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General changes

Namespace change: Plant Anatomical Entity

The former plant structure branch of the PO was renamed from Plant Structure Ontology (PSO) to Plant Anatomical Ontology (PAO). The namespace for all anatomical entities is now plant_anatomy, instead of plant_structure. The default namespace for the PO remains plant_ontology, and all PO term ID's will continue to begin with "PO:"

This change reflects the new root term plant anatomical entity (PO:0025131), which was added during the January 2011 release. It also better reflects the content of this branch of the PO, which includes not only plant structures (PO:0009011), but also plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

Translations

New subsets for Spanish and Japanese synonyms were added to the PO, with the scope exact synonym. All plant anatomy terms now have Spanish synonyms, and most have Japanese synonyms. Spanish synoyms will be incorporated into the live version of the PO, but because of issues with displaying special characters, the Japanese synonyms may be available through a separate file.

New subsets

Add subsets for bryophytes, pteridophytes and gymnosperms (in addition to the existing subset for angiosperms)

Changes to the top level of the PAO

Disjoints between upper level terms

Where appropriate, disjoint_from relations were added among the top level plant structure terms. These relations help to insure that annotations go to the correct class, and can aid in logical reasoning.

New relations added:

portion of plant tissue disjoint_from cardinal organ part

cardinal organ part disjoint_from plant cell

collective organ part structure disjoint_from plant cell

collective plant structure disjoint_from plant cell

plant cell disjoint_from plant organ

collective organ part structure disjoint_from portion of plant tissue

collective plant structure disjoint_from portion of plant tissue

plant cell disjoint_from portion of plant tissue

plant organ disjoint_from portion of plant tissue

cardinal organ part disjoint_from vascular system

collective organ part structure disjoint_from vascular system

collective plant structure disjoint_from vascular system

plant cell disjoint_from vascular system

plant organ disjoint_from vascular system

portion of plant tissue disjoint_from vascular system

cardinal organ part disjoint_from whole plant

collective organ part structure disjoint_from whole plant

collective plant structure disjoint_from whole plant

plant cell disjoint_from whole plant

plant organ disjoint_from whole plant

portion of plant tissue disjoint_from whole plant

vascular system disjoint_from whole plant

Partonomy of plant structures no longer rooted in whole plant

We removed the part_of relationships to whole plant from all of the other descendents of plant structure, such as plant cell, plant organ and portion of plant tissue. Because plant structure is defined as "An anatomical structure that is or was part of a plant, or was derived from a part of a plant," all children of plant structure can be part of a plant, a former part of a plant (e.g., a piece of wood or a cut flower), or derived from a part of a plant (e.g., and in vitro plant structure). There are many instances of plant structures such as cells, tissue, and organs that are not part of a whole plant, so it is inaccurate to specify the part_of relation between those structures and whole plant. This is particularly true in contemporary plant science, where so many plant structures are grown in plant culture.

New upper-level categories

collective organ part structure (PO:0025269)

This term was need to describe structures that would not fit in any other category.

Definition: A plant structure composed of two or more cardinal organ parts from adjacent organs and any associated portions of plant tissue.

Comment: A collective organ part structure is composed of parts of multiple organs, but no complete organs. The organ parts are often of the same type (e.g., petioles, carpel walls), but may be of different types. Includes plant structures like a septum that consists of the walls of two fused carpels or a pseudostem that consist of multiple, overlapping leaf sheaths. Unlike a collective plant structure, a collective organ part structure does not contain any complete organs.

For now, it only has three children: fruit operculum (PO:0025298), pseudostem (PO:0025248), and septum (PO:0000030).

rhizoid (PO:0030078)

Like trichomes, rhizoids can be either uni- or multi-cellular, which prevents us from defining them as either a plant cell or a portion of plant tissue, so we created a separate upper-level term for rhizoids.

Definition: A plant structure that is a uniseriate filament with positive geotropism that grows from an epidermis or protonema.

Comment: May be unicellular or multicellular. Serves to anchor the plant to the substrate, and may function in nutrient and water uptake. Usually lacks chlorophyll. Includes epidermal rhizoids that grow from the epidermis of bryophytes and pteridophytes in the gametophytic phase or from the stems of some monocots, and protonemal rhizoids that branch from a protonema.

Many types of rhizoids grow from an epidermis, and could be classified trichomes, however, making rhizoid a child of trichome would prevent us from including protonemal rhizoids in the same category (because unlike epidermal rhizoids and trichomes, they do not develop from a type of epidermal initial).

