Difference between revisions of "Summary of Changes to PO April 2012"

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More detailed descriptions of the changes made to the Plant Ontology file are available on the [[POC Meetings Minutes]] and the [http://sourceforge.net/tracker/?group_id=76834&atid=835555 SourceForge tracker].
 +
 
=New and Obsolete Terms=
 
=New and Obsolete Terms=
  
−
See separate page for a list of [[New_terms_and_obsolete_terms-March_2012_Release]].
+
102 new terms for plant anatomical entities and 34 new terms for plant structure development stages were added in this release.
 +
 
 +
See separate page for a complete list of [[New_terms_and_obsolete_terms-April_2012_Release]].
 +
 
 +
=General changes=
 +
We have begun including the ids of PO and GO terms used in PO definitions and comments. This allows users to link directly to those terms from the AmiGO browser and provides additional quality control. An id is listed in parentheses after the first mention of a term in a definition or comment. All new definitions have ids in them, and ids are being added to older definitions as part of an ongoing process.
 +
 
 +
=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.
 +
 
 +
The decision was made to define stages as occurring during the interval between two landmarks (e.g., the ''sporophyte development stage'' occurs between fertilization and death). This means that any stage which occurs during that interval is a subtype of the longer stage, rather than a part of it (e.g., ''sporophyte vegetative stage'' is_a ''sporophyte development stage'', not part_of ''sporophyte development stage''). The part_of and has_part relations can still be used for development stages where appropriate, e.g., ''seed development stage'' has_part ''embryo development stage''.
 +
 
 +
==Change to root node==
 +
''Plant structure development stage'' (PO:0007021) was merged into the original root node ''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.
 +
 
 +
The aspect (namespace in OboEdit) was changed from plant_growth_and_development_stage to
 +
plant_structure_development_stage.
 +
 
 +
==Changes to ''whole plant growth stage'' and its subtypes==
 +
 
 +
Made whole plant growth stage (PO:0007033) is_a ''plant structure development stage'', renamed ''whole plant development stage'' and updated the definition.
 +
 
 +
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'' but remain as subtypes of ''whole plant development stage'', because not every gametophyte or sporophyte development stage is a ''life of whole plant'', but all are part_of some ''life of whole plant'' .
 +
 
 +
Made the following terms subtypes of ''sporophyte development stage'' (were subtypes of ''whole plant development stage''), because they were already defined for sporophytes:
 +
*sporophyte vegetative stage (PO:0007134)
 +
*sporophyte reproductive stage (PO:0007130)
 +
*sporophyte senscent stage (PO:0007017)
 +
*sporophyte dormant stage (PO:0007132)
 +
 
 +
Added new terms for corresponding stages in gametophytes:
 +
*gametophyte vegetative development stage (PO:0025340)
 +
*gametophyte reproductive development stage (PO:0025341)
 +
*gametophyte dormant stage (PO:0025342)
 +
*gametophyte senescent stage (PO:0025343)
 +
 
 +
Made ''protonema whole plant development stage'' (PO:0030006) is_a ''gametophyte vegetative development stage'' (was a ''whole plant development stage'') and updated definition.
 +
 
 +
Renamed "embryo development stages" (PO:0007631) to ''plant embryo stage'', made it is_a ''sporophyte vegetative stage'', and updated the definition.
 +
 
 +
Renamed "A zygotic stage" (PO:0001097) to ''plant zygote stage'', made it is_a ''sporophyte development stage'', and updated the definition.
 +
 
 +
Added relation ''seed dormant stage'' has_part ''plant embryo dormant stage''.
  
−
=Term changes=
+
==Changes to other types of development stages==
−
Made whole plant growth stage (PO:0007033) is_a plant structure development stage, changed definition and renamed whole plant development stage
+
The subtypes of ''plant structure development stage'' were organized to reflect the structure of the ''plant anatomical entity'' branch of the PO. These subtypes include ''whole plant development stage (existing term, see details above), plus new terms for ''collective plant structure development stage'', ''plant organ development stage'', ''plant tissue development stage'', and ''trichome development stage''. ''Seed development stage'' was made a subtype of ''plant structure development stage'', rather than a subtype of ''sporopyhyte vegetative development stage''.
  
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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.
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*''Flower development stage'', ''fruit development stage'', and ''inflorescence development stage'' are now subtypes of ''collective plant structure development stage'' (PO:0025338).
  
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Made gametophyte development stage and sporophyte development stage part_of life of whole plant (PO:0025337).
+
*''Leaf development stage'' and ''root development stage'' are now subtypes of ''plant organ development stage''.
  
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Made flower, fruit and inflorescence development stage is_a collective plant structure development stage (PO:0025338)
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*''Leaf trichome development stage'' is now a subtype of ''trichome development stage''.
  
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Made leaf development stage and root development stage is_a plant organ development stage.
 
  
−
Made the following terms subtypes of sporophyte development stage:
+
Added new terms for ''seed trichome development stage'' and its subtypes, at the request of annotators describing cotton development.
  
−
sporophyte vegetative stage (PO:0007134)
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Added new terms for '''vascular tissue development stage'', ''phloem development stage'', and ''xylem development stage'' as subtypes of ''plant tissue development stage''.
  
−
sporophyte reproductive stage (PO:0007130)
+
Added ''secondary xylem development stage'' and its subtypes, as part of an ongoing project to add terms to the PO for wood anatomy and development, in collaboration with a group of wood scientists (see [[Wood anatomy ontology meeting, 2012 at NYBG, agenda]].
  
