Items In Progress
This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.
Please include the date when the item was added; topics will move off of here as they are dealt with.
- Go back to POC_Meetings_Minutes main page
- All new terms and changes should be listed here: Release_21
To do:
- Next: start working on the fruit ripening stages, leaf and and tuber development stages- see below
- Complete edits on prothallial cell and prothallium
- Post list of phloem terms to tracker- what needs to be done on them?
- follow up with French fern folks about terms for ferns - email inquiry, terms on tracker
- reopen gametophyte and sporophyte?
- Resolve the question about axis vs stem
- Open tracker for new term for caryopsis, other types of fruit
- look at spikelet rachilla (PO:0009080): The axis of the spikelet, above the glumes. is_a inflorescence branch (PO:0025111). needs to be revised. tracker?
- spikelet needs to be revised
- ovary wall should not be a cardinal organ part as ovary is not an organ See Items_for_future_meetings#ovary_and_the_like below.
- pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.
- egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant This was classified back when we were looser with putting things under COP. Need to propose an alternative classification. Maybe a portion of plant tissue?
- there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.
- Need to revisit the AISO annotations of segmented images, as some of the protoxylem terms are not in the live version yet (will be in Release #20).
- Need to work on the development of the gametophytes in moss Moss Physcomitrella patens Reproductive Organ Development, Plant Phys, 2013
- Add PO:id for tapetum (PO:0025313) to comment on tapetum cell (PO:0025543)
- need to fix: paraclade cortex PO:0004721: A portion of ground tissue that is part of a cortex and part of a paraclade. - change to 'primary inflorescence branch cortex'; add PO:Ids
- Add preceded_by to the sub-classes of floral organ formation stage (PO:0025585):
- Need to fix: spikelet rachilla: (PO:0009080): The axis of the spikelet, above the glumes. [source: POC:curators] - Should be an inflorescence branch (primary?), add PO:Ids
- look at caruncle (PO:0020060) again- came up in the contest of the arillode and arilloid.
- Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.
- should we add a costa has part hydrome and leptome, they are not always there?
- fix comment on receptacle- strawberry is an accessory fruit, post on tracker
Annotation Guidelines
Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR
-This will also be helpful when applying for new grants
-it would be helpful to have a detailed guide on our wiki for collaborators
- Need to update the Annotation_Association_File_Format page
Revisions to Plant Structure Development Stages:
POC 9-10-13: Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point
Stages of Plant Embryo Development
- These need to be addressed:
Suggested revisions to the embryo development terms from Dora Szakonyi (from 2012-06-27):
- See Open SF tracker: #488 embryo development terms
- At the moment B proembryo stage_PO:0001180 is a synonym for both 'eight-celled stage in Arabidopsis' and 'two-celled stage in Arabidopsis'. Maybe it would be good to introduce as child terms separately:
* B proembryo stage_PO:0001180 (= preglobular stage)
- two-celled stage in Arabidopsis
- four-celled stage in Arabidopsis (= quadrant stage)
- eight-celled stage in Arabidopsis (= octant stage)
* Similarly, for C globular stage_PO:0001185 new child terms:
- dermatogen stage in Arabidopsis (=16-cell stage)
- early-globular stage in Arabidopsis (32-cell stage)
- mid-globular stage in Arabidopsis
- late-globular stage in Arabidopsis
* For D bilateral stage_PO:0004507
- Transition stage in Arabidopsis (=triangular stage)
- early-heart stage in Arabidopsis
- mid-heart stage in Arabidopsis
- late-heart stage in Arabidopsis
* E expanded cotyledon stage_PO:0001078 Linear cotyledon stage embryo
- early-torpedo stage in Arabidopsis
- mid-torpedo stage in Arabidopsis
- late-torpedo stage in Arabidopsis
- Bent cotyledon stage (curled cotyledon stage/walking stick stage)
F mature embryo stage_PO:0001081
Older trackers:
fruit development stages (PO:0001002)
- See Google Doc for revisions in progress.
