Summary of Changes to PO May 2011

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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).

New subsets

New subsets for bryophytes, pteridophytes and gymnosperms were added, in addition to the existing subset for angiosperms. These subsets can be used to search for or filter classes that are relevant to particular taxa.

Please note that inclusion in a subset does not formally imply the class is only applicable to that subset (although that may be the case).

Classes may belong to multiple subsets. For example, antheridium belongs to the subset for bryophytes and the subset for pteridophytes.

Classes that apply to all plants (e.g., sporangium), are not necessarily placed in subsets, therefore, searching for terms in a taxonomic subset will not find all of the PO classes relevant to that taxon.

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.

Disjoint_from 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 needed 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.

Many types of rhizoids develop from a type of epidermal initial, and could be classified trichomes. However, making rhizoid a child of trichome would have prevented us from including protonemal rhizoids in the same category.

Definition: A plant structure that is a uniseriate filament with positive geotropism and without chlorophyll that grows from a plant structure such as 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, protonemal rhizoids that branch from a protonema, and rhizoids that develop from a basal cell of a gametophore bud.

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

We wanted to include all in vitro plant structures in their own category, but we felt it was also necessary to make them children of their respective plant structure categories. An in vitro plant cell is still a plant cell.

After consultation with PATO, OBI, and GO (CM), it was clear that there was 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 asserted 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 asserted dual inheritance, making all in vitro structures children of their respective plant structures (plant cell, portion of plant tissue or 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. Two new in vitro plant structures were added: cultured zygote-derived plant embryo (PO:0025304)and microspore-derived cultured plant embryo (PO:0025305).

New structure for in vitro plant structure and descendents:

Changes in embryo plant structure and its children

Embryo plant structure (PO:0025099) is a direct child of plant structure. The asserted children of embryo plant structure are plant structures that occur only in an embryo (embryo proper, scutellum, and suspensor). Embryo plant cell (PO:0025028) and portion of embryo plant tissue (PO:0025233) are also chidren of embryo plant structure, but these classes have no asserted is_a children.

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. 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. This allows us to classify, for example, embryo endodermis as is_a endodermis, but still infer that it is a portion of embryo plant tissue. All inferred is_a relations are asserted before each release, so users browsing in AmiGO will see both is_a parents. A version of the file without the asserted relations is also available.

There several plant structures that are found in embryos (e.g, hypocotyl, radicle), that persist beyond the embryo phase. To accomodate these structures, we have kept the original class a general parent term [e.g., hypocotyl (PO:0020100)] with specific children for the embryonic and seedling phase [e.g., embryo hypocotyl (PO:0025290) and seedling hypocotyl (PO:0025291)]. Because embryo hypocotyl is part_of embryo, but hypocotyl and seedling hypocotyl are not, only embryo hypocotyl is inferred to be an embryo plant structure.

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. If a user wishes to describe something like parenchyma tissue in an embryo, they should use both parenchyma (PO:0005421) and plant embryo (PO:0009009).

Here is a picture of how the inference works:

Inferred children of embryo plant structure

Classes that do not have a sibling term for seedlings:

• embryo axis (PO:0019018) - is_a plant axis

• embryonic leaf (PO:0006338) is_a vascular leaf

• embryo vascular system (PO:0008011) is_a vascular system

• plumule (PO:0020032) - is_a terminal bud

• scutellar node (PO:0004708) - is_a stem node

The definitions for some of these terms were modified

New classes that have a sibling term for seedling:

• embryonic coleoptile (PO:0025286) - is_a coleoptile (PO:0020033), also added seedling coleoptile (PO:0025287)

• embryo coleorhiza (PO:0025288) - is_a coleorhiza (PO:0020034), also added seedling coleorhiza (PO:0025289)

• embryo epicotyl (PO:0025292) - is_a epicotyl (PO:0020035), also added seedling epicotyl (PO:0025293)

• embryo hypotcotyl (PO:0025290) - is_a hypocotyl (PO:0020100), also added seedling hypocotyl (PO:0025291)

• embryo hypocotyl-root junction (PO:0025300) - is_a hypocotyl-root junction (PO:0004724), also added seedling hypocotyl-root junction (PO:0025301)

• embryo mesocotyl (PO:0025294) - is_a mesocotyl (PO:0020037), also added seedling mesocotyl (PO:0025295)

• embryo radicle (PO:0025296) - is_a radicle (PO:0020031), also added seedling radicle (PO:0025297)

Inferred children of embryo plant cell

• embryonic apical cell (PO:0030007; replaces apical cell PO:0004000)

• embryonic basal cell (formerly: basal cell) (PO:0002002)

• embryonic hypophysis (formerly hypophysis) (PO:0020109)

Inferred children of portion of embryo plant tissue

• embryo cortex (PO:0005014)

• embryo endodermis (PO:0005015)

• embryonic shoot apical meristem (PO:0006362)

• epiblast (PO:0020036)

• scutellar epithelium (PO:0008048)

• scutellum epidermis (PO:0006049)

Other changes to embryo plant structures:

Updated definition of radicle. Removed radicle part_of embryo axis, added embryo axis has_part radicle.

