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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=Term Requests from [http://www.agron-omics.eu/ Agron-Omics]=
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- All new terms and changes should be listed here: [[Release_21]]
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At the recent EBI Crop Ontology meeting PJ met with [http://atidb.org/group/projects.html Sean Walsh]  
 
  
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[http://www.agron-omics.eu/ Arabidopsis GROwth Network integrating OMICS technologies]
 
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459338&group_id=76834&atid=835555 epicuticular wax]: The plant cuticle is covered by epicuticular wax. It consists of a mixture of organic compounds. Epicuticular wax forms an above ground boundary layer between a plant and its environment.
 
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459336&group_id=76834&atid=835555 substomatal cavity]: Cavity located immediately proximal to the stoma.
 
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459332&group_id=76834&atid=835555 adaxial meristem]: The adaxial meristem is a meristematic tissue on the adaxial side of a young leaf primordium that contributes to the increase in the thickness of a leaf.
+
=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
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459331&group_id=76834&atid=835555 plate meristem]: Meristem established inside the leaf primordia. The plate meristem is a meristematic tissue consisting of parallel layers of cells dividing anticlinally (perpendicular to leaf surface) and contributes to the major part of leaf growth.
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* Need to update the [[Annotation_Association_File_Format]] page
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459318&group_id=76834&atid=835555 marginal meristem]: A region of meristematic tissue located along the edges of a leaf primordium. Repeated divisions of initials in this area give rise to the mesophyll and epidermal tissues of the blade.
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=Requests from SF- Anatomy terms in progress...=
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459287&group_id=76834&atid=835555 freely ending veinlet]: Part of leaf vein. Higher order veins that are only connected to other veins at one end.
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==Request for "rind" or outer layer of a maize or sorghum stem==
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459283&group_id=76834&atid=835555 leaf sinus]:Part of leaf margin. A small depression between two projecting lobes of a leaf.
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Request for a term for the outer covering of a maize or sorghum stalk.  
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459280&group_id=76834&atid=835555 cotyledon anlagen]:  A portion of meristem tissue that is a presumptive region on the embryo meristem where cotyledon primordia would initiate.
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[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/596/ link to #596]
  
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[https://sourceforge.net/tracker/?func=detail&aid=3459279&group_id=76834&atid=835555 leaf anlagen]:  A portion of meristem tissue that is a presumptive region on a vegetative meristem where leaf primordia would initiate
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[http://www.sciencedirect.com/science/article/pii/S2090447912000524 structure and properties of sorghum stalks]
  
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=User requests open on Source Forge; PSDSO =
 
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==[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed trichome development stages]==
 
  
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Requests for terms for cotton fiber development, Open since 07-28-2010, from AgBase curators
+
Propsed new terms:
  
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These items are on the agenda for [[POC_Conf._Call_11-15-11]] and [[POC_Conf._Call_11-22-11]].
+
=='''Abscission Zones'''==
 +
June 2014
  
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===Trichome development stages===
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Added new terms and revised existing:
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ fruit pedicel abscission zone (PO:0025605)].  Def'n: An abscission zone (PO:0000146) that forms as a swelling or joint on the fruit pedicel (PO:0004536).
  
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Need to address outstanding issues and wrap this up.
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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)
 +
* 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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References:  
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===New term needed: flower pedicel abscission zone (PO:0025608)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/590/ flower pedicel abscission zone (PO:0025608)]: An abscission zone (PO:0000146) that forms as a swelling or joint on the flower pedicel (PO:009052).
 +
 
 +
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)===
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/193/ flower abscission zone (PO:0006502)]:
 +
 
 +
Was: Zone at base of the flower that contains an abscission (or separation) layer and a protective layer, both involved in the abscission of the flower and its parts.
  
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Arabidopsis leaf trichomes: http://www.nature.com/nrm/journal/v5/n6/full/nrm1404.html (consistent with existing definitions of leaf trichome stage)
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This was revised as the AZ of a whole flower is different that that of the floral organs (sepals, petals and filaments).
  
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Alvin F. Reeves II. (1977) Tomato trichomes and mutation affecting their development. Amer. J. Bot. 64(2): 186-189.  http://www.jstor.org/stable/2442106
+
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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==from MaizeGDB:==
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Made this part_of a floral organ (PO:0025395), rather than a direct part_of a flower
  
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==[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence]==
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== New term request: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/589/ microgametophtye development stage]==
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This was discussed at the NYBG Meeting, on [[Sunday_Sept_11th,_2011]]
 
  
 +
'''Issue: We have megagametophyte development stage (PO:0007621), but do not have a similar term for microgametophtye development stage.'''
  
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We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.
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Question: how do the megagametophyte development stage (PO:0007621) and proposed microgametophtye development stage (new) fit in with the gametophyte development stage (PO:0028003)?? 
  
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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)
+
- multicellular plant gametangium (PO:0025124)- a plant organ- children: antheridium (PO:0025125) and archegonium (PO:0025126)
  
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This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.  
+
- unicellular plant gametangium (PO:0025521): a plant cell- no child terms...
  
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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.''
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''Currently, megagametophyte development stage (PO:0007621) is_a ovule development stage (PO:0007619), but it should be part_of.''
  
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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.
+
* 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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'''current structure:'''
+
* Moved megagametophyte development stage (PO:0007621) to be is_a gametophyte development stage (PO:0028003). part_of ovule development
 +
** Revised definition: A gametophyte development stage (PO:0028003) during which the megagametophyte (PO:0025279) develops.added dbxref to: OBO_SF2_PO: 589
 +
''This definition should be worked on further, and the child terms need work as well.''  
  
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[[File:germination_stages.jpg]]
+
* 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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Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.  
+
* pollen development stage (PO:0001007) should be a is_a microgametophtye development stage since pollen is_a microgametophyte (PO:0025280).
  
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Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
+
''Currently pollen development stage (PO:0001007) is_a androecium development stage (PO:0007605)- but it should probably be part_of.''
  
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===current and proposed terms and definitions===
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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).
−
'''All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.'''
 
  
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'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
 
  
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'''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 ???.
+
* 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: This terms is used only for seed plants.
+
Current definition: Stages of development of the pollen defined by characteristic morphological, cytological, histological or other visible features.
  
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'''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 ???.
+
Revised definition:  
 +
pollen development stage (PO:0001007): A microgametophtye development stage (PO:0025602) during which the pollen (PO:0025281) develops.
  
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Comment: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
+
''This definition should be worked on further, and the child terms need work as well.''
  
 +
==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.''
  
−
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
+
==[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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'''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 ???
+
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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Comment: This terms is used only for seed plants.
+
PMID:12610522
  
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'''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 ???
+
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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Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
+
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).
  
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'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]
+
==Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children==
  
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'''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 ???
+
See notes from discussion on POC call [[POC_Conf._Call_9-24-13]]
  
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Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
+
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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'''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 ???
+
[[File:Cortex terms.png]]
  
−
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.
 
  
 +
Fill in details here.....
  
  
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'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
+
==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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'''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 ???
+
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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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.
+
-Added Narrow synonyms: adnate perianth and connate perianth
  
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'''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 ???
+
*[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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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.  
+
*[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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'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
+
* [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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'''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 ???
+
***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: This terms is used only for seed plants. Occurs in plants with epigeal germination.
 
  
−
'''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 ???
+
*[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).
  
