Difference between revisions of "Eliminating Zea/Poaceae terms from PO"
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| + | Back to [[Summary_of_Changes to PO October 2011]] | ||
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=Annotations= | =Annotations= | ||
| − | If one term is merged with another, the IDs | + | If one term is merged with another, one of the IDs becomes a synonym (alt_id:PO:XXXXXXX) under the ID of the target term. |
| + | |||
| + | However, the annotations do not automatically move to the target term, they have to be moved manually. | ||
| + | |||
| + | We suggest running a check for annotations associated with alternate IDs with each new release, to make sure no merged terms were missed. | ||
See [[list of Poaceae/Zea terms with annotations]] | See [[list of Poaceae/Zea terms with annotations]] | ||
| + | |||
=Existing terms= | =Existing terms= | ||
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''suggest keeping the is_a children (PO:0006313-16)'' | ''suggest keeping the is_a children (PO:0006313-16)'' | ||
| − | ''suggest merging all of the part_of children with their is_a parent: androecium of tassel floret with Poaceae androecium,, lemma of tassel floret with lemma, etc. -- see below under [[Poaceae_terms_from_PO#Other_Poaceae-specific_terms]].'' | + | ''suggest merging all of the part_of children with their is_a parent: androecium of tassel floret with Poaceae androecium,, lemma of tassel floret with lemma, etc. -- see below under [[Eliminating_Zea/Poaceae_terms_from_PO#Other_Poaceae-specific_terms]].'' |
===PO:0006471 Zea androecium (0)=== | ===PO:0006471 Zea androecium (0)=== | ||
| Line 78: | Line 85: | ||
-Zea stamen is part_of | -Zea stamen is part_of | ||
| − | ''suggest merge this term plus all of its descendants into Poaceae androecium, then into androcium. Zea stamen will be merge into stamen.'' | + | '''x''' ''suggest merge this term plus all of its descendants into Poaceae androecium, then into androcium. Zea stamen will be merge into stamen.'' |
===PO:0006472 Zea stamen (1)=== | ===PO:0006472 Zea stamen (1)=== | ||
| Line 243: | Line 250: | ||
''Okay as is. Could give it a more generic name, like "functionally female inflorescence spikelet".'' | ''Okay as is. Could give it a more generic name, like "functionally female inflorescence spikelet".'' | ||
| + | |||
| + | '''x''' ''Kept as is.'' | ||
===PO:0006354 ear floret (0)=== | ===PO:0006354 ear floret (0)=== | ||
| Line 252: | Line 261: | ||
-androecium of ear floret, gynoecium of ear floret, lemma of ear floret, lodicule of ear floret, and 5 other parts are part_of | -androecium of ear floret, gynoecium of ear floret, lemma of ear floret, lodicule of ear floret, and 5 other parts are part_of | ||
| − | ''suggest merge Poaceae floret into floret, so ear floret will be a direct child of floret.'' | + | '''x''' ''suggest merge Poaceae floret into floret, so ear floret will be a direct child of floret.'' |
===PO:0006470 Zea carpel (0)=== | ===PO:0006470 Zea carpel (0)=== | ||
| Line 262: | Line 271: | ||
-silk, Zea ovary and Zea stigma are part | -silk, Zea ovary and Zea stigma are part | ||
| − | ''suggest merge into Poaceae carpel, then into carpel. Part_of children will also merge with more generic terms.'' | + | '''x''' ''suggest merge into Poaceae carpel, then into carpel. Part_of children will also merge with more generic terms.'' |
===PO:0006486 Zea ovary (0)=== | ===PO:0006486 Zea ovary (0)=== | ||
| Line 272: | Line 281: | ||
-Zea funicle, Zea ovary placenta, and Zea ovule are part_of | -Zea funicle, Zea ovary placenta, and Zea ovule are part_of | ||
| − | ''Suggest merging into poaceae ovary, and poaceae ovary into ovary. Will be part of carpel. Part_of children will merge into their parents.'' | + | '''x''' ''Suggest merging into poaceae ovary, and poaceae ovary into ovary. Will be part of carpel. Part_of children will merge into their parents.'' |
===PO:0006487 Zea stigma (56)=== | ===PO:0006487 Zea stigma (56)=== | ||
| Line 282: | Line 291: | ||
-no children | -no children | ||
| − | ''suggest merge with Poaceae stigma then with stigma. remove part_of Zea carpel relation.'' | + | '''x''' ''suggest merge with Poaceae stigma then with stigma. remove part_of Zea carpel relation.'' |
===PO:0006488 silk (56)=== | ===PO:0006488 silk (56)=== | ||
| Line 302: | Line 311: | ||
-Zea chalaza, Zea integument, and Zea nucellus are part_of | -Zea chalaza, Zea integument, and Zea nucellus are part_of | ||
| − | ''suggest merge with Poaceae ovule, then ovule. merge part_of children with their parents.'' | + | '''x''' ''suggest merge with Poaceae ovule, then ovule. merge part_of children with their parents.'' |
===PO:0006506 Zea chalaza (0)=== | ===PO:0006506 Zea chalaza (0)=== | ||
| Line 320: | Line 329: | ||
-no is_a children | -no is_a children | ||
| − | ''suggest merge with Poaceae integument, then integument. merge Zea ovule into ovule.'' | + | '''x''' ''suggest merge with Poaceae integument, then integument. merge Zea ovule into ovule.'' |
===PO:0006492 Zea nucellus (0)=== | ===PO:0006492 Zea nucellus (0)=== | ||
| Line 330: | Line 339: | ||
-Zea megasporocyte is part_of | -Zea megasporocyte is part_of | ||
| − | ''suggest merge with Poaceae nucellus, then nucellus. merge Zea ovule into ovule. Zea megasporocyte will merge with megasporocyte.'' | + | '''x''' ''suggest merge with Poaceae nucellus, then nucellus. merge Zea ovule into ovule. Zea megasporocyte will merge with megasporocyte.'' |
===PO:0006493 Zea megasporocyte (0)=== | ===PO:0006493 Zea megasporocyte (0)=== | ||
| Line 340: | Line 349: | ||
-Zea megaspore develops from | -Zea megaspore develops from | ||
