Difference between revisions of "Details of Changes in PO Release 19"

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Back to [[Release_19]]
 
Back to [[Release_19]]
  
−
=Modified or Updated definitions and/or comments: PAE terms=
+
=Revised or Updated definitions and/or comments: PAE terms=
 +
==Children of shoot axis tuber:(PO:0004543)==
 +
* shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073).
 +
** shoot axis tuber axillary bud meristem (PO:0025068): An axillary bud meristem (PO:0000232) that is part of a shoot axis tuber (PO:0004543).
 +
** shoot axis tuber axillary vegetative bud:  An axillary vegetative bud (PO:0004712) that is part of a shoot axis tuber (PO:0004543).
 +
** shoot axis tuber epidermis (PO:0025046): A portion of shoot axis epidermis (PO:0000112) that is part of a shoot axis tuber (PO:0004543).
 +
** shoot axis tuber periderm: A portion of shoot axis periderm (PO:0005048) that is part of a shoot axis tuber (PO:0004543).
 +
** aerial tuber (PO:0004548): A shoot axis tuber (PO:0004543) that develops above ground.
 +
**subterranean tuber (PO:0004547): A shoot axis tuber (PO:0004543) that develops below ground.
  
−
* basal axillary shoot system (PO:0005001)
+
==Children of multicellular plant gametangium (PO:0025124)==
 +
* multicellular plant gametangium (PO:0025124): A plant organ (PO:0009008) that produces one or more gametes (PO:0025006) and is part of a whole plant (PO:0000003) in the gametophyte development stage (PO:0028003).
  
−
* embryo sac egg cell (PO:0025123)
+
* archegonium (PO:0025126): A multicellular plant gametangium (PO:0025124) that develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038) and an archegonium neck (PO:0030039).
 +
**archegonium initial cell (PO:0025510): An initial cell (PO:0004011) that divides asymmetrically to form an archegonium central cell (PO:0025509) and a smaller archegonium neck canal cell (PO:0030035).
 +
** venter (PO:0030038): A cardinal organ part (PO:0025001) that is the enlarged basal part of an archegonium (PO:0025126) and has an archegonium egg cell (PO:0025122) located in it.
 +
**archegonium neck (PO:0030039): A cardinal organ part (PO:0025001) that is the elongated, apical part of an archegonium (PO:0025126).
 +
**archegonium neck canal (PO:0030066): A canal (PO:0025132) in the center of an archegonium neck (PO:0030039). Comment: Forms after the archegonium neck canal cells disintegrate.
 +
** archegonium neck canal cell (PO:0030065):  A plant cell that is one of the axial row of cells in an immature archegonium neck. Comment: As the archegonium matures, the archegonium neck canal cells disintegrate to form the archegonium neck canal.
 +
** archegoniophore (PO:0030034): revised def'n: A stalk (PO:0025066) that supports an archegonium head (PO:0030034).
 +
** archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the larger, distal cell arising from the first division of an archegonial initial cell (PO:0025510)
  
−
* embryo sac (PO:0025074)
 
  
−
* embryo sac central cell (PO:0020090)
+
* antheridium (PO:0025125): A multicellular plant gametangium (PO:0025124) that produces antheridium sperm cells (PO:0025120) and has as parts an antheridium jacket layer (PO:0030053) and an antheridium stalk (PO:0030035). Revised comment: An antheridium has a sterile jacket layer (PO:0030052). In both gymnosperms and angiosperms, the antheridium (PO:0025125) is replaced by pollen (PO:0025281). 
 +
** antheridium sperm cell (PO:0025120): A plant sperm cell (PO:0000084) that develops from a spermatogenous cell (PO:0025525) and is located in an antheridium (PO:0025125). Revised comment: Antheridium sperm cells are motile.
 +
** antheridiophore (PO:0030033): revised def'n: A stalk (PO:0025066) that supports an antheridium head (PO:0030075). Added relation has_part antheridium head (PO:0030075)
  
−
* laticifer cell (PO:0025031)
+
** spore capsule calyptra (PO:0030037): A cardinal organ part (PO:0025001) that develops from an archegonium venter (PO:0030038) and is a cap or hood enclosing the sporangium (syn: spore capsule; PO:0025094).comment:  Found in bryophytes. The spore capsule calyptra is a membranous or hairy cap or hood, composed of gametophytic tissue (venter; PO:0030038) that protects the embryonic sporophyte within the archegonium (PO:0025126). In some species, it may persist after the sporophyte develops and gets carried upward as the seta (PO:0030032) elongates. The spore capsule calyptra is usually lost before the spores are released, and its shape can be used for identification purposes.
  
