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)
- 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
Other:
Changed name of meristem (PO:0009013) to portion of meristem tissue
Added comment to antiraphe, chalaza, integument, nucellus, and raphe and funicle, and added PO ids to their definitions.
Changed embryo sac part_of plant ovary ovule to located_in. Will change others later, after we see how it works.
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: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.
