Summary of Changes to PO July 2012

See also: New terms and obsolete terms July 2012 Release

Back to July 2012 Release page.

Updated definitions and/or comments: PAE terms

areole bud (PO:0025353)

phyllome lamina areole (PO:0025391)

leaf lamina areole (PO:0025392)

leaf lamina vein (PO:0020138)

axillary vegetative bud (PO:0004712)

terminal vegetative bud (PO:0004716)

tuber (PO:0004543) (definition and comment)

subterranean tuber (PO:0004547) (comment)

phyllome marginal meristem (definitions and comments)

leaf marginal meristem (definitions and comments)

shoot apex (changed definition to: "has as parts ...the youngest phyllome primordia" instead of "...leaf primordia")

leaf sheath auricle

phyllome primordium (*updated definitions: part_of shoot apex)

cotyledon primordium (*updated definitions: part_of vegetative shoot apex)

vascular leaf primordium (*updated definitions: part_of vegetative shoot apex)

bract primordium (*updated definitions: part_of reproductive shoot apex) *relations were already there.

floral structure primordium (added "is part-of a reproductive shoot apex (PO:0025222)" to definition) Removed redundant relations from its subtypes.

plant organ (Modified comment)

ovule (PO:0020003) (modified def'n: use located in rather than contains)

gynoecium

androecium

subterranean tuber interfascicular region (comment)

lateral root

root primordium

lateral root primordium

root anlagen (comment)

whole plant (removed example seed example in comment)

phyllome anlagen (added "part_of peripheral zone (PO:0000225)" to definition of, relation was already there)

antiraphe, chalaza, integument, nucellus, raphe, funicle (Added comment and added PO ids to their definitions)

• Updated definition of primordium and its subtypes:

primordium (PO:0025127)

androecium primordium

anther primordium

carpel primordium

cotyldeon primordium

gynoecium primordium

lateral root primordium

lodicule primordium

ovule primordium

petal primordium

phyllome primordium

sepal primordium

stamen primordium

root anlagen

root primordium

vascular leaf primordium

• other changes to primordium terms:

Made primordium (PO:0025127) is_a meristem

Made 8 terms subtypes of the bin term floral structure primordium (PO:0025477) (and removed redundant relations from its subtypes)

Added "portion of xxx primordium tissue" as synonyms to all primordium types.

Removed the relation: lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.

Made root anlagen is_a portion of plant tissue

Added adventitious root primordium as synonym of basal root primordium and shoot-borne root primordium.

New or modified synonyms

Added tuber branch as exact synonym of tuber.

Added "vascular tissue" exact synonym of "portion of vascular tissue".

Added promeristem as synonym of apical meristem and shoot apical meristem (broad). (Was synonym of only root apical meristem).

Added "pistil primordium" as exact synonym of gynoecium primordium.

Changed "pistil", as synonym of gynoecium, from related to exact.

Changed pistil to broad synonym of gynoecium and carpel

Added "AM" as exact synonym of apical meristem

Added syncarpous gynoecium and apocarpous gynoecium as synonyms of gynoecium

New or modified relations

Made leaf sheath auricle part_of leaf sheath, rather than part_of vascular leaf to

Added phyllome margin part_of phyllome lamina

Removed phyllome marginal meristem part_of phyllome (now redundant)

Removed phyllome marginal meristem part_of phyllome primordium

Removed leaf marginal meristem part_of vascular leaf primordium

Removed relation: ovule part_of ovary

Changed funicle from part_of ovary to part of_ovule

Removed ovule part_of ovary

Changed ovule from is_a cardinal organ part to is_a plant organ

Made embryo sac part_of ovarian ovule instead of part of ovule

Added relations:

Added relation "located_in". Need to check on how to link to BFO/RO

bract primordium develops_from bract anlagen

lodicule primordium develops_from lodicule anlagen

petal primordium develops_from petal anlagen

sepal primordium develops_from sepal anlagen

stamen primordium develops_from stamen anlagen

embryo sac part_of plant ovary ovule changed to located_in

Other changes:

Changed name of meristem (PO:0009013) to portion of meristem tissue

New term: multi-tissue plant structure (PO:0025496): A plant structure (PO:0009011) that has as parts two or more portions of plant tissue (PO:0009007) of at least two different types and which through specific morphogenetic processes forms a single structural unit demarcated by primarily bona-fide boundaries from other structural units of different types. [source: CARO:0000055, POC:curators]

fruit (PO:0009001)- A multi-tissue plant structure (PO:0025496) that develops from a gynoecium (PO:0009062) and may have as parts one or more seeds (PO:0009010).

seed (PO:0009010)- A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088).