−
* articulated laticifer cell (PO:0006221)
+
* seta: A stalk (PO:0025066)that supports a spore capsule, the sporangium (PO:0025094).
  
−
* non-articulated laticifer cell (PO:0006222)
+
==Other PAE terms==
 +
* axillary shoot system (PO:0006343): A shoot-borne shoot system (PO:0004545) that develops_from an axillary bud (PO:0004709). (was develops_from a vegetative axillary bud).
  
−
* articulated laticifer (PO:0005008)
+
* axillary reproductive bud (PO:0025072): An axillary bud (PO:0004709) that develops into an reproductive shoot system (PO:0025082).
 +
* basal axillary shoot system (PO:0005001):An axillary shoot system (PO:0006343) that develops from an axillary vegetative bud (PO:0004712) that is part of a stem base (PO:0008039). (Needs further revision - [[Items_for_future_meetings]] page.
 +
* axillary bud meristem (PO:0000232): A shoot meristem (PO:0006079) formed in an axil (PO:0025224)
 +
* shoot system meristem (PO:0006079): A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
 +
* shoot apical meristem (PO:0020148): A shoot meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
 +
----
 +
* embryo sac egg cell (PO:0025123): A plant egg cell (PO:0020094) that is part of an egg apparatus (PO:0020096). Comment: The egg apparatus is part of an embryo sac (PO:0025074).
  
−
* gametophyte development stage (PO:0028003): removed the phrase "or fertilization" from the definition, added PO ids. Added new sentence to comment.
+
* embryo sac (PO:0025074): A megagametophyte (PO:0025279) that is located in a plant ovary ovule (PO:0025490). Comment: Produces an embryo sac egg cell (PO:0025123).
  
−
* placenta (PO:0025078): made it broader (any interface between a gametophyte and a sporophyte with transfer cells)
+
* embryo sac central cell (PO:0020090): An embryo sac cell (PO:0025026) that is largest cell in a mature embryo sac (PO:0025074).
 +
----
 +
* laticifer cell (PO:0025031): A ground tissue cell (PO:0025030) that contains latex. Comment: May be simple or branched.
  
−
* second order inflorescence (PO:0025240): fixed def'm: changed second order inflorescence branch to "second order inflorescence axis", because that is the correct term name. Added PO ids
+
* articulated laticifer cell (PO:0006221): A laticifer cell (PO:0025031) that is joined longitudinally to other articulated laticifer cells to form a tube.
  
−
* leaf sinus (PO:0025384): Added comment that it can be rounded or angled.
+
* non-articulated laticifer cell (PO:0006222): A laticifer cell (PO:0025031) that is not joined longitudinally to other laticifer cells to form a tube.
  
 +
* articulated laticifer (PO:0005008): A portion of secretory tissue (PO:0005656) that has as parts articulated laticifer cells (PO:0006221).
 +
----
 
* pericarp  and child terms exocarp, mesocarp, endocarp- Updated definitions:
 
* pericarp  and child terms exocarp, mesocarp, endocarp- Updated definitions:
 +
** pericarp (PO:0009084): A portion of plant tissue (PO:0009007) that is the outer layer (wall) of a fruit (PO:0009001), and develops from a plant ovary (PO:0009072) or a carpel (PO:0009030) wall.Added comment: May be fleshy in fruits such as grape.
 +
**exocarp (PO:0009085): A portion of plant tissue (PO:0009007) that is the outer layer of a pericarp (PO:0009084). Added fruit epidermis as a synonym.
 +
** mesocarp (PO:0009087): A portion of plant tissue (PO:0009007) that is the middle layer of a pericarp (PO:0009084).
 +
** endocarp (PO:0009086): A portion of plant tissue (PO:0009007) that is the innermost differentiated layer of a pericarp (PO:0009084).
 +
----
 +
* placenta (PO:0025078): made it broader (any interface between a gametophyte and a sporophyte with transfer cells)
  
−
pericarp (PO:0009084): A portion of plant tissue (PO:0009007) that is the outer layer (wall) of a fruit (PO:0009001), and develops from a plant ovary (PO:0009072) or a carpel (PO:0009030) wall.Added comment: May be fleshy in fruits such as grape.  
+
* second order inflorescence (PO:0025240): fixed def'n: changed 'second order inflorescence branch' to 'second order inflorescence axis', because that is the correct term name.
  
−
exocarp (PO:0009085): A portion of plant tissue (PO:0009007) that is the outer layer of a pericarp (PO:0009084). Added fruit epidermis as a synonym.
+
* leaf sinus (PO:0025384): Added comment that it can be rounded or angled.
  