Updated definition of hypocotyl and made it is_a stem internode, instead of is_a cardinal organ part.

Updated definition of epicotyl and made it is_a stem internode, instead of is_a embryonic plant structure.

Made hypocotyl-root junction is_a cardinal organ part. Already part of embryo axis.

Made mesocotyl is_a stem internode.

Made embryonic leaf is_a leaf, part_of embryo.

Made plumule is_a terminal bud, part_of embryo.

Made scutellar node is_a stem node, part_of embryo axis.

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)

New relations

More details on relations is available at Relations in the Plant Ontology.

participates_in

The participates_in relation provides a link between an independent occurant in the PAO (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)

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.

A participates_in B Should be read to mean: Every A participates in to some B.

adjacent_to

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

Example: anther wall endothecium adjacent_to anther wall exothecium

A adjacent_to B Should be read to mean: Every A is adjacent to some B. This does not imply that every B is adjacent to some A.

derives_from

Used to indicate that one plant structure succeeds another across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier structure is inherited by the later.

Example: leaf-derived cultured plant cell derives_from leaf indicates that a significant portion of the matter (in fact, all of it) of a leaf-derived cultured plant cell is inherited from some cell in a leaf.

A derives_from B Should be read to mean: Every A derives from some B. This does not imply that every B derives from some A.

intersection_of (cross-product definitions)

Cross-product definitions using intersection_of relations specify the sufficient conditions for a definition. So, if we say "embryo plant structure intersection_of: is_a plant structure" and "embryro plant structure intersection_of: part_of embryo", then every plant structure that is part_of an embryo (either directly, or through transitivity), will be inferred to be is_a embryo plant structure.

This is particularly useful when there is a need to organize concepts under multiple ontology classes, because the primary class can be asserted, and the other classes can be inferred by the reasoner.

For this revision, the intersection_of relation was added for two classes of structures:

embryo plant structures

embryo plant structure: intersection_of: is_a plant structure and intersection_of: part_of embryo

embryo plant cell: intersection_of: is_a plant cell and intersection_of: part_of embryo

portion of embryo plant tissue: intersection_of: is_a portion of plant tissue and intersection_of: part_of embryo

See above for more details of embryo plant structure.

portions of phyllome epidermis

For all of the children of phyllome epidermis (except the various leaf abaxial and leaf adaxial stomatal epidermises), we added intersection_of: is_a epidermis, intersection_of: part_of xx (e.g., part_of stamen for stamen epidermis, part_of petal for petal epidermis).

This allows stomatal complexes and prickles to be inferred is_a children of their respective portions of epidermal tissue, without creating dual parentage (e.g., stamen stomatal complex is asserted to be is_a stomatal complex and inferred to be is_a portion of stamen epidermis; leaf prickle is asserted to be is_a prickle and inferred to be is_a portion of leaf epidermis

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

The new terms for bryophytes and pteridophytes are summarized in this spread sheet: Media:NewBryophyteTerms_May2011releasePO(RW20-05-2011).pdf

Other

Changes to children of leaf (PO:0025034)

• Plant structures that can be part of either a vascular leaf or a non-vascular leaf were either left as or moved to be children of leaf (PO:0025034). These are: leaf aerenchyma, leaf apex, leaf base, leaf epidermis, leaf intercalary meristem, leaf lamina, leaf margin, leaf mesophyll, leaf prickle, leaf sheath, and leaf stomatal complex.

-Users who want to make an association to one of these structures should be sure to annotate to both the leaf part (e.g., leaf epidermis) and the correct type of leaf (vascular leaf or non-vascular leaf).

-Existing annotations for any of these terms should also be copied to vascular leaf (assuming they are all from vascular plants).

• Plant structures that can only be part of a vascular leaf were either left as or moved to be children of vascular leaf (PO:0009025). These are: auricle, bundle sheath, leaf abscission zone, leaf collar, leaf endodermis, leaf vascular system, ligule, petiole, stipule, and vascular leaf meristematic apical cell (for pteridophyte leaves).

• Plant structures that can only be part of a non-vascular leaf were either left as or moved to be children of non-vascular leaf (PO:0025075). These are: alar cell, costa, and non-vascular leaf meristematic apical cell.

• Moved juvenile leaf, transition leaf, and adult leaf, from is_a vascular leaf to is_a leaf.

(rosette leaf, cauline leaf, simple leaf, compound leaf, and cigar leaf are still children of vascular leaf)

• We added a comment to the structures listed below: “If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf."