| − | ''suggest merge with Poaceae megasporocyte, then megasporocyte. merge Zea ovule into ovule. Zea megaspore will merge with megaspore.'' | + | '''x''' ''suggest merge with Poaceae megasporocyte, then megasporocyte. merge Zea ovule into ovule. Zea megaspore will merge with megaspore.'' |
===PO:0006494 Zea megaspore (0)=== | ===PO:0006494 Zea megaspore (0)=== | ||
| Line 350: | Line 359: | ||
-no children | -no children | ||
| − | ''suggest merge with Poaceae megaspore, then megaspore. Zea megaspore will merge with megaspore.'' | + | '''x''' ''suggest merge with Poaceae megaspore, then megaspore. Zea megaspore will merge with megaspore.'' |
===PO:0006489 Zea funicle (0)=== | ===PO:0006489 Zea funicle (0)=== | ||
| Line 397: | Line 406: | ||
===PO:0006383 Poaceae androecium (0)=== | ===PO:0006383 Poaceae androecium (0)=== | ||
| − | Merge into PO:0009061 androecium | + | '''x''' Merge into PO:0009061 androecium |
===PO:0006442 Poaceae anther (6)=== | ===PO:0006442 Poaceae anther (6)=== | ||
| Line 409: | Line 418: | ||
===PO:0006455 Poaceae carpel (3)=== | ===PO:0006455 Poaceae carpel (3)=== | ||
| − | Merge into PO:0009030 carpel | + | '''x''' Merge into PO:0009030 carpel |
===PO:0006458 Poaceae chalaza (0)=== | ===PO:0006458 Poaceae chalaza (0)=== | ||
| − | Merge into PO:0006506 chalaza | + | '''x''' Merge into PO:0006506 chalaza |
===PO:0006443 Poaceae connective (0)=== | ===PO:0006443 Poaceae connective (0)=== | ||
| Line 421: | Line 430: | ||
===PO:0006495 Poaceae degenerate megaspore (0)=== | ===PO:0006495 Poaceae degenerate megaspore (0)=== | ||
| − | Merge into PO:0000245 degenerate megaspore | + | '''x''' Merge into PO:0000245 degenerate megaspore |
===PO:0006446 Poaceae endothecium (1)=== | ===PO:0006446 Poaceae endothecium (1)=== | ||
| Line 437: | Line 446: | ||
===PO:0006318 Poaceae floret (71)=== | ===PO:0006318 Poaceae floret (71)=== | ||
| − | Merge into floret | + | '''x''' Merge into floret |
===PO:0006329 Poaceae floret meristem (1)=== | ===PO:0006329 Poaceae floret meristem (1)=== | ||
| − | Merge into flower meristem | + | '''x''' Merge into flower meristem |
| + | |||
| + | Also merged '''ear floret meristem (PO:0006373)''' and '''tassel floret meristem (PO:0006374)''' into flower meristem. | ||
===PO:0006496 Poaceae functional megaspore (0)=== | ===PO:0006496 Poaceae functional megaspore (0)=== | ||
| − | Merge into PO:0000244 functional megaspore | + | '''x''' Merge into PO:0000244 functional megaspore |
===PO:0006466 Poaceae funicle (0)=== | ===PO:0006466 Poaceae funicle (0)=== | ||
| Line 453: | Line 464: | ||
===PO:0006384 Poaceae gynoecium (3)=== | ===PO:0006384 Poaceae gynoecium (3)=== | ||
| − | Merge into PO:0025088 gynoecium | + | '''x''' Merge into PO:0025088 gynoecium |
===PO:0025086 Poaceae gynoecium ridge (0)=== | ===PO:0025086 Poaceae gynoecium ridge (0)=== | ||
| − | Merge into PO:0009062 gynoecium ridge | + | '''x''' Merge into PO:0009062 gynoecium ridge |
===PO:0006000 Poaceae hull (11)=== | ===PO:0006000 Poaceae hull (11)=== | ||
Keep, and rename "hull"? Conflicts with other uses of the word hull. Need a better name. | Keep, and rename "hull"? Conflicts with other uses of the word hull. Need a better name. | ||
| + | |||
| + | '''x''' Renamed "caryopsis hull". | ||
===PO:0006460 Poaceae inner integument (0)=== | ===PO:0006460 Poaceae inner integument (0)=== | ||
| − | Merge into PO:0020022 inner integument | + | '''x''' Merge into PO:0020022 inner integument |
===PO:0006465 Poaceae integument (3)=== | ===PO:0006465 Poaceae integument (3)=== | ||
| − | Merge into PO:0020021 integument | + | '''x''' Merge into PO:0020021 integument |
===PO:0006508 Poaceae integument epidermis (1)=== | ===PO:0006508 Poaceae integument epidermis (1)=== | ||
| − | Merge into PO:0006043 integument epidermis | + | '''x''' Merge into PO:0006043 integument epidermis |
===PO:0006464 Poaceae megaspore (1)=== | ===PO:0006464 Poaceae megaspore (1)=== | ||
| − | Merge into PO:0020019 megaspore | + | '''x''' Merge into PO:0020019 megaspore |
===PO:0006463 Poaceae megasporocyte (2)=== | ===PO:0006463 Poaceae megasporocyte (2)=== | ||
| − | Merge into PO:0000431 megasporocyte | + | '''x''' Merge into PO:0000431 megasporocyte |
===PO:0006461 Poaceae micropyle (0)=== | ===PO:0006461 Poaceae micropyle (0)=== | ||
| − | Merge into PO:0020025 micropyle | + | '''x''' Merge into PO:0020025 micropyle |
===PO:0006444 Poaceae microsporangium (2)=== | ===PO:0006444 Poaceae microsporangium (2)=== | ||
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===PO:0006462 Poaceae nucellus (2)=== | ===PO:0006462 Poaceae nucellus (2)=== | ||
| − | Merge into PO:0020020 nucellus | + | '''x''' Merge into PO:0020020 nucellus |
===PO:0006459 Poaceae outer integumet (0)=== | ===PO:0006459 Poaceae outer integumet (0)=== | ||
| − | Merge into PO:0020023 outer integumet | + | '''x''' Merge into PO:0020023 outer integumet |
Need to fix spelling of this term (integumeNt) | Need to fix spelling of this term (integumeNt) | ||
| Line 511: | Line 524: | ||
===PO:0006456 Poaceae ovary (1)=== | ===PO:0006456 Poaceae ovary (1)=== | ||
| − | Merge into PO:0009072 ovary | + | '''x''' Merge into PO:0009072 ovary |
===PO:0006500 Poaceae ovary epidermis (0)=== | ===PO:0006500 Poaceae ovary epidermis (0)=== | ||
| − | Merge into PO:0006063 ovary epidermis | + | '''x''' Merge into PO:0006063 ovary epidermis |
===PO:0006467 Poaceae ovary placenta (0)=== | ===PO:0006467 Poaceae ovary placenta (0)=== | ||
| Line 523: | Line 536: | ||
===PO:0006457 Poaceae ovule (5)=== | ===PO:0006457 Poaceae ovule (5)=== | ||
| − | Merge into PO:0020003 ovule | + | '''x''' Merge into PO:0020003 ovule |
===PO:0006448 Poaceae placentoid (0)=== | ===PO:0006448 Poaceae placentoid (0)=== | ||
| Line 535: | Line 548: | ||