−
mesocarp (PO:0009087): A portion of plant tissue (PO:0009007) that is the middle layer of a pericarp (PO:0009084).
+
* tubercle (PO:0025352): An enlarged leaf base (PO:0020040) that is fused with adjacent shoot axis (PO:0025029) tissue. Modified comment: "In species with tubercles, the areole bud (PO:0025353) is often found at the distal end of the tubercle. The areole bud originates in the leaf axil (PO:0009023) of the leaf that becomes the tubercle, but is displaced to the tip through elongation of the tubercle."
  
−
endocarp (PO:0009086): A portion of plant tissue (PO:0009007) that is the innermost differentiated layer of a pericarp (PO:0009084).
+
* microgametophyte (PO:0025280): A whole plant (PO:0000003) in the gametophyte development stage (PO:0028003) that produces only plant sperm cells (PO:0000084).
  
 +
=New or Modified relations, PAE=
 +
see also the notes above
  
−
==New or modified relations, PAE==
+
* leaf develops_from vascular leaf primordium > vascular leaf develops_from vascular leaf primordium
  
−
===Removed:===
+
* archegonium egg cell (PO:0025122) part_of archegonium > archegonium egg cell located_in archegonium >archegonium egg cell located_in venter
 +
* petiole lamina (PO:0025129)is_a leaf lamina > petiole lamina is_a lamina
  
−
* peduncle part_of inflorescence (incorrect relation, does not work for cases of single flowers)
+
* lamina (PO:0025060) is_a cardinal organ part > lamina is_a cardinal part of multi-tissue plant structure, (to allow for lamina on seeds and fruits)
  
−
===Changed===
+
* tuber cortex (PO:0025055) is_a shoot axis cortex > tuber cortex is_a cortex
  
−
* 'leaf develops_from vascular leaf primordium' to 'vascular leaf develops_from vascular leaf primordium
+
* tuber pith (PO:0025052) is_a shoot axis pith > tuber pith is_a pith
  
−
* "archegonium egg cell part_of archegonium" to "archegonium egg cell located_in archegonium"
+
* tuber storage parenchyma (PO:0025036) part_of shoot axis tuber > tuber storage parenchyma part_of tuber (PO:0025522). Added comment: If you are annotating to this term, please add an additional annotation to either shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
  
−
* petiole lamina (PO:0025129) moved to is_a lamina, instead of is_a leaf lamina.
+
* Removed peduncle part_of inflorescence (incorrect relation, does not work for cases of single flowers)
−
* lamina (PO:0025060) Moved from is_a cardinal organ part to is_a cardinal part of multi-tissue plant structure, (to allow for lamina on seeds and fruits)
 
  
−
* tuber cortex (PO:0025055): moved to is a cortex, rather than a shoot axis cortex.
+
* antheridium sperm cell (PO:0025120) part_of antheridium > antheridium sperm cell (PO:0025120) located_in antheridium
−
A portion of cortex (PO:0005708) that is part of a tuber storage parenchyma (PO:0025036).
 
  
−
* tuber pith PO:0025052: Moved to is a pith, rather than a shoot axis pith. Def'n did not need to be changed.
+
* shoot axis tuber: (PO:0004543) is_a tuber (PO:0025522)
−
A portion of pith (PO:0006109) that is part of a tuber storage parenchyma (PO:0025036).
 
  
−
* tuber storage parenchyma moved to part_of a tuber (PO:0025522), added comment: 3005637
 
−
If you are annotating to this term, please add an additional annotation to either shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
 
  
−
===Added:===
+
* axillary shoot system (PO:0006343) develops_from axillary bud
−
* cardinal organ part (is_a cardinal part of MTPS and part_of plant organ); added cross product to definition
+
* cardinal organ part is_a cardinal part of MTPS and part_of plant organ, (added cross product to definition)
 
* organ margin (PO:0025005) part_of organ lamina
 
* organ margin (PO:0025005) part_of organ lamina
−
* phyllome margin (PO:0025018) part_of phyllome lamina (latter as XP).
+
* phyllome margin (PO:0025018) part_of phyllome lamina (latter as XP)
 
* laticiferous cell (PO:0004005, obsolete) replaced_by laticifer cell (PO:0025031)
 
