Difference between revisions of "Items In Progress"

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'''This page is a place holder for us to put items that will be scheduled for discussion at upcoming meetings.'''  
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'''This page is a place holder for us to put items that are being worked on or under development.'''  
  
 
Please include the date when the item was added;  topics will move off of here as they are dealt with.
 
Please include the date when the item was added;  topics will move off of here as they are dealt with.
  
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-Go back to [[POC_Meetings_Minutes]] main page
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- Go back to [[POC_Meetings_Minutes]] main page
  
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=User requests open on Source Forge: PAO=
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- All new terms and changes should be listed here: [[Release_21]]
  
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==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
 
  
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submitted by Austin Mast
 
  
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Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
 
  
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See agenda for 7-05-2011.
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=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
  
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'''
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-This will also be helpful when applying for new grants
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Remaining:'''
 
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]===
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-it would be helpful to have a detailed guide on our wiki for collaborators
  
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These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 [[Sunday_Sept_11th,_2011]]
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* Need to update the [[Annotation_Association_File_Format]] page
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
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=Requests from SF- Anatomy terms in progress...=
  
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This item is on the agenda for [[POC_Conf._Call_9-20-11]]
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==Request for "rind" or outer layer of a maize or sorghum stem==
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
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Request for a term for the outer covering of a maize or sorghum stalk.  
  
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(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
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[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/596/ link to #596]
  
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''Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should add terms needed to PATO.''
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[http://www.sciencedirect.com/science/article/pii/S2090447912000524 structure and properties of sorghum stalks]
  
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We have the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
 
  
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A bristle is a single thing, like a stiff hair, but many things can be bristled. Better to add bristled as an adjective in PATO (like ovate or acute).
+
Propsed new terms:
  
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There are two meanings for bristled:
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=='''Abscission Zones'''==
 +
June 2014
  
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!. Stiff and sharp (e.g., a bristled trichome)
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Added new terms and revised existing:
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ fruit pedicel abscission zone (PO:0025605)]. Def'n: An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
  
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2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
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Ref: http://www.plantphysiol.org/content/158/1/439 (PMID:22106095)
  
 +
See also:
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* Mao et al., Nature, 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development 
 +
(http://www.nature.com/nature/journal/v406/n6798/full/406910a0.html)
 +
* Szymkowiak and Irish Plant Cell. 1999. Interactions between jointless and wild-type tomato tissues during development of the pedicel abscission zone and the inflorescence meristem. (http://www.ncbi.nlm.nih.gov/pubmed/9927636?dopt=Abstract)
  
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Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
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===New term needed: flower pedicel abscission zone (PO:0025608)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ flower pedicel abscission zone (PO:0025608)]: An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
  
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'''1. bristle-like:'''
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PMID:24744429
 +
Nakano T, et al.  (2014) The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato. Journal of Experimental Botany.
  
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This is a combination of two PATO descriptors:
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http://jxb.oxfordjournals.org/content/early/2014/04/15/jxb.eru154.full
  
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Something describing the shape:
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Added relations:  
 +
* flower pedicel abscission zone (PO:0025608) part_of flower pedicel
 +
* fruit pedicel (PO:0004536) develops_from flower pedicel (PO:0009052)
 +
* fruit pedicel abscission zone (PO:0025605) develops_from flower pedicel abscission zone (PO:0025608)
  
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PATO:0001954 (subulate, awl-shaped, needle-shaped): A shape quality inhering in a bearer by virtue of the bearer's being linear, very narrow, tapering to a very fine point from a narrow base.
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===Renamed existing term: pedicel > flower pedicel (PO:0009052)===
  
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or
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Currently: pedicel (PO:0009052): An inflorescence branch (PO:0009081) that supports an individual flower (PO:0009046) in an inflorescence (PO:0009049).
  
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PATO:0001873 (cylindrical): A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section.
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Renamed: "flower pedicel"  to differentiate it from the fruit pedicel (PO:0004536), which is an infructescence branch.
  
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and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
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===Renamed existing term: flower abscission zone > floral organ abscission zone (PO:0006502)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/193/ flower abscission zone (PO:0006502)]:
  
 +
Was: Zone at base of the flower that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the flower and its parts.
  
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and something describing a quality of a substance:
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This was revised as the AZ of a whole flower is different that that of the floral organs (sepals, petals and filaments).
  
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PATO has:
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Revised name and definition:  
 +
* floral organ abscission zone (PO:0006502): An abscission zone (PO:0000146) at the base of a flower (PO:0009001) where a floral organ (PO:0025395) separates during floral organ abscission (GO:0010227).
  
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PATO:0001544 (flexible): A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking. (bendy)
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Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower
  
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PATO:0001545 (inflexibile): A physical quality inhering in a bearer by virtue of the bearer's inability of being turned, bowed, or twisted without breaking. (stiff)
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== New term request: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/589/ microgametophtye development stage]==
  
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A bristle is stiff but also bendy! I think in addition to flexible/inflexible, PATO needs terms for stiff or rigid/flacid, and that stiff should be a related synonym of inflexible, rather than exact.
+
'''Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.'''
  
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PATO:
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Question: how do the megagametophyte development stage (PO:0007621) and proposed microgametophtye development stage (new) fit in with the gametophyte development stage (PO:0028003)?? 
  
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quality of a substance (existing)
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- multicellular plant gametangium (PO:0025124)- a plant organ- children: antheridium (PO:0025125) and archegonium (PO:0025126)
  
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>flexibility (existing)
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- unicellular plant gametangium (PO:0025521):  a plant cell- no child terms...
  
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>>flexible (existing)
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''Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.''
  
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>>inflexible (existing)
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* plant ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
  
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>rigidity (new)
+
* Moved megagametophyte development stage (PO:0007621) to be is_a gametophyte development stage (PO:0028003). part_of ovule development
 +
** Revised definition: A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.added dbxref to: OBO_SF2_PO: 589
 +
''This definition should be worked on further, and the child terms need work as well.''
  
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>>rigid (new)
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* Created new term: microgametophtye development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
  
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>>flacid (new)
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* pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).
  
 +
''Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.''
  
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'''2. bristle-bearing:''' A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
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androecium (PO:0009061): A collective phyllome structure (PO:0025023) composed all of the stamens (PO:0009029) in a flower (PO:0009046).
  
