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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=Vascular tissues and cell types=
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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=3476730&group_id=76834&atid=835555 leaf vein, primary vein, mid vein]==
 
  
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''These changes have been made to the obo file.''
 
  
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*'''leaf vein (PO:0020138)'''
 
  
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May want to rename "leaf lamina vein".
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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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'''current definition:''' A strand of vascular tissue in the leaf blade.
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-This will also be helpful when applying for new grants
  
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'''revised definition, leaf lamina vein (PO:0020138):''' A vascular bundle that is part of a leaf lamina vascular system.
+
-it would be helpful to have a detailed guide on our wiki for collaborators
  
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part_of leaf lamina vascular system
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* Need to update the [[Annotation_Association_File_Format]] page
  
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synonym: leaf lamina vascular bundle
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=Requests from SF- Anatomy terms in progress...=
  
 +
==Request for "rind" or outer layer of a maize or sorghum stem==
  
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*'''primary leaf vein (new term)'''
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Request for a term for the outer covering of a maize or sorghum stalk.
  
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proposed def'n: A leaf vein (PO:0020138) that connects directly to a petiole vascular system (PO:0000052) or a shoot axis vascular system (PO:0000039).
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[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/596/ link to #596]
  
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Comment: Generally the largest and most prominent of the leaf veins. A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139). Vein orders only apply to hierarchically branching vein patterns, not to dichotomously branching vein patterns, as in some ferns and gymnosperms.
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[http://www.sciencedirect.com/science/article/pii/S2090447912000524 structure and properties of sorghum stalks]
  
  
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*'''midvein (PO:0020139)'''
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Propsed new terms:
  
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'''revised def'n:''' A primary leaf vein (PO:0025413) that is the central vein of a vascular leaf (PO:0009025).
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=='''Abscission Zones'''==
 +
June 2014
  
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Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf (PO:0025075).
+
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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broad synonyms: mid rib, midrib, mid-rib; exact synonym: vascular leaf midvein; related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
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Ref: http://www.plantphysiol.org/content/158/1/439 (PMID:22106095)
  
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We already have terms for secondary, tertiary, quaternary, and higher order veins.
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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)
 +
* 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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==Primary and secondary growth, etc.==
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===New term needed: flower pedicel abscission zone (PO:0025608)===
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''request has been made to GO.''
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[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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===proposed terms for GO===
 
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'''primary growth (new term):'''
 
  
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'''proposed definition:''' Growth of a plant structure from the time of its initiation by an apical meristem until its expansion is completed. Ref: Esau (ISBN:0471245208 or 9780471245209)
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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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comment: Has its inception in the apical meristems (PO:0020144) and continues in their derivative meristems - protoderm (PO:0006210) and procambium (PO:0025275) - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.  
+
http://jxb.oxfordjournals.org/content/early/2014/04/15/jxb.eru154.full
  
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is_a growth (GO:0040007)
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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)
  
 +
===Renamed existing term: pedicel > flower pedicel (PO:0009052)===
  
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'''secondary versus lateral growth'''
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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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GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290 
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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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Secondary growth from the vascular cambium does not occur in monocots, but there is a secondary thickening meristem that may be discontinuous from apical meristem that can contribute to another kind of secondary growth. See paper by [http://www.jstor.org/stable/10.2307/4354165 Rudall et al.] in Botanical Review (JSTOR:4354165).
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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)]:
  
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I suggest that GO add a general term for '''lateral growth''' (to mirror PO, see below), with specific subtypes for growth from the vascular cambium and growth from other types of lateral meristems.
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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).
  
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'''lateral growth (GO:new term):''' Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).
+
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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Comment: Includes thickening of plant axes (PO:0025004) due to the activity of a cambium (PO:0005597), known as secondary growth and found in most gymnosperms and dicotyledons, a primary thickening meristem (PO:0005039) as found in many monocotyledons, some ferns and some cycads, or secondary thickening meristem, (PO:0025414) as found in some monocotyledons.
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Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower
  
 +
== New term request: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/589/ microgametophtye development stage]==
  
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'''proposed new def., secondary growth (GO:0080117):''' Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of secondary vascular tissues by the vascular cambium (PO:0005598). Ref: Esau (ISBN:0471245208 or 9780471245209)
+
'''Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.'''
  
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Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium  or phellogen (PO:0005599). Monocotyledons do not have secondary growth, but may undergo primary thickening (GO:xxx) or secondary thickening (GO:xxx), which can give the appearance of secondary growth. Primary and secondary growth can occur simultaneously in the same organism.
+
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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Add exact synonym "cambial secondary growth", which is makes the meaning clearer.
+
- 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...
  
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'''secondary thickening (GO:new term):''' Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:0025414).
+
''Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.''
  
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comment: Occurs in shoot axes in some monocotyledons such as Dracaena, and rarely in roots of monocotyledons. Distinct from primary thickening, because it is distant from and generally discontinuous with the apical meristem.
+
* 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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References: Fahn 1990, ISBN:0080374903; Rudall 1991, JSTOR:4354165
+
* 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.
  
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'''primary thickening (GO:new term):'''  Lateral growth of a plant axis (PO:0025004, shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)  
+
* pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).
  
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comment: Occurs in shoot axes and rarely in roots in many monocotyledons.
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''Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.''
  
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Ref: JSTOR:4354165, Rudall 1991; and Esau ISBN:0471245208
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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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'''diffuse secondary thickening (GO:new term)''': Lateral growth of the older parts of a stem that occurs when the central parenchyma cells and the not yet fully differentiated fiber cells of the bundle sheaths continue to undergo cell division and expansion for a long period of time, leading to an increase in girth of the stem.
+
* 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)
  
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comment: Occurs in the stems (PO:0009047) of some Arecaceae (palms).
+
Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.
  
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Ref.: Fahn 1990, ISBN:0080374903
+
Revised definition:
 +
pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.
  
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==[https://sourceforge.net/tracker/?func=detail&aid=3481640&group_id=76834&atid=835555 PO terms for lateral meristems]==
+
''This definition should be worked on further, and the child terms need work as well.''
  
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''These edits have been done in the obo file, except as noted below.''
+
==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.''
  
