Difference between revisions of "Details of Changes to Release 21"

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Go back to main page: [[Release_21]]
 
Go back to main page: [[Release_21]]
  
−
* Includes all revisions from [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=log 2228] and up to #2407.
+
=Notes=
 +
* Includes all revisions of the plant_ontology.obo file from Aug 2013  (#2228) to July 2015 (#3502) on the [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/plant_ontology.obo?view=log PO SVN site].
  
 +
* After August 1, 2015, all the ontology files were moved to [https://github.com/Planteome/plant-ontology  Planteome GitHub Repository]
  
−
=Merged or Obsoleted terms=
+
* This Release includes all the changes from Aug. 6th, 2015 [https://github.com/Planteome/plant-ontology/commit/33ae100 #33ae100] to Sep 25, 2015  [https://github.com/Planteome/plant-ontology/commit/01901fa #01901fa]
−
None found so far....
 
  
 
=New PAE terms:=
 
=New PAE terms:=
  
−
* phyllome founder cell (PO:0025586): A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).
+
==portion of plant substance:==
 +
* plant resin (PO:0025603): A portion of plant substance (PO:0025161) that consists of a complex mixture of organic aromatic compounds such as mono-, sesqui-, and diterpenoids.
  
−
* leaf lamina tip (PO:0025589): A leaf tip (PO:0025142) area that is the distal portion of the leaf lamina (PO:00200039). Comment: This is the portion of the leaf lamina (PO:0020039) that is furthest away from the stem (PO:0009047).
+
==plant structure terms==
  
−
* receptacle pith (PO:0025590): A portion of pith (PO:0006109) that is part of a receptacle (PO:0009064). part_of receptacle.
+
==native plant cell and new child terms==
 +
* native plant cell (PO:0025606): A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in_natura' (i.e. part of a natural environment).
  
−
* receptacle cortex (PO:0025591): A portion of cortex (PO:0005708) that is part of a receptacle (PO:0009064).
+
* phyllome founder cell (PO:0025586): A native plant cell (PO:0025606) that is part of the phyllome anlagen (PO:0025430).
  
 
* vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).
 
* vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).
  
−
* shoot-borne internode root (PO:0025593): A shoot-borne root (PO:0000042) that arises from a shoot axis internode (PO:0005005).
+
==meristem terms==
  
 
* ground meristem (PO:0025594): A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
 
* ground meristem (PO:0025594): A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
Line 27: Line 30:
 
* root system ground meristem (PO:0025596): A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the root system (PO:0025025).
 
* root system ground meristem (PO:0025596): A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the root system (PO:0025025).
  
−
* ear infructescence (PO:0025597): An infructescence (PO:0006342) in Zea spp. that bears kernels (i.e. fruit; PO:0009001) on a compact infructescence axis (PO:0025242) and develops from the ear inflorescence (PO:0020136).
+
==Terms describing special types of flowers, inflorescences, strobili and infructesences==
  
 
* pistillate inflorescence (PO:0025598): An inflorescence (PO:0009049) that includes as part only pistillate flowers (PO:0025599).
 
* pistillate inflorescence (PO:0025598): An inflorescence (PO:0009049) that includes as part only pistillate flowers (PO:0025599).
Line 37: Line 40:
 
* staminate inflorescence (PO:0025601): An inflorescence (PO:0009049) that includes as part only staminate flowers (PO:0025600).
 
* staminate inflorescence (PO:0025601): An inflorescence (PO:0009049) that includes as part only staminate flowers (PO:0025600).
  
−
* plant resin (PO:0025603): A portion of plant substance (PO:0025161) that consists of a complex mixture of organic aromatic compounds such as mono-, sesqui-, and diterpenoids.
+
* microsporangiate strobilus (PO:0005031): A strobilus (PO:0025083) that bears only pollen (PO:0025281).
 +
 
 +
* megasporangiate strobilus (PO:0005032): A strobilus (PO:0025083) that bears only plant ovules (PO:0020003).
 +
 
 +
* ear infructescence (PO:0025597): An infructescence (PO:0006342) in Zea spp. that bears kernels (i.e. fruit; PO:0009001) on a compact infructescence axis (PO:0025242) and develops from the ear inflorescence (PO:0020136).
 +
 
 +
==Various other new terms==
 +
* vegetative shoot system (PO:0025607): A shoot system (PO:0009006) that has as parts only vegetative tissues and organs.
 +
 
 +
* lupulin gland (PO:0005030): A glandular trichome (PO:0004509) that synthesizes terpenophenolic resins and prenylflavonoids.
  