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is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
 
  
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Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
+
* moved pollen development stage (PO:0001007) to be is_a child of the new term: microgametophtye development stage (PO:0025602). part of androecium development stage_ (PO:0007605)
  
 +
Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.
  
 +
Revised definition:
 +
pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.
  
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To describe legume stipules, we may also need a term '''brush-like:''' A shape quality inhering in a bearer by virtue of the bearer's having a shape that is a cluster of bristle-like structures.
+
''This definition should be worked on further, and the child terms need work as well.''
  
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Then if we want to, we could add terms like '''brush-like stipule''' (is_a stipule) or '''bristle-like stipule''' (is_a stipule) or '''bristle-bearing stipule''', or users could post-compose these terms on their own.
+
==caryopsis hull (PO:0006000)==
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/239/ 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]
 +
** Comment: None
 +
''I think in maize, the hull is actually pericarp tissue, perhaps we should not include the last part.''
  
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==TraitNet requests==
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==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/575/ founder cells]==
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===[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]===
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New terms:
 +
phyllome founder cell (PO:0025586)]: A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).
  
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Their comment: is synonym to tubercle (but it isn't exactly the same)
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Comment: As a group, the phyllome founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a phyllome anlagen (PO:0025430). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.
  
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podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
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PMID:12610522
  
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tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are enlarged modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
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vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).
  
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[[http://docs.google.com/viewer?a=v&q=cache:NuEGm3IiDYAJ:www.fcla.edu/FlaEnt/fe84p474.pdf+cactus+morphology&hl=en&gl=us&pid=bl&srcid=ADGEEShKIXm284nTEhC69_8ZMUsUqJCxZF-KpqW7C_7nqrap5cB6PoZqgFe_R19AFvRD7j59jql-ugEv-Dfv0aNgJ1RcHunV0oxR67OB_e9iY4b1hBRqkXBK29vi3NYbon9rCkAm2fRR&sig=AHIEtbRWmPk6sb2L0_VDc_CoSY2U8RRYjA This article]] describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:
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Comment: As a group, the vascular leaf founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a vascular leaf anlagen (PO:0025431). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.
  
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"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."
+
Revised:
 +
vascular leaf anlagen formation stage PO:0001003: A vascular leaf initiation stage (PO:0007040) during which the vascular leaf founder cells (PO:0025592) of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).
  
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'''proposed def. podarium or tubercle:''' ''under construction''
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==Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children==
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]===
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See notes from discussion on POC call [[POC_Conf._Call_9-24-13]]
  
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'''proposed def:''' A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
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Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)
  
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child of stem (PO:0009047).
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[[File:Cortex terms.png]]
  
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]===
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Fill in details here.....
  
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definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
 
  
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'''proposed def:''' A root that is erect and protrudes above the soil.  
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==New terms Added in Release #20:==
 +
*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ 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.
  
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Comment: Pneumatophores are found in trees that live in flooded habitats such as mangroves. May provide oxygen to below ground roots growing in flooded soils.
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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
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]===
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused corolla (new PO:0025581)]: A corolla (PO:0009059) that is composed of fused petals (PO:0009032).
 +
** exact synonym: connate petal structure
  
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Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused calyx (new PO:0025582)]: - A calyx (PO:0009060) that is composed of fused sepals (PO:0025584). 
 +
**Exact synonym: connate sepal structure
  
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tendrils can be (evolutionarily) derived from multiple types of structures. Suggest we make separate terms:  
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ 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.
  
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'''branch tendril''' (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
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* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/542/ 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).
  
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'''leaf tendril''' (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
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***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.
  
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'''leaflet tendril''' (child of leaflet): A leaflet that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
 
  
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'''leaf apex tendril''' (child of leaf apex): A leaf apex that is slender and coiling. Comment: Found at the apex of a leaf lamina, but the leaf apex tendril is not laminar. Aids plant in climbing.
+
*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ fused sepal (new PO:0025584)] - A sepal (PO:0009031) that is part of the fused calyx (PO:0025582) or a fused perianth (PO:0025580).  
  
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Can add other types of tendrils if they come up or users need them.
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*[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/549/ 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).
  
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This is the way we defined spine (no parent class spine, only leaf spine and stipule spine with is_a relations to leaf and stipule).
+
**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]
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** 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]
  
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Alternative is to create a parent 'tendril'(is_a plant structure) with children that are part_of the other structures:
 
  
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'''tendril''': A plant structure that is slender and coiling. Comment: Aids plant in climbing.
+
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]
  
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'''branch tendril''' is_a tendril part_of branch
+
* 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
  
−
'''leaf tendril''' is_a tendril part_of leaf
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/98/ epicalyx] ==
  
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'''leaflet tendril''' is_a tendril part_of leaflet
+
* epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]
  
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'''leaf apex tendril''' is_a tendril part_of leaf apex
+
''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] 
  
−
The part_of relations are technically correct (not proper part), but I don't think it conveys the proper meaning. Also, according to the formal definitions, a leaflet tendril or a leaf apex tendril would be a leaf tendril as well.
+
''Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx''
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]===
+
''Example from MAG: In the [http://www.plantsystematics.org/imgs/dws/r/Trochodendraceae_Trochodendron_aralioides_26193.html Trocodondraceae], the perianth is completely lacking, but they have little bracts subtending the reproductive structure.
  
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definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
+
''Decided that we needed to add a new term:''
  
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We could add this term as a kind of upper level bin term (similar to trichome)
+
''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==
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]===
+
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''
  
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Synonym of strobilus (PO:0025083) or child?
+
* '''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.
  
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proposed def: A strobilus that is woody?
+
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)
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]===
+
*'''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.
  
−
from Crum (2001): a cluster of fern sporangia
+
Synonyms exact: carúncula (Spanish)
−
from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
 
  
−
Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
+
*aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
  
−
Part_of vascular leaf, has_part sporangium
+
Synonyms
 +
exact: arilo (Spanish)
 +
exact: 仮種皮 (Japanese)  
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
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.
  