−
See [[Items_for_future_meetings#Primary_and_secondary_growth.2C_etc.]] for more details on terms that will be requested in GO.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/575/ founder cells]==
 +
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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The PO has a general term for lateral meristem, of which cambium is a subtype:
+
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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[[File:lateral_meristem1.jpg]]
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PMID:12610522
  
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'''lateral meristem (PO:0020145)'''
+
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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'''revised def'n:''' A portion of meristem (PO:0009013) tissue located parallel to the circumference of a plant organ (PO:0009008).
+
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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comment: Participates in lateral growth (request has been made for lateral growth in GO) of a plant organ, primarily shoot axes (PO:0025029) and roots (PO:0009005). Contrast with apical meristem (PO:0020144).
+
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==
  
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'''cambium (PO:0005597)'''
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See notes from discussion on POC call [[POC_Conf._Call_9-24-13]]
  
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'''revised def'n:''' A lateral meristem that is part of a plant axis (PO:0025004) and has as part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files.  (Ref.: Esau)
+
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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comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).
+
[[File:Cortex terms.png]]
  
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''Changed cambial initial from part_of vascular cambium to part_of cambium, because that is how it was defined.''
 
  
 +
Fill in details here.....
  
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'''root lateral meristem (PO:0006308)'''
 
  
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''didn't do this edit yet''
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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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This is just a lateral meristem in the root, which is only the cambium (vascular cambium and phellogen). Therefore, it makes more sense to call it a root cambium.
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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.
  
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'''proposed new name and def'n: root cambium:''' A cambium that is part of a root.
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-Added Narrow synonyms: adnate perianth and connate perianth
  
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This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.
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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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Suggest that we also add root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium. Set up root cambium and shoot lateral meristem as XPs, so we don't have multiple inheritance.
+
*[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
  
 +
*[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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'''vascular cambium (PO:0005598)'''
+
* [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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'''revised def'n:''' A cambium (PO:0005597) that is located between and gives rise to secondary xylem (PO:0005848) and secondary phloem (PO:0005043).
+
***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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comment: Vascular cambium gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis (PO:0025004).
 
  
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''Got rid of relation vascular cambium part_of vascular bundle.''
+
*[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).  
  
 +
*[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).
  
−
'''cork cambium/phellogen (PO:0005599)'''
+
**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.
  
−
'''revised def'n:''' A cambium (PO:0005597) that is part of a shoot axis periderm (PO:0005048) and produces phellem (PO:0004003) and phelloderm (PO:0005050).
+
==Need to look at these associated terms:==
 +
* is_a:
 +
** PO:0025324 : banner petal [0]
 +
** PO:0025326 : keel petal [0]
  
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comment: Cork cambium is located between the phellem and phelloderm and produces phellem toward the outside and phelloderm toward the inside of a plant axis.
+
* 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]
  
  
−
'''primary thickening meristem (PO:0005039)'''
+
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]
  
−
Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.  
+
* 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
  
−
'''revised def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0009047) and has a parts multiple layers of meristematic cells (PO:0004010) located near the shoot apical meristem (PO:0020148).
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/98/ epicalyx] ==
  
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comment: Contributes to primary thickening of a stem (PO:0009047), adventitious (shoot-borne) root (PO:0000042) formation, and formation of linkages between shot axis (PO:0000039), leaf (PO:0000036), and root (PO:0003011) vascular systems. Contiguous with the shoot apical meristem (PO:0020148) in some species, but not all. Produces more or less distinct vascular bundles (PO:0005020) surrounded by ground tissue (PO:0025059), as opposed to the more or less continuous xylem (PO:0005352) and phloem (PO:0005417) produced by a vascular cambium (PO:0005598). A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
+
* 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.''
  
−
'''secondary thickening meristem (new term)'''
+
Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators] 
  
−
'''proposed def'n:''' A shoot lateral meristem (PO:0006344) that is part of a stem (PO:0025029) not contiguous with the shoot apical meristem (PO:0020148) and has a parts multiple layers of meristematic cells (PO:0004010).
+
''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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comment: Contributes mainly to formation of the body of a stem (PO:0009047), but may also produce adventitious (shoot-borne) roots (PO:0000042). May be continuous or discontinuous with the primary thickening meristem (PO:0005039). Found in some monocot species of the Liliales and Asperigales.
+
''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.
  
 +
''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.''
  
−
'''Other types of lateral meristems'''
+
==arilloid and arillode and caruncle==
  
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''didn't do these edits yet''
+
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''
  
−
PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel meristem (PO:0009107), plus their subtypes.
+
* '''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.
  
−
Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches develop from apical meristems, not a lateral meristem.
+
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.
  
−
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.
+
Synonyms exact: ariloide (Spanish)
  
−
Shoot lateral meristem should be set up as an xp, so subtypes and be inferred, just like root lateral meristem. Same for root meristem and shoot meristem.
+
*'''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.
  
−
'''inflorescence lateral meristem (PO:0009105)'''
+
Synonyms exact: carúncula (Spanish)
  
−
'''current def'n:''' The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.
+
*aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
  
−
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
+
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.
  
−
'''ear lateral meristem (PO:0009110)'''
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609179&group_id=76834&atid=835555 floral node]==
  
−
This should be called '''ear inflorescence branch meristem''', and be a subtype of inflorescence branch meristem (PO:0009105). Will need to add XP definitions to the different types of meristems so that they don't have dual parentage (e.g., ear inflorescence meristem XP of is_a inflorescence meristem and part_of ear inflorescence).
+
suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise
  
−
'''revised def'n:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.
+
Parent/relationship: is_a shoot node (PO:0005004)
  
−
==conductive and related cell types==
+
Submitted: Johnny Lloyd
−
===Current parent: axial cell===
 
−
'''Existing structure:'''
 
  
−
axial cell (PO:0000081)
 
  
−
>sieve tube member (PO:0000289, alt: PO:0000286)
+
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
  
−
>phloem fiber (PO:0004519)
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/535/ spine petiole]==
  
−
>xylem element (PO:0000273)
+
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
  
−
>>tracheary element (PO:0000273)
+
The petiole abscisses longitudinally and the blade withers.
  
−
>>>tracheid (PO:0000301)
+
See the photo and description on this page: [http://waynesword.palomar.edu/ecoph30a.htm "Spines From Modified Petioles"]
  
−
>>>vessel member (PO:0002003)
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609178&group_id=76834&atid=835555 adventitious branch]==
  
−
>>xylem fiber (PO:0000274)
 
  
−
>>>fiber tracheid (PO:0000355)
+
Definition: A shoot axis (PO:00025029) that develops in an unusual place
  
−
>>>libriform fiber (PO:0004520)
+
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
  
−
>>>septate fiber (PO:0004521)
 
  
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481651&group_id=76834&atid=835555 axial cell]====
+
adventitious shoot axis
−
'''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]
 
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
==shoot-borne root (PO:0000042)==
 +
synonym: adventitious root
  
−
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).
+
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
  
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.
+
==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.
  