Added definition dbxref to CARO:0000055 for multi-tissue plant structure

Made collective organ part structure (PO:0025269) a child of new CPS (PO:0025497), revised def'n: A collective plant structure (PO:0025497) composed of two or more cardinal organ parts (PO:0025001) from adjacent plant organs (PO:0009008) and any associated portions of plant tissue (PO:0009007).

Sub-classes of new MTPS: plant organ (PO:0009008): revised def'n: A multi-tissue plant structure (PO:0025496) that is a functional unit, is a proper part of a whole plant (PO:0000003), and includes portions of plant tissue (PO:0009007) of at least two different types that derive from a common developmental path.

Revised comment: Examples include stem (PO:0009047), leaf (PO:0025034), and root (PO:0009005). May include individual cell types that are not part of tissues (e.g., idioblasts (PO:0000283)). A plant organ may have one or more different plant organs as parts, such as sporophyll (PO:0009026) that may have as part a sporangium (PO:0025094) or a carpel that may have as part an plant ovule (PO:0020003).

Changed definition of pollen sac to say : "A microsporangium that is part of a sporophyll..." rather than "A microsporangium that is located in a sporophyll ...", because it was incorrect use of located in. We are reserving located in for different organisms, and sporangium is still same organism as the sporophyll.

Added protonema develops_from plant spore, because that is what the definition says.

Moved the following terms from is_a cardinal organ part to is_a cardinal part of MTPS: fruit distal end PO:0008001, fruit proximal end PO:0008002, arilloid PO:0019022, hilum PO:0020063, seed raphe PO:0006331

Changed seed funicle from is_a stalk to is_a cardinal part of MTPS.

Changed strophiole from part of raphe to part of seed raphe.

Changed hilum groove from is_a cardinal organ part to is_a canal.

Changed vascular system (PO:0000034) from is_a plant structure to is_a portion of vascular tissue, and changed definition. Removed relation vascular system disjoint from portion of plant tissue.

Removed relation fruit pedicel part of fruit.

Updated definition of hilum groove to say that it is a canal, instead of cardinal organ part

Updated definitions of arilloid, hilum, seed funicle, seed raphe, fruit proximal end, and fruit distal end to say that they are now cardinal part of multi-tissue plant structure, instead of cardinal organ part, and added PO ids.

Changed definition of fruit proximal end to say it is the proximal end of a fruit, instead of saying it is the stem end of a fruit.

Updated comment of plant organ (PO:0009008).

Updated definition of collective organ part structure (small change) Updated comment to include ids and remove references to PO terms that don't exist, like carpel wall.

Removed "collective plant organ structure" as exact synonym from PO:0025007, because it is now the primary name, and moved Spanish and Japanese synonyms to collective plant structure.

Revised comment of cardinal organ part, and added cardinal part of plant organ as synonym.

PSDS term revisions

Name changes:

Added "stage" to the end of these terms: "done for July 2012 release- note many of these are obsoletes- highlighted"