−
Submitted by Rich Zobel (Nov 2009).
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609179&group_id=76834&atid=835555 floral node]==
  
−
Still need to work on definitions for these terms.
+
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)
  
−
==New children of [https://sourceforge.net/tracker/index.php?func=detail&aid=3241802&group_id=76834&atid=835555 calyptra perianth]==
+
Submitted: Johnny Lloyd
  
  
−
This item is on the agenda for [[POC_Conf._Call_9-20-11]].
+
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
  
−
=User requests still open on Source Forge; PGDSO =
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/535/ spine petiole]==
  
−
==from MaizeGDB:==
+
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
−
See discussion of these items on [[POC Conf. Call 8-30-11]]
 
  
−
===[http://sourceforge.net/tracker/?func=detail&aid=3357762&group_id=76834&atid=835555 IL.03 full infloresecence length reached]===
+
The petiole abscisses longitudinally and the blade withers.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3357766&group_id=76834&atid=835555 LP.18 eighteen leaves visible]===
+
See the photo and description on this page: [http://waynesword.palomar.edu/ecoph30a.htm "Spines From Modified Petioles"]
  
−
===[http://sourceforge.net/tracker/?func=detail&aid=3324099&group_id=76834&atid=835555 3 infloresence visible]===
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609178&group_id=76834&atid=835555 adventitious branch]==
  
−
----
 
  
−
===[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence -- definition]===
+
Definition: A shoot axis (PO:00025029) that develops in an unusual place
  
−
These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 [[Sunday_Sept_11th,_2011]]
+
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
  
−
===[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3374186&group_id=76834 5 fruit formation; FF.00 fruit size 10%]===
 
  
−
These were dealt with at the NYBG Meeting, on Saturday, Sept 10th, 2011 [[Sunday_Sept_11th,_2011]]
+
adventitious shoot axis
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed trichome development stages]==
+
==shoot-borne root (PO:0000042)==
 +
synonym: adventitious root
  
−
Open since 07-28-2010
+
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
  
−
===Request===
+
==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. 
  
−
The following terms have been requested for cotton fiber development (their structure and defintions):
+
*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.
  
−
seed development stages PO: 0001170
+
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.
  
−
---[part_of]Seed hair development stages
 
  
−
---[part_of]seed hair initiation stage: The earliest histological
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/521/ Ultimate Unit (UU)]==
−
evidence of seed hair initiation, ie, a change in the orientation of cell
+
Requested by: Corvez Adele  Created: 2013-02-01
−
division in the ovule epidermises occurs at or just before anthesis. (Ruan
 
−
YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].
 
  
−
---[part_of]seed hair elongation stage: A period of rapid elongation
+
* 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.
−
of hair initials without cell division for 16-25 days. (Lee JJ, 2007,
+
Corvez et al., 2012
−
Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964)
 
−
[Sources:PMID: 17905721, PMID: 12671090].
 
  
−
---[part_of] seed hair secondary wall biosynthesis stage: A phase of
+
suggested parentage: Ultimate unit is_a cardinal organ part
−
the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ,
 
−
2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell
 
−
15:952-964) [Sources: PMID:17905721, PMID:12671090].
 
  
−
---[part_of]seed hair maturation stage: A period of seed hair
+
==moss capsule==
−
maturation from 50 to 60 days post-anthesis (DPA).
+
need to open tracker for this: [https://sourceforge.net/tracker/?func=detail&aid=3140824&group_id=76834&atid=835555 moss capsule]
−
(Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant
 
−
Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].
 
  
−
===Suggested terms and definitions:===
+
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell] and prothallium ==
  
−
'''Do we want to use stage or phase throughout PGDSO?'''
+
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
  
−
'''seed development stages (PO:0001170)'''
+
prothallial cell (PO:0025533):
  
−
'''Current definition:''' Stages of seed development, from fertilization to the dry or quiescent state. [source: TAIR:ki]
+
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.
  
−
'''Proposed name and definition:''' seed development stage: A plant structure development stage that begins with fertilization and ends with seed maturation.
+
''should add the PO id for microgametophyte (PO:0025280) to the definition''
  
−
Comment: Only used for seed plants. Some seeds may enter a period of dormancy after seed development is complete.
 
  
−
is_a plant structure development stage; part_of sporophyte phase; subset for gymnosperms and angiosperms; add relation: seed participates_in seed development stage
+
For reference about prothallial cells in gymnosperms see:  
  
−
====New terms and proposed definitions:====
+
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
  
−
'''seed trichome development stage:''' A plant structure development stage that is part of a seed development stage during which one or more seed trichomes develop.
+
Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
  
−
is_a plant structure development stage; part_of seed development stage; add seed trichome participates_in seed trichome development stage
 
  
−
synonym: seed hair development stage
+
Note: prothallium is a synonym for thallus (PO:0030027) and ....
  
 +
How does prothallial cell compare to microgametophyte vegetative cell?
  
−
seed trichome initiation stage: The earliest histological
+
prothallial cell (PO:0025533):
−
evidence of seed hair initiation, ie, a change in the orientation of cell
+
current 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.
−
division in the ovule epidermises occurs at or just before anthesis. (Ruan
 
−
YL, 2003, Plant Cell 15:952-964) [Source:PMID: 12671090].
 
  
−
synonym: seed hair initiation stage
+
Revised: A native plant cell (PO:0025606) which is vegetative and develops from the division of the microspore (PO:0020048) of vascular plants other than angiosperms.
  
 +
Revised comment:
 +
The prothallial cell (PO:0025533) is part of the microgametophyte (PO:0025280) and is believed to be the remnant of the vegetative tissue of the male gametophyte.
  
−
seed trichome elongation stage: A period of rapid elongation
+
==[https://sourceforge.net/tracker/?func=detail&aid=3080945&group_id=76834&atid=835555 common primordium]==
−
of hair initials without cell division for 16-25 days. (Lee JJ, 2007,
+
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)
−
Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell 15:952-964)
 
−
[Sources:PMID: 17905721, PMID: 12671090].
 
  
−
synonym: seed hair elongation stage
+
"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.
  
−
seed trichome secondary wall biosynthesis stage: A phase of
+
''We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.''
−
the massive amounts of secondary cell wall cellulose synthesis. (Lee JJ,
 
−
2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant Cell
 
−
15:952-964) [Sources: PMID:17905721, PMID:12671090].
 
  
−
synonym: seed hair secondary wall biosynthesis stage
+
==[https://sourceforge.net/tracker/?func=detail&aid=3082379&group_id=76834&atid=835555 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.
  