Parts of leaves:

leaf aerenchyma (PO:0006215)

leaf apex (PO:0020137)

leaf tip (PO:0025142)

leaf base (PO:0020040)

leaf epidermis (PO:0006016)

leaf abaxial epidermis (PO:0006019)

leaf adaxial epidermis (PO:0006018)

leaf lamina epidermis (PO:0000047)

leaf lamina abaxial epidermis (PO:0000049)

leaf lamina adaxial epidermis (PO:0000050)

leaf papilla cell (PO:0025167)

leaf pavement cell (PO:0025212)

buliform cell (PO:0004001)

leaf abaxial pavement cell (PO:0025213)

leaf adaxial pavement cell (PO:0025214)

long cell (PO:0004717)

short cell (PO:0004718)

leaf sheath epidermis (PO:0025249)

leaf sheath abaxial epidermis (PO:0025250)

leaf sheath adaxial epidermis (PO:0025251)

leaf trichome (PO:0006504)

leaf abaxial trichome (PO:0025210)

leaf adaxial trichome (PO:0025211)

petiole epidermis (PO:0000051)

petiole abaxial epidermis (PO:0008029)

petiole adaxial epidermis (PO:0008027)

leaf intercalary meristem (PO:0006346)

leaf lamina (PO:0020039)

central zone of the leaf lamina (PO:0008020)

leaf lamina base (PO:0008019)

leaf lamina stomatal complex (PO:0025185)

petiole lamina (PO:0025129)

leaf margin (PO:0020128)

leaf lamina margin (PO:0025009)

leaflet margin (PO:0006034)

petiole margin (PO:0025010)

leaf mesophyll (PO:0005645)

palisade mesophyll (PO:0005648)

palisade mesophyll cell (PO:0006206)

spongy mesophyll (PO:0005647)

spongy mesophyll cell (PO:0006205)

leaf prickle (PO:0025175)

leaf sheath (PO:0020104

leaf sheath pulvinus (PO:0008017)

leaf stomatal complex (PO:0025183)

leaf abaxial stomatal complex (PO:0025190)

leaf adaxial stomatal complex (PO:0025191)

petiole stomatal complex (PO:0025189)

leaf guard cell (PO:0025237)

leaf stomatal pore (PO:0025235)

• Added a slightly different comment to the following terms, which only occur in vascular leaves: “If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025).”

flag leaf (PO:0020103)

epidermal cork cell (PO:0000041)

silica cell (PO:0004009)

List of annotations on terms that are part_of leaf

In vascular plants, these structures may be part_of a vascular leaf. In non-vascular plants, they may be part_of a non-vascular leaf. Any existing annotation for these terms should also be copied to vascular leaf. Future annotations should go to both the part and to the appropriate leaf type.

Term name (id) number of annotations (from live AmiGO, not from most recent association files)

• leaf aerenchyma (PO:0006215) 1

• leaf apex (PO:0020137) 12890

• leaf base (PO:0020040) 5

• leaf epidermis (PO:0006016)365

includes:

buliform cell (PO:0004001) 1

leaf abaxial epidermis (PO:0006019) 4

leaf adaxial epidermis (PO:0006018) 4

leaf lamina epidermis (PO:0000047) 1

leaf trichome (PO:0006504) 63

• leaf intercalary meristem (PO:0006346) 1

• leaf lamina (PO:0020039) 12800

includes:

leaf lamina base (PO:0008019) 12614

leaf lamina vascular system (PO:0000048) 1

• leaf margin (PO:0020128) 100

• leaf mesophyll (PO:0005645) 762

includes:

palisade mesophyll cell (PO:0006206) 1

spongy mesophyll (PO:0005647) 1

spongy mesophyll cell (PO:0006205) 2

• leaf prickle (PO:0025175) 0

• leaf sheath (PO:0020104) 205

includes:

• leaf sheath pulvinus (PO:0008017) 2

• leaf stomatal complex (PO:0025183) 0

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 to be taxon neutral:

• 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

• theca (PO:0009069) > anther theca

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 adjective/noun synonym pairs. For example, archegonial egg cell as synonym for archegonium egg cell, antheridial jacket layer as synonym of antheridium jacket layer.

Added prothallium as narrow synonym of whole plant.

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

Added new synonym type "plural". Used for terms that have Latin names that change in the plural. For example, gametangia is a plural synonym of gametangium.

Miscellaneous Changes

Made pollen sac (PO:0025277) part_of microsporophyll, instead of part_of anther, and added anther has_part pollen sac.

Made anther wall (PO:0000002) is_a microsporangium wall

Made nucellar epidermis (PO:0008006) is_a megasporangium exothecium

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

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

Removed modified aleurone (PO:0008008) part_of aleurone layer, because it was already is_a aleurone layer.

Made old term procambium (PO:0006074) obsolete and replaced by procambium (PO:0025275), with new definition.

Made anther theca (PO:0009069) is_a collective organ part structure (new term), part of anther, has_part pollen sac.

Made microsporocyte (PO:0020047) part of microsporangium, instead of part of pollen sac. Made sporocyte (PO:0006204) part of sporangium.

Removed has_part relations from all pairs of terms that has reciprocal has_part/part_of relations. Although this is logically valid, the reasoner does not treat has_part relations correctly, so the reciprocal relations caused a circularity.

Updated definition of embryo sac (PO:0025074).

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

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 new term archesporial cell (PO:0030056)