−
See [[Items for future meetings#other wood terms]], below.
+
*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.  
  
−
===New proposed hierarchy (children of plant cell):===
+
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.
  
−
plant cell
 
  
−
>sieve element (new term)
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/521/ Ultimate Unit (UU)]==
 +
Requested by:  Corvez Adele  Created: 2013-02-01
  
−
>>sieve tube member (syn.: sieve tube element)
+
* 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
  
−
>>sieve cell (new term)
+
suggested parentage: Ultimate unit is_a cardinal organ part
  
−
>tracheary element
+
==moss capsule==
 +
need to open tracker for this: [https://sourceforge.net/tracker/?func=detail&aid=3140824&group_id=76834&atid=835555 moss capsule]
  
−
>>tracheid
+
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell] and prothallium ==
  
−
>>vessel member
+
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
  
−
>ground tissue cell (PO:0025030)
+
prothallial cell (PO:0025533):
  
−
>>sclerenchyma cell (PO:0000077)
+
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.
  
−
>>>sclerid (new term)
+
''should add the PO id for microgametophyte (PO:0025280) to the definition''
  
−
>>>fiber cell (new term)
 
  
−
>>>>phloem fiber cell
+
For reference about prothallial cells in gymnosperms see:
  
−
>>>>xylem fiber cell
+
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
  
−
>>>>other kinds of fiber cells?
+
Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
  
−
===New definitions - [https://sourceforge.net/tracker/?func=detail&aid=3481654&group_id=76834&atid=835555 sieve elements]===
 
−
Definitions from Esau's Anatomy of Seed Plants
 
  
−
'''sieve element (new term)'''
+
Note: prothallium is a synonym for thallus (PO:0030027) and ....
  
−
From Esau (glossary): The cell in the phloem tissue concerned mainly with longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
+
How does prothallial cell compare to microgametophyte vegetative cell?
  
−
Also from Esau (in text): Their principal morphological characteristics are sieve areas (modified pits) in their walls and the absence of nuclei in mature protoplasts.
+
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.
  
−
'''proposed def.:''' A plant cell that is part of a portion of phloem tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.
+
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.
  
−
Comment: Sieve cells function mainly in longitudinal conduction of organic solutes. Classified into sieve cells and sieve tube members based on the presence of sieve plates and specialization of sieve areas in different parts of the cell. Develops from either a cambial initial or a cell of the procambium.
+
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.
  
−
part_of phloem, participates_in sporophyte stage
+
==[https://sourceforge.net/tracker/?func=detail&aid=3080945&group_id=76834&atid=835555 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."
  
−
'''sieve cell (new term)'''
+
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.
  
−
proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.
+
''We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.''
  
−
Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas. 
+
==[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.
  
−
'''sieve tube member (PO:0000289)'''
+
''This definition is specific to grasses, and should be rephrased, so it is more general.''
  
−
'''current def.:''' One of the series of cells that make up a sieve tube; it shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores).
+
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?
  
−
comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.
+
''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).
  
−
'''proposed def.:''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
+
comment: Found a caryopsis in Poaceae.  
  
−
Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.
+
part_of nucellus
  
−
syn.: sieve tube element, sieve tube segment
+
==[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.
  
−
part_of sieve tube (new term)
+
'''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.
  
−
'''See below for companion cells and other parenchyma cells found in vascular tissue.'''
+
comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.
  
−
====New term for sieve tube====
+
'''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.
  
−
'''sieve tube, proposed definition:''' A portion of phloem tissue that has as parts a series of sieve tube members arranged end to end and interconnected through sieve plates.
+
comment: In Arabidopsis, refers to the leaves that are borne on ''the elongated inflorescence branches''.
  
−
Comment: A sieve plate (GO:0097218) is part of a sieve tube member.
 
  
−
====New terms for GO====
+
Perhaps we should use the appropriate growth stages in their definitions,
−
These subcellular components have been added to GO:
+
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
  
−
*GO:0097217 sieve area
+
'''proposed definitions'''
−
*GO:0097218 sieve plate
 
−
*GO:0097219 compound sieve plate
 
−
*GO:0097220 simple sieve plate
 
  
−
'''sieve area:''' A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.
+
'''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).
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment
+
comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.
  
  
−
'''sieve plate:''' A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.
+
'''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: Typical of angiosperms.
+
comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).
+
Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?
  
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
 
  
 +
Links from Lol:
  
−
'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
+
http://www.arabidopsis.org/portals/education/growth.jsp
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.  
+
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.
  
−
is_a sieve plate
+
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?
  
−
'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
+
''Don't need these''
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3299941&group_id=76834&atid=835555 sporocyte]==
 +
'''Existing definitions:'''
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3481658&group_id=76834&atid=835555 New definitions - tracheary elements]===
+
'''sporocyte (PO:0006204):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.
  
−
''These edits are done in the obo file.''
+
'''microsporocyte (PO:0020047):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]
  
−
'''xylem element (PO:0000273):''' A cell making up xylem tissue.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
Currently, this is parent of tracheary element and xylem fiber. I suggest we '''obsolete''' it and make xylem fiber cell a child of fiber cell. Xylem element could be a broad synonym of tracheary element and xylem fiber.
+
'''megasporocyte (PO:0000431):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]
  
 +
synonyms: megaspore mother cell, MMC
  
−
'''tracheary element (PO:0000290)'''
 
  
−
current def.: General term for any water conducting cell, tracheid or vessel member.
+
At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.
  
−
Currently is part_of primary xylem and part_of secondary xylem.
+
Already have:
  
−
proposed def.: A plant cell (PO:0009002O) that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.
+
megasporocyte develops_from female archesporial cell
  
−
comment: More or less elongated and with pits of various types in the cell wall. Tracheary elements function in the conduction of water and dissolved substances such as mineral nutrients from the roots to the shoot system. Tracheary elements can be distinguished from fiber cells (PO:0025407) by the presence of bordered pits, although there are intermediate forms called fiber tracheids (PO:0000355).
+
microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell
  
−
participates_in sporophyte stage, part_of xylem, disjoint from hydroid
 
  
 +
'''Proposed definitions:'''
  
−
'''tracheid (PO:0000301)'''
+
'''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).
  
