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); 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

Priorities for this release

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

2. Incorporate user requests

3. Add terms for non-angisperm structures (begin, mostly will be done in next release)

4. Update PGDSO (begin, mostly will be done in next release)

List of Changes

• 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 work on user term requests. About half way done -- will finish during next round of revisions.

Added terms for Musa (Generation Challenge Program), legumes (Austin Mast, FSU) and TraitNet.

Started working on root terms from Rich Zobel

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

New terms (as parents to terms without): gynoecium ridge, dehiscence zone,

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 root elongation zone, because definition was incorrect, and added new term with same name.

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.

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.