- To avoid confusion, the whole plant fruit development stages (PO:0025500) were renamed in Release_19 to make it clear that they apply to whole plants.
- The plant phenotype pilot project needs terms for grain (fruit) development stages such as milk stage (as synonym for more general term) and mature or dry stage.
- We currently have terms for two sub-classes:
- fruit formation stage PO:0025501 [145]
- PO:0025503 : fruit initiation stage [0]
- PO:0025505 : fruit size 10 to 30% stage [0]
- PO:0025506 : fruit size 30 to 50% stage [0]
- PO:0025507 : fruit size 50 to 70% stage [0]
- PO:0025508 : fruit size 70% to final size stage [0]
- PO:0025504 : fruit size up to 10% stage [0]
- PO:0025502 : fruit ripening stage [118]
- fruit formation stage PO:0025501 [145]
fruit ripening stage PO:0025502 and sub-classes
New terms are needed to describe the stages of ripening for individual fruits. Have a revised parent term; need the sub-classes.
fruit ripening stage: A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).
Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. Fruit ripening (GO:0009835) is defined as: an aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).
fruit ripening (GO:0009835): An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.
related synonyms: fruit maturation; fruit senescence
PO:0001170 : seed development stage [33916]
- PO:0004506 : developing seed stage [10]
- PO:0001040 : dry seed stage [19]
- PO:0007633 : endosperm development stage [33495]
- PO:0004505 : fertilized ovule stage [4]
- PO:0025374 : seed dormant stage [23]
- PO:0007632 : seed maturation stage [12]
plant organ development stage (PO:0025339) and child terms:
- phyllome development stage (PO:0025579): A plant organ development stage (PO:0025339) that has a primary participant a phyllome (PO:0025023) (Created in Release Version #19 )
- moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
reproductive shoot system development stage (PO:0025530)
- Is_a: collective plant organ structure development stage (PO:0025338)
- We need to build a hierarchy for the development of conifer cones- as they are also reproductive shoot systems
- A conifer cone is a strobilus (PO:0025083): A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem. [source: ISBN:0716710072, POC:curators]
- Comment: May be simple or compound. Found in lycophytes such as Selaginella and Lycopodium, sphenophytes such as Equisetum, gymnosperms such as cycad, conifers, gnetophytes and the pollen producing structures of Gingko. The term cone is often used for strobili that are woody. Flowers are sometimes considered bisexual strobili. Some flowering plants such as Alnus have inflorescences called catkins that resemble strobili, but are not.
- A conifer cone is a strobilus (PO:0025083): A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem. [source: ISBN:0716710072, POC:curators]
- moss reproductive structures: these would both be children of plant organ development, as moss lacks a shoot system.
- multicellular plant gametangium (PO:0025124):- antheridium (PO:0025125) and archegonium (PO:0025126)- produce the gametes
- sporangium (PO:0025094): A plant organ in which spores are produced.
Need to look at the fern sporangia- that is the reproductive structure for those plants
- This would parallel the two existing sub-classes:
inflorescence development stage (PO:0021004)and sub-classes
- Currently linked to tracker for: shoot system development stages and child terms
- Currently this has two sub-classes:
- PO:0021004 : inflorescence initiation stage [0]
- PO:0007037 : inflorescence bifurcation stage [0]
- Inflorescence development stage (PO:0001083):A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
- inflorescence initiation stage (PO:0021004): Stage of inflorescence development marked by the formation of the inflorescence meristem on a vegetative branch. [source: POC:Felipe_Zapata]
- inflorescence bifurcation stage ( PO:0007037): Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem. [source: POC:curators]
These need to be revised and additional stages need to be developed.
flower development stage:
This is mostly done- this reference might be helpful for the legume flowers and have annotations to add. Floral Development in Legumes: (Plant Physiol, March 2003, Vol. 131, pp. 911-926)
collective phyllome structure development stage (PO:0025578) and child terms
collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).
- Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
- androecium development stage (PO:0007605): A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).
- calyx development stage (PO:0007603):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
- corolla development stage (PO:0007604):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).
- gynoecium development stage (PO:0007606): A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
New term flower bract development stage (new po:id)
flower bract development stage (new po:id):
- will be parent to lemma development stage and palea development stage
- lemma development stage (PO:0001047): A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).
- PO:0001055 : lemma primordia visible stage [1]
- PO:0001056 : lemma differentiation and expansion stage [0]
- PO:0001057 : fully expanded lemma stage [0]
- palea development stage (PO:0001048): A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).
- PO:0001058 : palea primordia visible stage [1]
- PO:0001070 : palea differentiation and expansion stage [0]
- PO:0001071 : fully expanded palea stage [0]
anther development stage (PO:0001004) and its child terms
- anther development stage (PO:0001004): Stages of development of the anther defined by characteristic morphological, cytological, histological or other visible features.
- Is_a androecium development stage (PO:0007605):
- In Release #19, we renamed anther wall tapetum degeneration initiated stage (PO:0001032): An anther development stage during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.
Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498
tuber growth and development stages
This item has been open on SF since 6/2009, How we work these in will depend on restructuring of PSDS
We will have to differentiate between the two sub-types of tuber (PO:0025522), as they will have different development:
- tuber (PO:0025522): A plant axis (PO:0025004) that is radially enlarged. [source: POC:curators]
- PO:0004543: shoot axis tuber [6]
- PO:0025476: tuberous root tuber [0]
So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)
From Naama Menda: "I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).
Suggested stages:
- tuber initiation
- tuber growth
- tuber maturation
Would these be the same for the two different types of tubers? Also need: tuber dormancy
- sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
- All the SGN annotations refer to potato, which is a subterranean tuber (PO:0004547)
- part_of children:
- PO:0025070 : subterranean tuber axillary bud meristem
- PO:0025081 : subterranean tuber axillary shoot (exact synonym: tuber sprout)
- PO:0025042 : subterranean tuber axillary vegetative bud (narrow synonym: potato eye)
- PO:0025048 : subterranean tuber epidermis
- PO:0025045 : subterranean tuber periderm
- PO:0025038 : subterranean tuber storage parenchyma
- part_of children:
Further info and references:
Tuber on a chip: differential gene expression during potato tuber development
xylem developmental stages:
See discussions of primary xylem on POC_Conf._Call_6-11-13
Existing definitions:
* secondary xylem development stage (PO:0025427): A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem. [source: POC:wood_curators]
- Need: primary xylem development stage (PO:new): A xylem development stage (PO:0025425) that has as primary participant a primary xylem (PO:0005849) tissue. needs to be expanded
whole plant development stages (PO:0007033)
- sporophyte vegetative stage (PO:0007134):
child terms need to be revised:
- plant embryo stage (PO:0007631)
- 0 seed germination stage (PO:0007057)
- coleoptile emergence stage (PO:0007045)
- 1 main shoot growth stage (PO:0007112)
- 2 formation of axillary shoot stage (PO:0007073)
- seedling development stage (PO:0007131)
whole plant flowering stage PO:0007016
- Now that we have revived the flowering stages, we need to revisit the whole plant flowering stages:
whole plant flowering stage (PO:0007016): A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.
- child terms need to be revised and the synonyms need to be reviewed, compare synonyms and stages
- FL.00 first flower(s) open stage (PO:0007026) [24868]
- FL.01 1/4 of flowers open stage PO:0007034
- PO:0007053 : FL.02 1/2 of flowers open stage [0]
- PO:0007052 : FL.03 3/4 of flowers open stage [0]
- PO:0007024 : FL.04 end of flowering stage [2]
Why are there ~25,000 associations on the first one and none on the rest? They look like they are all from Zea Mays, and 1 from SGN.
whole plant fruit ripening stage (PO:0007010)
- whole plant fruit ripening stage: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
Comment: Succeeds a whole plant fruit formation stage (PO:0007042). This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant.
