Summary of Changes to PO Jan2011

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Summary of changes: October 2010 through January 2011:

Curators (in alphabetical order): Cooper, Laurel D. (1); Elser, Justin (1); Gandolfo, Maria A. (2); Jaiswal, Pankaj (1), Mungall, Christopher (3); Preece, Justin (1); Smith, Barry (4); Stevenson, Dennis W. (5); Walls, Ramona L. (5)

1. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 2. Department of Plant Biology, Cornell University, Ithaca, NY
 3. Lawrence Berkeley National Lab, Berkeley, CA 4. Department of Philosophy, University at Buffalo, NY 5. The New York Botanical Garden, Bronx, NY

Overview and general changes

The Plant Structure Ontology (PSO) and Plant Growth and Development Stage Ontology (PGDSO) into one file. The two ontologies still have separate name spaces. This should make little difference for most users, and was done mostly to make editing easier.

169 new terms have been added (see New_terms_and_obsolete_terms_for_Jan2011_release). These include several new top-level terms, a number of mid-level generic terms (such as stele) that were added to provide parents for more specific terms, and a number of bottom or leaf-level terms. See summary below for a more detailed description.

All terms in the PSO now have is_a parents, as well as all but three terms in the PGDSO.

About 10 terms were made obsolete (see New_terms_and_obsolete_terms_for_Jan2011_release). These were primarily terms that are sub-celluar components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and replaced by new terms with the same name but correct definition.

The defintions of many existing terms were re-written in the genus-differntia form, as well as the definitions for all new terms.

Several new sub-sets were created: one for TraitNet (general terms need for plant ecology), one for Musa species, and one for angiosperms. The angiosperms subset is still incomplete, but can be added to as revisions progress.

The relationship has_part was added to the ontology. For example, inflorescence has_part flower.

All terms with sensu their names were changed from "structure (sensu Taxon)" to "Taxon structure."

Priorities for this release

1. Compliance with OBO Foundry Principles (is_a parents for all terms, BFO compliance)

Status: All but three terms now have is_a parents. The three remaining terms without parents [imbibition (PO:0007022), seedling growth (PO:0007131), shoot emergence (PO:0007030)] are processes that are part_of seed germination. Since we don't yet have a category for processes (may move to GO), we can't give them is_a parents.

2. Incorporate user requests

Status: All terms requested byGeneration Challenge Program for Musa spp., have been added, either as new terms or synonyms. Several of terms for legumes have been added, as requested by Austin Mast of FSU, as well as several general terms requested by TraitNet and several root terms requested by Rich Zobel. Remaining user requests will be dealt with during future revisions.

3. Add terms for non-angisperm structures

Status: New upper level terms have been added: sporangium, microsporangium, megasporangium, gametangium, antheridium, archegonium. Also, several more specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121, archegonium egg cell (PO:0025122)

4. Update PGDSO

Status: A new structure for the PGDSO was developed, but it awaits testing and approval. May be incorporated during next release.

Summary of specific changes

General changes are describe in the overview, above

Upper-level terms

There were fewer changes to the upper-level terms during this revision than during the last, but several important new terms were added. The Plant Structure Ontology (PSO) got a new root term: plant anatomical entity (PO:0025131). Plant anatomical entity is now parent to the original root term plant structure (PO:0009011), plus the new terms plant anatomical space (PO:0025117) and portion of plant substance (PO:0025161). Children of plant anatomical space include existing terms like stomatal pore, micropyle and stomium, plus new terms like anther pore (PO:0025118), axil (PO:0025224), and canal (PO:0025132). Cuticle (PO:0000022) is currently the only child of portion of plant substance, but later it could have siblings like latex or xylem sap.

Also at the upper levels, a new term embryonic plant structure (PO:0025099) was added, as a direct child of plant structure. Analogous to the existing term in vitro plant structure (PO:0000004), embryonic plant structures do not have part_of relationships to whole plant, and remain separate from other, mature, plant structures. Only structures that occur exclusively in embryos are children of embryonic plant structure (e.g., coleoptile, suspensor or embryo proper). Plant structures that may part of either an embryo or an adult plant structure (e.g. hypocotyl, parenchyma) remain as they were.