 
* resin cell (PO:0025604): An epidermal cell (PO:0004013) that secretes plant resin (PO:0025603) and may line resin canals (PO:0005665) and/or be associated with resin blisters (or cysts).
 
* resin cell (PO:0025604): An epidermal cell (PO:0004013) that secretes plant resin (PO:0025603) and may line resin canals (PO:0005665) and/or be associated with resin blisters (or cysts).
Line 43: Line 55:
 
* fruit pedicel abscission zone (PO:0025605): An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
 
* fruit pedicel abscission zone (PO:0025605): An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
  
−
* native plant cell (PO:0025606): A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in_natura' (i.e. part of a natural environment).
+
* flower pedicel abscission zone (PO:0025608): An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
  
−
*proteoid root (PO:0000067): A root (PO:0009005) that forms one or more clusters of closely spaced lateral roots (PO:0020121) of limited growth along its length.
+
* shoot axis tegument layer (PO:0025609): A portion of plant tissue (PO:0009007) that forms a tough, protective outer layer on a shoot axis and includes as parts a shoot axis hypodermis (PO:0005057) and a shoot axis epidermis (PO:0000112).
  
−
*lupulin gland (PO:0005030): A glandular trichome (PO:0004509) that synthesizes terpenophenolic resins and prenylflavonoids.
+
* stem cortex (PO:0025612): A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047).
  
−
*microsporangiate strobilus (PO:0005031): A strobilus (PO:0025083) that bears only pollen (PO:0025281).
+
* stem hypodermis (PO:0025610): A portion of hypodermis (PO:0005051) that is part of a stem cortex (PO:0025612).
  
−
*megasporangiate strobilus (PO:0005032): A strobilus (PO:0025083) that bears only plant ovules (PO:0020003).
+
* receptacle pith (PO:0025590): A portion of pith (PO:0006109) that is part of a receptacle (PO:0009064). (added for strawberry annotations- fleshy part)
  
−
*vascular leaf development stage (PO:0025570): A leaf development stage (PO:0001050) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
+
* receptacle cortex (PO:0025591): A portion of cortex (PO:0005708) that is part of a receptacle (PO:0009064).
  
−
*multi-tissue plant structure development stage (PO:0025571): A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure (PO:0025496).
+
* stem tegument layer (PO:0025611): A portion of shoot axis tegument layer (PO:0025609) that a tough, protective outer layer on a stem (PO:0009047) and includes as parts a stem hypodermis (PO:0025610) and a stem epidermis (PO:0025178).
  
−
*vascular leaf primordium polarity determination stage (PO:0025572): A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).
+
* spine petiole (PO:0025613): A petiole (PO:0020038) that is sclerified and persistent.
  
−
*non-vascular leaf development stage (PO:0025573): A leaf development stage (PO:0001050) that has as a primary participant a non-vascular leaf (PO:0025075).
+
* rosette (PO:0025615): A collective leaf structure (PO:0025022) consisting of a group of rosette leaves (PO:0000014), generally borne at the base of the plant, that are separated by very short stem internodes (PO:0020142).
  
−
*vascular leaf differentiation stage (PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf *epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
+
* leaf lamina tip (PO:0025589): A leaf tip (PO:0025142) area that is the distal portion of the leaf lamina (PO:00200039). Comment: This is the portion of the leaf lamina (PO:0020039) that is furthest away from the stem (PO:0009047).
  
−
*microgametophyte development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
+
* gemma (PO:0025614): A portion of plant tissue (PO:0009007) which is a small ball of cells born on a thallus (PO:0030027) and is involved in asexual reproduction.
  
