Summary of Changes to PO April 2012

New and Obsolete Terms

See separate page for a list of New_terms_and_obsolete_terms-March_2012_Release.

Term changes

Made whole plant growth stage (PO:0007033) is_a plant structure development stage, changed definition and renamed whole plant development stage

Merged plant structure development stage (PO:0007021) into plant growth and development stage (PO:0009012) and made plant structure development stage the primary name and changed definition. Still need to fix comment based on BS's comment.

Made gametophyte development stage and sporophyte development stage part_of life of whole plant (PO:0025337).

Made flower, fruit and inflorescence development stage is_a collective plant structure development stage (PO:0025338)

Made leaf development stage and root development stage is_a plant organ development stage.

Made the following terms subtypes of sporophyte development stage (were subtypes of whole plant development stage):

• sporophyte vegetative stage (PO:0007134)
• sporophyte reproductive stage (PO:0007130)
• sporophyte senscent stage (PO:0007017)
• sporophyte dormant stage (PO:0007132)

Made protonema whole plant development stage (PO:0030006) is_a gametophyte vegetative development stage, redefined and removed part_of relation to gametophyte phase.

Wrote new definitions for gametophyte and sporophyte dormant stage.

Changed name of awn (PO:0006032) to lemma awn. Modified text definition to reflect that it is part of lemma. Existing annotations should stay with PO:0006032. Added new general term for awn (PO:0025349), plus new subtypes for palea awn (PO:0025350) and glume awn (PO:0025351)

Added leaf venation as a related synonym of leaf vascular system (PO:0000036)

Added tendril as broad synonym of all tendril types: leaf tendril (PO:0025361), leaflet tendril (PO:0025362), leaf apex tendril (PO:0025363), branch tendril (PO:0025364), stem apex tendril (PO:0025365), leaf rachis tendril (PO:0025366), prophyll tendril (PO:0025367)

Added diaspore as broad synonym to seed (PO:0009010), fruit (PO:0009001), spore (PO:0025017), corm (PO:0025355), bulb (PO:0025356), tuber (PO:0004543)

updated the names and definitions of gametophyte/sporophyte development stage and their direct descendents to match what is on SF tracker.

Renamed PO:0007631 from embryo development stages to embryo stage, and made is_a sporophyte vegetative stage. New definition.

Renamed PO:0001097 from A zygotic stage to zygote stage, and made is_a sporophyte development stage. New definition.

Changed definition of of plant embryo (PO:0009009) to say that it participates in the embryo stage. Changed wording in comment to say "embryo stage" instead of "embryonic phase".

carpel anlagen (PO:0006005) (revised)

-made flower meristem is_a reproductive shoot apical meristem, revised def'n

-made phyllome marginal meristem part_of phyllome

-added exact synonym to leaf marginal meristem: leaf margin blastozone

Changed the aspect (namespace) from plant_growth_and_development_stage to plant_structure_development_stage

Moved leaf trichome development stage (PO:0007039) to be is_a trichome development stage. new def'n: A trichome development stage that has as primary participant a leaf trichome. (POC:Curators)

Modified def'n: seed trichome: (PO:0004511): A trichome that develops from seed coat epidermis.

Got rid of old GRO synonyms on sporophyte dormant stage.

Made seed is_a plant structure. Updated definition. Removed seed part_of fruit and added develops_from ovule, has_part embryo

Added seed dormant stage has_part plant embryo dormant stage

As part of a general overhaul of the definitions of vascular tissue and cell types, updated definitions of: vascular tissue, vascular bundle, phloem, primary phloem, secondary phloem, protophloem, metaphloem, plant spore, xylem, primary xylem, protoxylem, metaxylem, secondary xylem, tracheid bar, leaf vein, midvein, primary vein, lateral meristem, cambium, vascular cambium, cork cambium, sieve tube member, tracheary element, xylem fiber cell, fiber tracheid, libriform fiber cell, axial system, ray system, wood parenchyma, axial wood parenchyma, ray wood parenchyma, wood parenchyma cell, ray wood parenchyma cell, upright wood parenchyma cell, procumbent wood parenchyma cell, axial wood parenchyma cell, tracheary element, tracheid, vessel member, schlerencyma cell, companion cell, sapwood, heartwood, early wood, late wood, growth ring, growth ring boundary.

Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it is defined.

Made growth ring boundary part_of growth ring, instead of is_a. This means it has no is_a parent for the moment.

Added comment to all leaf vein orders that they should only not be used with dichotomously branching vein patterns.

Updated definitions of second through higher order veins, renamed them leaf lamina veins

Updated definition of carpel anlagen.

Set up shoot and root lateral meristems as XPs

Changed phellem and phelloderm to part_of periderm, from part_of shoot axis periderm.

Changed definition of fruit nucellus (PO:0008005).

Udated definitions of intercalary meristem (PO:0006073), leaf intercalary meristem (PO:0006346), stem intercalary meristem (PO:0006347), lateral meristem (PO:0020145), vascular cambium (PO:0005598), and secondary thickening meristem (PO:0025414). Renamed tassel branch meristem to tassel inflorescence branch meristem.

Updated definition of companion cell (PO:0000071), sclerenchyma cell (PO:0000077) and sclerid cell (PO:0025418), sapwood (PO:0004513), heartwood (PO:0004512), early wood (PO:0004515), late wood (PO:0004516), growth ring (PO:0004514), plus wood parenchyma types and wood parenchyma cell types, early wood, late wood, growth ring, growth ring boundary, plant fiber cell, gelatinous fiber cell, septate fiber cell.

Logical definitions

We have begun to add logical or "cross-product" definitions for PO terms that can be defined by other PO terms. These are mostly for structures that are part of another plant structure.

For example: root meristem intersection_of is_a meristem and part_of root, shoot mersitem intersection_of is_a meristem and part_of shoot system.

More of these relations will be incorporated into the PO as we move forward.

Relation changes

Added new relation has_participant. Following BFO, the domain is "occurent" and range is "continuant", which correspond to PO "plant structure development stage" and "plant anatomical entity".

Added has_participant relations between the following terms:

-trichome development stage (PO:0025368) and trichome (PO:0000282)

-seed trichome development stage (PO:0025369) and seed trichome (PO:0004511)

-leaf trichome development stage (PO:0007039) and leaf trichome (PO:0006504)

-plus other plant structure development stages, as appropriate

Added xrefs to BFO or RO for develops_from, has_part, part_of, and adjacent_to.

Changed id of derives_by_manipulation_from from derives_from to derives_by_manipulation_from, so it will not be confused with the more general relation derives_from.

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