−
seed trichome maturation stage: A period of seed hair
+
''This definition is specific to grasses, and should be rephrased, so it is more general.''
−
maturation from 50 to 60 days post-anthesis (DPA).
 
−
(Lee JJ, 2007, Annals of Botany 100:1391-1401 and Ruan YL, 2003, Plant
 
−
Cell 15:952-964) [Sources: PMID:17905721, PMID:12671090].
 
  
−
synonym: seed hair maturation stage
+
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?
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
+
''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
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3205381&group_id=76834&atid=835555 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''
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3299941&group_id=76834&atid=835555 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''
 +
 
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007126 meiosis (GO:0007126)]
 +
 
 +
 
 +
'''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?
 +
 
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007140 male meiosis (GO:0007140)]
 +
 
 +
''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
 +
 
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007143 female meiosis (GO:0007143)]
 +
 
 +
''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.''
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3405173&group_id=76834&atid=835555 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)
 +
 
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 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 [http://dev.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0009027&session_id=4901b1372716379 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?''
 +
 
 +
* open tracker for pericarp cell types for PJ: "There are a number of pericarp components which may need PO terms".
 +
see: http://www.relata.info/docs/RT%202008%201.pdf
 +
 
 +
 
 +
 
 +
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 [http://www.flickr.com/photos/fostert/5236399328/ 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.
 +
 
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 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. [http://www.plantcell.org/content/early/2012/03/12/tpc.111.092924.abstract 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: [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3298006&group_id=76834 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
 +
 
 +
[http://onlinelibrary.wiley.com.ezproxy.proxy.library.oregonstate.edu/doi/10.1111/j.1469-8137.1973.tb02093.x/abstract link]
 +
 
 +
[http://books.google.com/books?id=xBR5KMLYGkUC&pg=PA8&lpg=PA8&dq=glandular+tapetum&source=bl&ots=P8Dfiew3_r&sig=0-Nr93OoExcRcqFFRTGnhKKMQ4A&hl=en&sa=X&ei=CUxkUaucFjriwLEqICoBA&ved=0CGAQ6AEwCA%23v=onepage&q=glandular%20tapetum&f=false#v=snippet&q=glandular%20tapetum&f=false link to book]
 +
 
 +
[http://ir.library.oregonstate.edu/xmlui/handle/1957/9976 link to OSU Thesis]
 +
 
 +
 
 +
==Organizing the types of plant cells ==
 +
 
 +
New term added: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/586/ native plant cell (PO:0025606)] and moved all the non cultured types of cells there, but it really needs some organization.
 +
 
 +
In CL, they are organized by type: 
 +
* absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
 +
 
 +
* ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
 +
 
 +
* barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
 +
 
 +
* defensive cell  CL:0000473  A cell whose primary function is to protect the organism.
 +
 
 +
* diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes.  xref_analog FMA:72300
 +
 
 +
* haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
 +
 
 +
* gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
 +
 
 +
* polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
 +
 
 +
* secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
 +
 
 +
* transporting cell ID: CL:0000627 A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances.  xref_definition TAIR:sr
 +
 
 +
* supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
 +
 
 +
* somatic cell ID: CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
 +
 
 +
* stem cell CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
 +
 
 +
* storage cell ID: CL:0000629 A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
 +
 
 +
* stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).
 +
 
 +
=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''
 +
 
 +
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ Stages of Plant Embryo Development]==
 +
 
 +
Currently: in Version #20, Aug 2013:
 +
 
 +
[[File:Plant Embryo Dev Stages.png]]
 +
 
 +
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). ''
 +
 
 +
===Revisions June-July 2014:===
 +
[[File:Screen Shot 2014-07-14 at 2.33.52 PM.png]]
 +
 
 +
* '''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=1#fde8 plant embryo development stage (PO:0007631)]''': A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the '''first cell division of a plant zygote (PO:0000423)''' and one of the following:
 +
** the beginning of the seed germination stage (PO:0007057) in seed plants,
 +
** the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
 +
** formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes,
 +
 
 +
 +
''An issue with the current definition is that it excludes the cotyledonary and true leaf formation stages, no?  Also, the seed germination stage (PO:0007057) is defined as starting with seed imbibition.  ''
 +
 
 +
 
 +
 
 +
 
 +
** Comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo development stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. No plant species undergoes all of the sub-stages listed here.
 +
 
 +
===Sub-classes:===
 +
 
 +
====plant proembryo stage (PO:0001180)]====
 +
'''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#859b plant proembryo stage (PO:0001180)]''': A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).
 +
*comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).
 +
 
 +
 
 +
-
 +
 
 +
====plant embryo globular stage (PO:0001185)====
 +
''' [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#58b6 plant embryo globular stage (PO:0001185)]''': A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.
 +
** comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
 +
 
 +
Comments from SF-RW:
 +
''"We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants."''
 +
 
 +
''"According to Howell 1998, "Proembryo is the term given to describe the embryo up to the stage when the protoderm can be recognized, which is usually the globular stage." (reference?)''
 +
 
 +
''"Of course, the problem with this is that we define the protoderm as arising from an apical meristem, and that is not the case in the embryo. Seems like some authors refer to it as an epidermis and some as a protoderm at this stage. I am not an expert in this, but I think I feel more comfortable with calling it a protoderm rather than a fully developed epidermis. In that case, I suggest modifying the definition of protoderm, which I will post on isssue 125."''
 +
 
 +
''presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)''
 +
 
 +
 
 +
''proposed definition RW:''
 +
* '''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).
 +
 
 +
New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).
 +
 
 +
''Propose re-revised def'n LC'':
 +
* '''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry, with the concomitant formation of a protoderm (PO:0006210), and the onset of a plant embryo bilateral stage (PO:0004507).
 +
 
 +
comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
 +
 
 +
I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).
 +
 
 +
 
 +
[http://www.sciencemag.org/content/266/5185/605.abstract?sid=b709ed1b-8241-480e-82d2-17a5d62dfbce Goldberg et al, 1994 Science]:
 +
""Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."
 +
 
 +
 
 +
 
 +
''Revised def'n LC:''
 +
 
 +
'''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry (with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).
 +
 
 +
 
 +
--
 +
 
 +
====plant embryo bilateral stage (PO:0004507)====
 +
'''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#1329 plant embryo bilateral stage (PO:0004507)]''':  was: Change from radial to bilateral symmetry takes place during this embryonic stage.
 +
 