−
*vegetative shoot system (PO:0025607): A shoot system (PO:0009006) that has as parts only vegetative tissues and organs.
+
===root terms===
  
−
*flower pedicel abscission zone (PO:0025608): An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
+
* shoot-borne internode root (PO:0025593): A shoot-borne root (PO:0000042) that arises from a shoot axis internode (PO:0005005).
  
−
*shoot axis tegument layer (PO:0025609): A portion of plant tissue (PO:0009007) that forms a tough, protective outer layer on a shoot axis and includes as parts a shoot axis hypodermis (PO:0005057) and a shoot axis epidermis (PO:0000112).
+
* proteoid root (PO:0000067): A root (PO:0009005) that forms one or more clusters of closely spaced lateral roots (PO:0020121) of limited growth along its length.
  
−
*stem hypodermis (PO:0025610): A portion of hypodermis (PO:0005051) that is part of a stem cortex (PO:0025612).
+
=New PSDS terms:=
  
−
*stem tegument layer (PO:0025611): A portion of shoot axis tegument layer (PO:0025609) that a tough, protective outer layer on a stem (PO:0009047) and includes as parts a stem hypodermis (PO:0025610) and a stem epidermis (PO:0025178).
 
  
−
*stem cortex (PO:0025612): A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047).
+
* '''multi-tissue plant structure development stage''' (PO:0025571): A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure  (PO:0025496).
  
−
*spine petiole (PO:0025613): A petiole (PO:0020038) that is sclerified and persistent.
 
  
−
*gemma (PO:0025614): A portion of plant tissue (PO:0009007) which is a small ball of cells born on a thallus (PO:0030027) and is involved in asexual reproduction.
 
−
 
−
*rosette (PO:0025615): A collective leaf structure (PO:0025022) consisting of a group of rosette leaves (PO:0000014), generally borne at the base of the plant, that are separated by very short stem internodes (PO:0020142).
 
−
 
−
=New PSDS terms:=
 
  
−
*''' vascular leaf development stage (PO:0025570)''': A leaf development stage (PO:0001051) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
+
* '''vascular leaf primordium polarity determination stage''' (PO:0025572): A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).
  
−
* '''multi-tissue plant structure development stage (PO:0025571)''': A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure  (PO:0025496).
+
* '''vascular leaf development stage''' (PO:0025570): A leaf development stage (PO:0001051) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
  
−
* '''vascular leaf primordium polarity determination stage (PO:0025572)''': A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).
+
* '''vascular leaf differentiation stage''' (new PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
  
−
* '''non-vascular leaf development stage (PO:0025573)''': A leaf development stage (PO:0001050) that begins with the non-vascular leaf initiation stage and ends with the non-vascular leaf senescence stage.  ''these are not added yet''
+
* '''non-vascular leaf development stage''' (PO:0025573): A leaf development stage (PO:0001050) that begins with the non-vascular leaf initiation stage and ends with the non-vascular leaf senescence stage.  ''(these child terms are not added yet)''
  
−
* '''vascular leaf differentiation stage (new PO:0025574)''': A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
 
  
−
* '''microgametophtye development stage (PO:0025602)''': A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
+
* '''microgametophtye development stage''' (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
  
 
=Renamed terms=
 
=Renamed terms=
Line 101: Line 105:
  
 
Format 'new_name'(PO:ID); was:'old_name'
 
Format 'new_name'(PO:ID); was:'old_name'
 +
 +
Note: This list may not be exhaustive
  
 
==Renamed PAE terms==
 
==Renamed PAE terms==
 +
===plant embryo terms===
 +
* plant embryo proper (PO:0000001); was: embryo proper
 +
 +
* plant embryo coleoptile (PO:0025286); was: embryo coleoptile
 +
 +
* plant embryo radicle (PO:0025296); was: embryo radicle
 +
 +
* plant embryo cotyledon (PO:0025470); was: embryo cotyledon
  
 +
===vascular leaf terms===
  
 
* vascular leaf primordium adaxial side (PO:0004726); was: 'adaxial side of leaf primordium'  
 
* vascular leaf primordium adaxial side (PO:0004726); was: 'adaxial side of leaf primordium'  
Line 109: Line 124:
 
* vascular leaf primordium abaxial side (PO:0004725); was: 'abaxial side of leaf primordium'
 
