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
- need to revisit the portion of meristem tissue definition- about 2 dozen direct is_a children, many of which are actually determinate tissues such as the phyllome anlagen (PO:0025430) and child terms, the primordium, etc
- Need to revisit shoot node (PO:0005004): A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud, or leaf may arise. Refer to the POC call 10-1-13 for more details.
- Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see POC_Conf._Call_10-29-13)
- Consider getting rid of apical meristem (PO:0020144)- it forces dual parentage on the two child terms- shoot apical meristem (PO:0020148) and root apical meristem (PO:0020147) and forms a loop/cycle.
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
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.
This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants
- child terms need to be revised and the synonyms need to be reviewed, compare synonyms and stages
- PO:0007026 : FL.00 first flower(s) open stage [24,868]
- PO:0007034 : FL.01 1/4 of flowers open stage
- 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.
Stages of Plant Embryo Development
- These need to be addressed:
Note: Not sure where the coleoptilar stage (PO:0001094) fits in- it has no letter code and apparently never has (at least in the last 4 years). The A zygotic stage term was removed sometime in 2011. Currently the heirarchy looks quite odd as starts with "B- proembryo stage"
-Removed the letters in the names and added preceded_by to order the stages. made coleoptilar stage (PO:0001094) a subclass of bilateral stage (PO:0004507).
Suggested revisions:
- 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:
References:
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 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.
**Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**
See comments from BS from email:
- On Wed, Sep 18, 2013
- A lot of this needs to go, I think:
- early, middle and late are okay, but then we need to define them non-circularly and if you want to keep whole plant f.r. complete stage' then you have to define it so that it differs from 'late ...'
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 requests:
Multicellular organism senescence/aging (GO:0010259)
- Multicellular organism senescence/aging (GO:0010259): includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.
Link to PO tracker: gametophyte/sporophyte senescent stage
PJ Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.
apoplast and symplast
- 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
- Submit tracker for GO biol process term to describe callus formation
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).