−
current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.
+
Add: sporocyte develops_from archesporial cell
  
−
proposed def.: A tracheary element (PO:0000290) that has no perforations in its cell wall.
+
Should we add spore develops_from sporocyte? ''yes''
  
−
comment: May have any of the kinds of secondary wall thickenings found in tracheary elements. The area of contact between two tracheids has only bordered pits, whereas in vessel members (PO:0002003) it has openings in the cell wall called perforations, organized into perforation plates (term has been requested in GO).
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007126 meiosis (GO:0007126)]
  
  
−
'''vessel member (PO:0002003)'''
+
'''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]
  
−
current def.: One of the cellular components of a vessel, a dead cell with the wall between adjacent members being variously perforated and the walls that persist variously thickened.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
proposed def.: A tracheary element (PO:0000290) that is part of a vessel (PO:0025417) and has as parts perforation plates.
+
Should we add microspore develops_from microsporocyte?
  
−
Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (term has been requested in GO). These are usually on the end walls of a cell, but may also be on the side walls. A perforation plate may be simple, with one perforation, or multiperforate, with more than one perforation.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007140 male meiosis (GO:0007140)]
  
−
syn.: vessel element, vessel segment
+
''Better to use meiosis, rather than male meiosis.''
  
−
part_of vessel (new term)
 
  
 +
'''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]
  
−
'''vessel (PO:0025417)'''
+
synonyms: megaspore mother cell, MMC
  
−
proposed def.: A portion of xylem (PO:0005352) tissue that has as parts a tube-like series of vessel members (PO:0002003), the common walls of which have perforations.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007143 female meiosis (GO:0007143)]
  
 +
''Better to use meiosis, rather than female meiosis.''
  
−
'''perforation plate''' (for GO)
 
  
−
proposed def.: A cell wall part that is the part of a wall of a vessel member and bears one or more openings (perforations).
+
'''Also need to address:'''
  
−
comment: Part of a vessel member (PO:0002003). May be simple, with one perforation, or multiperforate, with more than one perforation. Perforation plates are usually on the end walls of a cell, but may also be on the side walls.
+
'''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.
  
−
Reference ISBN:0471245194 (Esau's Anatomy of Seed Plants).
 
  
−
===New definitions - ground tissue 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).
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481660&group_id=76834&atid=835555 sclerenchyma cells]====
 
−
''These edits are done in the obo file.''
 
  
−
'''sclerenchyma cell (PO:0000077)'''
+
''okay''
  
−
current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.
 
  
−
proposed def.: A ground tissue cell (PO:0025030) with thickened secondary cell walls that are lignified.
+
''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.''
  
−
comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from tracheary elements (PO:0000290) or sclerified parenchyma cells (PO:0000074). Distinguishable from collenchyma cells (PO:0000075) because collenchyma cells alive at maturity. Collenchyma cells provides flexibility while sclerenchyma cells provide hardness.
+
==[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.
  
−
Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.
+
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).
  
−
'''sclerid (PO:0025418)'''
 
  
−
proposed def.: A sclerenchyma cell (PO:0000077) that has thick secondary walls with many pits.
+
Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.
  
−
comment: Usually not very elongated.
+
Comment: Part of a spike type inflorescence as found in grasses and other Poales.
  
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481662&group_id=76834&atid=835555 parenchyma cells in phloem tissue]====
+
From Ale:
−
''These edits are done in the obo file.''
 
  
−
'''companion cell (PO:0000071)'''
+
spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards
  
−
'''current definition:''' A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.
+
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)
  
−
'''proposed definition:''' A parenchyma cell (PO:0000074) that is adjacent to a sieve-tube member (PO:0000289) and arises from the same initial cell (PO:0004011) as the sieve-tube member.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 lamina areole]==
 +
Propose new definitions:
  
−
comment: Found in angiosperms. Compare to albuminous cells (PO:0025412), which are found in gymnosperms.
+
'''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.
  
−
Currently part_of primary phloem '''and''' part_of secondary phloem, which can't be true. Should change to part_of phloem.
+
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
  
−
Suggest that we add relation companion cell adjacent_to sieve tube member.
 
  
−
'''Need to check definition of phloem mother cell. Does it only differentiate into secondary phloem, or can it be for primary phloem too?'''
+
'''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
  
−
'''albuminous cell (new term)'''
+
==ovuliferous scale==
 +
New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).
  
−
'''proposed def.:''' A parenchyma cell (PO:0000074) that is morphologically and physiologically associated with a sieve cell (PO:0025415) but does is not derived from the same initial cell (PO:0004011) as the sieve cell.
+
"Ovuliferous scale" seems to be the more commonly used name.
  
−
comment: May be found in the ray system (PO:0025411) and sometimes the axial system (PO:0025410) of gymnosperms. Compare to companion cells (PO:0000071), which are found in angiosperms.
+
'''proposed def., ovuliferous scale:''' A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).  
  
−
is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.
+
Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().
  
−
====[https://sourceforge.net/tracker/?func=detail&aid=3481665&group_id=76834&atid=835555 fiber cells]====
+
''need to review this''
−
''These edits are done in the obo file.''
 
  
−
'''fiber cell (new term, PO:0025407)'''
+
''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]''
  
−
proposed def.: An elongated, tapering schlerenchyma cell (PO:0000077) with a more or less thick secondary cell wall.
 
  
−
comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from tracheary elements (PO:0000290).
 
  
 +
'''ovulate cone, new term:''' A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).
  
−
'''phloem fiber cell (PO:0004519)''' (was called phloem fiber)
+
synonym: female cone (related)
  
−
current def.: A fiber in phloem.
+
''Move more specific synonyms form strobilus to these terms.''
  
−
proposed def.: A fiber cell (PO:0025407) that is part of a portion of phloem (PO:0005417) tissue.
+
'''microsporangiate cone, new term:''' A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).
  
−
Made part_of phloem, instead of part_of secondary phloem.
 
  
 +
'''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 ().
  
−
'''xylem fiber cell (PO:0000274)''' (was called xylem fiber)
 
  
−
current def.: A fiber in xylem.
+
'''ovuliferous scale sterile bract''': A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().
  