Changes in in vitro plant structure (PO:0000004), and its children

After consultation with PATO, OBI, and GO (CM), it was clear that there no suitable ontology category for in vitro growth or similar in the OBO community. Although it would have been preferable to make all of the in vitro structures children of their respective plant structures (plant cell, etc.) and have their relationship to in vitro plant structure be inferred (as we did for embryo plant structure), this was not possible, because no differentia for in vitro growth existed. Therefore, we made all in vitro structures children of their respective plant structures (plant cell, portion of plant tissue and plant embryo) was well as be children of in vitro plant structure.

In addition to asserting dual inheritance for all in vitro plant structures, we renamed all terms to include "plant" in their names and to remove ambiguity from their names (e.g., leaf-derived cultured plant cell, instead of cultured leaf cell). We also modified the definitions to make them clearer and convert them to the genus-differentia form. Several new in vitro plant structures were added: cultured zygote-derived plant embryo (PO:0025304)and microspore-derived cultured plant embryo (PO:0025305).

Changes in embryo plant structure and its children

Also at the third level, a new term embryonic plant structure was added, as a direct child of plant structure. Only structures that occur exclusively in embryos are defined as children of embryonic plant structure (e.g., coleoptile, suspensor or embryo proper), while plant structures that may be part of either an embryo or an adult plant structure (e.g., parenchyma) are not classified as embryonic plant structures. Embryonic plant structure is defined logically using intersection_of relations, as the intersection of is_a plant structure and part_of embryo. Thus, embryo vascular system, which is_a vascular system and part_of embryo, is automatically inferred to be an embryonic plant structure (see below under “Cross-products in the ontology using the intersection_of relation”). Likewise, embryonic plant cell is defined as the intersection of is_a plant cell and part_of embryo, and portion of embryonic plant tissue is defined as the intersection of is_a portion of plant tissue and part_of embryo.

New relations

participates_in

Unlike other relations in the PO, participates_in provides a link between an independent occurant in the PSO (a plant anatomical entity) and a continuant in the PGDSO (a growth and developmental stage). Participates_in is a specific case of the more general inheres_in relation, as occurrants (i.e., things) generally inhere in continuants (i.e., processes) (Grennon et al., 2004). The addition of the participates_in relation allowed us to remove whole plant structures such as gametophyte, sporophyte, and seedling from the PSO, and describe them as whole plants that participate in their respective life-cycle phases. It also provides a way of more clearly defining structures that occur only in the gametophytic or sporophytic phase, such as, archegonium participates_in gametophytic phase or vascular tissue participates_in sporophytic phase. This allows for comparisons of analogous structures in the gametophytic phase or sporophytic phase that would not normally be grouped together based on homology (such as vascular versus non-vascular leaves, fig. x – still under construction).

adjacent_to

Used when one plant structure (the child) is in permanent contact with another plant structure (the parent).

intersection_of (cross-product definitions)

Cross-product definitions using intersection_of relations are particularly useful when there is a need to organize concepts under multiple ontology classes.

embryo plant structures

Portion of embryonic plant tissue is defined as the intersection_of: is_a portion of plant tissue and intersection_of: part_of embryo. Therefore, we are able to classify, for example, embryo epidermis as a sub-class of epidermis (which is a subclass of portion of plant tissue), yet also infer that embryo epidermis is a subclass of embryonic plant structure. Users who wish to examine all types of plant tissue will still find embryo epidermis under portion of plant tissue, while users who wish to examine all types of embryonic plant structures will also find embryo epidermis under portion of embryonic plant tissue, and therefore under embryonic plant structure.

portions of phyllome epidermis

Added stamen epidermis intersection_of is_a epidermis, intersection_of part_of stamen. Did the same thing for other phyllome epidermises (except the various leaf abaxial and leaf adaxial stomatal epidermises). This allows stomatal complexes and prickles to be inferred is_a children of their respective portions of epidermal tissue, without creating dual parentage.

User requests

Terms requested by TAIR

dispersed meristematic cell

We add leaf procambial cell, in response to the request for "dispersed meristematic cell". Dispersed meristematic cell and DMC were added as exact synonyms.

To accomodate this request, the following changes were made to the PO hierarchy:

meristematic cell (PO:0004010)

-[is_a] procambial cell (PO:0025258) (new)

- -[is_a] leaf procambial cell (PO:0000063) (new)

procambium (PO:0006074)

-[is_a] leaf procambium (PO:0025259) (new)

- -[part_of] leaf procambial cell (PO:0000063) (new)

ovary septum vs. carpel septum

TAIR request for a new term ovary septum.