* vascular leaf primordium abaxial side (PO:0004725); was: 'abaxial side of leaf primordium'
  
−
* vascular leaf adaxial meristem (PO:0025401); was 'leaf adaxial meristem'
+
* vascular leaf adaxial meristem (PO:0025401); was: 'leaf adaxial meristem'
  
 
* vascular leaf abaxial meristem (PO:0025403); was: leaf abaxial meristem (PO:0025403)
 
* vascular leaf abaxial meristem (PO:0025403); was: leaf abaxial meristem (PO:0025403)
  
 +
===meristem terms===
 
* meristem L1 layer (PO:0009020); was: meristem L1
 
* meristem L1 layer (PO:0009020); was: meristem L1
  
Line 119: Line 135:
 
* meristem L3 layer  (PO:0009022); was: meristem L3
 
* meristem L3 layer  (PO:0009022); was: meristem L3
  
−
* shoot axis node (PO:0005004); was: shoot node
+
===Terms for shoot-borne (adventitious) roots etc ===
 +
* shoot-borne root meristem (PO:0006021); was: adventitious root apical meristem
  
−
* shoot-borne root meristem (PO:0006021); was: adventitious root apical meristem
+
* shoot-borne root epidermis (PO:0006039): was: adventitious root epidermis
  
 
* shoot-borne nodal root  (PO:0003005); was: nodal root
 
* shoot-borne nodal root  (PO:0003005); was: nodal root
 +
 +
* shoot-borne root apical meristem (PO:0006021); was: adventitious root apical meristem
 +
 +
=== Other PAE terms===
 +
 +
* shoot system epidermis (PO:0006035); was: shoot epidermis
 +
 +
* shoot axis node (PO:0005004); was: shoot node
  
 
* shoot axis internode (PO:0005005);  was: shoot internode
 
* shoot axis internode (PO:0005005);  was: shoot internode
  
 
* shoot system meristem (PO:0006079); was shoot meristem
 
* shoot system meristem (PO:0006079); was shoot meristem
 +
 +
* inflorescence axis internode (PO:0006326); was: inflorescence internode
 +
 +
* floral organ abscission zone (PO:0006502); was: flower abscission zone
 +
 +
* flower pedicel (PO:0009052); was: pedicel
 +
 +
* microgametophyte vegetative cell (PO:0020099); was: vegetative cell
  
 
==Renamed PSDS terms==
 
==Renamed PSDS terms==
 +
 +
===vascular leaf development terms===
  
 
* vascular leaf initiation stage (PO:0001051); was: 1 leaf initiation stage
 
* vascular leaf initiation stage (PO:0001051); was: 1 leaf initiation stage
 +
** vascular leaf anlagen formation stage (PO:0001003) was: formation of leaf founder cells stage >> vascular leaf founder cells formation stage
 +
** vascular leaf primordium formation stage (PO:0001019); was: formation of leaf primordium stage
  
 
* vascular leaf expansion stage (PO:0001052); was: 2 leaf expansion stage
 
* vascular leaf expansion stage (PO:0001052); was: 2 leaf expansion stage
 +
** rapid elongation of vascular leaf lamina stage (PO:0001023); was: rapid elongation of leaf blade stage
 +
** formation of vascular leaflet primordia stage (PO:0004500); was: formation of leaflet primordia stage
  
−
* vascular leaf post-expansion stage (or maybe "mature vascular leaf stage ") (PO:0001053); was: 3 leaf fully expanded stage  
+
* vascular leaf post-expansion stage (PO:0001053); was: 3 leaf fully expanded stage  
  
 +
* vascular leaf senescent stage (PO:0001054); was: 4 leaf senescence stage  > vascular leaf senescence stage
  
 +
===plant embryo development terms===
  
−
* vascular leaf senescent stage (PO: 0001054); was: vascular leaf senescence stage
+
* plant embryo development stage (PO:0007631): was plant embryo stage
  
−
* vascular leaf senescence stage (PO:0001054); was: 4 leaf senescence stage
+
* plant proembryo stage (PO:0001180); was: B proembryo stage >  proembryo stage
  
−
* vascular leaf anlagen formation stage (PO:0001003); was: formation of leaf founder cells stage
+
* plant embryo globular stage (PO:0001185); was: C globular stage > globular stage > plant globular embryo stage
  