−
proposed def.: A fiber cell (PO:0025407) that is part of a portion of xylem (PO:0005352) tissue.
+
===Definitions of megasporophyll and microsporophyll===
 +
move part about angiosperms to the comment
  
−
comment: It may be difficult to distinguish xylem fiber cells from tracheary elements (PO:0000290).
+
Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
  
−
Made part_of xylem, instead of part_of secondary xylem.
+
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?''
  
−
'''libriform fiber cell (PO:0004520)'''
+
* 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
  
−
current def.: A xylem fiber commonly with thick walls and simple pits.
 
  
−
proposed def.: A xylem fiber cell (PO:0000274) with simple pits.
 
  
−
Comment: Libriform fiber cells have unbordered pits while fiber tracheids (PO:0000355) have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fiber cells and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Libriform fiber cells have a slit-like aperture toward the cell lumen, but no pit cavity.  
+
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
  
 +
Synonyms related: fruit peel, fruit rind
  
−
'''fiber tracheid (PO:0000355)'''
+
New def.: ''A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.''
  
−
current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.
+
comment: ''Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.''
  
−
proposed definition: A xylem fiber cell (PO:0000274) with bordered pits with pit cavities.
+
endocarp ; PO:0009086, synonym inner epidermis of pericarp
  
−
comment: Commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures. If both libriform fiber cells (PO:0004520) and fiber tracheids are present, the libriform fiber cells usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessel members (PO:0002003) or tracheids (PO:0000301) of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.
+
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
  
  
−
'''septate fiber (PO:0004521)'''
+
seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
  
−
current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.
+
Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument
  
−
Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.
+
Get rid of "usually" in def. of integument.  From: http://en.wikipedia.org/wiki/Caryopsis
  
−
'''proposed definition, septate fiber tracheid:''' A fiber tracheid (PO:0000355) that has as parts one or more thin internal partitions or septa.
+
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.
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.
  
−
'''proposed definition, septate libriform fiber cell:''' A libriform fiber cell (PO:0004520) that has as parts one or more thin internal partitions or septa.
+
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.
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
  
−
'''proposed definition, septate phloem fiber cell:''' A phloem fiber cell (PO:0004519) that has as parts one or more thin internal partitions or septa.
 
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
we also have the term:
  
−
====other kinds of fiber cells?====
+
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]
  
−
'''gelatinous fiber cell (new term, PO:0025422):''' A xylem fiber cell (PO:0000274) in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.
+
==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.  
  
−
comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.
+
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).
  
−
ref: Fahn
 
  
−
synonym: mucilaginous fiber cell
+
'''ovary wall:''' Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.
  
−
==other wood terms==
+
'''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.
−
'''Wood''' is a synonym for secondary xylem (PO:0005848) -- see definition above.
 
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3483855&group_id=76834&atid=835555 axial system and ray system]===
+
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.
  
−
'''axial system (new term, PO:0025410):'''  
+
'''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.
  
−
'''proposed definition:''' A portion of vascular tissue (PO:0009015) that has as parts cells derived from fusiform initials (PO:0000079) and oriented with their longest diameter parallel to a plant axis (PO:0025004).
+
'''anther and filament'''
  
−
comment: Includes portions of secondary xylem (PO:0005848) and axial wood parenchyma (PO:0004533).  
+
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]).
  
−
synonyms: vertical system, longitudinal system
+
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
  
−
'''ray system (new term, PO:0025411):'''
+
In Beentje, spinule is defined as a small spine.
  
−
'''proposed definition:''' A portion of vascular tissue (PO:0009015) that develops from ray initials (PO:0000082) and extends radially in the secondary xylem (PO:0005848) and secondary phloem (PO:0005848) of a plant axis (PO:0025004) and has as part ray wood parenchyma (PO:0004534).
+
Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.
  
−
comment: May include ray tracheids, as in Pinaceae and some Cupressaceae.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
 +
From Beentje:
  
−
synonyms: radial system (exact), horizontal system (exact), ray (broad)
+
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
  
−
===Existing terms===
+
phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.
−
'''wood parenchyma (PO:0004532):'''
 
  
−
Current def.: Parenchymatous tissue occurring in the wood.
+
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
  
−
Currently is_a secondary xylem. Should be is_a parenchyma.
+
proposed definition:
  
−
Proposed def.: A portion of parenchyma tissue that is part of a portion of secondary xylem and has as parts wood parenchyma cells.  
+
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.
  
−
'''axial wood parenchyma (PO:0004533):'''
+
synonyms: phylloclade, cladophyll
  
−
Current def.: Parenchyma tissue in the axial system of secondary xylem.
+
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
−
Proposed def.: A portion of wood parenchyma that is part of an axial system and has as parts axial wood parenchyma cells.
+
synonyms are not so much synonyms as they are subsets.
  
−
part_of axial system
+
''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:
  
−
'''ray wood parenchyma (PO:0004534):'''
+
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].
  
−
Current def.: Radially oriented parenchyma tissue in secondary xylem.
+
PMID:22415273
  
−
Proposed def.: A portion of parenchyma tissue that is part of a ray system and has as parts ray wood parenchyma cells.
+
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)?
  
−
comment: Occurs in bands or rays of variable width and height that extend radially in the secondary xylem and phloem of a plant axis.
+
===rib===
 +
Should also add 'rib' for cacti and other plants.
  
−
part_of ray system
+
Definition:
  
−
synonym:  ray (broad)
+
-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.
  
−
'''wood parenchyma cell (PO:0004525):'''
+
See tracker at: [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3298006&group_id=76834 tapetum types]
  
−
Current def.: Parenchyma cell occurring within secondary xylem.
+
Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:  
  
−
Proposed def.: A parenchyma cell that is part of a portion of wood parenchyma.
+
Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum.
  
−
comment: Found in secondary xylem.
+
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
  
−
part_of wood parenchyma
+
[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]
  
−
'''ray wood parenchyma cell (PO:0004527):'''
+
[http://ir.library.oregonstate.edu/xmlui/handle/1957/9976 link to OSU Thesis]
  
−
Current def.: Parenchyma cell of a ray in secondary xylem.
 
  
−
Proposed def.: A parenchyma cell that is part of a portion of ray wood parenchyma. develops from ray initials
+
==Organizing the types of plant cells ==
  
−
part_of ray wood parenchyma
+
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.
  