Proposed Revisions to sub-classes:
Comment from RW: The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point.
need to open tracker for this set:
* whole plant beginning of fruit ripening stage (PO:0007036):
current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
Add related synonyms:
- BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
- grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison
- whole plant early fruit ripening stage (PO:0007001)
current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening
proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
Add related synonyms:
- middle of veraison
- BBCH principal growth stage 83
* whole plant mid fruit ripening stage (PO:0007031): current name and def'n: FR.02 mid stage of fruit ripening (PO:0007031) The stage when fruit ripening is midway.
proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.
proposed comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
* whole plant late fruit ripening stage (PO:0007050):
current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.
proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.
comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
* whole plant fruit ripening complete stage (PO:0007038):
current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
Proposed Def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.
comment: This term is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.
related synonyms:
- BBCH principal growth stage 89
- grape E-L stage: 38; Berries ripe for harvest
GO cellular component requests
Existing terms in GO:
apoplast (GO:0048046): The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.
includes tracheids
This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.
symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
- all the plasma connected, through plasmodesmata, transport through the cytoplasm
See: Link to diagram Apoplast_and_symplast_pathways
See: Apoplastic versus Symplastic Pathways in roots
Suggest revised GO definitions for apoplast and symplast and add transport terms
Parent term:
- transport (GO:0006810): The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
- apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)
- symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)
comments: symplastic transport is a diffusion process
Other Requests from SF- Anatomy terms in progress...
Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children
See notes from discussion on POC call POC_Conf._Call_9-24-13
Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)
Fill in details here.....
New terms Added in Release #20:
- fused perianth (new PO:0025880): A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused.
Comment: The petals (PO:0009032), sepals (PO:0009031) and tepals (PO:0009033) may be fused anywhere along the phyllome margin (PO:0025018). In some cases where the calyx (PO:0009060) and corolla (PO:0009060) are fused at the base it is referred to as a perianth tube.
-Added Narrow synonyms: adnate perianth and connate perianth
- fused corolla (new PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0009032).
- exact synonym: connate petal structure
- fused calyx (new PO:0025582): - A calyx (PO:0009060) that is composed of fused sepals (PO:0025584).
- Exact synonym: connate sepal structure
- fused petal (new PO:0025583): - A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).
- Comment: In fused perianth (PO:0025580), the fused petal (PO:0025583) may be joined to a fused sepal (PO:0025584) or another fused petal.
- free petal (PO:0025569): A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
- comment: A free petal (PO:0025569) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a petal (PO:0009032) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use petal.
- fused sepal (new PO:0025584) - A sepal (PO:0009031) that is part of the fused calyx (PO:0025582) or a fused perianth (PO:0025580).
- free sepal (PO:0025587): A sepal (PO:0009031)that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
- comment: A free sepal (PO:0025587) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a sepal (PO:0009031) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use sepal.
Need to look at these associated terms:
- is_a:
- PO:0025324 : banner petal [0]
- PO:0025326 : keel petal [0]
- part_of
- PO:0025144 : petal apex [0]
- PO:0025146 : petal base [0]
- PO:0006041 : petal epidermis [0]
- PO:0025008 : petal margin [0]
- PO:0006069 : petal parenchyma [0]
- PO:0025511 : petal spur [0]
- PO:0025218 : petal stomatal complex [0]
- PO:0000054 : petal vascular system [0]
- PO:0025325 : wing petal [0]
For corolla:
- part_of:
- corolla spur PO:0025512: Def'n: A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.
- should be is_a fused corolla?
- keel PO:0025327: A boat-shaped collective phyllome structure (PO:0025023) that consists of the two lowest petals (PO:0009032) of a papilionaceous corolla (PO:0009059). Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.
