera]), andcompound fruits, formed from multiple ovaries (e.g. pineapple[Ananas comosus] or mulberry [Morus]). Currently, this nodehas only one direct descendant, fruit, which refers to a simplefruit. Terms specifically describing compound fruit will beincluded at a later time. Similar to the embryo node, the fruitnode contains several part_of children and not every fruit typenecessarily has all part_of descendants. Overlapping subsetsof part_of terms can be created, each applicable to siliquesof Arabidopsis and other Brassicaceae, caryopsis in cereals,and berry, a fleshy type of fruit, in tomato (Solanum lycopersicum)and other Solanaceae.
Recently, terms relevant for the Solanaceae and Fabaceae families,perennials, and woody species were added to the PSO. For example,terms such as tuber (and its children terms subterranean tuberand aerial tuber) and root nodule (with children terms adventitiousroot nodule, determinate nodule, and indeterminate nodule) wereadded to accommodate annotations to genes and germplasms inthe Solanaceae and Fabaceae families. In addition, the firstattempt to add terms relevant for perennials and woody specieswas made (such as epicomic shoot, defined as a shoot developingfrom a trunk), with more terms still to be incorporated. A numberof terms for secondary growth were also added, grouped undersecondary xylem (such as heartwood, sapwood, growth ring, growthring boundary, and others), secondary phloem (such as bark,libriform fiber, septate fiber, and phloem fiber), and vascularcambium (such as ray initial and fusiform initial), includingseveral cell-type terms under parenchyma cell, such as woodparenchyma cell, with direct descendants, axial wood parenchymacell, and ray wood parenchyma cell (with additional childrenterms underneath). At the very top level of the hierarchy is the node obsolete.As in the GO, a term that has been removed from the ontologyis never permanently deleted. Instead, the term and its assignedidentifier are kept in the ontology file for the record. Thedefinition is appended with OBSOLETE and an explanation is providedas to why a term was removed. The note in the definition orcomment field might also contain suggested terms for searchingand annotating. Obsoleted terms are not intended for use. Consequently,obsoleted terms do not have any annotations associated withthem. In many cases, terms in the obsolete node are valid botanicalterms (such as tunica and corpus); they are simply no longerin use in the PSO, mainly to avoid having duplicated terms thatdescribe a similar plant structure. Instead of using the outdatedconcept of tunica and corpus, shoot apex organization is describedby the following terms: central zone, peripheral zone, and ribzone. Other examples include terms depicting plant-specificsubcellular structures (e.g. filiform apparatus), all of whichwere made obsolete in the PSO to avoid overlap with the GO.Users are advised to use cellular component terms in the GOinstead.
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