Summary of Changes to PO July 2012

See also: New terms and obsolete terms July 2012 Release

Back to July 2012 Release page.

Updated definition of 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)

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

Modified definition and comment of tuber (PO:0004543) and comment of subterranean tuber (PO:0004547).

Made 8 terms subtypes the bin term floral structure primordium (PO:0025477).

Made primordium (PO:0025127) is_a meristem, and updated definition.

Updated definitions of subtypes of primordium: androecium primordium, anther primordium, gynoecium primordium, ovule primordium, phyllome primordium, vascular leaf primordium, carpel primordium, cotyldeon primordium, lodicule primordium, petal primordium, sepal primordium, stamen primordium

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

Updated definition of root primodrium and lateral root primordium, and removed relation lateral root primordium develops_from pericycle (PO:0006203), because it is not always true.

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

pericyclic and non-pericyclic lateral root and lateral root primordium - new terms

Updated definition of root anlagen. Made it is_a portion of plant tissue

Added tuber branch as exact synonym of tuber.

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

Changed definition of shoot apex to say "has as parts ...the youngest phyllome primordia" instead of "...leaf primordia".

Updated definition of leaf sheath auricle, and changed from part_of vascular leaf to part_of leaf sheath.

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

Updated definitions and comments of phyllome marginal meristem and leaf marginal meristem.

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

Updated definitions of phyllome primordium to say that it is part of shoot apex, plus definition of cotyledon and vascular leaf primordium to say they are part_of vegetative shoot apex, and definition of bract primordium part of reproductive shoot apex. Relations were already there. Added "is part of a reproductive shoot apex (PO:0025222)" to definition of floral structure primordium and removed redundant relations from its subtypes.

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

Added relations: 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

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

Added "AM" as exact synonym of apical meristem.

Changed pistil to broad synonym of gynoecium and carpel

Added syncarpous gynoecium and apocarpous gynoecium as synonyms of gynoecium.

Modified comment for plant organ.

Updated definition of ovule (PO:0020003). 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.

Removed relation ovule part of ovary.

Modified definition of ovule to use located in rather than contains.

Added comment to Antiraphe, chalaza, integument, nucellus, and raphe and funicle, and added PO ids to their definitions.

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

Changed embryo sac part_of plant ovary ovule to located_in. Will change others later, after we see how it works.

Updated definition of gynoecium and androecium.

Changed comment of subterranean tuber interfascicular region.

Updated definition of lateral root.

Updated definition of root primordium and lateral root primordium.

Updated comment of root anlagen.

Updated comment of whole plant to remove example of seed.

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).

seed (PO:0009010) revised def'n: 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).

fruit (PO:0009001)- revised def'n: A multi-tissue plant structure (PO:0025496) containing one or more plant embryos (PO:0009009), which as a whole, develops from a gynoecium (PO:0009062). (RW changed it again after this -- waiting for final definition approval).

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.

Made CPS is_a plant structure (not is_a MTPS).

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

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 definition of multi-tissue plant structure (PO:0025496), fruit (PO:0009001).

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: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:0001005 A archesporial cells visible

PO:0007623 A megaspore mother cell enlarges

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:0001018 B formation of primary parietal and sporogenous cells

PO:0007624 B meiosis of megaspore mother cell

PO:0007524	B1 primary root meristem formation

PO:0007539	B2 lateral root meristem formation

PO:0007514	B3 crown root meristem formation

PO:0001008 C callose wall formation in pollen mother cells

PO:0001025 C four anther lobes formed

PO:0007625 C tetrad of megaspores

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: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:0007529	E emerged root elongation

PO:0001032 E tapetum degeneration initiated

PO:0007627 E two nucleate megagametophyte

PO:0007081 early rosette growth

PO:0001028	elongation zone formation

PO:0007523	establishment of initial cells

PO:0007628 F four nucleate megagametophyte

PO:0007531	F1 root hair initiation

PO:0007526	F2 root hair elongation

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:0001098	formation of starchy endosperm

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

See also: New terms and obsolete terms July 2012 Release

Back to July 2012 Release page.