−
'''upright wood ray parenchyma cell (PO:0004528)'''
+
* ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  
−
Current def.: Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
+
* barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
  
−
Proposed def.: A ray wood parenchyma cell that is oriented with its longest dimension parallel to the axis in which it is found.
+
* 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
  
−
'''procumbent wood ray parenchyma cell (PO:0004529)'''
+
* haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  
−
Suggest naming it "procumbent ray wood parenchyma cell".
+
* gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
  
−
Current def.: Ray cell within secondary xylem having its longest axis in radial direction.
+
* polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
  
−
Proposed def.: A ray wood parenchyma cell that is oriented with its longest dimension radial to the axis in which it is found.
+
* 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
  
−
'''axial wood parenchyma cell (PO:0004526)'''
+
* supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  
−
Current def.: Parenchyma cell in the axial system of secondary xylem.
+
* 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).
  
−
Proposed def.: A wood parenchyma cell that is part of a portion of axial wood parenchyma.
+
* 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.
  
−
===wood types===
+
* 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.
−
'''sapwood (PO:0004513):'''
 
  
−
Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.
+
* stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).
  
−
From Esau: Wood that in the living tree contains living cells and reserve materials.
+
=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''
  
−
Proposed def.: A portion of secondary xylem that has as parts living wood parenchyma cells.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ Stages of Plant Embryo Development]==
  
−
comment: Sapwood contains reserve materials and is where the conduction of water takes place. It is generally lighter colored than the heartwood (PO:0004512) and is located between the heartwood the vascular cambium (PO:xxx) of a plant axis.
+
Currently: in Version #20, Aug 2013:
  
 +
[[File:Plant Embryo Dev Stages.png]]
  
−
'''heartwood ; PO:0004512'''
+
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"
  
−
Current def.:  The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.
+
''-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). ''
  
−
Proposed def.: A portion of secondary xylem (wood) which lacks living wood parenchyma cells.
+
===Revisions June-July 2014:===
 +
[[File:Screen Shot 2014-07-14 at 2.33.52 PM.png]]
  
−
comment: Heartwood has ceased to function in storage and conduction and the reserve materials have been removed or converted into heartwood substances. It is generally darker colored than sapwood (PO:0004513) and is found in the center of a plant axis, interior to the sapwood.
+
* '''[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.  ''
  
−
'''early wood ; PO:0004515'''
 
  
−
Current def.:  The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
 
  
−
Proposed def.: A portion of secondary xylem (wood) that is characterized by a lower density and larger cells than late wood and is formed in the first part of a growing season.
 
  
 +
** 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.
  
−
'''late wood ; PO:0004516'''
+
===Sub-classes:===
  
−
Current def.: The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
+
====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)).
  
−
Proposed def.: A portion of secondary xylem (wood) that is characterized by a higher density and smaller cells than early wood and formed in the later part of a growing season.
 
  
 +
-
  
 +
====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.
  
−
'''NOTE: do we need a term for reaction wood?'''
+
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."''
  
−
'''growth ring ()
+
''"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?)''
  
−
'''growth ring boundary (PO:0004517):'''
+
''"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."''
  
−
=Unfinished items from older agendas and user requests=
+
''presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)''
−
==[https://sourceforge.net/tracker/?func=detail&aid=3474999&group_id=76834&atid=835555 lobe and tooth]==
 
−
On 1-10-12, we added the term "sinus" and agreed to add the related terms for tooth and lobe, all part_of some margin.
 
  
−
We currently have organ margin (PO:0025005), phyllome margin (PO:0025018) without part of relations. Suggest that we add organ margin is part_of lamina, phyllome margin part_of phyllome lamina.
 
  
−
Leaf margin (PO:0020128) is already part of leaf and leaf lamina margin (PO:0025009) is part_of leaf lamina.
+
''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).
  
−
'''proposed definition, lobe:''' A cardinal organ part that is a rounded projection on the margin of an organ.
+
''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).
  
−
part_of organ margin
+
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).
  
−
'''proposed definition, phyllome lobe:''' A lobe that is a rounded projection on the margin of a phyllome.
 
  
−
part_of leaf phyllome margin
+
[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)."
  
  
−
'''proposed definition, leaf lamina lobe:''' A phyllome lobe that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
 
  
−
part_of leaf lamina margin
+
''Revised def'n LC:''
  
−
can add other types of lobes as we want, or wait until they are requested.
+
'''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).
  
  
−
'''proposed definition, plant organ tooth:''' A cardinal organ part that is a pointed projection on the margin of an organ.
+
--
  
−
part_of organ margin
+
====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.
  
−
'''proposed definition, phyllome tooth:''' A plant organ tooth that is a pointed projection on the margin of a phyllome.
 
  
−
part_of leaf phyllome margin
+
''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).
  
−
'''proposed definition, leaf lamina tooth:''' A phyllome tooth that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only? - no)
+
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).
  
−
part_of leaf lamina margin
+
Ref: [http://www.ncbi.nlm.nih.gov/pubmed/24784759 PMID:24784759]
  
−
can add other types of teeth as we want, or wait until they are requested.
 
  
−
Be sure to add "teeth" as exact plural synonym to all.
+
--
  
−
Ref.: Harris and Harris, ISBN:0964022168.
 
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3438986&group_id=76834&atid=835555 bud areole and lamina areole]==
 
  
−
At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina.
 
  
−
'''Proposed definition, bud areole (PO:0025353):''' An axillary bud that does not elongate, in which the leaves develop as spine leaves.
 
  
−
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
 
  
−
is_a axillary bud
 
  
−
ref.: Bell and Bryan, ISBN:9780881928501
+
--
  
 +
===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:
  
−
Suggest we add a general term for lamina areole, which will cover petals, etc., and a more specific term for leaf lamina areole.
+
'''* 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)
  
−
'''Proposed definition for lamina areole (PO:0025391):''' A cardinal organ part that is the smallest part of a lamina that is completely surrounded by veins.
+
'''* Similarly, for '''C globular stage_PO:0001185''' new child terms:'''
−
Comment: Any order of vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a lamina.
+
# dermatogen stage in Arabidopsis (=16-cell stage)
−
part_of lamina
+
# early-globular stage in Arabidopsis (32-cell stage)
 +
# mid-globular stage in Arabidopsis
 +
# late-globular stage in Arabidopsis
  
−
'''Proposed definition for leaf lamina areole (PO:0025392):''' A lamina areole that is the smallest part of a leaf lamina that is completely surrounded by leaf veins.
+
'''* For D bilateral stage_PO:0004507'''
−
Comment: Any order of leaf vein can form the sides of an areole. Taken together, the 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.
+
# Transition stage in Arabidopsis (=triangular stage)
−
part_of leaf lamina
+
# early-heart stage in Arabidopsis
 +
# mid-heart stage in Arabidopsis
 +
# late-heart stage in Arabidopsis
  
−
Ref: ISBN:9780801475184
+
'''* 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)
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3463382&group_id=76834&atid=835555 colony/ramet/genet]==
+
'''* F mature embryo stage_PO:0001081'''
−
This is a request from Daniel, from the Physco group.
 