===PO:0006468 Poaceae stigma (0)=== | ===PO:0006468 Poaceae stigma (0)=== | ||
| − | Merge into PO:0009073 stigma | + | '''x''' Merge into PO:0009073 stigma |
===PO:0006497 Poaceae stigma epidermis (3)=== | ===PO:0006497 Poaceae stigma epidermis (3)=== | ||
| Line 545: | Line 558: | ||
'''x''' Merge into PO:0020101 stomium | '''x''' Merge into PO:0020101 stomium | ||
| − | ===PO:0006469 Poaceae style (100 | + | ===PO:0006469 Poaceae style (100)=== |
'''x''' Merge into PO:0009074 style | '''x''' Merge into PO:0009074 style | ||
| Line 570: | Line 583: | ||
See SF tracker for [http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 infloresence visible] | See SF tracker for [http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 infloresence visible] | ||
| + | |||
| + | Merged Poaceae inflorescence visible (PO:0007012) into 3 inflorescence detectable phase (PO:0007047) and made booting (PO:0007014) a subtype of IL.00 inflorescence just visible phase (PO:0007006) | ||
==Plant G&D stages with Zea in the name:== | ==Plant G&D stages with Zea in the name:== | ||
| Line 581: | Line 596: | ||
===PO:0006337 inflorescence bract of ear (26)=== | ===PO:0006337 inflorescence bract of ear (26)=== | ||
| − | Merge this into PO:0009054 inflorescence bract. Mary is already putting the new annotations for husk on PO:0009054. | + | '''x''' Merge this into PO:0009054 inflorescence bract. Mary is already putting the new annotations for husk on PO:0009054. |
==merge into PO:0009061 androecium== | ==merge into PO:0009061 androecium== | ||
| + | No annotations directly on any of these terms. | ||
| + | |||
PO:0006355 androecium of ear floret | PO:0006355 androecium of ear floret | ||
| Line 607: | Line 624: | ||
==merge into gynoecium== | ==merge into gynoecium== | ||
| + | No annotations directly on any of these terms. | ||
| + | |||
| + | PO:0006384 Poaceae gynoecium | ||
| + | |||
PO:0006365 gynoecium of ear floret | PO:0006365 gynoecium of ear floret | ||
| Line 626: | Line 647: | ||
PO:0006394 gynoecium of upper floret of sessile spikelet of tassel | PO:0006394 gynoecium of upper floret of sessile spikelet of tassel | ||
| + | |||
| + | '''Done. See below for comment.''' | ||
==merge into lemma== | ==merge into lemma== | ||
| + | No annotations directly on any of these terms. | ||
PO:0006363 lemma of ear floret | PO:0006363 lemma of ear floret | ||
| Line 648: | Line 672: | ||
PO:0006395 lemma of upper floret of sessile spikelet of tassel | PO:0006395 lemma of upper floret of sessile spikelet of tassel | ||
| + | |||
| + | '''Done. Also changed definition and added comment. See [https://sourceforge.net/tracker/?func=detail&aid=3400245&group_id=76834&atid=835555 SF tracker].''' | ||
==merge into lodicule PO:0009036 (6)== | ==merge into lodicule PO:0009036 (6)== | ||
| Line 658: | Line 684: | ||
==merge into palea== | ==merge into palea== | ||
| + | No annotations directly on any of these terms. | ||
PO:0006361 palea of ear floret | PO:0006361 palea of ear floret | ||
| Line 678: | Line 705: | ||
PO:0006401 palea of upper floret of sessile spikelet of tassel | PO:0006401 palea of upper floret of sessile spikelet of tassel | ||
| + | |||
| + | '''Done''' | ||
| + | |||
| + | New definition: A flower bract that is part of a spikelet and is the | ||
| + | upper/distal of two bracts enclosing a spikelet floret. | ||
| + | |||
| + | Comment: Found in Poaceae such as Zea mays. Possibly a prophyll/bracteole. A palea subtends an individual floret while glumes subtend the pair of florets. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311). | ||
| + | |||
| + | See [https://sourceforge.net/tracker/index.php?func=detail&aid=3400245&group_id=76834&atid=835555 SF tracker] | ||
| + | |||
| + | ==glume== | ||
| + | There are already annotations on glume of ear spikelet and glume of tassel spikelet, so suggest we should keep these terms. | ||
| + | |||
| + | Also suggest fixing dual parentage by using cross-product definitions for glume of ear spikelet and glume of tassel spikelet. | ||
| + | |||
| + | '''x''' ''Kept descendants of glume. Eliminated dual parentage and changed definitions, as described below.'' | ||
| + | |||
| + | Current: | ||
| + | |||
| + | [[File:glume.jpg]] | ||
| + | |||
| + | Proposed (without merging): | ||
| + | |||
| + | [[File:glume2.jpg]] | ||
| + | |||
| + | |||
| + | ===Changes=== | ||
| + | '''glume (PO:0009039, PO:0006026)''' | ||
| + | |||
| + | current def: A "bract" in the inflorescence of a grass, sedge or similar plant. | ||
| + | |||
| + | proposed def: One of a pair of inflorescence bracts that is part of a spikelet and subtends the two florets. | ||
| + | |||
| + | Comment: Found in Poaceae and Cyperaceae. Glumes subtends the pair of florets while a lemma or palea subtend the individual florets. | ||
| + | |||
| + | |||
| + | '''glume of ear spikelet (PO:0006367)''' | ||
| + | |||
| + | current def: A bract in the ear inflorescence of a maize plant, subtending two florets. | ||
| + | |||
| + | proposed def: A glume that is part of an ear spikelet. | ||
| + | |||
| + | intersection_of: is_a glume and part_of ear spikelet | ||
| + | |||
| + | |||
| + | '''glume of tassel spikelet (PO:0006368)''' | ||
| + | |||
| + | current def: A bract in the tassel inflorescence of a maize plant, subtending two florets. | ||
| + | |||
| + | proposed def: A glume that is part of a tassel spikelet. | ||
| + | |||
| + | intersection_of: is_a glume and part_of tassel spikelet | ||
==keep for now== | ==keep for now== | ||
| Line 732: | Line 811: | ||
===Add comments to the following terms:=== | ===Add comments to the following terms:=== | ||
| − | + | ====androecium and parts==== | |
