Details of Changes to Release 21

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Notes

• Includes all revisions of the plant_ontology.obo file from Aug 2013 (#2228) to July 2015 (#3502) on the PO SVN site.

• After August 1, 2015, all the ontology files were moved to Planteome GitHub Repository

• 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.

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