−
sporophyte senscent stage (PO:0007017)
+
Updated definitions of ''radicle emergence stage'', ''coleoptile emergence stage'', ''epicotyl emergence stage'', ''hypocotyl emergence stage'' so that they are now defined as emerging from the seed coat, rather than the soil.
  
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sporophyte dormant stage (PO:0007132)
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See [[New_terms_and_obsolete_terms-April_2012_Release#New_plant_structure_development_stage_terms]] for a complete list of new and renamed terms. No plant structure development stage terms were made obsolete in this release.
  
 +
==General changes to ''plant structure development stage'' terms==
  
 +
A decision was made not to prefix new ''plant structure development stage'' terms with numbers or letters, and number/letter prefixes are being removed from existing terms as we update them. This means that terms may not be displayed in chronological order in the PO browser but makes the names clearer. Chronological order may be described by comments such as "stage X precedes stage Y", "stage Y is preceded by stage X", or "stage Y succeeds stage X". In future releases, this temporal relations may be specified in the PO.
  
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Made protonema whole plant development stage (PO:0030006) is_a gametophyte vegetative development stage, redefined and removed part_of relation to gametophyte phase.
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"Stage" has been appended to the end of most ''plant structure development stage'' term names.
  
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Wrote new definitions for gametophyte and sporophyte dormant stage. Need to put on SF.
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All term names are now singular.
  
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Changed name of awn (PO:0006032) to lemma awn. Modified text definition to reflect that it is part of awn. Existing annotations should stay with PO:0006032.  
+
=Changes to plant anatomical entities=
 +
Major revisions to the overall structure of the ''plant anatomical entity'' branch of the PO were completed during previous revisions. Ongoing work on this branch is aimed at refining definitions (including converting text definitions to genus-differentia form and adding logical or cross-product definitions) and adding new terms to meet users needs.
  
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Added leaf venation as a related synonym of leaf vascular system (PO:0000036)
+
==Definition updates==
 +
Definition updates to the terms listed below the updates converted the definitions to the genus-differentia format and made them clearer and/or more precise.
  
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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)  
+
As part of a PO-led initiative to incorporate term to describe wood anatomy, development, and phenotypes, the definitions of most vascular tissue and cell types and related terms were reviewed, and many were updated.
 +
Updated terms include:
 +
portion of vascular tissue (PO:0009015), vascular bundle (PO:0005020), phloem (PO:0005417), primary phloem (PO:0006075), secondary phloem (PO:0005043), protophloem (PO:0006077), metaphloem (PO:0006076), secondary phloem (PO:0005043), xylem (PO:0005352), primary xylem (PO:0005849), protoxylem (PO:0000272), metaxylem (PO:0000372), secondary xylem (PO:0005848), tracheid bar (PO:0019026), leaf lamina vein (PO:0020138), leaf midvein (PO:0020139), secondary leaf vein (PO:0020140), lateral leaf vein (PO:0006011), tertiary leaf vein (PO:0008021), quaternary leaf vein (PO:0008022), higher order leaf vein (PO:0008023), lateral meristem (PO:0020145, cambium (PO:0005597), vascular cambium (PO:0005598), cork cambium (PO:0005599), sieve tube element (PO:0000289), tracheary element (PO:0000290), xylem fiber cell (PO:0000274), fiber tracheid (PO:0000355), libriform fiber cell (PO:0004520), secondary xylem parenchyma (PO:0004532), axial secondary xylem parenchyma (PO:0004533), ray secondary xylem parenchyma (PO:0004534), secondary xylem parenchyma cell (PO:0004525), ray secondary xylem parenchyma cell (PO:0004527), upright ray secondary xylem parenchyma cell (PO:0004528), procumbent ray secondary xylem parenchyma cell (PO:0004529), axial secondary xylem parenchyma cell (PO:0004526), tracheary element (PO:0000290), tracheid (PO:0000301), xylem vessel member (PO:0002003), schlerencyma cell (PO:0000077), companion cell (PO:0000071), sapwood (PO:0004513), heartwood (PO:0004512), early wood (early wood), late wood (PO:0004516), growth ring (PO:0004516), growth ring boundary (PO:0004517), cambial initial cell (PO:0000295), plant fiber cell (PO:0025407), xylem fiber cell (PO:0000274), phloem fiber cell (PO:0004519), and septate fiber cell (PO:0004521).
  
−
Added '''diaspore''' as broad synonym to seed (PO:0009010), fruit (PO:0009001), spore (PO:0025017), corm (PO:0025355), bulb (PO:0025356), tuber (PO:0004543)
+
Other terms with modified definitions include: intercalary meristem (PO:0006073), leaf intercalary meristem (PO:0006346), stem intercalary meristem (PO:0006347), seed trichome (PO:0004511), carpel anlagen (PO:0006005), stipule (PO:0020041), stolon (PO:0003024), arilloid (PO:0019022), strophiole (PO:0019023), caruncle (PO:0020060), aril (PO:0009090), elaiosome (PO:0020062), tassel inflorescence branch meristem (PO:0009107), ear inflorescence branch meristem (PO:0009110), fruit nucellus (PO:0008005), and leaf lamina (PO:0020039).
  
−
updated the names and definitions of gametophyte/sporophyte development stage and their direct descendents to match what is on SF tracker.
+
Made ''seed'' is_a ''plant structure'', instead of is_a ''whole plant'' and updated the definition.  Removed the relation ''seed'' part_of ''fruit'' and added ''seed'' develops_from ''ovule'', ''seed '' has_part ''embryo''.
  