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| − | + | Complete androecium development in Maize normally occurs only in tassel florets, so for anther and its parts and filament, only listed tassel floret types in comments. Because there may be rudimentary development of the androecium in all floret types, listed all floret types in comment for stamen and androecium. There is nothing to stop people from annotating to other floret types for mutants. | |
| − | PO: | + | '''PO:0009061 androecium and PO:0009029 stamen'''(first part only for stamen): ''If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). The development of an androecium in an ear floret of a normal maize plant is aborted and is present in a rudimentary state, while the development of an androecium in a tassel floret leads to a functional androecium.'' |
| − | |||
| − | PO: | + | '''terms:''' PO:0009066 anther, PO:0000002 anther wall, PO:0009068 connective, PO:0020002 anther wall endothecium, PO:0020004 anther wall exothecium, PO:0009067 filament, PO:0025277 pollen sac, PO:0020048 microspore, PO:0020047 microsporocyte, PO:0006448 placentoid, PO:0020101 stomium, PO:0009071 anther wall tapetum, PO:0009069 anther theca |
| − | PO: | + | '''comment:''' If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). |
| − | + | ====lemma, palea==== | |
| − | + | Lemma and palea are part_of spikelet floret, but an annotation can also be made to the more specific floret type. | |
| − | PO: | + | ''Found in Poaceae such as Zea mays. A lemma and a palea enclose an individual floret while glumes subtend a pair of florets. Lemma/palea is part_of spikelet floret, but if you are annotating to this structure for Zea mays or other similar grasses, an annotation can also be made to the more specific floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).'' |
| − | PO: | + | ====flower meristem (PO:0000229)==== |
| − | + | In grasses, the flower meristem (floret meristem) is part of a spikelet and it develops into a floret. | |
| − | |||
| − | PO: | + | ''In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).'' |
| − | + | An additional annotation can be added for the type of floret the meristem will develop into, if we had a develops_into relation, but we don't! | |
| − | + | ====ovary and parts==== | |
| + | For ovary and its parts, in the comment, I only included the types of florets that normally have fully developed gynoecia: | ||
| − | PO:0020003 ovule | + | '''Terms:''' PO:0020006 funicle, PO:0020022 inner integument, PO:0020021 integument, PO:0006043 integument epidermis, PO:0020023 outer integument, PO:0006045 outer integument epidermis, PO:0006044 inner integument epidermis, PO:0006506 chalaza, PO:0020001 ovary placenta, PO:0000245 degenerate megaspore, PO:0000244 functional megaspore, PO:0020019 megaspore, PO:0000431 megasporocyte, PO:0020020 nucellus, PO:0009072 ovary, PO:0006063 ovary epidermis, PO:0020003 ovule, micropyle (PO:0020025), PO:0020102 portion of transmitting tissue |
| + | |||
| − | PO: | + | '''Comment:''' ''If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).'' |
| − | + | ====gynoecium and parts==== | |
| − | + | For carpel (including stigma, style, stigma epidermis, and style epidermis), in the comment, I included the upper florets of both ears and tassels, because occasionally gynoecia develop there. | |
| − | + | '''Terms:''' PO:0009030 carpel, PO:0009074 style, PO:0009073 stigma, PO:0006062 style epidermis, PO:0006061 stigma epidermis | |
| − | PO: | + | '''Comment:''' ''If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).'' |
| − | |||
| − | |||
| − | PO: | + | '''PO:0025088 gynoecium''' ''In some cases the gynoecium may consist of only one carpel. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).'' |
| − | |||
| − | PO: | + | '''PO:0009062 gynoecium ridge''' ''Common in monocots, including species of Poaceae such as Zea mays. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). In Zea mays, development of the gynoecium ridge of the upper floret of pedicellate spikelet of ear occurs via continued overgrowth of the shoot apex (which becomes the ovule primordium) by a ring of gynoecial tissue, leading to the formation of a stylar canal that is detected as a slight protuberance on the mature ovary. Early development of the gynoecium ridge of the lower floret of pedicellate spikelet of ear is very similar to that of the upper floret of the pedicellate spikelet of ear, except the development does not proceed beyond the early ridge stage.'' |
Latest revision as of 01:22, 9 December 2011
Back to Summary_of_Changes to PO October 2011
Annotations
If one term is merged with another, one of the IDs becomes a synonym (alt_id:PO:XXXXXXX) under the ID of the target term.
However, the annotations do not automatically move to the target term, they have to be moved manually.
We suggest running a check for annotations associated with alternate IDs with each new release, to make sure no merged terms were missed.
See list of Poaceae/Zea terms with annotations
Existing terms
(as of 7/2011)
Plant anatomical entities with Zea in the name (28):
(x indicates that the merge has already been done)
Male parts:
PO:0020126 tassel (~150)
-is_a inflorescence
-five part_of children
suggest that we keep this term and it's part_of children. Mary suggested giving it a more generic name, like "functionally male inflorescence"
x At the POC_Conf._Call_8-23-11 we decided to rename this term "tassel inflorescence".
PO:0006309 tassel spikelet (0)
-is_a spikelet
-part_of tassel
-develops_from spikelet pair meristem
-has 2 is_a and three part_of children, including tassel floret
suggest that we keep this term and it's children. Mary suggested giving it a more generic name, like "functionally male inflorescence spikelet"
x Kept as is.