Mid-level terms

Many new terms were added at the middle levels of the ontology (usually 3rd to 5th levels). These terms were added to provide parents to existing terms that did not have is_a parents (for example, a general term axil was added as a parent to the existing term leaf axil), or they were added to provide more general instances of classes (for example, plant axis differentiation zone was added as a more general parent for root differentiation zone and stem internode differentiation zone). Often, when a new general term was added, additional specific children were added for completeness (for example, after the general term phyllome epidermis was added, new children for bract epidermis and tepal epidermis were added).

New mid-level terms:

• primordium (PO:0025127). Made all other primordia descendents of PO:0025127. Deleted the is_a relationships between 'primordia' and the structures they develop into and replaced with develops_from relations (e.g., 'leaf' develops_from 'leaf primordium'). Also added new term phyllome primordium (PO:0025128), which is parent to leaf primordium, petal primordium, etc. Updated definitions for different types of primordia so they are consistent and fit the genus-differentia form.

• plant axis differentiation zone (PO:0025119). Parent to root differentiation zone (PO:0020135; renaming of old term differentiation zone), stem internode differentiation zone (PO:0008042), plus new terms shoot internode differentiation zone (PO:0025102) and branch internode differentiation zone (PO:0025103).

• plant axis elongation zone (PO:0025180). Parent to root elongation zone (PO:0025181) and shoot internode elongation zone (PO:0025100). Old terms elongation zone (PO:0020125), lateral root elongation zone(PO:0003014), and primary root elongation zone (PO:0003003) were made obsolete, because definitions were incorrect. Replaced by root elongation zone (PO:0025181), lateral root elongation zone (PO:0025256), and primary root elongation zone (PO:0025257). Old term stem internode elongation zone (PO:0008041) remained, but got standardized definition, and branch internode elongation zone (PO:0025101) was added.

• valve (PO:0000033). Added as a general term for all organ parts that split apart, with children fruit valve (PO:0000033; renamed from old term valve) and new term moss capsule valve (PO:0025229).

• columella. Made fruit columella (PO:0004540; renamed from old term columella) a child of this, plus new term moss capsule columella (PO:0025231).

• stele (PO:0025197). Parent to existing term root stele (PO:0020124), plus new terms shoot axis stele (PO:0025198), branch stele(PO:0025199), and stem stele (PO:0025200).

• sporangium (PO:0025094; added during last release but didn’t have definition), megasporangium (PO:0025201), and microsporangium (PO:0025202). Existing terms nucellus (PO:0020020) and pollen sac (PO:0009070) are children of mega- and microsporangium, respectively.

• canal, parent of petiole canal

• axil (PO:0025224) as a child of plant anatomical space. Made leaf axil (PO:0009023), branch axil (new) and bract axil (new) children of it.

• gynoecium ridge (PO:0025088). Parent to new terms Poaceae gynoecium ridge (PO:0025086) and Zea gynoecium ridge (PO:0025087)

• dehiscence zone (PO:0025092). Parent of existing terms anther dehiscence zone (PO:0005011) and fruit dehiscence zone (PO:0004707), plus new term moss capsule annulus (PO:0025093).

• gametangium (PO:0025124) Parent of new terms antheridium (PO:0025125) and archegonium (PO:0025126).

• shoot system vascular system (PO:0025205). Made different vascular systems of above ground parts child of this, plus new terms phyllome vascular system (PO:0025206) and tepal vascular system (PO:0025207)

• phyllome apex (PO:0025139), phyllome base (PO:0025140) and phyllome tip (PO:0025141), plus new terms for many of their children (e.g., sepal apex PO:0025145)

Lower level terms:

Many of these terms are at lower levels of the ontology and represent user requests or terms that were inspired by user requests (for example, if a user requested tepal apex, we added terms for other types of phyllome apices).

Created a new term root parenchyma (PO:0025095): A portion of parenchyma tissue that is part of a root system.

• Trichomes: added top level term trichome as a synonym for the different types of trichomes. Also have multicellular trichome, trichome cell (synonym: unicellular trichome), and multicellular trichome branch (is a trichome cell).