 +
revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.
 +
 
 +
 
 +
''RW: New proposed definition:''
 +
 
 +
'''* plant embryo bilateral stage (PO:0004507)''': A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).
 +
 
 +
new comment: During a plant embryo expanding cotyledon stage, the embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) begin to elongate. A plant embryo bilateral stage contains the stage commonly known as the heart stage. Preceded by a plant embryo globular stage (PO:0001185).
 +
 
 +
Ref: [http://www.ncbi.nlm.nih.gov/pubmed/24784759 PMID:24784759]
 +
 
 +
 
 +
--
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
 
 +
--
  
−
This item has been open on SF since 6/2009
+
===Suggested revisions from Dora Szakonyi (from 2012-06-27):===
 +
* See Open SF tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/488/ #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:
  
−
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).
+
'''* 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)
  
−
Suggested stages:
+
'''* 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
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
+
'''* 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
  
−
-tuber initiation
+
'''* 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)
  
−
-tuber growth
+
'''* F mature embryo stage_PO:0001081'''
  
−
-tuber maturation
 
  
−
How we work these in will depend on restructuring of PGDSO
+
Older trackers:
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ #400 plant embryo stage]
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/ #426 spore and embryo dormant stages]
  
−
=Conductive cells and tissues for vascular and non-vascular plants=
+
References:
 +
* [https://www.mcdb.ucla.edu/Research/Goldberg/research/Pdf/Science-1994-Goldberg-605-14.pdf Goldberg et al, 1994 Science]
 +
* [http://masish.uab.cat/masish/images/maizeseedanatomy2.pdf maize embryo development]
  
−
THIS PART IS STILL UNDER CONSTRUCTION
+
=Other "To do" items:=
 +
* 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?
 +
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3405173&group_id=76834&atid=835555 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 [http://www.plantphysiol.org/content/162/3/1406.full 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?
  
−
==conductive tissue for bryophytes and vascular plants==
+
* fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  
−
trace as possible name for category for veins, central strands, and costas
+
* 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
  
−
===vascular tissue===
+
* Need to revisit [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/145/  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.''
  
−
For vascular plants, we have the class:
+
* Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see [[POC_Conf._Call_10-29-13]])
  
−
'''portion of vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
+
* 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.
  
−
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
 
  
−
part_of vascular bundle (which is part_of vascular system)
 
  
−
This is okay, but suggest that we make it a child of the new class '''portion of axial tissue''' (see below), and also change definition to include xylem '''or''' phloem.
 
  
  
−
'''Proposed definition:''' A portion of plant tissue that has as parts tracheary elements or sieve tube members.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/499/ whole plant flowering stage PO:0007016]==
 +
* Now that we have revived the flowering stages, we need to revisit the whole plant flowering stages:
  
−
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or may occur as scattered vascular bundles. May include other types of tissue, such as fibers.
+
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.  
  
−
part_of vascular system (should add vascular system participates_in sporophytic phase)
+
''This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants''
  
−
currently part_of vascular bundle. Removed this relation, because it is not true for all plants. Also vascular bundle is now a portion of vascular tissue, so it can't be part_of.
+
* 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. ''
  
−
'''children of vascular tissue:'''
 
  
−
'''hydathode''' (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]
+
==fruit development stages (PO:0001002)==
 +
* See [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdDZEMzBVdXJWZjVubkJNVlBtSmQ2WFE&usp=sharing Google Doc] for revisions in progress.
  
−
Should be is_a cardinal organ part. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?
+
* 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.
  
−
'''proposed definition:''' A cardinal organ part that releases water through a pore.
+
* 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.  
  
−
Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.
+
* 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 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.
  
−
'''leaf vein''' (PO:0005417) - see more below details below
+
[https://sourceforge.net/tracker/index.php?func=detail&aid=3577380&group_id=76834&atid=835555 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).
  
−
'''phloem''' (PO:0005417): A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]
 
  
−
'''proposed definition:''' A portion of vascular tissue that has as parts sieve tube members.
+
[http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=GO&termId=GO%3A0009835&termName=fruit%20ripening 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.
  
−
Comment: Functions in the conduction of organic substances in vascular plants.
+
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]
  
−
'''metaphloem''' (PO:0006076): Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
+
==plant organ development stage (PO:0025339) and child terms:==
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/548/ 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 )
  
−
'''proposed definition:''' A portion of phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
+
* moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
  
 +
[[File: phyllome_snap_shot.jpg]]
  
−
'''protophloem''' (PO:0006077): The first-formed elements of the primary phloem.
+
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
  
−
'''proposed definition:''' A portion of phloem tissue that has as parts the first-formed elements of the primary phloem.
+
==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
  
−
'''tracheid bar''' (PO:0019026): A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]
+
** 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.
  
−
-should be is_a xylem
+
* 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.
  
  
−
'''xylem''' (PO:0005352): A portion of vascular tissue composed of (''that has as parts'') xylem elements.
+
''Need to look at the fern sporangia- that is the reproductive structure for those plants''
  
  
−
'''vascular bundle (PO:0005020):''' A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]
 
  
−
This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.
+
* This would parallel the two existing sub-classes:
  
−
'''proposed definition:''' A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.
+
==inflorescence development stage (PO:0021004)and sub-classes==
 +
* Currently linked to  tracker for: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/517/ shoot system development stages and child terms]
  
−
Comment: Usually contains both xylem or phloem. May also contain other types of tissue such as plant fibers or vascular cambium. May also contain portions of ground tissue.
+
* Currently this has two sub-classes:
 +
 +
** PO:0021004 : inflorescence initiation stage [0]
 +
** PO:0007037 : inflorescence bifurcation stage [0]
  
−
part_of vascular system
+
* 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.
  
−
====New children of plant tissue:====
+
==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)
  
−
'''hydrome:''' A portion of axial tissue that has as parts hyrdoids.
+
==collective phyllome structure development stage (PO:0025578) and child terms==
  
−
Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support, similar to xylem in vascular plants.
+
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/547/ 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).  
  
−
Synonyms: hydrom, leptoxylem (Hebant)
+
* 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).
  
−
'''leptome:''' A portion of axial tissue that has as parts leptoids.
+
** '''calyx development stage (PO:0007603):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
  
−
Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.  
+
** '''corolla development stage (PO:0007604):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).  
  