−
* vascular leaf primordium formation stage (PO:0001019); was: formation of leaf primordium stage
 
  
−
* formation of vascular leaflet primordia stage (PO:0004500); was: formation of leaflet primordia stage
+
* plant embryo cotyledonary stage (PO:0001078); was: E expanded cotyledon stage
  
−
* rapid elongation of vascular leaf lamina stage (PO:0001023); was: rapid elongation of leaf blade stage
+
* mature plant embryo stage (PO:0001081); was: F mature embryo stage
  
 +
* plant embryo coleoptilar stage (PO:0001094); was: coleoptilar stage
  
 +
* plant embryo true leaf formation stage (PO:0001095); was: true leaf formation stage
  
−
* XXXX (PO:0001024); was: rapid elongation of leaf sheath stage (PO:0001024)
+
* plant embryo bilateral stage (PO:0004507); was: D bilateral stage > plant bilateral embryo stage
  
−
* XXXX (PO:0001021); was: ligule primordial stage (PO:0001021)
+
* plant embryo coleoptilar stage (PO:0001094): was: coleoptilar stage  
  
−
* XXXX (PO:0001020); was: hood-shaped primordium stage (PO:0001020)
+
* plant embryo cotyledonary stage (PO:0001078): was: expanded cotyledon stage; plant embryo expanded cotyledon stage
  
−
=Other Fixes=
+
* plant embryo true leaf formation stage (PO:0001095) was: true leaf formation stage
 +
 
 +
* mature plant embryo stage (PO:0001081): was mature embryo stage
 +
 
 +
===Other stage terms revised===
 +
* seed germination stage (PO:0007057); was: 0 seed germination stage
 +
 
 +
=Merged or Obsoleted terms=
 +
None

Latest revision as of 21:50, 8 October 2015

Go back to main page: Release_21

Notes

  • Includes all revisions of the plant_ontology.obo file from Aug 2013 (#2228) to July 2015 (#3502) on the PO SVN site.
  • This Release includes all the changes from Aug. 6th, 2015 #33ae100 to Sep 25, 2015 #01901fa

New PAE terms:

portion of plant substance:

  • plant resin (PO:0025603): A portion of plant substance (PO:0025161) that consists of a complex mixture of organic aromatic compounds such as mono-, sesqui-, and diterpenoids.

plant structure terms

native plant cell and new child terms

  • native plant cell (PO:0025606): A plant cell (PO:0009002) that is either part of a multicellular whole plant (PO:0000003) 'in vivo' or a unicellular organism 'in_natura' (i.e. part of a natural environment).
  • phyllome founder cell (PO:0025586): A native plant cell (PO:0025606) that is part of the phyllome anlagen (PO:0025430).
  • vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).

meristem terms

  • ground meristem (PO:0025594): A portion of meristem tissue (PO:0009013) that gives rise to a portion of ground tissue (PO:0025059).
  • shoot system ground meristem (PO:0025595): A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the shoot system (PO:0009006).
  • root system ground meristem (PO:0025596): A ground meristem (PO:0025594) that gives rise to a portion of ground tissue (PO:0025059) in the root system (PO:0025025).

Terms describing special types of flowers, inflorescences, strobili and infructesences

  • pistillate inflorescence (PO:0025598): An inflorescence (PO:0009049) that includes as part only pistillate flowers (PO:0025599).
  • pistillate flower (PO:0025599): A flower (PO:0009046) that includes as part a single carpel (PO:0009030) or a gynoecium (PO:0009062), but the androecium (PO:0009061) is absent or has aborted during development.
  • staminate flower (PO:0025600): A flower (PO:0009046) that includes as part an androecium (PO:0009061), and the gynoecium (PO:0009062) is absent or has aborted during development.
  • staminate inflorescence (PO:0025601): An inflorescence (PO:0009049) that includes as part only staminate flowers (PO:0025600).
  • microsporangiate strobilus (PO:0005031): A strobilus (PO:0025083) that bears only pollen (PO:0025281).
  • megasporangiate strobilus (PO:0005032): A strobilus (PO:0025083) that bears only plant ovules (PO:0020003).
  • ear infructescence (PO:0025597): An infructescence (PO:0006342) in Zea spp. that bears kernels (i.e. fruit; PO:0009001) on a compact infructescence axis (PO:0025242) and develops from the ear inflorescence (PO:0020136).

