Difference between revisions of "Summary of Changes to PO April 2012"
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See separate page for a list of [[New_terms_and_obsolete_terms-March_2012_Release]]. | See separate page for a list of [[New_terms_and_obsolete_terms-March_2012_Release]]. | ||
| − | + | =Changes to plant structure development stages= | |
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The release marks a major revision to the ''plant structure development stage branch'' of the PO. The bulk of the changes were in to ''whole plant development stage'' and its subtypes, but there were substantial changes made throughout this branch of the PO. | The release marks a major revision to the ''plant structure development stage branch'' of the PO. The bulk of the changes were in to ''whole plant development stage'' and its subtypes, but there were substantial changes made throughout this branch of the PO. | ||
| − | + | ==Change to root node== | |
''Plant structure development stage'' (PO:0007021) was merged into ''plant growth and development stage'' (PO:0009012) and ''plant structure development stage'' was made the primary name. The definition of this term was also updated. | ''Plant structure development stage'' (PO:0007021) was merged into ''plant growth and development stage'' (PO:0009012) and ''plant structure development stage'' was made the primary name. The definition of this term was also updated. | ||
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plant_structure_development_stage | plant_structure_development_stage | ||
| − | + | ==Changes to whole plant growth stage== | |
| − | Made whole plant growth stage (PO:0007033) is_a plant structure development stage, changed definition and renamed whole plant development stage | + | Made whole plant growth stage (PO:0007033) is_a plant structure development stage, changed definition and renamed ''whole plant development stage'' |
| − | + | Added a new term for ''life of whole plant'' (PO:0025337). The only instances of ''life of whole plant'' are a maximal ''gametophyte development stage'' and a maximal ''sporophyte development stage''. ''Gametophyte development stage'' and ''sporophyte development stage'' are part_of ''life of whole plant''. | |
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Made the following terms subtypes of sporophyte development stage (were subtypes of whole plant development stage): | Made the following terms subtypes of sporophyte development stage (were subtypes of whole plant development stage): | ||
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Wrote new definitions for gametophyte and sporophyte dormant stage. | Wrote new definitions for gametophyte and sporophyte dormant stage. | ||
| − | ==Changes to plant anatomical entities | + | updated the names and definitions of gametophyte/sporophyte development stage and their direct descendents to match what is on SF tracker. |
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| + | Renamed PO:0007631 from embryo development stages to embryo stage, and made is_a sporophyte vegetative stage. New definition. | ||
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| + | Renamed PO:0001097 from A zygotic stage to zygote stage, and made is_a sporophyte development stage. New definition. | ||
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| + | 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) | ||
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| + | Added seed dormant stage has_part plant embryo dormant stage | ||
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| + | ==Changes to other types of development stages== | ||
| + | Made flower, fruit and inflorescence development stage is_a collective plant structure development stage (PO:0025338) | ||
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| + | Made leaf development stage and root development stage is_a plant organ development stage. | ||
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| + | =Changes to plant anatomical entities= | ||
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) | 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) | ||
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Added '''diaspore''' as broad synonym to seed (PO:0009010), fruit (PO:0009001), spore (PO:0025017), corm (PO:0025355), bulb (PO:0025356), tuber (PO:0004543) | Added '''diaspore''' as broad synonym to seed (PO:0009010), fruit (PO:0009001), spore (PO:0025017), corm (PO:0025355), bulb (PO:0025356), tuber (PO:0004543) | ||
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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". | 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". | ||
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Modified def'n: seed trichome: (PO:0004511): A trichome that develops from seed coat epidermis. | Modified def'n: seed trichome: (PO:0004511): A trichome that develops from seed coat epidermis. | ||
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Made seed is_a plant structure. Updated definition. Removed seed part_of fruit and added develops_from ovule, has_part embryo | Made seed is_a plant structure. Updated definition. Removed seed part_of fruit and added develops_from ovule, has_part embryo | ||
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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. | 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. | ||
Revision as of 13:43, 26 March 2012
This page is under construction.
New and Obsolete Terms
See separate page for a list of New_terms_and_obsolete_terms-March_2012_Release.
Changes to plant structure development stages
The release marks a major revision to the plant structure development stage branch of the PO. The bulk of the changes were in to whole plant development stage and its subtypes, but there were substantial changes made throughout this branch of the PO.
Change to root node
Plant structure development stage (PO:0007021) was merged into plant growth and development stage (PO:0009012) and plant structure development stage was made the primary name. The definition of this term was also updated.
Changed the aspect (namespace) from plant_growth_and_development_stage to plant_structure_development_stage
Changes to whole plant growth stage
Made whole plant growth stage (PO:0007033) is_a plant structure development stage, changed definition and renamed whole plant development stage
Added a new term for life of whole plant (PO:0025337). The only instances of life of whole plant are a maximal gametophyte development stage and a maximal sporophyte development stage. Gametophyte development stage and sporophyte development stage are part_of life of whole plant.
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.
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.
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)
Added seed dormant stage has_part plant embryo dormant stage
Changes to other types of development stages
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.
Changes to plant anatomical entities
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)
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
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
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.
Updated definition of root hair cell (PO:0000256). Renamed PO:0000263 from atrichoblast to non-hair root epidermal cell. Atrichoblast is exact synonym. Updated definition.
Relation changes
Added new relation has_participant. Following BFO, the domain is occurent and range is "continuant", which correspond to plant structure development stage and plant anatomical entity, respectively, in the PO.
Added has_participant relations between a number of terms, such as:
-whole plant development stage (PO:0007033) has_participant whole plant (PO:0000003)
-trichome development stage (PO:0025368) has_participant trichome (PO:0000282)
-leaf trichome development stage (PO:0007039) has_participant leaf trichome (PO:0006504)
-xylem development stage (PO:0025425) has_participant xylem (PO:0005352)
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.
Logical definitions
The PO currently has 64 terms with logical or "cross-product" definitions
New relations added for this release include:
More of these relations are being incorporated into the PO as we move forward.
Back to March_2012_Release_Page
Other
Links to images
We have added several test links to images on PlantSystematics.org:
Image_at_PlantSystematics:1597 to septum (PO:0000030) and fruit septum (PO:0025268)
Image_at_PlantSystematics:14891 and Image_at_PlantSystematics:8662 to pappus (PO:0025393) and pappus element (PO:0025394)
These show up as External References (near the bottom of the page, on AmiGO).
