Eliminating Zea/Poaceae terms from PO

Annotations

If one term is merged with another, the IDs merge too. This means any annotations should automatically move to the target term, but we should double check it.

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 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

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".

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

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

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

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

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

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

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

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

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)

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)

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)

Merge into floret

PO:0006329 Poaceae floret meristem (1)

Merge 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)

Merge into PO:0025088 gynoecium

PO:0025086 Poaceae gynoecium ridge (0)

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.

PO:0006460 Poaceae inner integument (0)

x Merge into PO:0020022 inner integument

PO:0006465 Poaceae integument (3)

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)

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)

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)

Merge into PO:0009072 ovary

PO:0006500 Poaceae ovary epidermis (0)

Merge into PO:0006063 ovary epidermis

PO:0006467 Poaceae ovary placenta (0)

x Merge into PO:0020001 ovary placenta

PO:0006457 Poaceae ovule (5)

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)

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, but AmiGO says 57, also, no pie chart for getting annotation distribution)

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

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)

Merge this into PO:0009054 inflorescence bract. Mary is already putting the new annotations for husk on PO:0009054.

merge into PO:0009061 androecium

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

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

merge into lemma

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

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

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

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:

(There may be other parts of flowers. These were all the terms with Poaceae children.)

PO:0009061 androecium 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:0009066 anther

PO:0000002 anther wall

PO:0009030 carpel

PO:0009068 connective

PO:0020002 anther wall endothecium

PO:0020004 anther wall exothecium

PO:0009067 filament

PO:0020025 micropyle

PO:0025277 pollen sac

PO:0020048 microspore

PO:0020047 microsporocyte

PO:0006448 placentoid

PO:0009029 stamen

PO:0020101 stomium

PO:0009074 style

PO:0006062 style epidermis

PO:0009071 anther wall tapetum

PO:0009069 anther theca

PO:0020102 portion of transmitting tissue

PO:0025088 gynoecium In Zea mays, gynoecia of tassel florets and of the lower florets of ear spikelets usually do not develop fully.

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.

ovary and parts

For ovary and its parts, I only suggest the types of florets that normally have fully developed gynoecia:

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:0009073 stigma, PO:0006061 stigma epidermis, 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

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).