* laticiferous cell (PO:0004005, obsolete) replaced_by laticifer cell (PO:0025031)
 +
* stele (PO:0025197) part_of plant axis (PO:0025004)
 +
* tuberous root tuber (PO:0025476) develops_from tuberous root (PO:0025523)
 +
* archegonium (PO:0025126) develops_from archegonium initial cell (PO:0025510)
 +
* ventral canal cell (PO:0025524) part_of the venter (PO:0030038)
 +
* ventral canal cell (PO:0025524) develops_from archegonium central cell (PO:0025509)
 +
* archegonium initial cell (PO:0025510) part_of archegonium megagametophyte (PO:0025282)
 +
* archegonium central cell (PO:0025509) develops_from archegonium initial cell (PO:0025510)
 +
* archegonium neck canal cell (PO:0030035) develops_from archegonium initial cell (PO:0025510)
  
 
=Updated definitions and/or comments: PSDS terms=
 
=Updated definitions and/or comments: PSDS terms=
 +
* gametophyte development stage (PO:0028003): removed the phrase "or fertilization" from the definition, added PO ids. Added new sentence to comment.
 +
 
* flower development stage (PO:0007615)
 
* flower development stage (PO:0007615)
  
Line 83: Line 125:
 
* whole plant flowering stage (PO:0007016)
 
* whole plant flowering stage (PO:0007016)
  
 +
* K second mitotic division stage (PO:0001015)
  
−
==New or modified relations, PSDS==
+
*(PO:0007032) whole plant fruit formation stage up to 10%
−
* Made fruit development stage is_a plant structure development stage (instead of collective plant organ structure development stage)
 
  
−
Added relation collective plant organ structure development stage has_participant collective plant organ structure, using intersection_of tags.
+
*(PO:0007009) whole plant fruit formation stage 10 to 30%
  
−
Made whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010) subclasses of whole plant fruit development stage and updated their definitions.
+
*(PO:0007029) whole plant fruit formation stage 30 to 50%
  
−
Updated names and definitions of:
 