- PO:0009032 : petal [0]
- fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
- calyptra corolla (PO:0025330): A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583). Very similar definitions
epicalyx
- epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]
Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.
Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators]
Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx
Example from MAG: In the Trocodondraceae, the perianth is completely lacking, but they have little bracts subtending the reproductive structure.
Decided that we needed to add a new term:
epicalyx bract (new PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063). It will be sibling to the existing terms lemma and palea.
arilloid and arillode and caruncle
There is an issue in OE with these that the exact synonyms are the same in Spanish, so it generates an error.this was resolved in Release #20
- arilloid (PO:0019022): A cardinal part of multi-tissue plant structure (PO:0025498) that is a fleshy outgrowth of a seed (PO:0009010). [source: ISBN:9780881928501]
Comment: Often conspicuous and found on seeds with a hard testa that are dispersed by animals. There is some variation in how different sources define the subtypes of arilloids.
Synonyms narrow: arillode; exact: ariloide (Spanish)
- arillode (PO:0025378): An arilloid that is an elaborate outgrowth of a seed at the micropyler end. [source: ISBN:9780881928501]
Comment: Generally larger than a caruncle and not hard.
Synonyms exact: ariloide (Spanish)
- caruncle (PO:0020060): An arilloid that is an outgrowth of a seed next to the micropyle. [source: ISBN:9780881928501]
Comment: Often hard and generally smaller and less elaborate than a arillode.
Synonyms exact: carúncula (Spanish)
- aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
Synonyms exact: arilo (Spanish) exact: 仮種皮 (Japanese)
Comment : Usually envelopes most of the seed and is fleshy. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.
floral node
suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise
Parent/relationship: is_a shoot node (PO:0005004)
Submitted: Johnny Lloyd
inflorescence node: A shoot node that is part of an inflorescence axis and where a spikelet, flower, floret or inflorescence branch is attached. [source: GR:Pankaj_Jaiswal].
PO:0006325
spine petiole
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
The petiole abscisses longitudinally and the blade withers.
See the photo and description on this page: "Spines From Modified Petioles"
adventitious branch
Definition: A shoot axis (PO:00025029) that develops in an unusual place
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
adventitious shoot axis
shoot-borne root (PO:0000042)
synonym: adventitious root
Need to align these three with the shoot-borne root
- adventitious root apical meristem ; PO:0006021
- adventitious root epidermis ; PO:0006039
- adventitious root nodule ; PO:0000040
leaf lamina PO:0020039
-fix typo in comment
- Def'n: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
- Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae.
If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.
Ultimate Unit (UU)
Requested by: Corvez Adele Created: 2013-02-01
- Ultimate units are last branching-orders inserted at extremities of lateral branching systems. Each unit can divide several times, they are mostly tridimensional and their last dichotomies form ultimate appendages.
Corvez et al., 2012
suggested parentage: Ultimate unit is_a cardinal organ part
moss capsule
need to open tracker for this: moss capsule
prothallial cell and prothallium
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
prothallial cell (PO:0025533):
proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.
should add the PO id for microgametophyte (PO:0025280) to the definition
For reference about prothallial cells in gymnosperms see:
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
Available online: Coulter + Chamberlain, 1910
common primordium
This request was made by Elena Kramer during the beta review: , I wondered if there was some way to incorporate ...the phenomenon of common primordia (...would only apply to the development ontology)
"During floral development (at least in peas, maybe others), petals and stamens (and maybe other floral organs) may share a common primordium before development of a distinct petal or stamen primordia. We may want to add this to the flower developmental stage branch of the PGDSO."
This could be a structure in the PAE branch, and we can consider adding it as a stage when we work on flower development stages.
We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.
nucellar projections
The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.
This definition is specific to grasses, and should be rephrased, so it is more general.