−
Renamed PO:0007631 from embryo development stages to embryo stage, and made is_a sporophyte vegetative stage. New definition.
+
Renamed "spore" (PO:0025017) ''plant spore'' and made it is_a ''whole plant'' as well as is_a ''plant cell''. Updated the definition to refer to the ''plant spore stage'' (PO:0025375).
  
−
Renamed PO:0001097 from A zygotic stage to zygote stage, and made is_a sporophyte development stage. New definition.
+
Renamed "atrichoblast" (PO:0000263) ''non-hair root epidermal cell'', made "atrichoblast" an exact synonym, and updated definition. Also updated definition of ''root hair cell'' (PO:0000256).
  
−
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".
+
==other changes==
 +
*Replaced "wood" in term names with "secondary xylem" (e.g., ''wood parenchyma'' became ''secondary xylem parenchyma''), but kept names with wood as synonyms. However, the commonly used terms ''late wood'', ''early wood'', ''heartwood'', ''sapwood'', and ''reaction wood'' were kept as primary names.
  
 +
*Changed name of "awn" (PO:0006032) to ''lemma awn'', because it was already part_of ''lemma''. Modified text definition to reflect that it is part of lemma. Added new general term for ''awn'' (PO:0025349), plus new subtypes for ''palea awn'' (PO:0025350) and ''glume awn'' (PO:0025351)
  
−
carpel anlagen (PO:0006005) (revised)
+
*Made ''flower meristem'' is_a ''reproductive shoot apical meristem'', revised definition
  
 +
*Added comment to all leaf vein orders that they should not be used with dichotomously branching vein patterns.
  
−
-made flower meristem is_a reproductive shoot apical meristem, revised def'n
+
*Changed ''phellem'' and ''phelloderm'' to part_of ''periderm'', instead of part_of ''shoot axis periderm'', because it can also be found in ''roots''.
  
−
-made phyllome marginal meristem part_of phyllome
+
====Revised def'ns:====
 +
* Sporophyte vegetative stage (PO:0028002): A sporophyte development stage (PO:0007134) that occurs during the interval between fertilization and the first cell division of the plant zygote.  Revised comment: Precedes the plant embyro stage (PO:0007631). Refers to the GO Biological Process term: fertilization (GO:0009566).
  
−
-added exact synonym to leaf marginal meristem: leaf margin blastozone
+
* sporophyte development stage (PO:0028002), sporophyte vegetative stage (PO:0007134) and seedling development stage (PO:0007131) with Po ids.
  
 +
==Changes to radicle emergence stage (PO:0007015), coleoptile emergence stage (PO:0007045) and related terms:==
  
−
added has_participant relations between the following terms:
 
  
−
-trichome development stage (PO:0025368) and trichome (PO:0000282)
+
* coleoptile (PO:0020033): A plant organ (PO:0009008) that surrounds the plumule (PO:0020032) of a plant embryo (PO:0009009) or the emerging shoot apex (PO:0000037) of a seedling.  (is_a plant organ).
  
−
-seed trichome development stage (PO:0025369) and seed trichome (PO:0004511)
+
* embryo coleoptile (PO:0025286) and seedling coleoptile (PO:0025287)  
  
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-leaf trichome development stage (PO:0007039) and leaf trichome (PO:0006504)
+
* plumule (PO:0020032): The shoot apex (PO:0000037) of the plant embryo (PO:0009009), above the cotyledonary node (PO:0025321).
  
 +
* cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003). (added new child  terms: embryo cotyledon (PO:0025470) and seedling cotyledon (PO:0025471)).
  
 +
* radicle (PO:0020031): An embryo root (PO:0000045) that is the basal continuation of a hypocotyl (PO:0020100) in a plant embryo (PO:0009009) or a seedling (PO:0000003).
  
−
Changed the aspect (namespace) from plant_growth_and_development_stage to
+
* embryo radicle (PO:0025296) (is_a embryo root), seedling radicle (PO:0025297)  
−
plant_structure_development_stage
 
  
 +
* coleorhiza (PO:0020034): A sheath-like plant organ (PO:0009008) that surrounds the radicle (PO:0020031) of a plant embryo (PO:0009009) or the emerging root (PO:0009005) of a seedling (PO:0000003).
  
 +
* embryo coleorhiza (PO:0025288), seedling coleorhiza (PO:0025289) 
  
−
Moved leaf trichome development stage (PO:0007039) to be is_a trichome development stage.
+
* hypocotyl (PO:0020100): A stem internode (PO:0020142) below the cotyledonary node (PO:0025321) and transitional to a root (PO:0009005) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
−
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.
+
* embryo hypocotyl (PO:0025290) and seedling hypocotyl (PO:0025291)
  
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Got rid of old GRO synonyms on sporophyte dormant stage.
+
* epicotyl (PO:0020035): The first stem internode (PO:0020142) above the cotyledonary node (PO:0025321) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
  
−
Made seed is_a plant structure. Updated definition.  Removed seed part_of fruit and added develops_from ovule, has_part embryo
+
* embryo epicotyl (PO:0025292) and seedling epicotyl (PO:0025293)
  
−
Added seed dormant stage has_part plant embryo dormant stage
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* plant embryo stage (PO:0007631) and plant embryo (PO:0009009): removed reference to cotyledons in pteridophytes, added Po ids and terms names.
 +
* Updated the comment on plant embryo (PO:0009009) to include the details of the end of the plant embryo stage in various taxa.
 +
 +
* radicle emergence stage (PO:0007015): A root development stage (PO:0007520) during which a radicle (PO:0020031) emerges from the seed coat (PO:0009088). (part_of seed germination stage (PO:0007057)).
  