−
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.
+
*[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).
  
 +
**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]
  
−
Could also add terms for feeder emergence for some gymnosperms.
+
* 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 all of the above terms, need to check existing synonyms and move or copy them as needed.
 
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
+
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]
  
−
This item has been open on SF since 6/2009
+
* 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
  
−
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).
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/98/ epicalyx] ==
  
−
Suggested stages:
+
* epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
+
''Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.''
  
−
-tuber initiation
+
Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators] 
  
−
-tuber growth
+
''Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx''
  
−
-tuber maturation
+
''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.
  
−
How we work these in will depend on restructuring of PGDSO
+
''Decided that we needed to add a new term:''
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
''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.''
  
−
=User requests open on Source Forge: PAO=
+
==arilloid and arillode and caruncle==
−
==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
+
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''
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 areole]===
+
* '''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.
  
−
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
+
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.
  
−
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).
+
Synonyms exact: ariloide (Spanish)
  
−
is_a axillary bud
+
*'''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.
  
−
ref.: Bell and Bryan, Plant Form
+
Synonyms exact: carúncula (Spanish)
  
−
===glochid===
+
*aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
+
Synonyms
−
From Beentje:
+
exact: arilo (Spanish)
 +
exact: 仮種皮 (Japanese)  
  
−
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
+
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.
  
−
phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609179&group_id=76834&atid=835555 floral node]==
  
−
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
+
suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise
  
−
proposed definition:
+
Parent/relationship: is_a shoot node (PO:0005004)
  
−
cladode: A shoot axis that is flattened and expanded.
+
Submitted: Johnny Lloyd
  
−
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
+
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
  
−
Need to open a SF tracker for these
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/535/ spine petiole]==
  
−
Should also add 'rib' for cacti and other plants
+
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
The petiole abscisses longitudinally and the blade withers.
  
−
Submitted by Rich Zobel (Nov 2009).
+
See the photo and description on this page: [http://waynesword.palomar.edu/ecoph30a.htm "Spines From Modified Petioles"]
  
−
Still need to work on definitions for these terms.
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609178&group_id=76834&atid=835555 adventitious branch]==
  
−
=Vascular tissues and cell types=
 
  
−
THIS PART IS STILL UNDER CONSTRUCTION
+
Definition: A shoot axis (PO:00025029) that develops in an unusual place
  
−
These terms will need to be fixed before the Wood Ontology meeting in February.
+
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
  
−
==vascular tissue types==
 
  
−
For vascular plants, we have the class:
+
adventitious shoot axis
  
−
'''portion of vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]
+
==shoot-borne root (PO:0000042)==
 +
synonym: adventitious root
  
−
Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.
+
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
  
−
part_of vascular bundle (which is part_of vascular 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. 
  
−
This is okay, but suggest that we change definition to include xylem '''or''' phloem, and it may not always be part_of vascular bundle.
+
*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.
  
−
'''Proposed definition:''' A portion of plant tissue that has as parts tracheary elements or sieve elements.
 
  
−
Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or as scattered vascular bundles. May include other types of tissues or cells, such as parenchyma or fibers.
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/521/ Ultimate Unit (UU)]==
 +
Requested by:  Corvez Adele  Created: 2013-02-01
  
−
part_of vascular system (should add vascular system participates_in sporophytic phase)
+
* 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
  
−
'''vascular bundle (PO:0005020) current def.:''' A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]
+
==moss capsule==
 +
need to open tracker for this: [https://sourceforge.net/tracker/?func=detail&aid=3140824&group_id=76834&atid=835555 moss capsule]
  
−
This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.
+
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell] and prothallium ==
  
−
'''proposed definition:''' A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.
+
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
  
−
Comment: Usually contains both xylem and phloem. May also contain other types of cells or tissue such as fibers, vascular cambium, or portions of ground tissue.
+
prothallial cell (PO:0025533):
  
−
part_of vascular system
+
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.
  
−
add vein as exact synonym -- can be in any organ
+
''should add the PO id for microgametophyte (PO:0025280) to the definition''
  
−
===primary and secondary vascular tissue===
 
−
'''primary vascular tissue:''' A portion of vascular tissue that develops from a procambium. (ref: Esau)
 
  
−
comment: Forms as part of primary growth (GO:xxxx).
+
For reference about prothallial cells in gymnosperms see:  
  
−
'''secondary vascular tissue:''' A portion of vascular tissue that develops from a vascular cambium. (ref: Esau)
+
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
  
−
comment: Forms as part of secondary growth (GO:0080117) in vascular plants. Often differentiated into the axial system and ray system.
+
Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
  
−
If we '''set both of these up as a cross products''', then primary and secondary xylem and phloem will be inferred children.
 
  
−
===phloem===
+
Note: prothallium is a synonym for thallus (PO:0030027) and ....
  
−
'''phloem (PO:0005417) current def.:''' A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]
+
How does prothallial cell compare to microgametophyte vegetative cell?
  
−
'''proposed definition:''' A portion of vascular tissue that has as parts sieve elements.
+
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.
  
−
Comment: Functions in the conduction of organic substances in vascular plants.
+
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.
  
−
''Note: currently, sieve element is listed as a synonym of sieve tube member, but this does not correctly follow Esau's usage. It was okay when we only had angiosperms in PO, but is no longer valid. Suggest we make a new term for sieve element, rather than have it as synonym. See below under conductive_and_related_cell_types.''
+
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.
  
 +
==[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)
  
−
'''metaphloem (PO:0006076) current def.:''' Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.
+
"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."
  
−
'''proposed definition:''' A portion of primary phloem that differentiates after the protophloem.
+
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.
  
−
Comment: Differentiates before the secondary phloem, if any is formed.
+
''We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.''
  
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3082379&group_id=76834&atid=835555 nucellar projections]==
  
−
'''protophloem (PO:0006077) current def.:''' The first-formed elements of the primary phloem.
+
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.
  
−
'''proposed definition:''' A portion of primary phloem tissue that has as parts the first-formed sieve elements of the primary phloem.
+
''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?
  
−
'''primary phloem (PO:0006075) current def.:''' A portion of phloem tissue of the primary plant body.
+
''No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.''
  
−
'''proposed definition:''' A portion of phloem tissue that develops from the procambium.
+
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: Primary phloem develops as part of GO:xxxx primary growth. (''see below'')
+
comment: Found a caryopsis in Poaceae.  
  
−
develops_from PO:0025275 procambium
+
part_of nucellus
  
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3205381&group_id=76834&atid=835555 rosette leaf and cauline leaf]==
 +
The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.
  
−
'''secondary phloem (PO:0005043) current def.:''' A portion of phloem tissue formed by the activity of the vascular cambium.
+
'''Current definitions:'''
  
−
'''proposed definition:''' A portion of phloem tissue that develops from the vascular cambium.
+
'''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: Secondary phloem develops as part of GO:0080117 secondary growth.
+
comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.
  
−
develops_from PO:0005598 vascular cambium
+
'''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.
  
−
===xylem===
+
comment: In Arabidopsis, refers to the leaves that are borne on ''the elongated inflorescence branches''.
  
−
'''xylem (PO:0005352) current def.:''' A portion of vascular tissue composed of xylem elements.
 
