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

169 new terms have been added. They are summarized on the page: New_terms_and_obsolete_terms_for_Jan2011_release.

There were fewer changes to the upper-level terms during this revision than during the last, but there were several important new terms 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.

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). Many terms were also added at the middle levels of the ontology (3rd to 5th levels)

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.

List of Changes

List of new terms and obsolete terms for Jan2011 release

• 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.

Added has_part relationship

• Added TraitNet slim - could be used as a generic slim for plant ecologists

• Merged PSO and PGDSO into one file. Still have separate name spaces. Little difference for users, mostly a convenience for the editors.

• All terms in PSO now have is_a parents. A few in PGDSO without, but that may undergo major restructuring.

Began a collaboration with Physco group (Stefan Rensing and Daniel Lang)

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.

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.

New term primordium. Made all definitions of types of primordia consistent. Removed is_a relations between primordia and the structures they develop into. Instead added relations that the structures develop from the primordia.

• 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 term primordium (PO:0025127). Made all other primordia a child of this term, 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'). lso added new term: phyllome primordium, 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.

• Added new terms: thorn, prickle, spine

Reorganization of PSO top level terms:

• Added plant anatomical entity as a new root node. Plant structure (old term), plant anatomical space and portion of plant structure are new children of this node.

Children of plant anatomical space include stomatal pore, micropyle and stomium. Cuticle is the only child of portion of plant substance, but later could add children like latex, xylem sap, etc.

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

Fixed definitions and added is_a parents for parts of the root tip, like root cap, quiescent center. Added new terms differentiation zone and elongation zone.

Added new term: plant axis differentiation zone (PO:0025119), which is parent to root differentiation zone (PO:0020135; renaming of old term differentiation zone) and new term stem internode differentiation zone (PO:0008042). Also added new term plant axis elongation zone (PO:0025180).

Obsoleted elongation zone, because definition was incorrect, and added new term root elongation zone.

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.

Destroyed leaf lamina ab/adaxial stomatal complex and petiole ab/adaxial stomatal complex, because we decided not to add them at the POC meeting on 12-15-10. Added new terms leaf abaxial stomatal complex and leaf adaxial stomatal complex.

The reason I destroyed them (rather than obsolete) is because they were never on the live site. This has been my practice all along (whenever I add a term to try it out, then it is subsequently rejected by the group, I destroy it, since it was never live. Although PJ suggested yesterday that we merge new term and old terms for those few examples for sensu terms, I think generally it is a better idea to destroy experimental terms that never make it to the live site. Users who download from SVN are using it at their own risk and are aware that the editors file can be changed at any moment, so they should know better than to make associations from terms that are only on the dev browser. If we have to obsolete every term we add experimentally, the file will get really cluttered. We should discuss this more at a future meeting, in case other people don't agree with me on this issue.

Notes from 12-15-10 onward:

Added a general term for stomatal complex, with phyllome stomatal complex and leaf stomatal complex as descendants. Obsoleted floral stomatal complex (see below).

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.

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.

Decided to keep terms leaf abaxial epidermis and leaf adaxial epidermis, even though this means that terms like petiole abaxial epidermis will have two is_a parents (petiole epidermis and leaf abaxial epidermis).

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.

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

Made tetrad of microspores (PO:0000032) is_a portion of plant tissue, added new term tetrad of megaspores.

Made valve (PO:0000033) a general term for all organ parts that split apart, added new child fruit valve.

Made new general term for columella. Made fruit columella (PO:0004540) a child of this, plus new term moss capsule columella. Also had to add term for moss capsule.

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.

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).

Added new term stele, parent to existing term root stele (PO:0020124).

Added new terms for sporangium, megasporangium, and microsporangium. Existing terms nucellus (PO:0020020) and pollen sac (PO:0009070) are children of mega- and microsporangium, respectively.

Made new term embryonic plant structure: A plant structure that is a proper part of an embryo. This term is for plant structures that are only parts of embryos. Structures like hypocotyl that can exist in embryonic and non-embryonic plants do not go here. This created is_a parents for 5 terms that did not have one.

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.

Changed all terms with sensu their names from "structure (sensu Taxon)" to "Taxon structure."

Made part_of children of leaf trichome development stage (PO:0007039) is_a children (1 pattern formation, 2 endoreplication, 3 branch formation 4 growth directionality).

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

canal, is_a plant anatomical canal, parent of petiole canal

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)

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