−
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.
+
* coleoptile emergence stage (PO:0007045): A sporophyte vegetative stage (PO:0007134) during which the coleoptile (PO:0020033) emerges from the seed coat (PO:0009088).
  
−
Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it is defined.
+
* cotyledon emergence stage (PO:0007049): A seedling development stage (PO:0007131) during which the cotyledon (PO:0020030) emerges from the seed coat (PO:0009088).
  
−
Made growth ring boundary part_of growth ring, instead of is_a. This means it has no is_a parent for the moment.
+
* epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the epicotyl (PO:0020035) emerges from the seed coat (PO:0009088).  
  
−
Added comment to all leaf vein orders that they should only not be used with dichotomously branching vein patterns.
+
* hypocotyl emergence stage (PO:0007043): A seedling development stage (PO:0007131) during which the hypocotyl (PO:0020100) emerges from the seed coat (PO:0009088).
  
−
Updated definitions of second through higher order veins, renamed them leaf lamina veins
+
===Added relations: ===
  
−
Updated definition of carpel anlagen.
+
* seedling hypocotyl (PO:0025291) participates_in seedling development stage (PO:0007131)
 +
 +
* plant zygote (PO:0000423) participates_in plant zygote stage
  
−
Set up shoot and root lateral meristems as XPs
+
* primary root develops from seedling radicle
  
−
Changed phellem and phelloderm to part_of periderm, from part_of shoot axis periderm.
+
* plant zygote stage (PO:0001097) is_a sporophyte development stage (PO:0028002)
  
 +
===Created new terms===
 +
* embryo cotyledon (PO:0025470) and seedling cotyledon (PO:0025471)
 +
* coleorhiza emergence stage (PO:0025475): A root development stage (PO:0007520) during which a coleorhiza (PO:0020034) emerges from the seed coat (PO:0009088). Added relation part_of the seed germination stage (PO:0007057).
  
 +
==Summary of new and obsolete terms==
 +
For a complete list of new, renamed, and obsolete terms, see [[New_terms_and_obsolete_terms-April_2012_Release#New_plant_anatomical_entity_terms]].
  
−
Changed definition of fruit nucellus (PO:0008005).
+
===New term highlights:===
  
−
Udated definitions of
+
'''New plant anatomical spaces:''' intercellular space (PO:0025379), leaf mesophyll intercellular space (PO:0025380), spongy mesophyll intercellular space (PO:0025381), palisade mesophyll intercellular space (PO:0025397), substomatal cavity (PO:0025382), phyllome substomatal cavity (PO:0025398), leaf substomatal cavity (PO:0025399), phyllome sinus (PO:0025383), leaf sinus (PO:0025384)  
−
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.
+
'''New portion of plant substance terms:''' cutin (PO:0025385), cuticular wax (PO:0025386), plant cuticle proper (PO:0025387), epicuticular wax (PO:0025388), intercuticular wax (PO:0025389), leaf primary vein (PO:0025413)
  
−
=Logical definitions=
+
'''New meristems:''' phyllome adaxial meristem (PO:0025400), leaf adaxial meristem (PO:0025401), phyllome abaxial meristem (PO:0025402), leaf abaxial meristem (PO:0025403), phyllome marginal meristem (PO:0025404), leaf marginal meristem (PO:0025405), secondary thickening meristem (PO:0025414), phyllome plate meristem: (PO:0025428), leaf plate meristem: (PO:0025429), phyllome anlagen: (PO:0025430), leaf anlagen (PO:0025431), cotyledon anlagen (PO:0025432), root anlagen (PO:0025433), shoot axis cork cambium (PO:0025435), root cork cambium (PO:0025436), shoot axis vascular cambium (PO:0025437), root vascular cambium (PO:0025438), cambial zone (PO:0025439), shoot axis cambial zone (PO:0025440), root cambial zone (PO:0025441), stem secondary thickening meristem (PO:0025442), root secondary thickening meristem (PO:0025443)
−
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.
+
'''New vascular and wood related terms:''' shoot axis cork cambium (PO:0025435), root cork cambium (PO:0025436), shoot axis vascular cambium (PO:0025437), root vascular cambium (PO:0025438), cambial zone (PO:0025439), shoot axis cambial zone (PO:0025440), root cambial zone (PO:0025441), primary xylem tracheary element (PO:0025444), secondary xylem tracheary element (PO:0025445), primary xylem tracheid (PO:0025446), secondary xylem tracheid (PO:0025447), primary xylem vessel member (PO:0025448), secondary xylem vessel member (PO:0025449), primary xylem vessel (PO:0025450), secondary xylem vessel (PO:0025451), primary phloem sieve element (PO:0025452), secondary phloem sieve element (PO:0025453), primary phloem sieve cell (PO:0025454), primary phloem sieve tube element (PO:0025455), secondary phloem sieve cell (PO:0025456), secondary phloem sieve tube element (PO:0025457), transfer companion cell (PO:0025458), ordinary companion cell (PO:0025459), intermediary companion cell (PO:0025460), early wood tracheary element (PO:0025461), late wood tracheary element (PO:0025462), reaction wood (PO:0025472), compression wood (PO:0025473), tension wood (PO:0025474)
  