Various other new terms

  • vegetative shoot system (PO:0025607): A shoot system (PO:0009006) that has as parts only vegetative tissues and organs.
  • lupulin gland (PO:0005030): A glandular trichome (PO:0004509) that synthesizes terpenophenolic resins and prenylflavonoids.
  • resin cell (PO:0025604): An epidermal cell (PO:0004013) that secretes plant resin (PO:0025603) and may line resin canals (PO:0005665) and/or be associated with resin blisters (or cysts).
  • fruit pedicel abscission zone (PO:0025605): An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
  • flower pedicel abscission zone (PO:0025608): An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
  • shoot axis tegument layer (PO:0025609): A portion of plant tissue (PO:0009007) that forms a tough, protective outer layer on a shoot axis and includes as parts a shoot axis hypodermis (PO:0005057) and a shoot axis epidermis (PO:0000112).
  • stem cortex (PO:0025612): A portion of shoot axis cortex (PO:0000223) that is part of a stem (PO:0009047).
  • stem hypodermis (PO:0025610): A portion of hypodermis (PO:0005051) that is part of a stem cortex (PO:0025612).
  • receptacle pith (PO:0025590): A portion of pith (PO:0006109) that is part of a receptacle (PO:0009064). (added for strawberry annotations- fleshy part)
  • receptacle cortex (PO:0025591): A portion of cortex (PO:0005708) that is part of a receptacle (PO:0009064).
  • stem tegument layer (PO:0025611): A portion of shoot axis tegument layer (PO:0025609) that a tough, protective outer layer on a stem (PO:0009047) and includes as parts a stem hypodermis (PO:0025610) and a stem epidermis (PO:0025178).
  • spine petiole (PO:0025613): A petiole (PO:0020038) that is sclerified and persistent.
  • rosette (PO:0025615): A collective leaf structure (PO:0025022) consisting of a group of rosette leaves (PO:0000014), generally borne at the base of the plant, that are separated by very short stem internodes (PO:0020142).
  • leaf lamina tip (PO:0025589): A leaf tip (PO:0025142) area that is the distal portion of the leaf lamina (PO:00200039). Comment: This is the portion of the leaf lamina (PO:0020039) that is furthest away from the stem (PO:0009047).
  • gemma (PO:0025614): A portion of plant tissue (PO:0009007) which is a small ball of cells born on a thallus (PO:0030027) and is involved in asexual reproduction.

root terms

  • shoot-borne internode root (PO:0025593): A shoot-borne root (PO:0000042) that arises from a shoot axis internode (PO:0005005).
  • proteoid root (PO:0000067): A root (PO:0009005) that forms one or more clusters of closely spaced lateral roots (PO:0020121) of limited growth along its length.

New PSDS terms:

  • multi-tissue plant structure development stage (PO:0025571): A plant structure development stage (PO:0009012) that has as primary participant a multi-tissue plant structure (PO:0025496).


  • vascular leaf primordium polarity determination stage (PO:0025572): A vascular leaf initiation stage (PO:0001051) during which the vascular leaf primordium (PO:0004725) develops an adaxial side (PO:0004726) and an abaxial side (PO:0004725).
  • vascular leaf development stage (PO:0025570): A leaf development stage (PO:0001051) which begins with the onset of the vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
  • vascular leaf differentiation stage (new PO:0025574): A vascular leaf development stage (PO:0025570) that begins with the formation of procambium (PO:0025275) and protoderm (PO:0006210) and ends with the formation and differentiation of the leaf epidermis (PO:0006016) and leaf vascular system (PO:0000036) and all the specialized cells of the vascular leaf.
  • non-vascular leaf development stage (PO:0025573): A leaf development stage (PO:0001050) that begins with the non-vascular leaf initiation stage and ends with the non-vascular leaf senescence stage. (these child terms are not added yet)


  • microgametophtye development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.