−
*(PO:0007032) whole plant fruit formation stage up to 10%
 
−
*(PO:0007009) whole plant fruit formation stage 10 to 30%
 
−
*(PO:0007029) whole plant fruit formation stage 30 to 50%
 
 
*(PO:0007007) whole plant fruit formation stage 50 to 70%  
 
*(PO:0007007) whole plant fruit formation stage 50 to 70%  
 +
 
*(PO:0007027) whole plant fruit formation stage 70% to final size
 
*(PO:0007027) whole plant fruit formation stage 70% to final size
 +
 +
==New or modified relations, PSDS==
 +
* fruit development stage is_a collective plant organ structure development stage > fruit development stage is_a plant structure development stage
 +
 +
* collective plant organ structure development stage has_participant collective plant organ structure (using intersection_of tags)
 +
 +
* Made whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010) subclasses of whole plant fruit development stage and updated their definitions.
 +
 +
=Added PO IDs to the definitions of the following terms:=
 +
* megagametophyte (PO:0025279)
 +
* antheridium jacket layer (PO:0030053)
 +
* antheridium stalk (PO:0030035)
 +
* antheridium sperm cell (PO:0025120)
 +
* antheridium head (PO:0030075)
 +
* antheridiophore (PO:0030033)
 +
* archegonium initial cell (PO:0025510)
 +
* archegonium neck (PO:0030039)
 +
* archegonium neck canal (PO:0030066)
 +
* venter PO:0030038
 +
* shoot sytem PO:0009006
 +
* axillary bud PO:0004709
 +
* antheridium jacket layer cell PO:0030052
 +
* anther PO:0009066
 +
* anther theca PO:0009069
 +
* root system PO:0025025
 +
* collective phyllome structure PO:0025023
 +
* root system PO:0025025
 +
* sorus PO:0025359
 +
* leaf PO:0025034
 +
* vascular leaf PO:0009025
 +
* collective plant organ structure PO:0025007
 +
* children of plant organ:PO:0009008
 +
* floral organ PO:0025395
 +
* subterranean tuber storage parenchyma PO:0025038
 +
* tuber storage parenchyma (PO:0025035)
 +
* ground tissue (PO:0025059)
 +
* parenchyma (PO:0005421)
 +
* portion of ground tissue (PO:0025059)
 +
* shoot axis cortex (PO:0000223)
 +
* aerial tuber storage parenchyma PO:0025039
 +
* pith (PO:0006109)
 +
* tuber pith PO:0025052
 +
* aerial tuber pith (PO:0025054)
 +
* subterranean tuber pith PO:0025053
 +
* perimedullary zone (PO:0025058)
 +
* shoot axis pith PO:0005041
 +
* root pith PO:0005040
 +
* shoot axis perimedullary zonePO:0025064
 +
* leaf tip (PO:0025142)
 +
* leaf apex (PO:0020137)
 +
* laticifer cell (PO:0025031)
 +
* articulated laticifer cell (PO:0006221)
 +
* non-articulated laticifer cell (PO:0006222)
 +
* articulated laticifer (PO:0005008)
 +
* gametophyte development stage (PO:0028003)
 +
* fruit development stage (PO:0001002)
 +
* fruit initiation stage (PO:0025503)
 +
* fruit size up to 10% stage (PO:0025504)
 +
* whole plant fruit development stage (PO:0025500)
 +
* whole plant fruit formation stage (PO:0007042)
 +
* whole plant fruit ripening stage (PO:0007010)
 +
* embryo sac egg cell (PO:0025123)
 +
* embryo sac (PO:0025074)
 +
* placenta (PO:0025078)
 +
* embryo sac central cell (PO:0020090)
 +
* leaf lamina (PO:0020039)
 +
* leaf lamina abaxial epidermis (PO:0000049)
 +
* leaf lamina adaxial epidermis (PO:0000050)
 +
* leaf lamina areole (PO:0025392)
 +
* leaf lamina base (PO:0008019)
 +
* leaf lamina crena (PO:0025519)
 +
* leaf lamina epidermis (PO:0000047)
 +
* leaf lamina intramarginal vein (PO:0025520)
 +
* leaf lamina lobe (PO:0025517)
 +
* leaf lamina margin (PO:0025009)
 +
* leaf lamina stomatal complex (PO:0025185)
 +
* leaf lamina tooth (PO:0025518)
 +
* leaf lamina vascular system (PO:0000048)
 +
* leaf lamina vein (PO:0020138)
 +
* leaf tip (PO:0025142)
 +
* organ lamina (PO:0025513)
 +
* petiole lamina (PO:0025129)
 +
* phyllome lamina (PO:0025396)
 +
* phyllome lamina areole (PO:0025391)
 +
* phyllome lamina crena (PO:0025516)
 +
* phyllome lamina lobe (PO:0025514)
 +
* phyllome lamina tooth (PO:0025515)
 +
* phyllome lamina vein (PO:0025348)
 +
* tubercle (PO:0025352)
 +
* leaf base PO:0020040
 +
* phyllome base (PO:0025140)
 +
* leaf (PO:0025034)
 +
~83

Latest revision as of 22:12, 4 January 2013

See also New_terms_and_obsolete_terms_Release_19

Back to Release_19

Revised or Updated definitions and/or comments: PAE terms

Children of shoot axis tuber:(PO:0004543)

  • shoot axis tuber (PO:0004543): A tuber (PO:0025522) that develops from a branch (PO:0025073).
    • shoot axis tuber axillary bud meristem (PO:0025068): An axillary bud meristem (PO:0000232) that is part of a shoot axis tuber (PO:0004543).
    • shoot axis tuber axillary vegetative bud: An axillary vegetative bud (PO:0004712) that is part of a shoot axis tuber (PO:0004543).
    • shoot axis tuber epidermis (PO:0025046): A portion of shoot axis epidermis (PO:0000112) that is part of a shoot axis tuber (PO:0004543).
    • shoot axis tuber periderm: A portion of shoot axis periderm (PO:0005048) that is part of a shoot axis tuber (PO:0004543).
    • aerial tuber (PO:0004548): A shoot axis tuber (PO:0004543) that develops above ground.
    • subterranean tuber (PO:0004547): A shoot axis tuber (PO:0004543) that develops below ground.

Children of multicellular plant gametangium (PO:0025124)

  • multicellular plant gametangium (PO:0025124): A plant organ (PO:0009008) that produces one or more gametes (PO:0025006) and is part of a whole plant (PO:0000003) in the gametophyte development stage (PO:0028003).
  • archegonium (PO:0025126): A multicellular plant gametangium (PO:0025124) that develops from an archegonium initial cell (PO:0025510) and has as parts a venter (PO:0030038) and an archegonium neck (PO:0030039).
    • archegonium initial cell (PO:0025510): An initial cell (PO:0004011) that divides asymmetrically to form an archegonium central cell (PO:0025509) and a smaller archegonium neck canal cell (PO:0030035).
    • venter (PO:0030038): A cardinal organ part (PO:0025001) that is the enlarged basal part of an archegonium (PO:0025126) and has an archegonium egg cell (PO:0025122) located in it.
    • archegonium neck (PO:0030039): A cardinal organ part (PO:0025001) that is the elongated, apical part of an archegonium (PO:0025126).
    • archegonium neck canal (PO:0030066): A canal (PO:0025132) in the center of an archegonium neck (PO:0030039). Comment: Forms after the archegonium neck canal cells disintegrate.
    • archegonium neck canal cell (PO:0030065): A plant cell that is one of the axial row of cells in an immature archegonium neck. Comment: As the archegonium matures, the archegonium neck canal cells disintegrate to form the archegonium neck canal.
    • archegoniophore (PO:0030034): revised def'n: A stalk (PO:0025066) that supports an archegonium head (PO:0030034).
    • archegonium central cell (PO:0025509): A plant cell (PO:0009002) that is the larger, distal cell arising from the first division of an archegonial initial cell (PO:0025510)