−
More of these relations will be incorporated into the PO as we move forward.
+
===Obsolete terms:===
 +
Only two terms were made obsolete (depricated) for this release:
 +
* '''xylem element''' (PO:0000273), consider ''tracheary element'' (PO:0000290) or ''xylem fiber cell'' (PO:0000274)
 +
* '''axial cell''' (PO:0000081), consider ''fiber cell'' (PO:0025407), ''sieve element'' (PO:0025406), or ''tracheary element'' (PO:0000290)
 +
 
 +
These terms were made obsolete because they did not represent valid anatomical groupings.
 +
 
 +
==Synonyms==
 +
 
 +
Many synonyms were added to the PO (see [[New_terms_and_obsolete_terms-April_2012_Release#New_synonyms]]), including 333 synonyms based on entries from the [http://huntbot.andrew.cmu.edu/hibd/departments/DB-INTRO/IntroFNA.shtml Flora of North America Glossary] that mapped to existing terms.
  
 
=Relation changes=
 
=Relation changes=
  
−
Added new relation '''has_participant'''. '''Domain''' = plant structure development stage, '''Range''' = plant anatomical entity.
+
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. This makes the PO file more compatible with other ontologies.
 +
 
 +
Changed the 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, and more of these relations are being incorporated into the PO as we move forward.
 +
 
 +
Examples of new cross-product (XP) relations added for this release include:
 +
 
 +
*''shoot lateral meristems'' and ''root lateral meristems'' as XPs of ''lateral mersistem'' and part_of ''shoot system'' or ''root'', respectively
 +
 
 +
*''primary vascular tissue'' and ''secondary vascular tissue'' as XPs of ''vacular tissue'' and develops_from ''procambium'' or ''cambium'', respectively
 +
 
 +
*''plant embryo stage'' as XP of ''sporophyte development stage'' and has_participant ''plant embryo''
 +
 
 +
*''plant spore development stage'' as XP of ''sporophyte development stage'' and has_participant ''plant spore''
 +
 
 +
*''xylem fiber cell'' and ''phloem fiber cell'' as XPs of ''plant fiber cell'' and part_of ''xylem'' or ''phloem'', respectively
 +
 
 +
=Other=
 +
==Links to images==
 +
 
 +
We have added several test links to images on PlantSystematics.org:
 +
 
 +
[http://www.plantsystematics.org/imagebyid_1597.html PlantSystematics_image_archive:1597] to septum (PO:0000030) and fruit septum (PO:0025268)
 +
 
 +
[http://www.plantsystematics.org/imagebyid_14891.html PlantSystematics_image_archive:14891]  and [http://www.plantsystematics.org/imagebyid_8662.html PlantSystematics_image_archive:8662] to pappus (PO:0025393) and pappus element (PO:0025394)
  
−
The '''participates_in relation''' was added during the last release. For improved reasoning, the domain and range were specified. '''Domain''' = plant anatomical entity, '''Range''' = plant structure development stage.
+
These show up as External References (near the bottom of the page) on AmiGO.
  
−
Changed name of derives_from to '''derives_by_manipulation_from''' and added definition and comment.
+
==Glossary of PO terms==
 +
The definitions of all ''plant anatomical entities'' are now available in glossary form: [http://www.plantontology.org/db/glossary/glossary Glossary of Plant Anatomy].
  
−
Back to [[March_2012_Release_Page]]
+
Back to [[April_2012_Release_Page]]

Latest revision as of 02:36, 14 June 2012

More detailed descriptions of the changes made to the Plant Ontology file are available on the POC Meetings Minutes and the SourceForge tracker.

New and Obsolete Terms

102 new terms for plant anatomical entities and 34 new terms for plant structure development stages were added in this release.

See separate page for a complete list of New_terms_and_obsolete_terms-April_2012_Release.

General changes

We have begun including the ids of PO and GO terms used in PO definitions and comments. This allows users to link directly to those terms from the AmiGO browser and provides additional quality control. An id is listed in parentheses after the first mention of a term in a definition or comment. All new definitions have ids in them, and ids are being added to older definitions as part of an ongoing process.

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.

The decision was made to define stages as occurring during the interval between two landmarks (e.g., the sporophyte development stage occurs between fertilization and death). This means that any stage which occurs during that interval is a subtype of the longer stage, rather than a part of it (e.g., sporophyte vegetative stage is_a sporophyte development stage, not part_of sporophyte development stage). The part_of and has_part relations can still be used for development stages where appropriate, e.g., seed development stage has_part embryo development stage.

Change to root node

Plant structure development stage (PO:0007021) was merged into the original root node 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.

The aspect (namespace in OboEdit) was changed from plant_growth_and_development_stage to plant_structure_development_stage.

Changes to whole plant growth stage and its subtypes

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

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 but remain as subtypes of whole plant development stage, because not every gametophyte or sporophyte development stage is a life of whole plant, but all are part_of some life of whole plant .

Made the following terms subtypes of sporophyte development stage (were subtypes of whole plant development stage), because they were already defined for sporophytes:

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

Added new terms for corresponding stages in gametophytes:

  • gametophyte vegetative development stage (PO:0025340)
  • gametophyte reproductive development stage (PO:0025341)
  • gametophyte dormant stage (PO:0025342)
  • gametophyte senescent stage (PO:0025343)

Made protonema whole plant development stage (PO:0030006) is_a gametophyte vegetative development stage (was a whole plant development stage) and updated definition.

