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) have been merged into one file (plant_ontology.obo), in order to faciliated cross-ontology cross products. The two ontologies still have separate name spaces. The separate files po_anatomy.obo and po_temporal.obo will be maintained for some period of time, but users should try to switch to using the combined file as soon as possible.

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_of_specific_changes' below for a more detailed description.

All terms in the PSO now have is_a parents.

Eleven 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components and have been requested in the Gene Ontology (GO), or terms that were incorrectly defined and have been replaced by new terms with the same name but correct definition.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 under development, but will be added to as revisions progress. For future releases, subsets for other taxa such as gymnosperms be added.

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, compliance with the Basic Formal Ontology (BFO)]

Status: All terms in the PSO now have is_a parents, as well as al but three terms in the PGDSO. 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. They will be assigned is_a parents during the next round of revisions, when the PGDSO is restructured. A draft version of a restructured PGDSO that is compliant with BFO criteria was prepared. This will be modified and incorporated into the PO during the next round of revisions.

2. Incorporate user requests

Status: All terms requested by Generation Challenge Program (GCP) for Musa spp., have been added, either as new terms or synonyms. Several new terms for legumes have been added, as requested by Austin Mast of Florida State University, 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 the next revision.

3. Add terms to PSO for non-angiosperm structures

Status: New upper level terms have been added: sporangium (PO:0025094), microsporangium (PO:0025202), megasporangium (PO:0025201), gametangium (PO:0025124), antheridium (PO:0025125), and archegonium (PO:0025126). Several more new, specific terms have been added: moss capsule(PO:0025232, moss capsule annulus (PO:0025093, moss capsule valve (PO:0025229, moss capsule columella (PO:0025231), antheridium sperm cell (PO:0025120), pollen sperm cell(PO:0025121), archegonium egg cell (PO:0025122)

4. Update PGDSO to accommodate a broader range of species

Status: A new structure for the PGDSO was developed, but it awaits testing and approval. Will be revised and incorporated for 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 of the Plant Structure Ontology (PSO) during this revision than during the last, but several important new terms were added. The 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. Only structures that occur exclusively in embryos are children of embryonic plant structure (e.g., coleoptile, suspensor, or embryo proper). Likewise, just as in vitro structures can have derives_from relations to in vivo structures, mature plant structures can have develops_from relations to embryonic plant structures. Plant structures that may be part of either an embryo or an adult plant structure (e.g. hypocotyl, parenchyma) do not go under embryonic plant structure.

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 (PO:0025230). 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 (PO:0025132), parent of petiole canal (PO:0025133)

• 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)

• trichome (PO:0000282). This was an existing term, but it was incorrectly placed as a child of epidermal cell. It is now a child of plant structure. PO:0000282 acts as a type of synonym for unicellular trichomes (plant cell) or multicellular trichoms (portion of plant tissue).

Lower level terms:

New terms added to the lower levels of the ontology represent user requests, terms that were inspired by user requests (for example, if a user requested tepal apex, we added terms for other types of phyllome apices), or terms that were added for completeness when we added a new mid-level term (for example, we added the mid-level term stele as a parent to root stele, so at the same time, we added shoot axis stele, stem stele and branch stele).

New lower level terms:

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

• trichomes: multicellular trichome (PO:0025162), multicellular trichome branch cell (PO:0025163), bract trichome (PO:0025098), peduncle trichome (PO:0025153), stem trichome (PO:0025176), branch trichome (PO:0025177), sepal trichome (PO:0025182), phyllome trichome (PO:0025186), petal trichome (PO:0025187), tepal trichome (PO:0025188), carpel trichome (PO:0025208), stamen trichome (PO:0025209), leaf abaxial trichome (PO:0025210) leaf adaxial trichome (PO:0025211). Also see above under new mid-level terms.

• thorn (PO:0025172), leaf spine (PO:0025173), stipule spine (PO:0025174), leaf prickle (PO:0025175), stem trichome (PO:0025176)

• children of stomatal complex: phyllome stomatal complex (PO:0025215), leaf stomatal complex (PO:0025183), leaf lamina stomatal complex (PO:0025185), petiole stomatal complex (PO:0025189), leaf abaxial stomatal complex (PO:0025190), leaf adaxial stomatal complex (PO:0025191), bract stomatal complex (PO:0025216), carpel stomatal complex (PO:0025217), petal stomatal complex (PO:0025218), sepal stomatal complex (PO:0025219), stamen stomatal complex (PO:0025220), tepal stomatal complex (PO:0025221)

• reproductive shoot apex (PO:0025222) and vegetative shoot apex (PO:0025223)

• root nodule meristem (PO:0025194)

• tetrad of megaspores (PO:0025227)

• moss capsule (PO:0025232), moss capsule valve (PO:0025229), and moss capsule columella (PO:0025231)

• basal endosperm transfer layer (PO:0025196) replaced obsolete term with same name(PO:0009019) because definition was wrong.

• second order inflorescence (PO:0025240) and second order infructescence (PO:0025241). Higher order terms could be added if needed.

• infructescence axis (PO:0025242), infructescence branch (PO:0025243), plus terms for all of the differnt orders of infructescence and inflorescence branches up to tenth order and higher [e.g., first order infructescence axis (PO:0025244)]

New terms for Musa

26 new terms or synonyms were added at the request of the Generation Challenge Program, to accomodate their descriptions of banana and other Musa species. Many of these terms are also present in other taxa. For a complete list, see the Source Forge tracker items for Musa terms, Musa flower terms, Musa shoot terms, and Musa fruit terms.

Some of the terms that were added for Musa species are considered "phenotype terms," meaning that they are a class of terms that represent what might normally be called a phenotype of a more general term, and that they are a combination of a PO class and a Phenotypic Attribute Ontology (PATO) class. For example, free tepal (PO:0025136) is a cross-product of PO:0025136 (tepal) and PATO:0001505 (separated from). We do not yet have the infrastructure to support cross-ontlogy cross products, so they are defined in the comment section.

Reworking of definitions, etc.:

• Revised the 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 the definitions of bract (PO:0009055) and leaf (PO:0025034)

• Redefined flower. Made it is_a reproductive shoot system (this change actually went in last release, but was not documented, because it was a last minute change).

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

• 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.

• 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.

• Obsoleted terms that were parts of cells: pollen tube, pollen tube tip, unicellular trichome branch, root hair, root hair tip, papillae. Requested these terms in GO. Added new terms: pollen tube cell, papilla cell, multicellular trichome branch cell.

• Renamed hull(PO:0006000)Poaceae hull; is_a collective phyllome structure.

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

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

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.