  • antheridium (PO:0025125): A multicellular plant gametangium (PO:0025124) that produces antheridium sperm cells (PO:0025120) and has as parts an antheridium jacket layer (PO:0030053) and an antheridium stalk (PO:0030035). Revised comment: An antheridium has a sterile jacket layer (PO:0030052). In both gymnosperms and angiosperms, the antheridium (PO:0025125) is replaced by pollen (PO:0025281).
    • antheridium sperm cell (PO:0025120): A plant sperm cell (PO:0000084) that develops from a spermatogenous cell (PO:0025525) and is located in an antheridium (PO:0025125). Revised comment: Antheridium sperm cells are motile.
    • antheridiophore (PO:0030033): revised def'n: A stalk (PO:0025066) that supports an antheridium head (PO:0030075). Added relation has_part antheridium head (PO:0030075)
    • spore capsule calyptra (PO:0030037): A cardinal organ part (PO:0025001) that develops from an archegonium venter (PO:0030038) and is a cap or hood enclosing the sporangium (syn: spore capsule; PO:0025094).comment: Found in bryophytes. The spore capsule calyptra is a membranous or hairy cap or hood, composed of gametophytic tissue (venter; PO:0030038) that protects the embryonic sporophyte within the archegonium (PO:0025126). In some species, it may persist after the sporophyte develops and gets carried upward as the seta (PO:0030032) elongates. The spore capsule calyptra is usually lost before the spores are released, and its shape can be used for identification purposes.
  • seta: A stalk (PO:0025066)that supports a spore capsule, the sporangium (PO:0025094).

Other PAE terms

  • axillary shoot system (PO:0006343): A shoot-borne shoot system (PO:0004545) that develops_from an axillary bud (PO:0004709). (was develops_from a vegetative axillary bud).
  • axillary reproductive bud (PO:0025072): An axillary bud (PO:0004709) that develops into an reproductive shoot system (PO:0025082).
  • basal axillary shoot system (PO:0005001):An axillary shoot system (PO:0006343) that develops from an axillary vegetative bud (PO:0004712) that is part of a stem base (PO:0008039). (Needs further revision - Items_for_future_meetings page.
  • axillary bud meristem (PO:0000232): A shoot meristem (PO:0006079) formed in an axil (PO:0025224)
  • shoot system meristem (PO:0006079): A portion of meristem tissue (PO:0009013) that is part of a shoot system (PO:0009006).
  • shoot apical meristem (PO:0020148): A shoot meristem (PO:0006079) formed at the apex of the shoot axis (PO:0025029), including those originating from an axillary bud meristem (PO:0000232).
  • embryo sac egg cell (PO:0025123): A plant egg cell (PO:0020094) that is part of an egg apparatus (PO:0020096). Comment: The egg apparatus is part of an embryo sac (PO:0025074).
  • embryo sac (PO:0025074): A megagametophyte (PO:0025279) that is located in a plant ovary ovule (PO:0025490). Comment: Produces an embryo sac egg cell (PO:0025123).
  • embryo sac central cell (PO:0020090): An embryo sac cell (PO:0025026) that is largest cell in a mature embryo sac (PO:0025074).
  • laticifer cell (PO:0025031): A ground tissue cell (PO:0025030) that contains latex. Comment: May be simple or branched.
  • articulated laticifer cell (PO:0006221): A laticifer cell (PO:0025031) that is joined longitudinally to other articulated laticifer cells to form a tube.
  • non-articulated laticifer cell (PO:0006222): A laticifer cell (PO:0025031) that is not joined longitudinally to other laticifer cells to form a tube.
  • articulated laticifer (PO:0005008): A portion of secretory tissue (PO:0005656) that has as parts articulated laticifer cells (PO:0006221).
  • pericarp and child terms exocarp, mesocarp, endocarp- Updated definitions:
    • pericarp (PO:0009084): A portion of plant tissue (PO:0009007) that is the outer layer (wall) of a fruit (PO:0009001), and develops from a plant ovary (PO:0009072) or a carpel (PO:0009030) wall.Added comment: May be fleshy in fruits such as grape.
    • exocarp (PO:0009085): A portion of plant tissue (PO:0009007) that is the outer layer of a pericarp (PO:0009084). Added fruit epidermis as a synonym.
    • mesocarp (PO:0009087): A portion of plant tissue (PO:0009007) that is the middle layer of a pericarp (PO:0009084).
    • endocarp (PO:0009086): A portion of plant tissue (PO:0009007) that is the innermost differentiated layer of a pericarp (PO:0009084).
  • placenta (PO:0025078): made it broader (any interface between a gametophyte and a sporophyte with transfer cells)
  • second order inflorescence (PO:0025240): fixed def'n: changed 'second order inflorescence branch' to 'second order inflorescence axis', because that is the correct term name.
  • leaf sinus (PO:0025384): Added comment that it can be rounded or angled.
  • tubercle (PO:0025352): An enlarged leaf base (PO:0020040) that is fused with adjacent shoot axis (PO:0025029) tissue. Modified comment: "In species with tubercles, the areole bud (PO:0025353) is often found at the distal end of the tubercle. The areole bud originates in the leaf axil (PO:0009023) of the leaf that becomes the tubercle, but is displaced to the tip through elongation of the tubercle."
  • microgametophyte (PO:0025280): A whole plant (PO:0000003) in the gametophyte development stage (PO:0028003) that produces only plant sperm cells (PO:0000084).