Renamed "embryo development stages" (PO:0007631) to plant embryo stage, made it is_a sporophyte vegetative stage, and updated the definition.

Renamed "A zygotic stage" (PO:0001097) to plant zygote stage, made it is_a sporophyte development stage, and updated the definition.

Added relation seed dormant stage has_part plant embryo dormant stage.

Changes to other types of development stages

The subtypes of plant structure development stage were organized to reflect the structure of the plant anatomical entity branch of the PO. These subtypes include whole plant development stage (existing term, see details above), plus new terms for collective plant structure development stage, plant organ development stage, plant tissue development stage, and trichome development stage. Seed development stage was made a subtype of plant structure development stage, rather than a subtype of sporopyhyte vegetative development stage.

  • Flower development stage, fruit development stage, and inflorescence development stage are now subtypes of collective plant structure development stage (PO:0025338).
  • Leaf development stage and root development stage are now subtypes of plant organ development stage.
  • Leaf trichome development stage is now a subtype of trichome development stage.


Added new terms for seed trichome development stage and its subtypes, at the request of annotators describing cotton development.

Added new terms for 'vascular tissue development stage, phloem development stage, and xylem development stage as subtypes of plant tissue development stage.

Added secondary xylem development stage and its subtypes, as part of an ongoing project to add terms to the PO for wood anatomy and development, in collaboration with a group of wood scientists (see Wood anatomy ontology meeting, 2012 at NYBG, agenda.

Updated definitions of radicle emergence stage, coleoptile emergence stage, epicotyl emergence stage, hypocotyl emergence stage so that they are now defined as emerging from the seed coat, rather than the soil.

See New_terms_and_obsolete_terms-April_2012_Release#New_plant_structure_development_stage_terms for a complete list of new and renamed terms. No plant structure development stage terms were made obsolete in this release.

General changes to plant structure development stage terms

A decision was made not to prefix new plant structure development stage terms with numbers or letters, and number/letter prefixes are being removed from existing terms as we update them. This means that terms may not be displayed in chronological order in the PO browser but makes the names clearer. Chronological order may be described by comments such as "stage X precedes stage Y", "stage Y is preceded by stage X", or "stage Y succeeds stage X". In future releases, this temporal relations may be specified in the PO.

"Stage" has been appended to the end of most plant structure development stage term names.

All term names are now singular.

Changes to plant anatomical entities

Major revisions to the overall structure of the plant anatomical entity branch of the PO were completed during previous revisions. Ongoing work on this branch is aimed at refining definitions (including converting text definitions to genus-differentia form and adding logical or cross-product definitions) and adding new terms to meet users needs.

Definition updates

Definition updates to the terms listed below the updates converted the definitions to the genus-differentia format and made them clearer and/or more precise.

As part of a PO-led initiative to incorporate term to describe wood anatomy, development, and phenotypes, the definitions of most vascular tissue and cell types and related terms were reviewed, and many were updated. Updated terms include: portion of vascular tissue (PO:0009015), vascular bundle (PO:0005020), phloem (PO:0005417), primary phloem (PO:0006075), secondary phloem (PO:0005043), protophloem (PO:0006077), metaphloem (PO:0006076), secondary phloem (PO:0005043), xylem (PO:0005352), primary xylem (PO:0005849), protoxylem (PO:0000272), metaxylem (PO:0000372), secondary xylem (PO:0005848), tracheid bar (PO:0019026), leaf lamina vein (PO:0020138), leaf midvein (PO:0020139), secondary leaf vein (PO:0020140), lateral leaf vein (PO:0006011), tertiary leaf vein (PO:0008021), quaternary leaf vein (PO:0008022), higher order leaf vein (PO:0008023), lateral meristem (PO:0020145, cambium (PO:0005597), vascular cambium (PO:0005598), cork cambium (PO:0005599), sieve tube element (PO:0000289), tracheary element (PO:0000290), xylem fiber cell (PO:0000274), fiber tracheid (PO:0000355), libriform fiber cell (PO:0004520), secondary xylem parenchyma (PO:0004532), axial secondary xylem parenchyma (PO:0004533), ray secondary xylem parenchyma (PO:0004534), secondary xylem parenchyma cell (PO:0004525), ray secondary xylem parenchyma cell (PO:0004527), upright ray secondary xylem parenchyma cell (PO:0004528), procumbent ray secondary xylem parenchyma cell (PO:0004529), axial secondary xylem parenchyma cell (PO:0004526), tracheary element (PO:0000290), tracheid (PO:0000301), xylem vessel member (PO:0002003), schlerencyma cell (PO:0000077), companion cell (PO:0000071), sapwood (PO:0004513), heartwood (PO:0004512), early wood (early wood), late wood (PO:0004516), growth ring (PO:0004516), growth ring boundary (PO:0004517), cambial initial cell (PO:0000295), plant fiber cell (PO:0025407), xylem fiber cell (PO:0000274), phloem fiber cell (PO:0004519), and septate fiber cell (PO:0004521).