  
−
"The description of moss phenotypes in many cases is at the level of (clonal) colony instead of single plant (which is IMO hard to define in this case). E.g. people measure colony area, diameter, branching etc. I want to annotate phenotypes using the EQ model by linking to PATO terms."
 
  
−
Suggest we add the following synonyms:
+
Older trackers:  
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ #400 plant embryo stage]
  
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/ #426 spore and embryo dormant stages]
  
−
to "gametophore" (PO:0030018) narrow synonym: "ramet"
+
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]
  
−
to "whole plant" (PO:0000003) related synonym: "ramet", narrow synonyms: "colony", "clonal colony", "genet"
+
=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?
  
 +
* fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  
−
On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "
+
* 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
  
−
=Primordia=
+
* 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.''
−
These issues came up while we were working on new term requests for Agron-Omics.  
 
  
−
primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]  
+
* Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see [[POC_Conf._Call_10-29-13]])
  
−
Comment: The primordium is the first distinct form in the development of a plant structure.
+
* 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.
  
−
leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]
 
  
−
Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).
 
  
−
I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.
 
  
−
''"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."''
 
  
−
General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.
+
==[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:
  
 +
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.
  
−
''We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).''
+
''This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants''  
  
−
''Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.''
+
* 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]
  
−
''Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ.  We were trying to get rid of that when we made it is_a tissue.''
+
''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. ''
  
−
''promeristem as synonym of AM, not RAM''
 
  
−
=User requests open on Source Forge; PSDS=
+
==fruit development stages (PO:0001002)==
−
==from MaizeGDB:==
+
* See [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdDZEMzBVdXJWZjVubkJNVlBtSmQ2WFE&usp=sharing Google Doc] for revisions in progress.
  
−
==[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence]==
+
* 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.
−
This was discussed at the NYBG Meeting, on [[Sunday_Sept_11th,_2011]]
 
  
 +
* 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 don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.
+
* 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]
  
−
From MS (MaizeGDB): It would be more useful for maize if the definition for '''coleoptile emergence PO:0007045''' were altered to be: Emergence of coleoptile from the seed. (rather than above ground)
+
====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.  
  
−
This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.  
+
[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).
  
−
At the POC meeting on [[Sunday_Sept_11th,_2011]], we agreed to keep the existing terms that reference emergence from the soil, but rename them as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.''
+
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).
  
−
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. Imbibition (sibling of shoot emergence) also has no is_a parent.
 
  
−
'''current structure:'''
+
[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.
  
−
[[File:germination_stages.jpg]]
+
related synonyms: fruit maturation; fruit senescence
  
−
Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.
+
==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]
  
−
Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
+
==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 )
  
−
===current and proposed terms and definitions===
+
* moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
−
'''All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.'''
 
  
−
'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
+
[[File: phyllome_snap_shot.jpg]]
  
−
'''proposed: shoot emergence from growth medium development stage (PO:0007030):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the growth medium and ???.  
+
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
  
−
Comment: This terms is used only for seed plants.
+
==reproductive shoot system development stage (PO:0025530)==
 +
* Is_a: collective plant organ structure development stage (PO:0025338)
  
−
'''proposed: shoot emergence from seed coat development stage (new number):''' A seedling growth stage that has as a participant a whole plant during the interval between emergence of a part of a shoot system from the seed coat and ???.
+
* We need to build a hierarchy for the development of '''conifer cones-''' as they are also reproductive shoot systems
  
−
Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
+
** 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.
  
−
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
 
  
−
'''proposed: coleoptile emergence from growth medium development stage (PO:0007045):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the growth medium and ???
+
''Need to look at the fern sporangia- that is the reproductive structure for those plants''
  
−
Comment: This terms is used only for seed plants.
 
  
−
'''proposed: coleoptile emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a coleoptile from the seed coat and ???
 
  
−
Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
+
* This would parallel the two existing sub-classes:
  
 +
==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]
  
−
'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]  
+
* Currently this has two sub-classes:
 +
 +
** PO:0021004 : inflorescence initiation stage [0]
 +
** PO:0007037 : inflorescence bifurcation stage [0]
  
−
'''proposed: cotyledon emergence from growth medium development stage (PO:0007049):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the growth medium and ???
+
* 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]
  
−
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
+
These need to be revised and additional stages need to be developed.
  
−
'''proposed: cotyledon emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a cotyledon from the seed coat and ???
+
==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)
  
−
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination. May occur simultaneously with cotyledon emergence form the growth medium.
+
==collective phyllome structure development stage (PO:0025578) and child terms==
  
 +
[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).
  
 +
* Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
  
−
'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
+
** '''androecium development stage (PO:0007605):''' A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).
  
−
'''proposed: epicotyl emergence from growth medium development stage (PO:0007054):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the growth medium and ???
+
** '''calyx development stage (PO:0007603):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
  
−
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination.
+
** '''corolla development stage (PO:0007604):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).  
  
−
'''proposed: epicotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of an epicotyl from the seed coat and ???
+
** '''gynoecium development stage (PO:0007606):''' A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
  
−
Comment: This terms is used only for seed plants. During this phase, only the first true foliage leaf or pair of leaves is visible. Occurs in plants with hypogeal germination. May occur simultaneously with epicotyl emergence form the growth medium.  
+
[[File: collective_phyllome_snap_shot.jpg]]
  
 +
===New term flower bract development stage (new po:id)===
 +
 +
flower bract development stage (new po:id):
  
−
'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
+
- will be parent to lemma development stage and palea development stage
  
−
'''proposed: hypocotyl emergence from growth medium development stage (PO:0007043):''' A shoot emergence stage has as a participant a whole plant during the interval between emergence of a hypocotyl from the growth medium and ???
+
* 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]
 +
  
−
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
+
* 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]
  
−
'''proposed: hypocotyl emergence from seed coat development stage (new number):''' A shoot emergence stage that has as a participant a whole plant during the interval between emergence of a hypocotyl from the seed coat and ???
+
==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: This terms is used only for seed plants. Occurs in plants with epigeal germination. May occur simultaneously with hypocotyl emergence form the growth medium.
+
* 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
  