New or Modified relations, PAE

see also the notes above

  • leaf develops_from vascular leaf primordium > vascular leaf develops_from vascular leaf primordium
  • archegonium egg cell (PO:0025122) part_of archegonium > archegonium egg cell located_in archegonium >archegonium egg cell located_in venter
  • petiole lamina (PO:0025129)is_a leaf lamina > petiole lamina is_a lamina
  • lamina (PO:0025060) is_a cardinal organ part > lamina is_a cardinal part of multi-tissue plant structure, (to allow for lamina on seeds and fruits)
  • tuber cortex (PO:0025055) is_a shoot axis cortex > tuber cortex is_a cortex
  • tuber pith (PO:0025052) is_a shoot axis pith > tuber pith is_a pith
  • tuber storage parenchyma (PO:0025036) part_of shoot axis tuber > tuber storage parenchyma part_of tuber (PO:0025522). Added comment: If you are annotating to this term, please add an additional annotation to either shoot axis tuber (PO:0004543) or tuberous root tuber (PO:0025476).
  • Removed peduncle part_of inflorescence (incorrect relation, does not work for cases of single flowers)
  • antheridium sperm cell (PO:0025120) part_of antheridium > antheridium sperm cell (PO:0025120) located_in antheridium
  • shoot axis tuber: (PO:0004543) is_a tuber (PO:0025522)


  • axillary shoot system (PO:0006343) develops_from axillary bud
  • cardinal organ part is_a cardinal part of MTPS and part_of plant organ, (added cross product to definition)
  • organ margin (PO:0025005) part_of organ lamina
  • phyllome margin (PO:0025018) part_of phyllome lamina (latter as XP)
  • laticiferous cell (PO:0004005, obsolete) replaced_by laticifer cell (PO:0025031)
  • stele (PO:0025197) part_of plant axis (PO:0025004)
  • tuberous root tuber (PO:0025476) develops_from tuberous root (PO:0025523)
  • archegonium (PO:0025126) develops_from archegonium initial cell (PO:0025510)
  • ventral canal cell (PO:0025524) part_of the venter (PO:0030038)
  • ventral canal cell (PO:0025524) develops_from archegonium central cell (PO:0025509)
  • archegonium initial cell (PO:0025510) part_of archegonium megagametophyte (PO:0025282)
  • archegonium central cell (PO:0025509) develops_from archegonium initial cell (PO:0025510)
  • archegonium neck canal cell (PO:0030035) develops_from archegonium initial cell (PO:0025510)

Updated definitions and/or comments: PSDS terms

  • gametophyte development stage (PO:0028003): removed the phrase "or fertilization" from the definition, added PO ids. Added new sentence to comment.
  • flower development stage (PO:0007615)
  • fruit development stage (PO:0001002)-
  • collective plant organ structure development stage (PO:0025338)- modified definition and comment to include PO:ids.
  • whole plant fruit formation stage (PO:0007042)
  • whole plant fruit ripening stage (PO:0007010)
  • whole plant flowering stage (PO:0007016)
  • K second mitotic division stage (PO:0001015)
  • (PO:0007032) whole plant fruit formation stage up to 10%
  • (PO:0007009) whole plant fruit formation stage 10 to 30%
  • (PO:0007029) whole plant fruit formation stage 30 to 50%
  • (PO:0007007) whole plant fruit formation stage 50 to 70%
  • (PO:0007027) whole plant fruit formation stage 70% to final size