  
−
comment: The principal function is the upward translocation of water and solutes. See also primary xylem and secondary xylem.
+
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 definition:''' A portion of vascular tissue that has as parts tracheary elements.
+
'''proposed definitions'''
  
−
comment: Functions in the translocation of water and solutes from roots to the shoot system and in support.
+
'''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.
  
−
'''primary xylem (PO:0005849) current def.:''' A portion of xylem tissue of the primary plant body. [source: GR:Pankaj_Jaiswal, ISBN:0122151704, ISBN:0471245194]
 
  
−
Comment: In stem or root it is differentiated behind the apical meristem.
+
'''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).
  
−
'''proposed definition:''' A portion of xylem tissue that differentiates from the procambium.
+
comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.
  
−
Comment: Primary xylem develops as part of GO:xxxx primary growth.
+
Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?
  
−
develops_from PO:0025275 procambium
 
  
 +
Links from Lol:
  
−
'''protoxylem (PO:0000272) current def.:''' A portion of xylem tissue composed of any of the first formed elements of the primary xylem. [source: ISBN:047125208]
+
http://www.arabidopsis.org/portals/education/growth.jsp
  
−
'''proposed definition:''' A portion of primary xylem that has as parts the first formed xylem elements of the primary xylem.
+
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.
  
−
'''metaxylem (PO:0000372) current def.:''' A portion of xylem tissue that is part of the primary xylem and differentiates after the protoxylem and before the secondary xylem, if any of the latter is formed. [source: ISBN:047125208]
+
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?
  
−
'''proposed definition:''' A portion of primary xylem that differentiates after the protoxylem.
+
''Don't need these''
  
−
Comment: Differentiates before the secondary xylem, if any is formed.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3299941&group_id=76834&atid=835555 sporocyte]==
 +
'''Existing definitions:'''
  
 +
'''sporocyte (PO:0006204):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.
  
−
'''secondary xylem (PO:0005848) current def.:''' A portion of xylem tissue that develops from a vascular cambium. [source: ISBN:0471245194, POC:Curators]  
+
'''microsporocyte (PO:0020047):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]
  
−
Comment: Absent in some dicots and most monocots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
Existing definition is okay.
+
'''megasporocyte (PO:0000431):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]
  
−
New comment: Secondary xylem develops as part of GO:0080117 secondary growth. Found in gymnosperms and most dicots. The "wood" of gymnosperm and dicot angiosperm trees, shrubs, and lianas. May be organized into axial and ray systems. Some monocots have a primary peripheral thickening meristem, located near shoot apical meristem, that gives the appearance of secondary growth and may produce lignified tissue that appears woody, but is not composed of secondary xylem.
+
synonyms: megaspore mother cell, MMC
  
−
develops_from PO:0005598 vascular cambium
 
  
 +
At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.
  
−
''Note: exarch, endarch, mesarch are descriptors for different types of xylem development.''
+
Already have:
  
 +
megasporocyte develops_from female archesporial cell
  
−
'''tracheid bar (PO:0019026) current def.:''' A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]
+
microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell
  
−
'''proposed definition:'''  A portion of xylem tissue that is a distinct ring-like structure, composed of tracheid cells, which surrounds the hilum and forms a groove in the surface of the pericarp immediately adjacent to the hilum.
 
  
−
Comment: Found some taxa such as Phaseolus. [ISBN:0080280293]
+
'''Proposed definitions:'''
  
−
part_of seed; adjacent_to hilum
+
'''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).
  
−
===leaf vein, midrib, costa===
+
Add: sporocyte develops_from archesporial cell
  
−
*'''leaf vein (PO:0020138), current def:''' A strand of vascular tissue in the leaf blade.
+
Should we add spore develops_from sporocyte? ''yes''
  
−
is_a portion of vascular tissue; part_of leaf vascular system
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007126 meiosis (GO:0007126)]
  
  
−
'''proposed definition, leaf vein (PO:0020138):''' A vascular bundle that is part of a leaf lamina in a vascular leaf.
+
'''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]
  
−
part_of leaf vascular system, part_of leaf lamina
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
synonym: leaf vascular bundle
+
Should we add microspore develops_from microsporocyte?
  
 +
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007140 male meiosis (GO:0007140)]
  
−
Suggest new term '''primary leaf vein''': A leaf vein that originates from the base of a leaf lamina  where it attaches to the petiole or to the shoot axis if no petiole is present.
+
''Better to use meiosis, rather than male meiosis.''
  
−
Comment: A leaf may have more than one primary vein. The central primary vein is the midvein (PO:0020139).
 
  
 +
'''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]
  
−
*'''midvein (PO:0020139):''' The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]
+
synonyms: megaspore mother cell, MMC
  
−
Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007143 female meiosis (GO:0007143)]
  
−
'''proposed definition:''' A primary leaf vein that is the central vein of a vascular leaf.
+
''Better to use meiosis, rather than female meiosis.''
  
−
Comment: Often the most prominent vein of a vascular leaf. See costa (PO:0030072) for the central conductive strand of a non-vascular leaf.
 
  
−
broad synonyms: mid rib, midrib, mid-rib, vascular leaf midvein
+
'''Also need to address:'''
  
−
related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128
+
'''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.
  
−
We already have terms for secondary, tertiary, quaternary, and higher order veins.
 
  
−
===Primary and secondary growth, lateral meristems, etc.===
+
'''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).
−
====proposed terms for GO====
 
−
'''primary growth (new term):'''
 
  
−
'''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)
+
''okay''
  
−
comment: Has its inception in the apical meristems and continues in their derivative meristems - protoderm and procambium - even in older tissues. Primary and secondary growth can occur simultaneously in the same organism.
 
  
−
is_a growth (GO:0040007)
+
''Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.''
  
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3405173&group_id=76834&atid=835555 spikelet]==
 +
At the POC meeting on 8-30-11, we decided that this definition needs some work.
  
−
'''secondary or lateral growth'''
+
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.
  
−
GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290 
+
Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).
  
−
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.
 
  
−
Perhaps GO should have 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.
+
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.
  
−
'''lateral growth (GO:new term):''' Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).
+
From Ale:
  
−
Comment: Includes thickening of plant axes due to the activity of a cambium (secondary growth, found in most gymnosperms and dicotyledons), a primary thickening meristem (found in many monocotyledons, some ferns and some cycads), or secondary thickening meristem (in some monocotyledons).
+
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)
  
−
'''proposed new def., secondary growth (GO:0080117):''' Lateral growth of a plant axis (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)
+
==[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 lamina areole]==
 +
Propose new definitions:
  
−
Comment: Occurs in vascular plants, including gymnosperms and most dicotyledons. Commonly supplemented by activity of the cork cambium (phellogen). 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.  
+
'''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.
  
−
Add synonym "cambial secondary growth", which is makes the meaning clearer.
+
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
  
  
−
'''secondary thickening (GO:new term):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from formation of tissue from a secondary thickening meristem (PO:xxxx).
+
'''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: Occurs 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.
+
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
  
−
References: Fahn 1990, ISBN:0080374903, Rudall 1991, JSTOR:4354165
+
==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.
  
−
'''primary thickening (GO:new term):''' Lateral growth of a plant axis (shoot axis or root) that is an increase in thickness resulting from the activity of a primary thickening meristem (PO:0005039)  
+
'''proposed def., ovuliferous scale:''' A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).
  
−
comment: Occurs in shoot axes and rarely in roots in many monocotyledons.
+
Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().
  