After extensive discussion, we decided to obsolete three existing terms for septum and replum, because there seemed to be some confusion as to where annotations should go. Many species have septa in their gynoecia and fruit, but in Brassicaceae and some legumes, there are repla.

Terms made obsolete, and their replacements:

obsolete fruit septum (PO:0005008) - consider fruit septum (PO:0025268) or fruit replum (PO:0025267);

carpel septum (PO:0005009) - consider ovary septum (PO:0025262) or ovary replum (PO:0025272)

replum (PO:0005016) - consider: ovary replum (PO:0025272) or fruit replum (PO:0025267)

All annotations from TAIR should go to ovary replum or fruit replum.

New terms and definitions:

ovary replum (PO:0025272): A portion of ovary placenta tissue that divides an ovary into two or more chambers and develops from contact of the placental tissue from opposite sides of the ovary early in gynoecium development.

Comment: An ovary replum develops along with the ovary and has no suture line in its center, while a true ovary septum (PO:0025262) is derived from the fusion two adjacent ovary walls. Common in Brassicaceae. Annotations for Arabidopsis should go here, and not under ovary septum.

fruit replum (PO:0025267): A portion of fruit placenta tissue that divides a fruit into two or more chambers and develops from a replum.

Comment: A fruit replum develops from the ovary replum and has no suture line in its center, while a fruit septum (PO:0025262) develops from an ovary septum via the fusion of two adjacent ovary walls. Common in Brassicaceae. Annotations for Arabidopsis fruit should go here, and not under fruit septum.

septum (PO:0000030): A collective organ part structure composed of two or more layers of various tissues that is a partition that divides a cavity formed by the fusion of two or more organs.

Comment: A septum is formed by the fusion of the walls of two adjacent organs (ovary walls or anther walls), for example, the partition between two sections of an orange, seen in cross-section.

ovary septum (PO:0025262): A septum that divides a multilocular ovary.

Comment: Found in species with syncarpous gynoecia (fused carpels). An ovary septum is derived from the fused walls of two adjacent carpels, while a replum (PO:0005016) develops from early contact of placental tissue from opposite sides of the ovary. Annotations for Arabidopsis should go under replum, not under ovary septum.

fruit septum (PO:0025268): A septum that divides a cavity or mass of tissue in a fruit and develops from an ovary septum.

Comment: Annotations for Arabidopsis should go under fruit replum (PO:0025267), not under fruit septum. The partition between two sections of an orange is a fruit septum.

stomatal meristemoid cell and meristemoid/initial cell

TAIR has requested the term stomatal meristemoid cell and the relation guard mother cell develops_from stomatal meristemoid cell.

Merged meristermoid (PO:0000070) into initial cell (PO:0004011). New definition: A meristematic cell that by division gives rise to two cells, one of which remains meristematic, while the other is added to the plant body.

Comment: Initial cells are often part of a portion of tissue that is composed mostly of somewhat older, differentiating cells. The division of an initial cell is often uneven, with the smaller daughter cell remaining meristematic.

Added new term stomatal initial (PO:0000062): An epidermal initial that undergoes several rounds of uneven division, each time giving rise to a larger daughter cell that differentiates into an epidermal ground cell and a smaller daughter cell that remains meristematic, until the meristematic cell differentiates into a guard mother cell. Synonyms: stomatal initial cell, stomatal meristermoid.

Guard mother cell now develops from stomatal initial, instead of both epidermal initial and meristemoid.

We couldn't find examples of other patterns of stomatal development. If users come to us in the future with different developmental patterns in other species, we can modify accordingly.

We also changed meristematic cell part_of meristem to meristem has_part meristematic cell, because not all meristematic cell occur as part of a meristem (e.g., in leaves).

xylem pole pericycle cell

TAIR requested a new term for xylem pole pericycle cell. We added two new terms:

xylem pole pericycle cell (PO:0000064): A pericycle cell that is adjacent to a protoxylem cell.

Comment: Xylem pole pericycle cells are cells in the pericycle that are adjacent to the protoxylem pole of a vascular bundle. Pericycle cells that are adjacent to other xylem cells in the vascular bundle are not considered xylem pole pericycle cells. Xylem pole pericycle cells may retain some meristematic activity and are the site of lateral root initiation.

phloem pole pericycle cell (PO:0000065): A pericycle cell that is adjacent to the protophloem of a vascular bundle.