• Secretory trichome was renamed glandular trichome. Non-secretory trichome was merged with trichome, made non-secretory trichome a synonym of trichome (PO:0000282), added narrow synonyms 'unicellular non-secretory trichome' and 'multicellular non-secretory trichome' for trichome cell and multicellular trichome, respectively. Made new term phyllome trichome, parent of existing term leaf trichome (PO:0006504), and added trichome terms for other types of phyllomes (like bract and carpel). Made seed trichome the primary name for PO:0004511, changed seed hair to exact synonym, added pubescence as related synonym. The more specific sub-terms can be post-compositionally created or we can add them as needed by our users.

• Added new terms: thorn, prickle, spine

• existing term stomatal complex (PO:0002000) was kept as a general term. Phyllome stomatal complex and leaf stomatal complex aredescendants. Obsoleted floral stomatal complex.

Added new terms leaf abaxial stomatal complex and leaf adaxial stomatal complex.

Obsoleted terms that were parts of cells: pollen tube, pollen tube tip, unicellular trichome branch, root hair, root hair tip, papilla (do you mean papillae; does not seem to be obsoleted)??. Requested in GO. Added new terms: pollen tube cell, papilla cell, multicellular trichome branch cell.

Modified definition of shoot apex slightly to make it is_a shoot axis. Added children reproductive shoot apex and vegetative shoot apex.

Made root nodule (PO:0003023) is_a cardinal organ part, and added new term root nodule meristem.

Made tetrad of microspores (PO:0000032) is_a portion of plant tissue, added new term tetrad of megaspores. Made Poaceae hull (PO:0006000) is_a collective phyllome structure

Obsoleted pollen tube (PO:0006345), requested in GO and added new term pollen tube cell.

Deleted floral epidermis and floral stomatal complex (obsoleted) and replaced it with terms for specific parts of the flower (such as petal epidermis and petal stomatal complex). This follows the organization of other plant parts.

Also had to add term for moss capsule.

Obsoleted the existing ID (PO:0009019) because definition was wrong. Created new ID for 'basal endosperm transfer layer'.

Updated definitions and added is_a parents for lodicule (PO:0009036), aril (PO:0009090), arilloid (PO:0019022), placentoid (PO:0020005), and egg apparatus (PO:0020096).

secondary inflorescence and infructescence, branch orders

New terms added at the request of GCP, for Musa (many are also present in other taxa):

collective tepal structure (synonym compound tepal)

second order infructescence (synonym hand of fruit)

pseudostem (is_a collective plant structure)

leaf sheath abaxial epidermis (synonym pseudostem underlayers)

Synonyms added at the request of GCP, for Musa (many are also present in other taxa):

bunch (infructescence) basal flower (flower), male inflorescence bud (inflorescence bud), Musa sucker (axillary shoot system)

sepal relic, tepal relic, and stamen relic (synonym flower relic)

Reworking of definitions, etc.:

reworked definitions of embryo, egg cell, sperm cell, plus added new terms archegonium egg cell, embryo sac egg cell, antheridium sperm cell, pollen sperm cell.

Revised definition of bract (PO:0009055) A phyllome, usually different in form from the foliage leaves, subtending a reproductive structure.

Revised definition of leaf (PO:0025034): A phyllome that is not associated with a reproductive structure. These new definitions make the terms more appropriate for all plants

• Redefined flower. Made it is_a reproductive shoot system (new term). inflorescence has_part flower

>>this change actually went in last release, not sure if it was documented, because it was a last minute change.

Fixed definitions and added is_a parents for parts of the root tip, like root cap, quiescent center.

Fixed part_of relations between leaf trichome and pavement cell, so that they are only part_of leaf epidermis. Added specific children (like leaf lamina trichome, etc.) with proper part_of relations.

renamed pavement cell (PO:0000332) epidermal pavement cell, do distinguish it from the term pavement cell used in embryology. Made pavement cell disjoint from other, specialized kinds of epidermal cells. Created new child leaf pavement cell, parent to existing terms like bulliform cell, long cell and short cell.

New definitions for inflorescence and infructescence. Renamed and more clearly defined various types of inflorescence axes (branches). Added terms for infructescence branches.

Changes to the PGDSO:

The PGDSO was largely unchanged during this revision. Three terms that were part_of children of leaf trichome development stage (PO:0007039), 1 pattern formation, 2 endoreplication, 3 branch formation 4 growth directionality, were made is_a children.