PO:0006310 tassel floret (0)
-is_a Poaceae floret
-part_of tassel spikelet
-four is_a children:
PO:0006313 : lower floret of pedicellate spikelet of tassel (0)
PO:0006315 : lower floret of sessile spikelet of tassel (0)
PO:0006314 : upper floret of pedicellate spikelet of tassel (0)
PO:0006316 : upper floret of sessile spikelet of tassel (0)
-five part_of children:
PO:0006366 : androecium of tassel floret (0)
PO:0006317 : gynoecium of tassel floret (0)
PO:0006356 : lemma of tassel floret (0)
PO:0006381 : lodicule of tassel floret (0)
PO:0006359 : palea of tassel floret (0)
suggest keep this term, make it a direct child of floret (will happen when we merge Poaceae floret with floret.
suggest keeping the is_a children (PO:0006313-16)
suggest merging all of the part_of children with their is_a parent: androecium of tassel floret with Poaceae androecium,, lemma of tassel floret with lemma, etc. -- see below under Eliminating_Zea/Poaceae_terms_from_PO#Other_Poaceae-specific_terms.
PO:0006471 Zea androecium (0)
-is_a Poaceae androecium, not part_of anything
-has children androecium of ear floret and androecium of tassel floret (plus their children)
-Zea stamen is part_of
x suggest merge this term plus all of its descendants into Poaceae androecium, then into androcium. Zea stamen will be merge into stamen.
PO:0006472 Zea stamen (1)
-is_a Poaceae stamen
-part_of androecium of tassel floret
-Zea anther and Zea filament are part_of
x suggest merge into Poaceae stamen, then into stamen. remove part_of androecium of tassel floret relation (stamen is part of androecium). Zea anther and Zea filament will be merged with their parent terms.
annotation for Zea stamen will move to stamen. Should also add annotation for tassel floret.
PO:0006473 Zea anther (363)
-is_a Poaceae anther
-part_of Zea stamen
-Zea connective and Zea microsporangium are part_of
x suggest merge into Poaceae anther, then into anther. remove part_of Zea stamen relation (anther is part of stamen). Zea connective and Zea microsporangium will be merged with their parent terms.
annotations for Zea anther will move to stamen. Should also add annotations for tassel floret.
PO:0006474 Zea filament (0)
-is_a Poaceae filament
-part_of Zea stamen
-no children
x suggest merge into Poaceae filament, then into filament. remove part_of Zea stamen relation.
PO:0006475 Zea connective (0)
-is_a Poaceae connective
-part_of Zea anther
-no children
x suggest merge into Poaceae connective, then into connective. remove part_of Zea anther relation.
PO:0006477 Zea anther wall (0)
-is_a Zea anther wall
-part_of Zea microsporangium
-Zea endothecium, Zea exothecium, Zea placentoid, Zea stomium, and Zea tapetum are parts
x suggest merge into Poaceae anther wall, then into anther wall. remove part_of Zea microsporangium relation. Child terms will be merged into their parents.
PO:0006481 Zea endothecium (0)
-is_a Poaceae endothecium
-part_of Zea anther wall
-no children
x suggest merge into Poaceae endothecium, then into anther wall endothecium. remove part_of Zea anther wall relation.
PO:0006482 Zea exothecium (0)
-is_a Poaceae exothecium
-part_of Zea anther wall
-no children
x suggest merge into Poaceae exothecium, then into anther wall exothecium. remove part_of Zea anther wall relation.
PO:0006484 Zea tapetum (0)
-is_a Poaceae tapetum
-part_of Zea anther wall
-no children
x suggest merge into Poaceae tapetum, then into anther wall tapetum. remove part_of Zea anther wall relation.
PO:0006483 Zea placentoid (0)
-is_a Poaceae placentoid
-part_of Zea anther wall
-no children
x suggest merge into Poaceae placentoid, then into placentoid. remove part_of Zea anther wall relation.
PO:0006485 Zea stomium (0)
-is_a Poaceae stomium
-part_of Zea anther wall
-no children
x suggest merge into Poaceae stomium, then into stomium. remove part_of Zea anther wall relation.
PO:0006478 Zea theca (0)
-is_a Poaceae theca
-is_a Zea microsporangium
x suggest merge into Poaceae theca, then into anther theca. remove is_a Zea microsporangium relation, because anther theca is now a collective plant structure.
PO:0006476 Zea microsporangium (0)
-is_a Poaceae microsporangium
-part_of Zea anther
-Zea theca is_a Zea microsporangium
-Zea anther wall and Zea microsporocyte are part_of
x suggest merge into Poaceae microsporangium, then into microsporangium. remove Zea theca is_a Zea microsporangium relation. part_of children will merge into their parent terms.
PO:0006479 Zea microsporocyte (0)
-is_a Poaceae microsporocyte
-part_of Zea microsporangium
-Zea microspore develops_from
x suggest merge into Poaceae microsporocyte, then into microsporocyte. remove part_of Zea microsporangium relation. Zea microspore will merge into microspore, which develops_from microsporocyte.
PO:0006480 Zea microspore (0)
-is_a Poaceae microspore
-develops_from Zea microsporocyte
-no children
x suggest merge into Poaceae microspore, then into microspore. remove develops_from Zea microsporocyte relation.
female parts:
PO:0020136 Zea ear (56)
-is_a inflorescence
-central spike of ear, ear meristem, ear peduncle, ear spikelet and infloreacence bract of ear are part
Should ear meristem be part_of ear, or should it be ear develops_from ear meristem?
suggest renaming "ear", then it would be like tassel (PO:0020126). Mary suggested giving it a more generic name, like "functionally female inflorescence"
x At the POC_Conf._Call_8-23-11 we decided to rename this term "ear inflorescence".
PO:0006320 ear spikelet (0)
-is_a spikelet, part_of ear
Okay as is. Could give it a more generic name, like "functionally female inflorescence spikelet".
x Kept as is.
PO:0006354 ear floret (0)
-is_a Poaceae floret
-part_of ear spikelet
-androecium of ear floret, gynoecium of ear floret, lemma of ear floret, lodicule of ear floret, and 5 other parts are part_of
x suggest merge Poaceae floret into floret, so ear floret will be a direct child of floret.
PO:0006470 Zea carpel (0)
-is_a Poaceae carpel
-part_of gynoecium of ear floret
-silk, Zea ovary and Zea stigma are part
x suggest merge into Poaceae carpel, then into carpel. Part_of children will also merge with more generic terms.
PO:0006486 Zea ovary (0)
-is_a Poaceae ovary
-part_of Zea carpel
-Zea funicle, Zea ovary placenta, and Zea ovule are part_of
x Suggest merging into poaceae ovary, and poaceae ovary into ovary. Will be part of carpel. Part_of children will merge into their parents.