New or modified relations, PSDS

  • fruit development stage is_a collective plant organ structure development stage > fruit development stage is_a plant structure development stage
  • collective plant organ structure development stage has_participant collective plant organ structure (using intersection_of tags)
  • Made whole plant fruit formation stage (PO:0007042) and whole plant fruit ripening stage (PO:0007010) subclasses of whole plant fruit development stage and updated their definitions.

Added PO IDs to the definitions of the following terms:

  • megagametophyte (PO:0025279)
  • antheridium jacket layer (PO:0030053)
  • antheridium stalk (PO:0030035)
  • antheridium sperm cell (PO:0025120)
  • antheridium head (PO:0030075)
  • antheridiophore (PO:0030033)
  • archegonium initial cell (PO:0025510)
  • archegonium neck (PO:0030039)
  • archegonium neck canal (PO:0030066)
  • venter PO:0030038
  • shoot sytem PO:0009006
  • axillary bud PO:0004709
  • antheridium jacket layer cell PO:0030052
  • anther PO:0009066
  • anther theca PO:0009069
  • root system PO:0025025
  • collective phyllome structure PO:0025023
  • root system PO:0025025
  • sorus PO:0025359
  • leaf PO:0025034
  • vascular leaf PO:0009025
  • collective plant organ structure PO:0025007
  • children of plant organ:PO:0009008
  • floral organ PO:0025395
  • subterranean tuber storage parenchyma PO:0025038
  • tuber storage parenchyma (PO:0025035)
  • ground tissue (PO:0025059)
  • parenchyma (PO:0005421)
  • portion of ground tissue (PO:0025059)
  • shoot axis cortex (PO:0000223)
  • aerial tuber storage parenchyma PO:0025039
  • pith (PO:0006109)
  • tuber pith PO:0025052
  • aerial tuber pith (PO:0025054)
  • subterranean tuber pith PO:0025053
  • perimedullary zone (PO:0025058)
  • shoot axis pith PO:0005041
  • root pith PO:0005040
  • shoot axis perimedullary zonePO:0025064
  • leaf tip (PO:0025142)
  • leaf apex (PO:0020137)
  • laticifer cell (PO:0025031)
  • articulated laticifer cell (PO:0006221)
  • non-articulated laticifer cell (PO:0006222)
  • articulated laticifer (PO:0005008)
  • gametophyte development stage (PO:0028003)
  • fruit development stage (PO:0001002)
  • fruit initiation stage (PO:0025503)
  • fruit size up to 10% stage (PO:0025504)
  • whole plant fruit development stage (PO:0025500)
  • whole plant fruit formation stage (PO:0007042)
  • whole plant fruit ripening stage (PO:0007010)
  • embryo sac egg cell (PO:0025123)
  • embryo sac (PO:0025074)
  • placenta (PO:0025078)
  • embryo sac central cell (PO:0020090)
  • leaf lamina (PO:0020039)
  • leaf lamina abaxial epidermis (PO:0000049)
  • leaf lamina adaxial epidermis (PO:0000050)
  • leaf lamina areole (PO:0025392)
  • leaf lamina base (PO:0008019)
  • leaf lamina crena (PO:0025519)
  • leaf lamina epidermis (PO:0000047)
  • leaf lamina intramarginal vein (PO:0025520)
  • leaf lamina lobe (PO:0025517)
  • leaf lamina margin (PO:0025009)
  • leaf lamina stomatal complex (PO:0025185)
  • leaf lamina tooth (PO:0025518)
  • leaf lamina vascular system (PO:0000048)
  • leaf lamina vein (PO:0020138)
  • leaf tip (PO:0025142)
  • organ lamina (PO:0025513)
  • petiole lamina (PO:0025129)
  • phyllome lamina (PO:0025396)
  • phyllome lamina areole (PO:0025391)
  • phyllome lamina crena (PO:0025516)
  • phyllome lamina lobe (PO:0025514)
  • phyllome lamina tooth (PO:0025515)
  • phyllome lamina vein (PO:0025348)
  • tubercle (PO:0025352)
  • leaf base PO:0020040
  • phyllome base (PO:0025140)
  • leaf (PO:0025034)

~83

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