−
Ref: JSTOR:4354165, Rudall 1991, and Esau ISBN:0471245208
+
''need to review this''
  
 +
''Currently, ovuliferous scale is a narrow synonym of [http://dev.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0009027&session_id=4901b1372716379 megasporophyll]''
  
−
'''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 fibers 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.
 
  
−
comment: Occurs in the stems of some Arecaceae (palms).
 
  
−
Ref.: Fahn 1990, ISBN:0080374903
+
'''ovulate cone, new term:''' A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).
  
−
====PO terms for lateral meristems====
+
synonym: female cone (related)
  
−
The PO has a general term for lateral meristem, of which cambium is a subtype:
+
''Move more specific synonyms form strobilus to these terms.''
  
−
[[File:lateral_meristem1.jpg]]
+
'''microsporangiate cone, new term:''' A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).
  
−
'''lateral meristem (PO:0020145)'''
 
  
−
'''current def.:''' A meristem containing cells along the stem or root that first differentiate and function as members of a mature tissue system but then again take up meristematic activity.
+
'''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 ().
  
−
'''proposed def.:''' A meristem located parallel to the circumference of a plant organ.
 
  
−
comment: Participates in lateral growth (GO:xxxx) of a plant organ, primarily shoot axes and roots. Contrast with apical meristem (PO:0020144).
+
'''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
  
−
'''root lateral meristem (PO:0006308)'''
+
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.:''' Meristem of the root located parallel to the sides of the axis.
+
Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.
  
−
comment: Generally causes root thickening. Not to be confused with lateral root meristem, which is the meristem of the lateral root.
+
==pericarp and seed coat==
 +
''What is the problem with pericarp?''
  
−
This is just a cambium in the root, which also has vascular cambium and phellogen.
+
* 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
  
−
'''proposed new name and def.: root cambium:''' A cambium that is part of a root.
 
  
−
This terms has six annotations. These should be checked, because it is not obvious what some of them have to do with roots.
 
  
−
If we are going to have this term, maybe we should have root vascular cambium and root cork cambium, plus shoot axis vascular cambium and shoot axis cork cambium?
+
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
  
 +
Synonyms related: fruit peel, fruit rind
  
−
'''cambium (PO:0005597)'''
+
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 lateral meristem, the cells of which divide mostly periclinally. [source: ISBN:0080374913]
+
comment: ''Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.''
  
−
'''proposed def.:''' A lateral meristem that has a part a single layer of cambial initial cells and their derivatives, arranged orderly in radial files.  (Ref.: Esau)
+
endocarp ; PO:0009086, synonym inner epidermis of pericarp
  
−
comment: This term is applied to only two types of meristems: vascular cambium (PO:0005598) and cork cambium/phellogen (PO:0005599).
+
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
  
  
−
'''vascular cambium (PO:0005598)'''
+
seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
  
−
'''current def.:''' A lateral meristem, the cells of which give rise to secondary xylem and phloem, leading to an increase in girth.
+
Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument
  
−
Current definition is okay, but needs minor changes.  
+
Get rid of "usually" in def. of integument.  From: http://en.wikipedia.org/wiki/Caryopsis
  
−
'''proposed def.:''' A cambium that gives rise to secondary xylem and secondary phloem.
+
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: Vascular cambium is located between the secondary xylem and secondary phloem and gives off cells in both directions by periclinal division, leading to an increase in girth of a plant axis.
+
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.
  
−
'''cork cambium/phellogen (PO:0005599)'''
+
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
  
−
'''current def.:''' Lateral meristem which produces the phellem (cork) and the phelloderm.
 
  
−
'''proposed def.:''' A cambium that is part of a periderm and produces phellem (cork) and phelloderm.
+
we also have the term:  
  
−
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.
+
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.
  
−
'''primary thickening meristem (PO:0005039)'''
+
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).
  
−
'''current def.:''' A meristem that develops from a peripheral zone of a shoot apical meristem and is responsible for the primary increase in thickness of a shoot axis.
 
  
−
comment: May appear as a distinct mantle like zone. Often found in monocotyledons.
+
'''ovary wall:''' Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.
  
−
Esau defines it as originating in the apical meristem, but Rudall's review shows that in some species, it is discontinuous with the SAM.  
+
'''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.
  
−
'''proposed def.:''' A lateral meristem that has a parts multiple layers of cells located near the shoot apical meristem.
+
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.
  
−
comment: Contributes to primary thickening of the stem, adventitious root formation, and formation of linkages between the stem, leaf, and root vasculature. Contiguous with the shoot apical meristem in some species, but not all. Produces more or less distinct vascular bundles surrounded by ground tissue, as opposed to the more or less continuous xylem and phloem produced by a vascular cambium. A primary thickening meristem is a multi-layered structure, compared to the single layer of a cambium. Found in many monocotyledons.
+
'''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'''
  
−
'''secondary thickening meristem (new term)'''
+
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]).
  
−
'''proposed def.:''' A lateral meristem has a parts multiple layers of cells in a shoot axis...
+
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).
  
−
comment: Contributes mainly to formation of the body of a stem, but may also produce adventitious roots. May be continuous or discontinuous with the primary thickening meristem. Found in some monocot species of the Liliales and Asperigales.
+
==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.
  
−
'''Other types of lateral meristems'''
+
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
 +
From Beentje:
  
−
PO has the terms shoot lateral meristem (PO:0006344), inflorescence lateral meristem (PO:0009105), ear lateral meristem (PO:0009110) and tassel merristem (PO:0009107), plus their subtypes.
+
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
  
−
Shoot lateral meristem is okay, but inflorescence lateral meristem and all the others are misleading. Inflorescence branches generall develop from apical meristems, not a lateral meristem.
+
phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.
  
−
There are three annotations on shoot lateral meristem and two on inflorescence lateral meristem that should be moved to shoot apical meristem.  
+
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
  
−
'''inflorescence lateral meristem (PO:0009105)'''
+
proposed definition:
  
−
'''current def.:''' The meristem which gives rise to the lateral structures of the inflorescence and contributes to their apical growth.
+
cladode: A shoot axis that is flattened and expanded.
  
−
This should be called '''inflorescence branch meristem''', and be a subtype of inflorescence meristem (PO:0000230), which should in turn be an apical meristem.
+
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
  
−
'''ear lateral meristem (PO:0009110)'''
+
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.
  
−
'''current def.:''' The meristem that gives rise to the lateral structures of a maize ear.
+
''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.''
  
−
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).
+
Recent interesting paper on cladodes in Asparagus:  
  
−
'''proposed def.:''' An inflorescence branch meristem that gives rise to the branches of an ear inflorescence.
+
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].
  
−
==conductive and related cell types==
+
PMID:22415273
−
''under costruction''
 
  
−
See [https://sourceforge.net/tracker/?func=detail&aid=3386970&group_id=76834&atid=835555 new vascular cell types].
+
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)?
  
−
===Current parent: axial cell===
+
===rib===
−
'''Existing structure:'''
+
Should also add 'rib' for cacti and other plants.
  
−
axial cell (PO:0000081)
+
Definition:
  
−
>sieve tube member (PO:0000289, alt: PO:0000286)
+
-caryopsis new child of fruit
  
−
>phloem fiber (PO:0004519)
+
-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.
  