−
Synonyms: leptom, leptophloem (Hebant)
+
** '''gynoecium development stage (PO:0007606):''' A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
  
 +
[[File: collective_phyllome_snap_shot.jpg]]
  
−
'''central strand:''' A unit strand of axial tissue that has as part hydrome or leptome.
+
===New term flower bract development stage (new po:id)===
 +
 +
flower bract development stage (new po:id):  
  
−
Comment: Often contains both hydrome and leptome. Found in bryophytes located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the costa of a non-vascular leaf.
+
- will be parent to lemma development stage and palea development stage
  
−
synonyms: conducting strand, central cylinder
+
* 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]
  
−
'''stereome:''' A portion of axial tissue that has as parts stereids.
+
==anther development stage (PO:0001004) and its child terms==
 +
* [https://sourceforge.net/tracker/?func=detail&aid=3613820&group_id=76834&atid=835555 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):
  
−
Comment: Found in bryophytes.
+
* 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.  
  
−
From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.
+
Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498
  
 +
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 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
  
−
'''portion of plant fiber:''' Currently fibers are plant cell types, but they should also be a tissue type.
+
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]
  
−
''Proposed definition: A portion axial tissue that has as parts fiber cells.
+
So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)
  
−
Comment: Contains elongated, lignified fiber cells that are dead at maturity.
 
  
−
'''phloem fiber:''' A portion of plant fiber that has as parts phloem fiber cells.
+
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).
  
−
'''xylem fiber:''' A portion of plant fiber that has as parts xylem fiber cells.
+
Suggested stages:
 +
* tuber initiation
 +
* tuber growth
 +
* tuber maturation
  
−
===leaf vein, midrib, costa===
+
''Would these be the same for the two different types of tubers? Also need: tuber dormancy''
  
−
*'''leaf vein (PO:0020138):''' A strand of vascular tissue in the leaf blade.
+
* sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  
−
is_a portion of vascular tissue; part_of leaf vascular system
+
* 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
  
−
This term only applies to vascular leaves, and should be renamed vascular leaf vein.
 
  
−
'''proposed definition, vascular leaf vein (PO:0020138):''' A strand of vascular tissue that is part of a leaf lamina in a vascular leaf.
+
===Further info and references:===
 +
[http://www.cals.uidaho.edu/potatoes/potatoproductionsystems/topics/growth&development.pdf Potato Growth & Development]
  
−
part_of leaf vascular system, part_of leaf lamina
+
[http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2005.00141.x/full Tuber on a chip: differential gene expression during potato tuber development]
  
 +
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540956/pdf/plntphys00369-0069.pdf Growth of the Potato Tuber]
  
−
*Suggest new term '''primary leaf vein''': A vascular leaf vein that originates from the base of a leaf lamina  where it attaches to the petiole or to the shoot axis if no petiole is present.
+
=xylem developmental stages: =
  
−
Comment: A leaf may have more than one primary vein. The central primary vein is the midvein.
+
See discussions of primary xylem on [http://wiki.plantontology.org/index.php/POC_Conf._Call_6-11-13 POC_Conf._Call_6-11-13]
  
 +
Existing definitions:
  
−
*'''midvein (PO:0020139):''' The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]  
+
'''* 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]  
  
−
Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ". Suggest we rename it '''vascular leaf midvein''' to distinguish it from '''costa'''.
+
*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''
  
−
'''proposed definition of vascular leaf midvein:''' A primary leaf vein that is the central vein of a leaf lamina in a vascular leaf.
+
=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)
  
−
Comment: Often the most prominent vein of a vascular leaf.
+
==whole plant fruit ripening stage (PO:0007010)==
 +
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3565059&group_id=76834&atid=835555 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.  
  
−
broad synonyms: mid rib, midrib, mid-rib
+
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.
  
−
related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
 
  
 +
  **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**
  
−
*Moss Ontology has requested the term '''midrib''' for bryophytes. It is often called a '''costa'''.
+
===See comments from BS from email:===
 +
* On Wed, Sep 18, 2013
  
−
''Proposed definition for costa:''' A central strand that is part of a non-vascular leaf.
+
- A lot of this needs to go, I think:
  
−
Comment: Found in bryophytes, especially mosses.
+
- 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 ...'
  
−
part_of non-vascular leaf
+
[[File:WPFRS.png]]
  
−
broad synonyms: mid rib, midrib, mid-rib
+
===Proposed Revisions to sub-classes:===
  
−
====Refs:====
+
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.
  
−
Sperry 2003, IJPS; Hebant 1977;
+
need to open tracker for this set:
  
 +
'''* whole plant beginning of fruit ripening stage (PO:0007036):'''
  
−
==conductive and related cell types for bryophytes and vascular plants==
+
current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
  
−
See also [https://sourceforge.net/tracker/?func=detail&aid=3386970&group_id=76834&atid=835555 conducting cells for non-vascular plants].
+
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.
  
−
===Current parent: axial cell===
+
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.
  
−
'''axial cell (PO:0000081):''' A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]
+
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 ''
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
* whole plant early fruit ripening stage (PO:0007001)
  
−
'''Existing descendents of axial cell:'''
+
current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening
  
−
sieve tube member (PO:0000289, alt: PO:0000286)
+
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.
  
−
phloem fiber (PO:0004519)
+
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.
  
−
xylem element (PO:0000273)
+
Add related synonyms:
 +
* middle of veraison''
 +
*BBCH principal growth stage 83
  
−
>tracheary element (PO:0000273)
+
'''* 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.
  
−
>>tracheid (PO:0000301)
+
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.
  
−
>>vessel member (PO:0002003)
+
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.
  
−
>xylem fiber (PO:0000274)
+
'''* whole plant late fruit ripening stage (PO:0007050):'''
  
−
>>fiber tracheid (PO:0000355)
+
current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.
  
−
>>libriform fiber (PO:0004520)
+
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.
  
−
>>septate fiber (PO:0004521)
+
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):'''
  
−
The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).
+
current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
  
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system
+
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.
  