PO:0006487 Zea stigma (56)
-is_a Poaceae stigma
-part_of Zea carpel
-no children
x suggest merge with Poaceae stigma then with stigma. remove part_of Zea carpel relation.
PO:0006488 silk (56)
-is_a Poaceae style
-part_of Zea carpel
-no children
x suggest merge with Poaceae style then with style. remove part_of Zea carpel relation.
PO:0006491 Zea ovule (0)
-is_a Poaceae ovule
-part_of Zea ovary
-Zea chalaza, Zea integument, and Zea nucellus are part_of
x suggest merge with Poaceae ovule, then ovule. merge part_of children with their parents.
PO:0006506 Zea chalaza (0)
-is_a Poaceae chalaza
-part_of Zea ovule
x suggest merge with Poaceae chalza, then chalaza. merge Zea ovule into ovule.
PO:0006507 Zea integument (0)
-is_a Poaceae integument
-part_of Zea ovule
-no is_a children
x suggest merge with Poaceae integument, then integument. merge Zea ovule into ovule.
PO:0006492 Zea nucellus (0)
-is_a Poaceae nucellus
-part_of Zea ovule
-Zea megasporocyte is part_of
x suggest merge with Poaceae nucellus, then nucellus. merge Zea ovule into ovule. Zea megasporocyte will merge with megasporocyte.
PO:0006493 Zea megasporocyte (0)
-is_a Poaceae megasporocyte
-part_of Zea ovule
-Zea megaspore develops from
x suggest merge with Poaceae megasporocyte, then megasporocyte. merge Zea ovule into ovule. Zea megaspore will merge with megaspore.
PO:0006494 Zea megaspore (0)
-is_a Poaceae megaspore
-develops_from Zea megasporocyte
-no children
x suggest merge with Poaceae megaspore, then megaspore. Zea megaspore will merge with megaspore.
PO:0006489 Zea funicle (0)
-is_a Poaceae funicle
-part_of Zea ovary
-no children
x suggest merge with Poaceae funicle, then funicle. merge Zea ovary into ovary.
PO:0006490 Zea ovary placenta (0)
-is_a Poaceae ovary placenta
-part_of Zea ovary
-no children
x suggest merge with Poaceae ovary placenta, then ovary placenta. merge Zea ovary into ovary.
PO:0025087 Zea gynoecium ridge (0)
-is_a Poaceae gynoecium ridge
-is_a gynoecium of ear floret
-has four children:
PO:0009024 : gynoecium ridge of lower floret of pedicellate spikelet of ear (0)
PO:0009076 : gynoecium ridge of lower floret of sessile spikelet of ear (0)
PO:0009079 : gynoecium ridge of upper floret of pedicellate spikelet of ear (0)
PO:0009092 : gynoecium ridge of upper floret of sessile spikelet of ear (0)
x suggest that each of the four children be merged into Zea gynoecium ridge, then Zea gynoecium ridge be merged into Poaceae gynoecium ridge then into gynoecium ridge. Also need to remove the is_a relationship between each of these and their respective gynoecia. need to condense merged comments
Plant anatomical entities with Poaceae in the name (42):
(x indicates that the merge has already been done)
PO:0006383 Poaceae androecium (0)
x Merge into PO:0009061 androecium
PO:0006442 Poaceae anther (6)
x Merge into PO:0009066 anther
PO:0006445 Poaceae anther wall (2)
x Merge into PO:0000002 anther wall
PO:0006455 Poaceae carpel (3)
x Merge into PO:0009030 carpel
PO:0006458 Poaceae chalaza (0)
x Merge into PO:0006506 chalaza
PO:0006443 Poaceae connective (0)
x Merge into PO:0009068 connective
PO:0006495 Poaceae degenerate megaspore (0)
x Merge into PO:0000245 degenerate megaspore
PO:0006446 Poaceae endothecium (1)
x Merge into PO:0020002 anther wall endothecium
PO:0006447 Poaceae exothecium (0)
x Merge into PO:0020004 anther wall exothecium
PO:0006454 Poaceae filament (0)
x Merge into PO:0009067 filament
PO:0006318 Poaceae floret (71)
x Merge into floret
PO:0006329 Poaceae floret meristem (1)
x Merge into flower meristem
Also merged ear floret meristem (PO:0006373) and tassel floret meristem (PO:0006374) into flower meristem.
PO:0006496 Poaceae functional megaspore (0)
x Merge into PO:0000244 functional megaspore
PO:0006466 Poaceae funicle (0)
x Merge into PO:0020006 funicle
PO:0006384 Poaceae gynoecium (3)
x Merge into PO:0025088 gynoecium
PO:0025086 Poaceae gynoecium ridge (0)
x Merge into PO:0009062 gynoecium ridge
PO:0006000 Poaceae hull (11)
Keep, and rename "hull"? Conflicts with other uses of the word hull. Need a better name.
x Renamed "caryopsis hull".