PO:0007601 1 flower meristem visible

PO:0007056 1 pattern formation

PO:0007505 1 root primordium formation

PO:0007058 2 endoreduplication

PO:0007602 2 flower meristem notched

PO:0007527 2 root meristem formation

PO:0007087 2.01 main shoot and axillary shoots visible at one node

PO:0007071 2.02 main shoot and axillary shoots visible at two nodes

PO:0007080 2.03 main shoot and axillary shoots visible at three nodes

PO:0007088 2.04 main shoot and axillary shoots visible at four nodes

PO:0007093 2.05 main shoot and axillary shoots visible at five nodes

PO:0007118 2.06 main shoot and axillary shoots visible at six nodes

PO:0007122 2.07 main shoot and axillary shoots visible at seven nodes

PO:0007077 2.08 main shoot and axillary shoots visible at eight nodes

PO:0007110 2.09 main shoot and axillary shoots visible at nine or more nodes

PO:0007059 3 branch formation

PO:0007525 3 establishment of tissue systems

PO:0001053 3 leaf fully expanded

PO:0007616 4 anthesis

PO:0007016 4 flowering

PO:0007135 4 growth directionality

PO:0001031 4 root elongation

PO:0007042 5 fruit formation

PO:0007617 5 post anthesis

PO:0007519 5 root hair formation

PO:0007010 6 ripening

PO:0001005 A archesporial cells visible

PO:0007623 A megaspore mother cell enlarges

PO:0001018 B formation of primary parietal and sporogenous cells

PO:0007624 B meiosis of megaspore mother cell

PO:0001008 C callose wall formation in pollen mother cells

PO:0001025 C four anther lobes formed

PO:0007625 C tetrad of megaspores

PO:0007618 carpel primordium visible

PO:0001041 chalazal and micropylar domain establishment

PO:0004502 closure of carpel(s)