−
At the bryophyte term meeting on 4-25-2011 (RW and MAG present), we decided that axial cell was not the correct term to use to describe all of the elongated cells associated with conducting tissue in plants. They are different cell types and have different origins, so they should not all be grouped together.
+
related synonyms:
 +
* BBCH principal growth stage 89
 +
* grape E-L stage: 38;  Berries ripe for harvest
  
 +
=GO requests:=
  
−
===New proposed hierarchy (children of plant cell):===
+
==[https://sourceforge.net/p/geneontology/ontology-requests/9075 Multicellular organism senescence/aging (GO:0010259)]==
  
−
plant cell
+
* 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.
  
−
>hydroid
 
  
−
>leptoid
+
Link to PO tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/392/ gametophyte/sporophyte senescent stage]
  
−
>vascular cell (new term)
 
  
−
>>sieve tube member
+
''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. ''
  
−
>>tracheary element
+
==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.
  
−
>>>tracheid
+
''includes tracheids''
  
−
>>>vessel member
+
This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.
  
−
>>phloem fiber cell
+
* symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
  
−
>>xylem fiber cell
+
- all the plasma connected, through plasmodesmata, transport through the cytoplasm
  
−
>>other kinds of fiber cells
+
See: Link to diagram Apoplast_and_symplast_pathways
  
−
>ground tissue cell (PO:0025030)
+
See: Apoplastic versus Symplastic Pathways in roots
  
−
>>stereid
+
* Suggest revised GO definitions for apoplast and symplast and add transport terms
  
−
>>collenchyma cell
+
Parent term:
  
−
>>sclerenchyma cell (PO:0000077)
+
* 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.
  
−
>>>fiber cell (new term)
+
* apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)  
  
−
>>>sclerid (new term)
+
* 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
  
−
'''Proposed definitions:'''
+
=Wood ontology terms=
 +
See separate page: [[Wood Ontology PO and GO Term Development]]
 +
 
 +
=[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]=
 +
 
 +
Submitted by Rich Zobel (Nov 2009).  Still need to work on definitions for these terms.
  
−
'''fiber cell:'''
+
=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).
  
−
'''vascular cell:'''
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3609139&group_id=36855&atid=440764 epidermis/epidermal cell : plant v. animal]==

Latest revision as of 20:26, 17 July 2014

This page is a place holder for us to put items that are being worked on or under development.

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



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

Requests from SF- Anatomy terms in progress...

Request for "rind" or outer layer of a maize or sorghum stem

Request for a term for the outer covering of a maize or sorghum stalk.

link to #596

structure and properties of sorghum stalks


Propsed new terms:

Abscission Zones

June 2014

Added new terms and revised existing:

Ref: http://www.plantphysiol.org/content/158/1/439 (PMID:22106095)

See also:

  • Mao et al., Nature, 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development

(http://www.nature.com/nature/journal/v406/n6798/full/406910a0.html)

New term needed: flower pedicel abscission zone (PO:0025608)

flower pedicel abscission zone (PO:0025608): An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).

PMID:24744429 Nakano T, et al. (2014) The AP2/ERF transcription factor SlERF52 functions in flower pedicel abscission in tomato. Journal of Experimental Botany.

http://jxb.oxfordjournals.org/content/early/2014/04/15/jxb.eru154.full

Added relations:

  • flower pedicel abscission zone (PO:0025608) part_of flower pedicel
  • fruit pedicel (PO:0004536) develops_from flower pedicel (PO:0009052)
  • fruit pedicel abscission zone (PO:0025605) develops_from flower pedicel abscission zone (PO:0025608)

Renamed existing term: pedicel > flower pedicel (PO:0009052)

Currently: pedicel (PO:0009052): An inflorescence branch (PO:0009081) that supports an individual flower (PO:0009046) in an inflorescence (PO:0009049).

Renamed: "flower pedicel" to differentiate it from the fruit pedicel (PO:0004536), which is an infructescence branch.

Renamed existing term: flower abscission zone > floral organ abscission zone (PO:0006502)

flower abscission zone (PO:0006502):

Was: Zone at base of the flower that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the flower and its parts.

This was revised as the AZ of a whole flower is different that that of the floral organs (sepals, petals and filaments).

Revised name and definition:

  • floral organ abscission zone (PO:0006502): An abscission zone (PO:0000146) at the base of a flower (PO:0009001) where a floral organ (PO:0025395) separates during floral organ abscission (GO:0010227).

Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower

New term request: microgametophtye development stage

Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.

Question: how do the megagametophyte development stage (PO:0007621) and proposed microgametophtye development stage (new) fit in with the gametophyte development stage (PO:0028003)??

- multicellular plant gametangium (PO:0025124)- a plant organ- children: antheridium (PO:0025125) and archegonium (PO:0025126)

- unicellular plant gametangium (PO:0025521): a plant cell- no child terms...

Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.

  • plant ovule (PO:0020003): A plant organ (PO:0009008) that has as parts a nucellus (PO:0020020) in which a female gametophyte (PO:0025279) is located, one or two integuments (PO:0020021), and a funicle (PO:0020006).
  • Moved megagametophyte development stage (PO:0007621) to be is_a gametophyte development stage (PO:0028003). part_of ovule development
    • Revised definition: A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.added dbxref to: OBO_SF2_PO: 589

This definition should be worked on further, and the child terms need work as well.

  • Created new term: microgametophtye development stage (PO:0025602): A gametophyte development stage (PO:0028003) during which a microgametophyte (PO:0025280) develops.
  • pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).

Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.

androecium (PO:0009061): A collective phyllome structure (PO:0025023) composed all of the stamens (PO:0009029) in a flower (PO:0009046).


  • moved pollen development stage (PO:0001007) to be is_a child of the new term: microgametophtye development stage (PO:0025602). part of androecium development stage_ (PO:0007605)

Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.

Revised definition: pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.

This definition should be worked on further, and the child terms need work as well.

caryopsis hull (PO:0006000)

  • 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]
    • Comment: None

I think in maize, the hull is actually pericarp tissue, perhaps we should not include the last part.

founder cells

New terms: phyllome founder cell (PO:0025586)]: A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).

Comment: As a group, the phyllome founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a phyllome anlagen (PO:0025430). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

PMID:12610522

vascular leaf founder cell (PO:0025592): A phyllome founder cell (PO:0025586) that is part of a vascular leaf anlagen (PO:0025431).

Comment: As a group, the vascular leaf founder cells encompass several layers of the shoot apical meristem (PO:0020148) and form a vascular leaf anlagen (PO:0025431). Founder cells do not function as stem cells but rather have a determinate fate and can be defined by histological, clonal and molecular criteria.