Actually, I can't find any references to this outside grasses, so perhaps it is fine as is. Does anyone know of an example of this outside grasses? Maybe in other monocots?
No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.
proposed def.: A portion of plant tissue (PO:0009007) that is a morphologically distinct part of a nucellus (PO:0020020) overlying the vascular bundles (PO:0005020).
comment: Found a caryopsis in Poaceae.
part_of nucellus
rosette leaf and cauline leaf
The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.
Current definitions:
rosette leaf (PO:0000014): One of multiple leaves borne in a rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.
comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.
cauline leaf (PO:0000013): Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.
comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.
Perhaps we should use the appropriate growth stages in their definitions,
e.g., PO:0007113 rosette growth, and PO:0007089 stem elongation. However, stem elongation is defined as a vegetative growth stage, so it doesn't really apply to plants that are bolting
proposed definitions
rosette leaf: A vascular leaf (PO:0009025) that is part of a collective leaf structure (PO:0025022) in which the leaves are borne on a stem base (PO:0008039) that has very short stem internodes (PO:0020142).
comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.
cauline leaf (PO:0000013): A vascular leaf (PO:0009025) that is borne on a stem (PO:0009047) or branch (PO:0025073) that has elongated shoot internodes (PO:0005005).
comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.
Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?
Links from Lol:
http://www.arabidopsis.org/portals/education/growth.jsp
http://www.jstor.org/stable/2656849
non-vascular rosette leaves?
At the POC meeting on 6/7/11, PJ suggested that we make new general terms for rosette leaf and cauline leaf, is_a children of leaf. Then we could make specific terms for vascular rosette leaf and vascular cauline leaf.
However, I don't know if the terms rosette leaf and cauline leaf are ever used for non-vascular plants. Certainly leaves occur on a stem in mosses and liverworts, but it is not the case that the leaves first form during a rosette stage then the stem elongates. Instead, leaves are formed from the stem apex as it elongates.
If rosette leaf and cauline leaf only have one child each (vascular rosette leaf or vascular cauline leaf), is there really a point in making the general category?
Don't need these
sporocyte
Existing definitions:
sporocyte (PO:0006204): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.
microsporocyte (PO:0020047): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]
synonyms: microspore mother cell, PMC, pollen mother cell
megasporocyte (PO:0000431): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]
synonyms: megaspore mother cell, MMC
At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.
Already have:
megasporocyte develops_from female archesporial cell
microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell
Proposed definitions:
sporocyte (PO:0006204): A plant cell (PO:0009002) that develops from an archesporial cell (PO:0030056) and undergoes meiosis (GO:0007126) to produces four plant spores (PO:0025017).
Add: sporocyte develops_from archesporial cell
Should we add spore develops_from sporocyte? yes
microsporocyte (PO:0020047): A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]
synonyms: microspore mother cell, PMC, pollen mother cell
Should we add microspore develops_from microsporocyte?
Better to use meiosis, rather than male meiosis.
megasporocyte (PO:0000431): A sporocyte (PO:0006204) that develops from a female archesporial cell (PO:0006015) and undergoes meiosis (GO:0007126) to produces four megaspores (PO:0020019). [source: ISBN:0471245208]
synonyms: megaspore mother cell, MMC
Better to use meiosis, rather than female meiosis.
Also need to address:
primary sporogenous cell (PO:0006088), current def.: It is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.
proposed def.: A plant cell (PO:0009002) that develops from a male archesporial cell (PO:0006014) and, after several mitotic divisions, develops into microsporocytes (PO:0020047).
okay
Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.
spikelet
At the POC meeting on 8-30-11, we decided that this definition needs some work.
Current def.: Ultimate and congested inflorescence branch of the grasses. [source: APWeb:Glossary] Comment: It consists of one to many closely-packed flowers and associated glumes etc.
Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).
Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.
Comment: Part of a spike type inflorescence as found in grasses and other Poales.