PO:0006460 Poaceae inner integument (0)
x Merge into PO:0020022 inner integument
PO:0006465 Poaceae integument (3)
x Merge into PO:0020021 integument
PO:0006508 Poaceae integument epidermis (1)
x Merge into PO:0006043 integument epidermis
PO:0006464 Poaceae megaspore (1)
x Merge into PO:0020019 megaspore
PO:0006463 Poaceae megasporocyte (2)
x Merge into PO:0000431 megasporocyte
PO:0006461 Poaceae micropyle (0)
x Merge into PO:0020025 micropyle
PO:0006444 Poaceae microsporangium (2)
x Merge into PO:0025277 pollen sac
PO:0006452 Poaceae microspore (22)
x Merge into PO:0020048 microspore
PO:0006451 Poaceae microsporocyte (1)
x Merge into PO:0020047 microsporocyte
PO:0006462 Poaceae nucellus (2)
x Merge into PO:0020020 nucellus
PO:0006459 Poaceae outer integumet (0)
x Merge into PO:0020023 outer integumet
Need to fix spelling of this term (integumeNt)
PO:0006456 Poaceae ovary (1)
x Merge into PO:0009072 ovary
PO:0006500 Poaceae ovary epidermis (0)
x Merge into PO:0006063 ovary epidermis
PO:0006467 Poaceae ovary placenta (0)
x Merge into PO:0020001 ovary placenta
PO:0006457 Poaceae ovule (5)
x Merge into PO:0020003 ovule
PO:0006448 Poaceae placentoid (0)
x Merge into PO:0006448 placentoid
PO:0006441 Poaceae stamen (7)
x Merge into PO:0009029 stamen
PO:0006468 Poaceae stigma (0)
x Merge into PO:0009073 stigma
PO:0006497 Poaceae stigma epidermis (3)
x Merge into PO:0006061 stigma epidermis
PO:0006449 Poaceae stomium (1)
x Merge into PO:0020101 stomium
PO:0006469 Poaceae style (100)
x Merge into PO:0009074 style
PO:0006498 Poaceae style epidermis (0)
x Merge into PO:0006062 style epidermis
PO:0006450 Poaceae tapetum (3)
x Merge into PO:0009071 anther wall tapetum
PO:0006453 Poaceae theca (0)
x Merge into PO:0009069 anther theca
PO:0006499 Poaceae transmitting tissue (0)
x Merge into PO:0020102 portion of transmitting tissue
Plant G&D stages with Poaceae in the name:
PO:0007012 Poaceae inflorescence visible
See SF tracker for 3 infloresence visible
Merged Poaceae inflorescence visible (PO:0007012) into 3 inflorescence detectable phase (PO:0007047) and made booting (PO:0007014) a subtype of IL.00 inflorescence just visible phase (PO:0007006)
Plant G&D stages with Zea in the name:
None
Other Poaceae-specific terms
These terms don't have Zea or Poaceae in the name, but should probably be merged as well:
PO:0006337 inflorescence bract of ear (26)
x Merge this into PO:0009054 inflorescence bract. Mary is already putting the new annotations for husk on PO:0009054.
merge into PO:0009061 androecium
No annotations directly on any of these terms.
PO:0006355 androecium of ear floret
PO:0006419 androecium of lower floret of pedicellate spikelet of ear
PO:0006406 androecium of lower floret of pedicellate spikelet of tassel
PO:0006420 androecium of lower floret of sessile spikelet of ear
PO:0006393 androecium of lower floret of sessile spikelet of tassel
PO:0006366 androecium of tassel floret
PO:0006422 androecium of upper floret of pedicellate spikelet of ear
PO:0006405 androecium of upper floret of pedicellate spikelet of tassel
PO:0006421 androecium of upper floret of sessile spikelet of ear
PO:0006392 androecium of upper floret of sessile spikelet of tassel
done - merged into Zea androecium, then Poaceae androecium, then into androecium
merge into gynoecium
No annotations directly on any of these terms.
PO:0006384 Poaceae gynoecium
PO:0006365 gynoecium of ear floret
PO:0006424 gynoecium of lower floret of pedicellate spikelet of ear
PO:0006403 gynoecium of lower floret of pedicellate spikelet of tassel
PO:0006423 gynoecium of lower floret of sessile spikelet of ear
PO:0006391 gynoecium of lower floret of sessile spikelet of tassel
PO:0006317 gynoecium of tassel floret
PO:0006426 gynoecium of upper floret of pedicellate spikelet of ear
PO:0006404 gynoecium of upper floret of pedicellate spikelet of tassel
PO:0006425 gynoecium of upper floret of sessile spikelet of ear
PO:0006394 gynoecium of upper floret of sessile spikelet of tassel
Done. See below for comment.
merge into lemma
No annotations directly on any of these terms.
PO:0006363 lemma of ear floret
PO:0006431 lemma of lower floret of pedicellate spikelet of ear
PO:0006407 lemma of lower floret of pedicellate spikelet of tassel
PO:0006433 lemma of lower floret of sessile spikelet of ear
PO:0006397 lemma of lower floret of sessile spikelet of tassel
PO:0006356 lemma of tassel floret
PO:0006432 lemma of upper floret of pedicellate spikelet of ear
PO:0006409 lemma of upper floret of pedicellate spikelet of tassel
PO:0006434 lemma of upper floret of sessile spikelet of ear
PO:0006395 lemma of upper floret of sessile spikelet of tassel
Done. Also changed definition and added comment. See SF tracker.
merge into lodicule PO:0009036 (6)
PO:0006382 lodicule of ear floret (0)
PO:0006381 lodicule of tassel floret (0)
Done. Added comment to lodicule: If you are annotating to this structure for Zea mays, please also add an annotation to the corresponding floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
merge into palea
No annotations directly on any of these terms.
PO:0006361 palea of ear floret
PO:0006430 palea of lower floret of pedicellate spikelet of ear
PO:0006411 palea of lower floret of pedicellate spikelet of tassel
PO:0006428 palea of lower floret of sessile spikelet of ear
PO:0006399 palea of lower floret of sessile spikelet of tassel
PO:0006359 palea of tassel floret
PO:0006429 palea of upper floret of pedicellate spikelet of ear
PO:0006413 palea of upper floret of pedicellate spikelet of tassel
PO:0006427 palea of upper floret of sessile spikelet of ear
PO:0006401 palea of upper floret of sessile spikelet of tassel
Done
New definition: A flower bract that is part of a spikelet and is the upper/distal of two bracts enclosing a spikelet floret.
Comment: Found in Poaceae such as Zea mays. Possibly a prophyll/bracteole. A palea subtends an individual floret while glumes subtend the pair of florets. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding spikelet type. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
See SF tracker
glume
There are already annotations on glume of ear spikelet and glume of tassel spikelet, so suggest we should keep these terms.
Also suggest fixing dual parentage by using cross-product definitions for glume of ear spikelet and glume of tassel spikelet.
x Kept descendants of glume. Eliminated dual parentage and changed definitions, as described below.
Current:
Proposed (without merging):
Changes
glume (PO:0009039, PO:0006026)
current def: A "bract" in the inflorescence of a grass, sedge or similar plant.
proposed def: One of a pair of inflorescence bracts that is part of a spikelet and subtends the two florets.