Revised: vascular leaf anlagen formation stage PO:0001003: A vascular leaf initiation stage (PO:0007040) during which the vascular leaf founder cells (PO:0025592) of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).

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)

Cortex terms.png


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 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.


  • 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


Note: prothallium is a synonym for thallus (PO:0030027) and ....

How does prothallial cell compare to microgametophyte vegetative cell?

prothallial cell (PO:0025533): current 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.

Revised: A native plant cell (PO:0025606) which is vegetative and develops from the division of the microspore (PO:0020048) of vascular plants other than angiosperms.

Revised comment: The prothallial cell (PO:0025533) is part of the microgametophyte (PO:0025280) and is believed to be the remnant of the vegetative tissue of the male gametophyte.

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

meiosis (GO:0007126)


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?

male meiosis (GO:0007140)

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

female meiosis (GO:0007143)

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?

  • open tracker for pericarp cell types for PJ: "There are a number of pericarp components which may need PO terms".

see: http://www.relata.info/docs/RT%202008%201.pdf


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

link

link to book

link to OSU Thesis


Organizing the types of plant cells

New term added: native plant cell (PO:0025606) and moved all the non cultured types of cells there, but it really needs some organization.

In CL, they are organized by type:

  • absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
  • ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  • barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
  • defensive cell CL:0000473 A cell whose primary function is to protect the organism.
  • diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes. xref_analog FMA:72300
  • haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  • gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
  • polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
  • secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
  • transporting cell ID: CL:0000627 A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances. xref_definition TAIR:sr
  • supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  • somatic cell ID: CL:0002371 A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell).
  • stem cell CL:0000034 A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
  • storage cell ID: CL:0000629 A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose.
  • stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).

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

Currently: in Version #20, Aug 2013:

Plant Embryo Dev Stages.png

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).

Revisions June-July 2014:

Screen Shot 2014-07-14 at 2.33.52 PM.png

  • plant embryo development stage (PO:0007631): A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and one of the following:
    • the beginning of the seed germination stage (PO:0007057) in seed plants,
    • the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
    • formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes,


An issue with the current definition is that it excludes the cotyledonary and true leaf formation stages, no? Also, the seed germination stage (PO:0007057) is defined as starting with seed imbibition.



    • Comment: Succeeds a plant zygote stage (PO:0001097). The plant embryo development stage generally starts after the first division of a plant zygote (PO:0000423), but in the case of a nucellar (adventitious) plant embryo (PO:0004537), somatic plant embryo (PO:0025302), microspore-derived cultured plant embryo (PO:0025305), and other embryos that arise through apogamy, it begins after the division of a single cell that is not a zygote. The end of the embryo stage varies among taxa. No plant species undergoes all of the sub-stages listed here.

Sub-classes:

plant proembryo stage (PO:0001180)]

plant proembryo stage (PO:0001180): A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).

  • comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).


-

plant embryo globular stage (PO:0001185)

plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.

    • comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.

Comments from SF-RW: "We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants."

"According to Howell 1998, "Proembryo is the term given to describe the embryo up to the stage when the protoderm can be recognized, which is usually the globular stage." (reference?)

"Of course, the problem with this is that we define the protoderm as arising from an apical meristem, and that is not the case in the embryo. Seems like some authors refer to it as an epidermis and some as a protoderm at this stage. I am not an expert in this, but I think I feel more comfortable with calling it a protoderm rather than a fully developed epidermis. In that case, I suggest modifying the definition of protoderm, which I will post on isssue 125."

presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)


proposed definition RW:

  • plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).

New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).

Propose re-revised def'n LC:

  • plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry, with the concomitant formation of a protoderm (PO:0006210), and the onset of a plant embryo bilateral stage (PO:0004507).

comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.

I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).


Goldberg et al, 1994 Science: ""Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."


Revised def'n LC:

plant embryo globular stage (PO:0001185): A plant embryo development stage (PO:0007631) that occurs during the interval between when a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry (with the concomitant formation of a protoderm (PO:0006210)), and the onset of a plant embryo bilateral stage (PO:0004507).


--

plant embryo bilateral stage (PO:0004507)

plant embryo bilateral stage (PO:0004507): was: Change from radial to bilateral symmetry takes place during this embryonic stage.

revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.


RW: New proposed definition:

* plant embryo bilateral stage (PO:0004507): A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).

new comment: During a plant embryo expanding cotyledon stage, the embryo axis (PO:0019018) and embryo cotyledons (PO:0025470) begin to elongate. A plant embryo bilateral stage contains the stage commonly known as the heart stage. Preceded by a plant embryo globular stage (PO:0001185).

Ref: PMID:24784759


--




--

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)

  1. two-celled stage in Arabidopsis
  2. four-celled stage in Arabidopsis (= quadrant stage)
  3. eight-celled stage in Arabidopsis (= octant stage)

* Similarly, for C globular stage_PO:0001185 new child terms:

  1. dermatogen stage in Arabidopsis (=16-cell stage)
  2. early-globular stage in Arabidopsis (32-cell stage)
  3. mid-globular stage in Arabidopsis
  4. late-globular stage in Arabidopsis

* For D bilateral stage_PO:0004507

  1. Transition stage in Arabidopsis (=triangular stage)
  2. early-heart stage in Arabidopsis
  3. mid-heart stage in Arabidopsis
  4. late-heart stage in Arabidopsis

* E expanded cotyledon stage_PO:0001078 Linear cotyledon stage embryo

  1. early-torpedo stage in Arabidopsis
  2. mid-torpedo stage in Arabidopsis
  3. late-torpedo stage in Arabidopsis
  4. Bent cotyledon stage (curled cotyledon stage/walking stick stage)

* F mature embryo stage_PO:0001081


Older trackers:

References:

Other "To do" items:

  • 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.



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.


fruit development stages (PO:0001002)

  • 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 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:

  • moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.

Phyllome snap shot.jpg

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.
  • 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 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).

Collective phyllome snap shot.jpg

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


Further info and references:

Potato Growth & Development

Tuber on a chip: differential gene expression during potato tuber development

Growth of the Potato Tuber

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 ...'

WPFRS.png

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).

epidermis/epidermal cell : plant v. animal

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