Other terms with modified definitions include: intercalary meristem (PO:0006073), leaf intercalary meristem (PO:0006346), stem intercalary meristem (PO:0006347), seed trichome (PO:0004511), carpel anlagen (PO:0006005), stipule (PO:0020041), stolon (PO:0003024), arilloid (PO:0019022), strophiole (PO:0019023), caruncle (PO:0020060), aril (PO:0009090), elaiosome (PO:0020062), tassel inflorescence branch meristem (PO:0009107), ear inflorescence branch meristem (PO:0009110), fruit nucellus (PO:0008005), and leaf lamina (PO:0020039).

Made seed is_a plant structure, instead of is_a whole plant and updated the definition. Removed the relation seed part_of fruit and added seed develops_from ovule, seed has_part embryo.

Renamed "spore" (PO:0025017) plant spore and made it is_a whole plant as well as is_a plant cell. Updated the definition to refer to the plant spore stage (PO:0025375).

Renamed "atrichoblast" (PO:0000263) non-hair root epidermal cell, made "atrichoblast" an exact synonym, and updated definition. Also updated definition of root hair cell (PO:0000256).

other changes

  • Replaced "wood" in term names with "secondary xylem" (e.g., wood parenchyma became secondary xylem parenchyma), but kept names with wood as synonyms. However, the commonly used terms late wood, early wood, heartwood, sapwood, and reaction wood were kept as primary names.
  • Changed name of "awn" (PO:0006032) to lemma awn, because it was already part_of lemma. Modified text definition to reflect that it is part of lemma. Added new general term for awn (PO:0025349), plus new subtypes for palea awn (PO:0025350) and glume awn (PO:0025351)
  • Made flower meristem is_a reproductive shoot apical meristem, revised definition
  • Added comment to all leaf vein orders that they should not be used with dichotomously branching vein patterns.
  • Changed phellem and phelloderm to part_of periderm, instead of part_of shoot axis periderm, because it can also be found in roots.

Revised def'ns:

  • Sporophyte vegetative stage (PO:0028002): A sporophyte development stage (PO:0007134) that occurs during the interval between fertilization and the first cell division of the plant zygote. Revised comment: Precedes the plant embyro stage (PO:0007631). Refers to the GO Biological Process term: fertilization (GO:0009566).
  • sporophyte development stage (PO:0028002), sporophyte vegetative stage (PO:0007134) and seedling development stage (PO:0007131) with Po ids.

Changes to radicle emergence stage (PO:0007015), coleoptile emergence stage (PO:0007045) and related terms:

  • coleoptile (PO:0020033): A plant organ (PO:0009008) that surrounds the plumule (PO:0020032) of a plant embryo (PO:0009009) or the emerging shoot apex (PO:0000037) of a seedling. (is_a plant organ).
  • embryo coleoptile (PO:0025286) and seedling coleoptile (PO:0025287)
  • plumule (PO:0020032): The shoot apex (PO:0000037) of the plant embryo (PO:0009009), above the cotyledonary node (PO:0025321).
  • cotyledon (PO:0020030): A vascular leaf (PO:0009025) formed at the first shoot node (PO:0005004) of a plant embryo (PO:0009009) or a seedling (PO:0000003). (added new child terms: embryo cotyledon (PO:0025470) and seedling cotyledon (PO:0025471)).
  • radicle (PO:0020031): An embryo root (PO:0000045) that is the basal continuation of a hypocotyl (PO:0020100) in a plant embryo (PO:0009009) or a seedling (PO:0000003).
  • embryo radicle (PO:0025296) (is_a embryo root), seedling radicle (PO:0025297)
  • coleorhiza (PO:0020034): A sheath-like plant organ (PO:0009008) that surrounds the radicle (PO:0020031) of a plant embryo (PO:0009009) or the emerging root (PO:0009005) of a seedling (PO:0000003).
  • embryo coleorhiza (PO:0025288), seedling coleorhiza (PO:0025289)
  • hypocotyl (PO:0020100): A stem internode (PO:0020142) below the cotyledonary node (PO:0025321) and transitional to a root (PO:0009005) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
  • embryo hypocotyl (PO:0025290) and seedling hypocotyl (PO:0025291)
  • epicotyl (PO:0020035): The first stem internode (PO:0020142) above the cotyledonary node (PO:0025321) of a plant embryo (PO:0009009) or a seedling (PO:0000003).
  • embryo epicotyl (PO:0025292) and seedling epicotyl (PO:0025293)
  • plant embryo stage (PO:0007631) and plant embryo (PO:0009009): removed reference to cotyledons in pteridophytes, added Po ids and terms names.
  • Updated the comment on plant embryo (PO:0009009) to include the details of the end of the plant embryo stage in various taxa.
  • radicle emergence stage (PO:0007015): A root development stage (PO:0007520) during which a radicle (PO:0020031) emerges from the seed coat (PO:0009088). (part_of seed germination stage (PO:0007057)).
  • coleoptile emergence stage (PO:0007045): A sporophyte vegetative stage (PO:0007134) during which the coleoptile (PO:0020033) emerges from the seed coat (PO:0009088).
  • cotyledon emergence stage (PO:0007049): A seedling development stage (PO:0007131) during which the cotyledon (PO:0020030) emerges from the seed coat (PO:0009088).
  • epicotyl emergence stage (PO:0007054): A seedling development stage (PO:0007131) during which the epicotyl (PO:0020035) emerges from the seed coat (PO:0009088).
  • hypocotyl emergence stage (PO:0007043): A seedling development stage (PO:0007131) during which the hypocotyl (PO:0020100) emerges from the seed coat (PO:0009088).