−
>xylem element (PO:0000273)
+
See tracker at: [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3298006&group_id=76834 tapetum types]
  
−
>>tracheary element (PO:0000273)
+
Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:  
  
−
>>>tracheid (PO:0000301)
+
Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum. 
  
−
>>>vessel member (PO:0002003)
+
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
  
−
>>xylem fiber (PO:0000274)
+
[http://onlinelibrary.wiley.com.ezproxy.proxy.library.oregonstate.edu/doi/10.1111/j.1469-8137.1973.tb02093.x/abstract link]
  
−
>>>fiber tracheid (PO:0000355)
+
[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]
  
−
>>>libriform fiber (PO:0004520)
+
[http://ir.library.oregonstate.edu/xmlui/handle/1957/9976 link to OSU Thesis]
  
−
>>>septate fiber (PO:0004521)
 
  
 +
==Organizing the types of plant cells ==
  
−
'''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]
+
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.
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
In CL, they are organized by type:
 +
* absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
  
−
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).
+
* ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.
+
* barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
  
−
====New tissue term:====
+
* defensive cell  CL:0000473  A cell whose primary function is to protect the organism.
−
'''axial system:''' A portion of plant tissue that has as parts cells derived from the fusiform cambial initials and oriented with their longest diameter parallel to a root or shoot axis.
 
  
−
synonyms: vertical system, longitudinal system
+
* diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes.  xref_analog FMA:72300
  
−
comment: Includes portions of secondary xylem tissue and axial wood parenchyma tissue.  
+
* haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  
−
See below for existing terms for ray wood parenchyma and axial wood parenchyma.
+
* gamete ID: CL:0000300 A mature sexual reproductive cell having a single set of unpaired chromosomes.
  
−
===New proposed hierarchy (children of plant cell):===
+
* polyploid cell ID: CL:0000412 A cell whose nucleus, or nuclei, each contain more than two haploid genomes.
  
−
plant cell
+
* secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
  
−
>sieve element (new term)
+
* 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
  
−
>>sieve tube member (syn.: sieve tube element)
+
* supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  
−
>>sieve cell (new term)
+
* 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).
  
−
>tracheary element
+
* 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.
  
−
>>tracheid
+
* 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.
  
−
>>vessel member
+
* stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).
  
−
>ground tissue cell (PO:0025030)
+
=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''
  
−
>>sclerenchyma cell (PO:0000077)
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ Stages of Plant Embryo Development]==
  
−
>>>sclerid (new term)
+
Currently: in Version #20, Aug 2013:
  
−
>>>fiber cell (new term)
+
[[File:Plant Embryo Dev Stages.png]]
  
−
>>>>phloem fiber cell
+
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"
  
−
>>>>xylem fiber cell
+
''-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). ''
  
−
>>>>other kinds of fiber cells?
+
===Revisions June-July 2014:===
 +
[[File:Screen Shot 2014-07-14 at 2.33.52 PM.png]]
  
−
===New definitions - sieve elements===
+
* '''[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:
−
Definitions from Esau's Anatomy of Seed Plants
+
** 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,
  
−
'''sieve element (new term)'''
+
 +
''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.  ''
  
−
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.
 
  
−
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.
 
  
−
'''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.
 
  
−
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.
+
** 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.
  
−
part_of phloem, participates_in sporophyte stage
+
===Sub-classes:===
  
 +
====plant proembryo stage (PO:0001180)]====
 +
'''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#859b plant proembryo stage (PO:0001180)]''': A plant embryo development stage (PO:0007631) that occurs during the interval between the first cell division of a plant zygote (PO:0000423) and the onset of the plant globular embryo stage (PO:0001185).
 +
*comment: The plant proembryo stage occurs prior to the differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)).
  
−
'''sieve cell (new term)'''
 
  
−
proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.
+
-
  
−
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.
+
====plant embryo globular stage (PO:0001185)====
 +
''' [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=2#58b6 plant embryo globular stage (PO:0001185)]''': A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) increases in diameter through cell division, but retains radial symmetry.
 +
** comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
  
 +
Comments from SF-RW:
 +
''"We need a way to distinguish the end of the proembryo and the beginning of this stage. I think the end can be distinguished by bilaterality. I will have to do some research to see if there are differences in when a proembryo stage ends across land plants."''
  
−
'''sieve tube member (PO:0000289)'''
+
''"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?)''
  
−
'''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).
+
''"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."''
  
−
comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.
+
''presumably, this is referring to: (https://sourceforge.net/p/obo/plant-ontology-po-term-requests/125/)''
  
  
−
'''proposed def.:''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
+
''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).
  
−
Comment: Sieve elements 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.
+
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).
  
−
syn.: sieve tube element, sieve tube segment
+
''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 sieve tube (new term)
+
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).
  
−
'''See below for companion cells and other parenchyma cells found in vascular tissue.'''
 
  
−
====New term for sieve tube====
+
[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)."
  
−
'''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.
 
  
−
====New terms for GO====
 
−
These subcellular components are missing from GO.
 
  
−
'''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.
+
''Revised def'n LC:''  
  
−
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
+
'''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).
  
  
−
'''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.
+
--
  
−
comment: Typical of angiosperms.
+
====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.
  
−
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).
+
revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.  
  
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
 
  
 +
''RW: New proposed definition:''
  
−
'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
+
'''* 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).
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.  
+
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).
  
−
is_a sieve plate
+
Ref: [http://www.ncbi.nlm.nih.gov/pubmed/24784759 PMID:24784759]
  
  
−
'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
+
--
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
 
  
−
===New definitions - tracheary elements===
 
  
−
'''xylem element (PO:0000273):''' A cell making up xylem tissue.
 
  
−
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.
 
  
  
−
'''tracheary element (PO:0000290)'''
 
  
−
current def.: General term for any water conducting cell, tracheid or vessel member.
+
--
  
−
Currently is part_of primary xylem and part_of secondary xylem.
+
===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:
  
−
proposed def.: A plant cell that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.
+
'''* 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)
  
−
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 by the presence of bordered pits, although there are intermediate forms called fiber tracheids.
+
'''* Similarly, for '''C globular stage_PO:0001185''' new child terms:'''
 +
# dermatogen stage in Arabidopsis (=16-cell stage)
 +
# early-globular stage in Arabidopsis (32-cell stage)
 +
# mid-globular stage in Arabidopsis
 +
# late-globular stage in Arabidopsis
  
−
participates_in sporophyte stage, part_of xylem, disjoint from hydroid
+
'''* For D bilateral stage_PO:0004507'''
 +
# Transition stage in Arabidopsis (=triangular stage)
 +
# early-heart stage in Arabidopsis
 +
# mid-heart stage in Arabidopsis
 +
# late-heart stage in Arabidopsis
  
 +
'''* E expanded cotyledon stage_PO:0001078'''
 +
Linear cotyledon stage embryo
 +
# early-torpedo stage in Arabidopsis
 +
# mid-torpedo stage in Arabidopsis
 +
# late-torpedo stage in Arabidopsis
 +
# Bent cotyledon stage (curled cotyledon stage/walking stick stage)
  
−
'''tracheid (PO:0000301)'''
+
'''* F mature embryo stage_PO:0001081'''
  
−
current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.
 
  
−
proposed def.: A tracheary element that has no perforations.
+
Older trackers:
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ #400 plant embryo stage]
  
−
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 it has perforations organized into perforation plates.
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/ #426 spore and embryo dormant stages]
  
 +
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]
  
−
'''vessel member (PO:0002003)'''
+
=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?
  