 +
==[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
  
−
Could also add terms for feeder emergence for some gymnosperms.
+
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]
  
−
For all of the above terms, need to check existing synonyms and move or copy them as needed.
+
So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)
  
−
==[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
+
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).
−
 
 
−
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:
 
Suggested stages:
 +
* tuber initiation
 +
* tuber growth
 +
* tuber maturation
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
+
''Would these be the same for the two different types of tubers? Also need: tuber dormancy''
  
−
-tuber initiation
+
* sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  
−
-tuber growth
+
* 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
  
−
-tuber maturation
 
  
−
How we work these in will depend on restructuring of PSDS
+
===Further info and references:===
 +
[http://www.cals.uidaho.edu/potatoes/potatoproductionsystems/topics/growth&development.pdf Potato Growth & Development]
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
[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]
  
−
=User requests open on Source Forge: Plant Anatomical Entities=
+
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540956/pdf/plntphys00369-0069.pdf Growth of the Potato Tuber]
−
==Cacti terms:==
 
−
spinule: word for when the spines are stipules – synonym of stipule spine
 
  
−
In Beentje, spinule is defined as a small spine. Could be narrow synonym for stipule spine and other kinds of spines
+
=xylem developmental stages: =
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 areole]===
+
See discussions of primary xylem on [http://wiki.plantontology.org/index.php/POC_Conf._Call_6-11-13 POC_Conf._Call_6-11-13]
  
−
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
+
Existing definitions:
  
−
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
+
'''* 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]
  
−
is_a axillary bud
+
*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''
  
−
ref.: Bell and Bryan, Plant Form
+
=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)
  
−
===glochid===
+
==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.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
+
Comment:
−
From Beentje:
+
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.
  
−
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 an dinternodes) flattened and expanded to serve the functions of a leaf.
+
  **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**
  
−
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
+
===See comments from BS from email:===
 +
* On Wed, Sep 18, 2013
  
−
proposed definition:
+
- A lot of this needs to go, I think:  
  
−
cladode: A shoot axis that is flattened and expanded.
+
- 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 ...'
  
−
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.
+
[[File:WPFRS.png]]
−
 
 
−
synonyms: phylloclade, cladophyll
 
−
 
 
−
Need to open a SF tracker for these
 
  
−
Should also add 'rib' for cacti and other plants
+
===Proposed Revisions to sub-classes:===
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
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.
  
−
Submitted by Rich Zobel (Nov 2009).
+
need to open tracker for this set:
  
−
Still need to work on definitions for these terms.
+
'''* whole plant beginning of fruit ripening stage (PO:0007036):'''
  
−
=[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]=
+
current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
  
−
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
+
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.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
+
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.
  
−
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
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 ''
  
−
''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.''
+
* whole plant early fruit ripening stage (PO:0007001)
  
−
''At the POC meeting on 9-27-11, it was decided that bristled stipules should best be handled as a phenotype term. Leaving these notes here for when we start to add phenotypic descriptors.''
+
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.
  
−
We have the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
+
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.
  
−
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).
+
Add related synonyms:
 +
* middle of veraison''
 +
*BBCH principal growth stage 83
  
−
There are two meanings for bristled:  
+
'''* 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.
  
−
!. Stiff and sharp (e.g., a bristled trichome)
+
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.
  
−
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
+
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):'''
  
−
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
+
current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.
  
−
'''1. bristle-like:'''
+
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.
  
−
This is a combination of two PATO descriptors:
+
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.
  
−
Something describing the shape:
+
'''* whole plant fruit ripening complete stage (PO:0007038):'''
  
−
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.
+
current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
  
−
or
+
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.
  
−
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.
+
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.
  
−
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
+
related synonyms:  
 +
* BBCH principal growth stage 89
 +
* grape E-L stage: 38;  Berries ripe for harvest
  
 +
=GO requests:=
  
−
and something describing a quality of a substance:
+
==[https://sourceforge.net/p/geneontology/ontology-requests/9075 Multicellular organism senescence/aging (GO:0010259)]==
  
−
PATO has:
+
* 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.
  
−
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)
 
  
−
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)
+
Link to PO tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/392/ gametophyte/sporophyte senescent stage]
  
−
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.
 
  
−
PATO:
+
''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. ''
  
−
quality of a substance (existing)
+
==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.
  
−
>flexibility (existing)
+
''includes tracheids''
  
−
>>flexible (existing)
+
This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.
  
−
>>inflexible (existing)
+
* symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.
  
−
>rigidity (new)
+
- all the plasma connected, through plasmodesmata, transport through the cytoplasm
  
−
>>rigid (new)
+
See: Link to diagram Apoplast_and_symplast_pathways
  
−
>>flacid (new)
+
See: Apoplastic versus Symplastic Pathways in roots
  
 +
* Suggest revised GO definitions for apoplast and symplast and add transport terms
  
−
'''2. bristle-bearing:''' A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
+
Parent term:
  
−
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
+
* 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.  
  
−
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
+
* 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)
  
−
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.
+
comments: symplastic transport is a diffusion process
  
−
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.
+
* Submit tracker for GO biol process term to describe callus formation
  
 +
=Wood ontology terms=
 +
See separate page: [[Wood Ontology PO and GO Term Development]]
  
−
=New Annotation Files=
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]=
  
−
===Strawberry===
+
Submitted by Rich Zobel (Nov 2009).  Still need to work on definitions for these terms.
  
−
* Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
+
=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).
  
−
===Potato Annotations===
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3609139&group_id=36855&atid=440764 epidermis/epidermal cell : plant v. animal]==
−
 
 
−
LC has been in contact with the group who published the [http://www.nature.com/nature/journal/v475/n7355/full/nature10158.html#/f4 potato genome paper] and they are interested in collaborating with us to assign ontology terms to the annotations.
 
−
 
 
−
From Dr. Richard Finker (Wageningen, The Netherlands):
 
−
 
 
−
"We are also interested to use trait ontologies to assist in candidate gene selection within regions of interest, I'm eager to discuss with you on the efforts of cross linking ontologies to biological relevant entities. e.g. a metabolite content trait to its e.g. chebi ontology ID, form which we could obtain info about the pathway."
 
−
 
 
−
''This will go in the next release, do they have expression data- RNA Seq?''
 
−
 
 
−
=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
 

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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