Added relations:

  • seedling hypocotyl (PO:0025291) participates_in seedling development stage (PO:0007131)
  • plant zygote (PO:0000423) participates_in plant zygote stage
  • primary root develops from seedling radicle
  • plant zygote stage (PO:0001097) is_a sporophyte development stage (PO:0028002)

Created new terms

  • embryo cotyledon (PO:0025470) and seedling cotyledon (PO:0025471)
  • coleorhiza emergence stage (PO:0025475): A root development stage (PO:0007520) during which a coleorhiza (PO:0020034) emerges from the seed coat (PO:0009088). Added relation part_of the seed germination stage (PO:0007057).

Summary of new and obsolete terms

For a complete list of new, renamed, and obsolete terms, see New_terms_and_obsolete_terms-April_2012_Release#New_plant_anatomical_entity_terms.

New term highlights:

New plant anatomical spaces: intercellular space (PO:0025379), leaf mesophyll intercellular space (PO:0025380), spongy mesophyll intercellular space (PO:0025381), palisade mesophyll intercellular space (PO:0025397), substomatal cavity (PO:0025382), phyllome substomatal cavity (PO:0025398), leaf substomatal cavity (PO:0025399), phyllome sinus (PO:0025383), leaf sinus (PO:0025384)

New portion of plant substance terms: cutin (PO:0025385), cuticular wax (PO:0025386), plant cuticle proper (PO:0025387), epicuticular wax (PO:0025388), intercuticular wax (PO:0025389), leaf primary vein (PO:0025413)

New meristems: phyllome adaxial meristem (PO:0025400), leaf adaxial meristem (PO:0025401), phyllome abaxial meristem (PO:0025402), leaf abaxial meristem (PO:0025403), phyllome marginal meristem (PO:0025404), leaf marginal meristem (PO:0025405), secondary thickening meristem (PO:0025414), phyllome plate meristem: (PO:0025428), leaf plate meristem: (PO:0025429), phyllome anlagen: (PO:0025430), leaf anlagen (PO:0025431), cotyledon anlagen (PO:0025432), root anlagen (PO:0025433), shoot axis cork cambium (PO:0025435), root cork cambium (PO:0025436), shoot axis vascular cambium (PO:0025437), root vascular cambium (PO:0025438), cambial zone (PO:0025439), shoot axis cambial zone (PO:0025440), root cambial zone (PO:0025441), stem secondary thickening meristem (PO:0025442), root secondary thickening meristem (PO:0025443)

New vascular and wood related terms: shoot axis cork cambium (PO:0025435), root cork cambium (PO:0025436), shoot axis vascular cambium (PO:0025437), root vascular cambium (PO:0025438), cambial zone (PO:0025439), shoot axis cambial zone (PO:0025440), root cambial zone (PO:0025441), primary xylem tracheary element (PO:0025444), secondary xylem tracheary element (PO:0025445), primary xylem tracheid (PO:0025446), secondary xylem tracheid (PO:0025447), primary xylem vessel member (PO:0025448), secondary xylem vessel member (PO:0025449), primary xylem vessel (PO:0025450), secondary xylem vessel (PO:0025451), primary phloem sieve element (PO:0025452), secondary phloem sieve element (PO:0025453), primary phloem sieve cell (PO:0025454), primary phloem sieve tube element (PO:0025455), secondary phloem sieve cell (PO:0025456), secondary phloem sieve tube element (PO:0025457), transfer companion cell (PO:0025458), ordinary companion cell (PO:0025459), intermediary companion cell (PO:0025460), early wood tracheary element (PO:0025461), late wood tracheary element (PO:0025462), reaction wood (PO:0025472), compression wood (PO:0025473), tension wood (PO:0025474)

Obsolete terms:

Only two terms were made obsolete (depricated) for this release:

  • xylem element (PO:0000273), consider tracheary element (PO:0000290) or xylem fiber cell (PO:0000274)
  • axial cell (PO:0000081), consider fiber cell (PO:0025407), sieve element (PO:0025406), or tracheary element (PO:0000290)

These terms were made obsolete because they did not represent valid anatomical groupings.

Synonyms

Many synonyms were added to the PO (see New_terms_and_obsolete_terms-April_2012_Release#New_synonyms), including 333 synonyms based on entries from the Flora of North America Glossary that mapped to existing terms.

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. This makes the PO file more compatible with other ontologies.

Changed the 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, and more of these relations are being incorporated into the PO as we move forward.

Examples of new cross-product (XP) relations added for this release include:

  • shoot lateral meristems and root lateral meristems as XPs of lateral mersistem and part_of shoot system or root, respectively
  • primary vascular tissue and secondary vascular tissue as XPs of vacular tissue and develops_from procambium or cambium, respectively
  • plant embryo stage as XP of sporophyte development stage and has_participant plant embryo
  • plant spore development stage as XP of sporophyte development stage and has_participant plant spore
  • xylem fiber cell and phloem fiber cell as XPs of plant fiber cell and part_of xylem or phloem, respectively

Other

Links to images

We have added several test links to images on PlantSystematics.org:

PlantSystematics_image_archive:1597 to septum (PO:0000030) and fruit septum (PO:0025268)

PlantSystematics_image_archive:14891 and PlantSystematics_image_archive:8662 to pappus (PO:0025393) and pappus element (PO:0025394)

These show up as External References (near the bottom of the page) on AmiGO.

Glossary of PO terms

The definitions of all plant anatomical entities are now available in glossary form: Glossary of Plant Anatomy.

Back to April_2012_Release_Page

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