−
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.
+
* fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  
−
proposed def.: A trachary element that is part of a vessel and has as parts perforation plates.
+
* 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
  
−
Comment: The cell wall of a vessel member has openings called perforations, which are organized into perforation plates (GO:xxxx). 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.
+
* 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.''
  
−
syn.: vessel element, vessel segment
+
* Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see [[POC_Conf._Call_10-29-13]])
  
−
part_of vessel (new term)
+
* 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.
  
  
−
'''vessel (new term)'''
 
  
−
proposed def.: A portion of vascular tissue that has as parts a tube-like series of vessel members, the common walls of which have perforations.
 
  
  
−
'''perforation plate''' (for GO)
+
==[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:
  
−
proposed def.: A cell wall part that is the part of a wall of a vessel member that bears one or more openings (perforations).
+
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.  
  
−
comment: 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.
+
''This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants''
  
−
===New definitions - ground tissue cells===
+
* 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]
  
−
'''sclerenchyma cell (PO:0000077)'''
+
''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. ''
  
−
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 with thickened secondary cell walls that are often lignified.
+
==fruit development stages (PO:0001002)==
 +
* See [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdDZEMzBVdXJWZjVubkJNVlBtSmQ2WFE&usp=sharing Google Doc] for revisions in progress.
  
−
comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from xylem tissue or sclerified parenchyma cells.
+
* 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.
  
−
Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.
+
* 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]
  
−
'''sclerid (new term)'''
+
====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.
  
−
proposed def.: A sclerenchyma cell that has thick, lignified secondary walls with many pits.
+
[https://sourceforge.net/tracker/index.php?func=detail&aid=3577380&group_id=76834&atid=835555 fruit ripening stage]: A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).
  
−
comment: Usually not much elongated.
+
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).
  
−
====parenchyma cells in vascular tissue====
 
  
−
'''companion cell (PO:0000071)'''
+
[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.
  
−
'''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.
+
related synonyms: fruit maturation; fruit senescence
  
−
'''proposed definition:''' A parenchyma cell associated with a sieve-tube member and arising from the same mother cell as the sieve-tube member.
+
==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]
  
−
comment: Found in angiosperms. Compare to albuminous cells (PO:xxxx), which are found in gymnosperms.
+
==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 )
  
−
Currently part_of primary phloem '''and''' part_of secondary phloem, which can't be true. Should change to part_of phloem.
+
* moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
  
−
Suggest that we add relation companion cell adjacent_to sieve tube element.
+
[[File: phyllome_snap_shot.jpg]]
  
 +
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
  
−
'''albuminous cell (new term)'''
+
==reproductive shoot system development stage (PO:0025530)==
 +
* Is_a: collective plant organ structure development stage (PO:0025338)
  
−
'''proposed def.:''' A parenchyma cell that is morphologically and physiologically associated with a sieve cell but does is not derived from the same initial cell as the sieve cell.
+
* We need to build a hierarchy for the development of '''conifer cones-''' as they are also reproductive shoot systems
  
−
comment: May be found in the rays and sometimes the axial system of gymnosperms. Compare to companion cells, which are found in angiosperms.
+
** 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.
  
−
is_a parenchyma cell, part_of phloem
+
* 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.
  
−
Should we have a term for phloem parenchyma cell?
 
  
−
====fiber cells====
+
''Need to look at the fern sporangia- that is the reproductive structure for those plants''
−
'''fiber cell (new term)'''
 
  
−
proposed def.:
 
  
  
−
'''phloem fiber cell (PO:0004519)''' (was called phloem fiber)
+
* This would parallel the two existing sub-classes:
  
−
current def.: A fiber in phloem.
+
==inflorescence development stage (PO:0021004)and sub-classes==
 +
* Currently linked to  tracker for: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/517/ shoot system development stages and child terms]
  
−
proposed def.:  
+
* 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]
  
−
'''xylem fiber cell (PO:0000274)''' (was called xylem fiber)
+
These need to be revised and additional stages need to be developed.
  
−
current def.: A fiber in xylem.
+
==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)
  
−
proposed def.:  
+
==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).
  
−
fiber tracheid (PO:0000355): A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.
+
* Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
  
−
libriform fiber (PO:0004520): A xylem fiber commonly with thick walls and simple pits.
+
** '''androecium development stage (PO:0007605):''' A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).  
  
−
septate fiber (PO:0004521): A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.
+
** '''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).
  
−
'''other kinds of fiber cells?'''
+
** '''gynoecium development stage (PO:0007606):''' A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
  
−
==other wood terms==
+
[[File: collective_phyllome_snap_shot.jpg]]
−
''this part is under construction''
 
  
−
'''Wood''' is a synonym for secondary xylem (PO:0005848) -- see definition above.
+
===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
  
−
axial wood parenchyma ; PO:0004533: Parenchyma tissue in the axial system of secondary xylem.
+
* 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]
 
 
−
axial wood parenchyma cell ; PO:0004526 Parenchyma cell in the axial system of secondary xylem.
 
−
plant anatomy
 
−
early wood ; PO:0004515 The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
 
  
−
heartwood ; PO:0004512 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.
+
* 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==
 +
* [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):
 +
 
 +
* 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
 +
 
 +
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)
 +
 
  
−
late wood ; PO:0004516 The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
+
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).
  
−
procumbent wood ray parenchyma cell ; PO:0004529 Ray cell within secondary xylem having its longest axis in radial direction.
+
Suggested stages:
 +
* tuber initiation
 +
* tuber growth
 +
* tuber maturation
  
−
ray wood parenchyma ; PO:0004534 Radially oriented parenchyma tissue in secondary xylem.
+
''Would these be the same for the two different types of tubers? Also need: tuber dormancy''
  
−
ray wood parenchyma cell ; PO:0004527 Parenchyma cell of a ray in secondary xylem.
+
* sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  
−
sapwood ; PO:0004513 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.
+
* 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
  
−
upright wood ray parenchyma cell ; PO:0004528 Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
 
  
−
wood parenchyma ; PO:0004532 Parenchymatous tissue occurring in the wood.
+
===Further info and references:===
 +
[http://www.cals.uidaho.edu/potatoes/potatoproductionsystems/topics/growth&development.pdf Potato Growth & Development]
  
−
wood parenchyma cell ; PO:0004525 Parenchyma cell occurring within secondary xylem.  
+
[http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2005.00141.x/full Tuber on a chip: differential gene expression during potato tuber development]
  
 +
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540956/pdf/plntphys00369-0069.pdf Growth of the Potato Tuber]
  
−
'''wood parenchyma''' is_a secondary xylem. Should be is_a parenchyma.
+
=xylem developmental stages: =
  
−
'''wood parenchyma (PO:0000272) current def.:''' Parenchymatous tissue occurring in the wood. [source: POC:Curators]  
+
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:'''
+
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]
  
−
'''ray:''' A contiguous band of parenchyma tissue that develops from ray initials and extends radially in the secondary xylem and phloem of a plant axis.
+
*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''
  
−
comment: Of variable width and height.  This term is used to describe individual rays, which ray system is used to describe all rays in a plant.
+
=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)
  
−
part_of ray system
+
==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.
  