From Ale:
spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards
spikelet: a small spike or secondary spike; the ultimate flower cluster of grasses and sedges, consisting of one to may flowers subtended by two bracts (glumes)
lamina areole
Propose new definitions:
phyllome lamina areole (PO:0025391): A cardinal organ part (PO:0025001) that is part of a phyllome lamina (PO:0025396) and is completely surrounded by phyllome lamina veins (PO:0025348) and cannot be divided into any smaller parts that are completely surrounded by phyllome lamina veins.
Comment: Any order of phyllome lamina vein can form the sides of a phyllome lamina areole. Taken together, the phyllome lamina areoles form a contiguous field of polygons over the area of a phyllome lamina. part_of phyllome lamina
leaf lamina areole (PO:0025392): A phyllome lamina areole (PO:0025391) that
is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf
lamina veins (PO:0020138) and cannot be divided into any smaller parts that
are completely surrounded by leaf lamina veins.
Comment: Any order of leaf lamina vein can form the sides of a leaf lamina areole. Taken together, the leaf lamina areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina
ovuliferous scale
New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).
"Ovuliferous scale" seems to be the more commonly used name.
proposed def., ovuliferous scale: A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).
Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().
need to review this
Currently, ovuliferous scale is a narrow synonym of megasporophyll
ovulate cone, new term: A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).
synonym: female cone (related)
Move more specific synonyms form strobilus to these terms.
microsporangiate cone, new term: A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).
seed-scale complex: A reproductive shoot system (PO:0025082) that is part of an ovulate cone (PO:0025083) and has as parts a ovuliferous scale () and a ovuliferous scale sterile bract ().
ovuliferous scale sterile bract: A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().
Definitions of megasporophyll and microsporophyll
move part about angiosperms to the comment
Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.
pericarp and seed coat
What is the problem with pericarp?
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
Synonyms related: fruit peel, fruit rind
New def.: A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.
comment: Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.
endocarp ; PO:0009086, synonym inner epidermis of pericarp
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument
Get rid of "usually" in def. of integument. From: http://en.wikipedia.org/wiki/Caryopsis
is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.
The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.
The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
we also have the term:
caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]
ovary and the like
An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.
The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).
ovary wall: Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.
style: (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.
If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.
stigma: Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.
anther and filament
Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this cool picture).
It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).
Cacti terms:
spinule: word for when the spines are stipules – synonym of stipule spine
In Beentje, spinule is defined as a small spine.
Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.
cladode and phylloclade
From Beentje:
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
proposed definition:
cladode: A shoot axis that is flattened and expanded.
comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.
synonyms: phylloclade, cladophyll
Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla? This does not work. The comment also does not work. Similarily the synonyms are not so much synonyms as they are subsets.
I don't know what the problem is with Cholla. As far as I know, it does not have cladodes or phylloclades, because the axes are round.
Recent interesting paper on cladodes in Asparagus:
Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. The Plant Cell Online, 24, 929 –940.
PMID:22415273
In Asparagus, some cladodes have re-evolved a rounded shape. Are they still cladodes, or just shoot axes again at that point (given that the PO is not based on homology)?
rib
Should also add 'rib' for cacti and other plants.
Definition:
-caryopsis new child of fruit
-adventitious root nodule
Make two sub-types of tapetum
Based on the discussion on the PO conf call 4-9-13, we need to add the two types of tapetum(s). Added as a comment on tapetum for now.
See tracker at: tapetum types
Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:
Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum.
See references in the literature to: Sporne KR (1973) A Note on the Evolutionary Status of Tapetal Types in Dicotyledons. New Phytologist 72: 1173–1174
Wood ontology terms
See separate page: Wood Ontology PO and GO Term Development
root terms
Submitted by Rich Zobel (Nov 2009). Still need to work on definitions for these terms.
Growth forms
From Daniel Hiss: "IMHO plant growth/life forms should be best integrated as an extension to PO." Also need acrocarpous and pleurocarpous moss (these could be growth forms).