Renamed terms

No substantial change in the meaning of the definition

Format 'new_name'(PO:ID); was:'old_name'

Note: This list may not be exhaustive

Renamed PAE terms

plant embryo terms

  • plant embryo proper (PO:0000001); was: embryo proper
  • plant embryo coleoptile (PO:0025286); was: embryo coleoptile
  • plant embryo radicle (PO:0025296); was: embryo radicle
  • plant embryo cotyledon (PO:0025470); was: embryo cotyledon

vascular leaf terms

  • vascular leaf primordium adaxial side (PO:0004726); was: 'adaxial side of leaf primordium'
  • vascular leaf primordium abaxial side (PO:0004725); was: 'abaxial side of leaf primordium'
  • vascular leaf adaxial meristem (PO:0025401); was: 'leaf adaxial meristem'
  • vascular leaf abaxial meristem (PO:0025403); was: leaf abaxial meristem (PO:0025403)

meristem terms

  • meristem L1 layer (PO:0009020); was: meristem L1
  • meristem L2 layer (PO:0009021); was: meristem L2
  • meristem L3 layer (PO:0009022); was: meristem L3

Terms for shoot-borne (adventitious) roots etc

  • shoot-borne root meristem (PO:0006021); was: adventitious root apical meristem
  • shoot-borne root epidermis (PO:0006039): was: adventitious root epidermis
  • shoot-borne nodal root (PO:0003005); was: nodal root
  • shoot-borne root apical meristem (PO:0006021); was: adventitious root apical meristem

Other PAE terms

  • shoot system epidermis (PO:0006035); was: shoot epidermis
  • shoot axis node (PO:0005004); was: shoot node
  • shoot axis internode (PO:0005005); was: shoot internode
  • shoot system meristem (PO:0006079); was shoot meristem
  • inflorescence axis internode (PO:0006326); was: inflorescence internode
  • floral organ abscission zone (PO:0006502); was: flower abscission zone
  • flower pedicel (PO:0009052); was: pedicel
  • microgametophyte vegetative cell (PO:0020099); was: vegetative cell

Renamed PSDS terms

vascular leaf development terms

  • vascular leaf initiation stage (PO:0001051); was: 1 leaf initiation stage
    • vascular leaf anlagen formation stage (PO:0001003) was: formation of leaf founder cells stage >> vascular leaf founder cells formation stage
    • vascular leaf primordium formation stage (PO:0001019); was: formation of leaf primordium stage
  • vascular leaf expansion stage (PO:0001052); was: 2 leaf expansion stage
    • rapid elongation of vascular leaf lamina stage (PO:0001023); was: rapid elongation of leaf blade stage
    • formation of vascular leaflet primordia stage (PO:0004500); was: formation of leaflet primordia stage
  • vascular leaf post-expansion stage (PO:0001053); was: 3 leaf fully expanded stage
  • vascular leaf senescent stage (PO:0001054); was: 4 leaf senescence stage > vascular leaf senescence stage

plant embryo development terms

  • plant embryo development stage (PO:0007631): was plant embryo stage
  • plant proembryo stage (PO:0001180); was: B proembryo stage > proembryo stage
  • plant embryo globular stage (PO:0001185); was: C globular stage > globular stage > plant globular embryo stage


  • plant embryo cotyledonary stage (PO:0001078); was: E expanded cotyledon stage
  • mature plant embryo stage (PO:0001081); was: F mature embryo stage
  • plant embryo coleoptilar stage (PO:0001094); was: coleoptilar stage
  • plant embryo true leaf formation stage (PO:0001095); was: true leaf formation stage
  • plant embryo bilateral stage (PO:0004507); was: D bilateral stage > plant bilateral embryo stage
  • plant embryo coleoptilar stage (PO:0001094): was: coleoptilar stage
  • plant embryo cotyledonary stage (PO:0001078): was: expanded cotyledon stage; plant embryo expanded cotyledon stage
  • plant embryo true leaf formation stage (PO:0001095) was: true leaf formation stage
  • mature plant embryo stage (PO:0001081): was mature embryo stage

Other stage terms revised

  • seed germination stage (PO:0007057); was: 0 seed germination stage

Merged or Obsoleted terms

None

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