PO:0007518 crown root emergence

PO:0007504 crown root primordium formation

PO:0001026 D locules established

PO:0007626 D megaspore degeneration

PO:0001032 E tapetum degeneration initiated

PO:0007627 E two nucleate megagametophyte

PO:0007081 early rosette growth

PO:0007628 F four nucleate megagametophyte

PO:0007026 FL.00 first flower(s) open

PO:0007034 FL.01 1/4 of flowers open

PO:0007053 FL.02 1/2 of flowers open

PO:0007052 FL.03 3/4 of flowers open

PO:0007024 FL.04 end of flowering

PO:0001099 formation of aleurone and starchy layers

PO:0001019 formation of leaf primordium

PO:0004500 formation of leaflet primordia

PO:0001021 formation of ligule primordium

PO:0001003 formation of the leaf founder cells

PO:0007036 FR.00 beginning of fruit ripening

PO:0007038 FR.04 fruit ripening complete

PO:0001057 fully expanded lemma

PO:0001079 fully expanded lodicule

PO:0001071 fully expanded palea

PO:0007612 fully expanded petal

PO:0001045 fully expanded sepal

PO:0001042 functional specialization of the endosperm

PO:0001035 G anther dehiscence

PO:0007629 G eight nucleate megagametophyte

PO:0004501 gynoecium differentiation and expansion

PO:0001036 H anther senescence

PO:0001020 hood-shaped primordium

PO:0007025 IE.00 inflorescence tip just visible above flag leaf sheath

PO:0007048 IE.01 1/4 of inflorescence emerged from flag leaf sheath

PO:0007008 IE.02 1/2 of inflorescence emerged from flag leaf sheath

PO:0007002 IE.03 3/4 of inflorescence emerged from flag leaf sheath

PO:0007023 IE.04 inflorescence fully emerged from flag leaf sheath

PO:0007076 late rosette growth

PO:0007517 lateral root emergence

PO:0007511 lateral root primordium formation

PO:0007133 leaf production

PO:0001055 lemma primordia visible

PO:0025337 life of whole plant

PO:0001072 lodicule primordia visible

PO:0007094 LP.01 one leaf visible

PO:0007098 LP.02 two leaves visible

PO:0007106 LP.03 three leaves visible

PO:0007115 LP.04 four leaves visible

PO:0007065 LP.05 five leaves visible

PO:0007123 LP.06 six leaves visible

PO:0007063 LP.07 seven leaves visible

PO:0007095 LP.08 eight leaves visible

PO:0007101 LP.09 nine leaves visible

PO:0007103 LP.10 ten leaves visible

PO:0007116 LP.11 eleven leaves visible

PO:0007064 LP.12 twelve leaves visible

PO:0007083 LP.13 thirteen leaves visible

PO:0007085 LP.14 fourteen leaves visible

PO:0007104 LP.15 fifteen leaves visible

PO:0007119 LP.16 sixteen leaves visible

PO:0007067 LP.17 seventeen leaves visible

PO:0007072 LP.18 eighteen leaves visible

PO:0007120 LP.19 nineteen leaves visible

PO:0007082 LP.20 twenty or more leaves whorls visible

PO:0007068 mid rosette growth

PO:0004504 ovule differentiation and expansion

PO:0007620 ovule primordium visible

PO:0001058 palea primordia visible

PO:0007608 petal primordium visible

PO:0007506 primary root primordium formation

PO:0001023 rapid elongation of leaf blade

PO:0001024 rapid elongation of leaf sheath

PO:0007501 root cap formation

PO:0007513 root cortex differentiation

PO:0007510 root emergence

PO:0007516 root epidermal differentiation

PO:0007509 root vascular cylinder differentiation

PO:0007113 rosette growth

PO:0007078 rosette growth complete

PO:0007079 SE.00 stem elongation begins

PO:0007091 SE.01 one node or internode visible

PO:0007117 SE.02 two nodes or internodes visible

PO:0007096 SE.03 three nodes or internodes visible

PO:0007092 SE.04 four nodes or internodes visible

PO:0007086 SE.05 five nodes or internodes visible

PO:0007062 SE.06 six nodes or internodes visible

PO:0007108 SE.07 seven nodes or internodes visible

PO:0007070 SE.08 eight nodes or internodes visible

PO:0007066 SE.09 nine nodes or internodes visible

PO:0007084 SE.10 ten nodes or internodes visible

PO:0007114 SE.11 eleven nodes or internodes visible

PO:0007111 SE.12 twelve nodes or internodes visible

PO:0007090 SE.13 thirteen nodes or internodes visible

PO:0007097 SE.14 fourteen nodes or internodes visible

PO:0007074 SE.15 fifteen nodes or internodes visible

PO:0007100 SE.16 sixteen or more nodes or internodes visible

PO:0007099 SE.97 flag leaf visible

PO:0007109 SE.99 maximum stem length reached

PO:0007607 sepal primordium visible

PO:0001380 sepals enclosing flower bud

PO:0001378 sepals enclosing meristem

PO:0007613 stamen primordium visible

PO:0007089 stem elongation

PO:0004503 stigma cell differentiation

PO:0001095 true leaf formation

PO:0001027 meristamtic zone formation

PO:0001000 meristem eloboration

PO:0007060 obsolete growth and development terms

PO:0007532 obsolete plant growth and development terms

PO:0007061 2.00 main shoot only

PO:0001030 specialization zone formation

PO:0007610 sepals 100% of final size

PO:0007609 sepals 50% of final size

PO:0007536 root primordium visible

PO:0028001 plant life cycle phase

PO:0007075 5.02 20% of inflorescence emerged.

PO:0007102 5.04 40% of inflorescence emerged

PO:0007105 5.06 60% of inflorescence emerged

PO:0007107 5.08 80% of inflorescence emerged

PO:0001098 formation of starchy endosperm

PO:0007529 E emerged root elongation

PO:0007531 F1 root hair initiation

PO:0007526 F2 root hair elongation

PO:0007121 6.01 10% of flowers open

PO:0007124 6.03 30% of flowers open

PO:0007125 6.04 40% of flowers open

PO:0007035 7-8 fruit formation and maturation

PO:0007126 7.02 fruit size 20%

PO:0007127 7.04 fruit size 40%

PO:0007128 7.06 fruit size 60%

PO:0007129 7.08 fruit size 80%

PO:0007503 A2.1 root intials differntiation of primary roots

PO:0007528 A2.2 root initials differentiation of lateral roots

PO:0007530 A2.3 founder cell derivatives of lateral root

PO:0007534 A2.4 root initials differentiation of crown roots

PO:0007524 B1 primary root meristem formation

PO:0007539 B2 lateral root meristem formation

PO:0007514 B3 crown root meristem formation

PO:0007521 C3.1 metaxylem differentiation of root.

PO:0007537 C3.2 maturation of phloem elements in root.

PO:0007533 C3.3 maturation of protoxylem elements in root.

PO:0021002 calyx absolute size

PO:0021003 calyx relationship

PO:0001028 elongation zone formation

PO:0007523 establishment of initial cells

See also: New terms and obsolete terms July 2012 Release

Back to July 2012 Release page.