Comment: Phloem pole pericycle cells are cells in the pericycle that are adjacent to the protophloem pole of a vascular bundle. Pericycle cells that are adjacent to other phloem cells in the vascular bundle are not considered phloem pole pericycle cells. Phloem pole pericycle cells are distinct from xylem pole pericycle cells in that they display cytoplasmic characteristics of a more differentiated status.

See PMID:17993548

Terms requested by Cosmoss/Moss Ontology for Physcomitrella

More that 40 new terms were added to the PO at the request of the Physcomitrella group.

In addition, 44 associated new terms were added that can be used for pteridophytes and bryopytes

21 existing terms got new synonyms or minor modifications to make them applicable to a broader range of plants.

A complete list of the terms added for bryophytes and pteridophytes can be found on New_terms_and_obsolete_terms_for_May2011_release#Terms_for_bryophytes_and_pteridophytes

Other

Renamed terms

Added "plant" to the name of embryo and its descendents:

embryo (PO:0009009) > plant embryo

cultured somatic embryo (PO:0000011) > cultured somatic plant embryo

etc.

Renamed parts of the anther wall:

endothecium (PO:0020002) > anther wall endothecium

exothecium (PO:0020004) > anther wall exothecium

middle layer (PO:0004700) > anther wall middle layer (definition needs work)

tapetum (PO:0009071) > anther wall tapetum

primary parietal cell layer (PO:0006006) > anther wall primary parietal cell layer

etc.

Changed names of child terms of sporangium/spore capsule:

PO:0025093 Moss capsule annulus > spore capsule annulus

PO:0025231 Moss capsule columella > spore capsule columella

PO:0025229 Moss capsule valve>spore capsule valve

Other:

bud scale (PO:0020054) > bud scale leaf.

adventitious embryo (PO:0004537) > nucellar plant embryo

New Synonyms

New synonyms for vascular leaf (PO:0009025): frond, needle-like leaf, scale-like leaf, and leaf, vascular

New synonyms for non-vascular leaf (PO:0025075): phyllid, gametophyll, gametophytic leaf, gametophyte leaf, phyllidium, and non-vascular leaflet (related)

Added a bunch of adjective/noun synonyms. For example, archegonium egg cell as synonym for archegonial egg cell, antheridial jacket layer as synonym of antheridium jacket layer.

Miscellaneous Changes

Made pollen sac part_of microsporophyll, instead of part_of anther, and added anther has_part pollen sac.

Made anther wall is_a microsporangium wall

Made nucellar epidermis (PO:0008006) is_a megasporangium exothecium

Removed anther wall tapetum develops-from anther wall inner secondary parietal cell layer. Made is_a microsporangium tapetum.

New term for locule (PO:0025263), plus various children

Removed modified aleurone part_of aleurone layer, because it was already is_a aleurone layer.

Added "portion of … tissue" as synonyms to several tissue types of tissue that had single word names (like epidermis, collenchyma).

Redefined procambium (had to obsolete and replace)

Made theca is_a collective organ part structure, part of anther, has_part pollen sac.

Made microsporocyte part of microsporangium, instead of part of microsporocyte. Made sporocyte part of sporangium.

Moved juvenile, transition and adult leaf from vascular leaf to leaf. Also simple leaf and compound leaf.

Moved leaf aerenchyma, leaf mesophyll, leaf lamina, leaf margin, leaf intercalary meristem and leaf sheath from part_of vascular leaf to part_of leaf.

Moved leaf endodermis from part_of leaf to part_of vascular leaf.

Removed has_part relations from all pairs of terms that has reciprocal has_part/part_of relations

Added formal relations for: sporophyte replaced_by saprophytic phase and gametophyte replaced by gametophytic phase. Couldn't do this for the previous release because of separate files. Did not add replaced by relation for seedling, b/c there is not seedling phase yet.

Updated definition of embryo sac.

Updated definitions of archegonium egg cell, embryo sac egg cell, antheridium sperm cell, and pollen sperm cell

Added vascular leaf and non-vascular leaf part_of vascular and non-vascular shoot system, respectively.

Changed embryo to plant embryo.

Removed embryonic axis has_part radicle, has_part hypocotyl, has_part epicotyl, hypocotyl-root junction, has_part root meristem (b/c not true in all plants)

Added prothallium as narrow synonym of whole plant.

Added appropriate subsets for apical cell terms and other terms.

Changed theca (PO:0009069) to anther theca

Made sporangium (PO:0025094) is_a plant organ instead of is_a cardinal organ part.

Made female archesporial cell (PO:0006015) and male archesporial cell (PO:0006014) children of archesporial cell (PO:0030056)

Summary of Changes to PO May 2011