−
'''ray system:''' A portion of parenchyma tissue that has as parts all of the rays in a plant structure.
+
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.
  
−
comment: May refer to the ray system of a shoot axis, a root, or an entire plant.
 
  
−
synonyms: radial system, horizontal system
+
  **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**
  
−
=[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]=
+
===See comments from BS from email:===
 +
* On Wed, Sep 18, 2013
  
−
All trackers are now closed. Leaving notes about bristle here for when we are ready to describe phenotypes.
+
- A lot of this needs to go, I think:
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
+
- 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 ...'
  
−
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
[[File:WPFRS.png]]
  
−
''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.''
+
===Proposed Revisions to sub-classes:===
  
−
''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.''
+
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:
  
−
We have the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
+
'''* whole plant beginning of fruit ripening stage (PO:0007036):'''
  
−
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).
+
current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.
  
−
There are two meanings for bristled:  
+
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.
  
−
!. Stiff and sharp (e.g., a bristled trichome)
+
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.
  
−
2. Bearing bristles (e.g, a bristled leaf bears many bristle-like hairs)
+
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)
  
−
Suggest two new phenotype descriptors (for PO phenotype branch or for PATO):
+
current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening
  
−
'''1. bristle-like:'''
+
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.
  
−
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:
+
Add related synonyms:
 +
* middle of veraison''
 +
*BBCH principal growth stage 83
  
−
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.
+
'''* 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.
  
−
or
+
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.
  
−
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.
+
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.
  
−
and/or PATO:0001154 (elongated): A quality inhering in a bearer by virtue of the bearer's length being notably higher than its width.
+
'''* 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.
  
−
and something describing a quality of a substance:
+
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.
  
−
PATO has:
+
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.
  
−
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)
+
'''* whole plant fruit ripening complete stage (PO:0007038):'''
  
−
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)
+
current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.
  
−
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.
+
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:
+
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.
  
−
quality of a substance (existing)
+
related synonyms:
 +
* BBCH principal growth stage 89
 +
* grape E-L stage: 38;  Berries ripe for harvest
  
−
>flexibility (existing)
+
=GO requests:=
  
−
>>flexible (existing)
+
==[https://sourceforge.net/p/geneontology/ontology-requests/9075 Multicellular organism senescence/aging (GO:0010259)]==
  
−
>>inflexible (existing)
+
* 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.
  
−
>rigidity (new)
 
  
−
>>rigid (new)
+
Link to PO tracker: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/392/ gametophyte/sporophyte senescent stage]
  
−
>>flacid (new)
 
  
 +
''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. ''
  
−
'''2. bristle-bearing:''' A pilosity quality inhering in a bearer by virtue of the bearer's having structures that are bristle-like.
+
==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.
  
−
is_a pilosity (PATO:0000066: A texture quality inhering in a bearer by virtue of the bearer's having hair or bristles.)
+
''includes tracheids''
  
−
Synonym: bristly (Beentje 2010: bearing stiff strong hairs or bristles).
+
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.
  
−
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.
+
- all the plasma connected, through plasmodesmata, transport through the cytoplasm
  
−
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.
+
See: Link to diagram Apoplast_and_symplast_pathways
  
 +
See: Apoplastic versus Symplastic Pathways in roots
  
−
=New Annotation Files=
+
* Suggest revised GO definitions for apoplast and symplast and add transport terms
  
−
===Strawberry===
+
Parent term:
  
−
* Strawberry is on SVN: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]
+
* 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.  
  
−
===Potato Annotations===
+
* apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)
  
−
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.
+
* symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)
  
−
From Dr. Richard Finker (Wageningen, The Netherlands):  
+
comments: symplastic transport is a diffusion process
  
−
"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."
+
* Submit tracker for GO biol process term to describe callus formation
  
−
''This will go in the next release, do they have expression data- RNA Seq?''
+
=Wood ontology terms=
 +
See separate page: [[Wood Ontology PO and GO Term Development]]
  
−
=Annotation Guidelines=
+
=[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]=
  
−
Comments from PJ from previous meeting (9-27-11):
+
Submitted by Rich Zobel (Nov 2009).  Still need to work on definitions for these terms.
−
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
+
=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).
  
−
-it would be helpful to have a detailed guide on our wiki for collaborators
+
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3609139&group_id=36855&atid=440764 epidermis/epidermal cell : plant v. animal]==

Latest revision as of 20:26, 17 July 2014

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

Please include the date when the item was added; topics will move off of here as they are dealt with.

- Go back to POC_Meetings_Minutes main page

- All new terms and changes should be listed here: Release_21



Annotation Guidelines

Comments from PJ from previous meeting (9-27-11): Ask MS if she can write up a small blurb on how she created the Maize annotations. Maize probe ids => gene ids methods and cut-offs, a guide for other collaborators and a page for the info. Maybe co-author it with SR

-This will also be helpful when applying for new grants

-it would be helpful to have a detailed guide on our wiki for collaborators

Requests from SF- Anatomy terms in progress...

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

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

link to #596

structure and properties of sorghum stalks


Propsed new terms:

Abscission Zones

June 2014

Added new terms and revised existing:

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

See also:

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

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

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

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

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

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

Added relations:

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

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

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

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

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

flower abscission zone (PO:0006502):

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

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

Revised name and definition:

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

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

New term request: microgametophtye development stage

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

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

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

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

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

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

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

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

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

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


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

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

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

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

caryopsis hull (PO:0006000)

  • caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]
    • Comment: None

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

founder cells

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

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

PMID:12610522

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

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

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

Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children

See notes from discussion on POC call POC_Conf._Call_9-24-13

Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)

Cortex terms.png


Fill in details here.....


New terms Added in Release #20:

  • fused perianth (new PO:0025880): A perianth (PO:0009058) in which one or more of the petals (PO:0009032), sepals (PO:0009031), and/or tepals (PO:0009033) are fused.

Comment: The petals (PO:0009032), sepals (PO:0009031) and tepals (PO:0009033) may be fused anywhere along the phyllome margin (PO:0025018). In some cases where the calyx (PO:0009060) and corolla (PO:0009060) are fused at the base it is referred to as a perianth tube.

-Added Narrow synonyms: adnate perianth and connate perianth

  • fused petal (new PO:0025583): - A petal (PO:0009032) that is part of a fused corolla (PO:0025581) or a fused perianth (PO:0025580).
    • Comment: In fused perianth (PO:0025580), the fused petal (PO:0025583) may be joined to a fused sepal (PO:0025584) or another fused petal.
  • free petal (PO:0025569): A petal (PO:0009032) that is part of a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
      • comment: A free petal (PO:0025569) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a petal (PO:0009032) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use petal.


  • free sepal (PO:0025587): A sepal (PO:0009031)that is part of a perianth (PO:0009058) that contains fused sepals (PO:0025584) and/or fused petals (PO:0025583), but is separate from the other sepals (PO:0009031) and petals (PO:0009032).
    • comment: A free sepal (PO:0025587) only occurs in a perianth (PO:0009058) that contains fused sepals (PO:PO:0025584) and/or fused petals (PO:0025583). If you are describing a sepal (PO:0009031) that is part of a perianth (PO:0009058) where none of the sepals (PO:0009031) and/or petals (PO:0009032) are fused, you should use sepal.

