Summary of Changes to PO Jan2011

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Organization and summary of changes to the Plant Ontology (PO)

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 (all terms have is_a parents)

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 my 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. 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 and trichome cell (synonym: unicellular trichome).

Reorganization of PSO root terms:

Fixed definitions and parents for parts of the root tip.