Comment: Found in Poaceae and Cyperaceae. Glumes subtends the pair of florets while a lemma or palea subtend the individual florets.
glume of ear spikelet (PO:0006367)
current def: A bract in the ear inflorescence of a maize plant, subtending two florets.
proposed def: A glume that is part of an ear spikelet.
intersection_of: is_a glume and part_of ear spikelet
glume of tassel spikelet (PO:0006368)
current def: A bract in the tassel inflorescence of a maize plant, subtending two florets.
proposed def: A glume that is part of a tassel spikelet.
intersection_of: is_a glume and part_of tassel spikelet
keep for now
PO:0006353 lower floret of pedicellate spikelet of ear
PO:0006313 lower floret of pedicellate spikelet of tassel
PO:0006351 lower floret of sessile spikelet of ear
PO:0006315 lower floret of sessile spikelet of tassel
PO:0006350 upper floret of pedicellate spikelet of ear
PO:0006314 upper floret of pedicellate spikelet of tassel
PO:0006352 upper floret of sessile spikelet of ear
PO:0006316 upper floret of sessile spikelet of tassel
Comments for former zea and Poaceae terms that are part_of a floret
Once the specific Zea terms are merged with their parents, the resulting term will no longer have a part_of relation to ear floret or tassel floret (or their children). For example, Zea carpel is part_of gynoecium of ear floret, but once Zea carpel is merged with carpel and gynoecium of ear floret is merged with gynoecium, gynoecium will not be part of ear floret.
We could add a comment to the parts of flower: "If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316)."
For structures that don't occur in all of these floret types, will provide a limited set of choices.
Floret types:
PO:0009082 spikelet floret
PO:0006310 tassel floret
PO:0006354 ear floret
PO:0006353 lower floret of pedicellate spikelet of ear
PO:0006313 lower floret of pedicellate spikelet of tassel
PO:0006351 lower floret of sessile spikelet of ear
PO:0006315 lower floret of sessile spikelet of tassel
PO:0006350 upper floret of pedicellate spikelet of ear
PO:0006314 upper floret of pedicellate spikelet of tassel
PO:0006352 upper floret of sessile spikelet of ear
PO:0006316 upper floret of sessile spikelet of tassel
Add comments to the following terms:
androecium and parts
Complete androecium development in Maize normally occurs only in tassel florets, so for anther and its parts and filament, only listed tassel floret types in comments. Because there may be rudimentary development of the androecium in all floret types, listed all floret types in comment for stamen and androecium. There is nothing to stop people from annotating to other floret types for mutants.
PO:0009061 androecium and PO:0009029 stamen(first part only for stamen): If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316). The development of an androecium in an ear floret of a normal maize plant is aborted and is present in a rudimentary state, while the development of an androecium in a tassel floret leads to a functional androecium.
terms: PO:0009066 anther, PO:0000002 anther wall, PO:0009068 connective, PO:0020002 anther wall endothecium, PO:0020004 anther wall exothecium, PO:0009067 filament, PO:0025277 pollen sac, PO:0020048 microspore, PO:0020047 microsporocyte, PO:0006448 placentoid, PO:0020101 stomium, PO:0009071 anther wall tapetum, PO:0009069 anther theca
comment: If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
lemma, palea
Lemma and palea are part_of spikelet floret, but an annotation can also be made to the more specific floret type.
Found in Poaceae such as Zea mays. A lemma and a palea enclose an individual floret while glumes subtend a pair of florets. Lemma/palea is part_of spikelet floret, but if you are annotating to this structure for Zea mays or other similar grasses, an annotation can also be made to the more specific floret type, if known. Choose the most specific term possible from: ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
flower meristem (PO:0000229)
In grasses, the flower meristem (floret meristem) is part of a spikelet and it develops into a floret.
In Zea mays and other grasses, the floret meristem is part of a spikelet and develops into a specific type of floret. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the spikelet type that the meristem is part of. Choose the most specific term possible from: spikelet (PO:0009051), ear spikelet (PO:0006320), ear pedicellate spikelet (PO:0006348), ear sessile spikelet (PO:0006349), tassel spikelet (PO:0006309), tassel pedicellate spikelet (PO:0006312), tassel sessile spikelet (PO:0006311).
An additional annotation can be added for the type of floret the meristem will develop into, if we had a develops_into relation, but we don't!
ovary and parts
For ovary and its parts, in the comment, I only included the types of florets that normally have fully developed gynoecia:
Terms: PO:0020006 funicle, PO:0020022 inner integument, PO:0020021 integument, PO:0006043 integument epidermis, PO:0020023 outer integument, PO:0006045 outer integument epidermis, PO:0006044 inner integument epidermis, PO:0006506 chalaza, PO:0020001 ovary placenta, PO:0000245 degenerate megaspore, PO:0000244 functional megaspore, PO:0020019 megaspore, PO:0000431 megasporocyte, PO:0020020 nucellus, PO:0009072 ovary, PO:0006063 ovary epidermis, PO:0020003 ovule, micropyle (PO:0020025), PO:0020102 portion of transmitting tissue
Comment: If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352).
gynoecium and parts
For carpel (including stigma, style, stigma epidermis, and style epidermis), in the comment, I included the upper florets of both ears and tassels, because occasionally gynoecia develop there.
Terms: PO:0009030 carpel, PO:0009074 style, PO:0009073 stigma, PO:0006062 style epidermis, PO:0006061 stigma epidermis
Comment: If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
PO:0025088 gynoecium In some cases the gynoecium may consist of only one carpel. In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully, and they are present in a rudimentary state. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352), tassel floret (PO:0006310), lower floret of pedicellate spikelet of tassel (PO:0006313), lower floret of sessile spikelet of tassel (PO:0006315), upper floret of pedicellate spikelet of tassel (PO:0006314), upper floret of sessile spikelet of tassel (PO:0006316).
PO:0009062 gynoecium ridge Common in monocots, including species of Poaceae such as Zea mays. If you are annotating to this structure for Zea mays or other grasses, please also add an annotation to the corresponding floret type. Choose the most specific term possible from: spikelet floret (PO:0009082), ear floret (PO:0006354), lower floret of pedicellate spikelet of ear (PO:0006353), lower floret of sessile spikelet of ear (PO:0006351), upper floret of pedicellate spikelet of ear (PO:0006350), upper floret of sessile spikelet of ear (PO:0006352). In Zea mays, development of the gynoecium ridge of the upper floret of pedicellate spikelet of ear occurs via continued overgrowth of the shoot apex (which becomes the ovule primordium) by a ring of gynoecial tissue, leading to the formation of a stylar canal that is detected as a slight protuberance on the mature ovary. Early development of the gynoecium ridge of the lower floret of pedicellate spikelet of ear is very similar to that of the upper floret of the pedicellate spikelet of ear, except the development does not proceed beyond the early ridge stage.