Need to look at these associated terms:

  • is_a:
    • PO:0025324 : banner petal [0]
    • PO:0025326 : keel petal [0]
  • part_of
    • PO:0025144 : petal apex [0]
    • PO:0025146 : petal base [0]
    • PO:0006041 : petal epidermis [0]
    • PO:0025008 : petal margin [0]
    • PO:0006069 : petal parenchyma [0]
    • PO:0025511 : petal spur [0]
    • PO:0025218 : petal stomatal complex [0]
    • PO:0000054 : petal vascular system [0]
    • PO:0025325 : wing petal [0]


For corolla:

  • part_of:
    • corolla spur PO:0025512: Def'n: A collective organ part structure (PO:0025269) that is a slender, hollow extension of a corolla and has as parts segments of two more fused petals.

- should be is_a fused corolla?

    • keel PO:0025327: A boat-shaped collective phyllome structure (PO:0025023) that consists of the two lowest petals (PO:0009032) of a papilionaceous corolla (PO:0009059). Comment: The two petals of the keel are often fused at the apex and free at the base. The keel projects toward the front of the flower. Found in the flowers of some Fabaceae.
    • PO:0009032 : petal [0]
  • fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
  • calyptra corolla (PO:0025330): A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583). Very similar definitions

epicalyx

  • epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]

Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.

Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators]

Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx

Example from MAG: In the Trocodondraceae, the perianth is completely lacking, but they have little bracts subtending the reproductive structure.

Decided that we needed to add a new term:

epicalyx bract (new PO:0025577): A flower bract (PO:0009034) that is part of the epicalyx (PO:0009063). It will be sibling to the existing terms lemma and palea.

arilloid and arillode and caruncle

There is an issue in OE with these that the exact synonyms are the same in Spanish, so it generates an error.this was resolved in Release #20

  • arilloid (PO:0019022): A cardinal part of multi-tissue plant structure (PO:0025498) that is a fleshy outgrowth of a seed (PO:0009010). [source: ISBN:9780881928501]

Comment: Often conspicuous and found on seeds with a hard testa that are dispersed by animals. There is some variation in how different sources define the subtypes of arilloids.

Synonyms narrow: arillode; exact: ariloide (Spanish)

  • arillode (PO:0025378): An arilloid that is an elaborate outgrowth of a seed at the micropyler end. [source: ISBN:9780881928501]

Comment: Generally larger than a caruncle and not hard.

Synonyms exact: ariloide (Spanish)

  • caruncle (PO:0020060): An arilloid that is an outgrowth of a seed next to the micropyle. [source: ISBN:9780881928501]

Comment: Often hard and generally smaller and less elaborate than a arillode.

Synonyms exact: carúncula (Spanish)

  • aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]

Synonyms exact: arilo (Spanish) exact: 仮種皮 (Japanese)

Comment : Usually envelopes most of the seed and is fleshy. If the ovule is pressed against the funicle to form a raphe, it may appear that the aril is growing from the raphe.

floral node

suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise

Parent/relationship: is_a shoot node (PO:0005004)

Submitted: Johnny Lloyd


inflorescence node: A shoot node that is part of an inflorescence axis and where a spikelet, flower, floret or inflorescence branch is attached. [source: GR:Pankaj_Jaiswal]. PO:0006325

spine petiole

Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.

The petiole abscisses longitudinally and the blade withers.

See the photo and description on this page: "Spines From Modified Petioles"

adventitious branch

Definition: A shoot axis (PO:00025029) that develops in an unusual place

Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud


adventitious shoot axis

shoot-borne root (PO:0000042)

synonym: adventitious root

Need to align these three with the shoot-borne root

  • adventitious root apical meristem ; PO:0006021
  • adventitious root epidermis ; PO:0006039
  • adventitious root nodule ; PO:0000040

leaf lamina PO:0020039

-fix typo in comment

  • Def'n: A phyllome lamina (PO:0025396) that is the part of a leaf (PO:0025034) exclusive of the petiole (PO:0020038) or leaf sheath (PO:0020104), if either is present.
  • Comment: A leaf lamina is usually dorsiventrally flattened, but may be flattened in a median plant (perpendicular to the axis) in the case of phyllodes (PO:0025335) or other ensiform leaves (PO:0025333). This term should not be used for leaves that are not laminar (flat), like round leaves in Allium or needle-like leaves in Pinus or some Proteaceae.

If you are annotating to this term, please add an additional annotation to vascular leaf (PO:0009025) or non-vascular leaf (PO:0025075), depending on the species. All annotations for angiosperms, gymnosperms, and pteridophytes should go to vascular leaf and all annotations for bryophytes should go to non-vascular leaf.


Ultimate Unit (UU)

Requested by: Corvez Adele Created: 2013-02-01

  • Ultimate units are last branching-orders inserted at extremities of lateral branching systems. Each unit can divide several times, they are mostly tridimensional and their last dichotomies form ultimate appendages.

Corvez et al., 2012

suggested parentage: Ultimate unit is_a cardinal organ part

moss capsule

need to open tracker for this: moss capsule

prothallial cell and prothallium

On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.

prothallial cell (PO:0025533):

proposed def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.

should add the PO id for microgametophyte (PO:0025280) to the definition


For reference about prothallial cells in gymnosperms see:

Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.

Available online: Coulter + Chamberlain, 1910


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

How does prothallial cell compare to microgametophyte vegetative cell?

prothallial cell (PO:0025533): current def'n: A vegetative plant cell (PO:0009002) that develops from the division of the microspore (PO:0020048) and is part of the microgametophyte of vascular plants other than angiosperms.

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

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

common primordium

This request was made by Elena Kramer during the beta review: , I wondered if there was some way to incorporate ...the phenomenon of common primordia (...would only apply to the development ontology)

"During floral development (at least in peas, maybe others), petals and stamens (and maybe other floral organs) may share a common primordium before development of a distinct petal or stamen primordia. We may want to add this to the flower developmental stage branch of the PGDSO."

This could be a structure in the PAE branch, and we can consider adding it as a stage when we work on flower development stages.

We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.

nucellar projections

The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.

This definition is specific to grasses, and should be rephrased, so it is more general.

Actually, I can't find any references to this outside grasses, so perhaps it is fine as is. Does anyone know of an example of this outside grasses? Maybe in other monocots?

No one know of an example outside grasses, so it is okay, but we can rephrase slightly to make it more braod.

proposed def.: A portion of plant tissue (PO:0009007) that is a morphologically distinct part of a nucellus (PO:0020020) overlying the vascular bundles (PO:0005020).

comment: Found a caryopsis in Poaceae.

part_of nucellus

rosette leaf and cauline leaf

The definitions for these terms need revision, especially cauline leaf. Rosette leaf is okay, but should be converted to genus-differentia form.

Current definitions:

rosette leaf (PO:0000014): One of multiple leaves borne in a rosette - a group of leaves, generally borne at the base of the plant, that are separated by very short internodes.

comment: Arabidopsis, vegetative development is characterized by the production of the rosette leaves.

cauline leaf (PO:0000013): Leaf or pairs/whorls of leaves borne on the stem. Comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.

comment: In Arabidopsis, refers to the leaves that are borne on the elongated inflorescence branches.


Perhaps we should use the appropriate growth stages in their definitions, e.g., PO:0007113 rosette growth, and PO:0007089 stem elongation. However, stem elongation is defined as a vegetative growth stage, so it doesn't really apply to plants that are bolting

proposed definitions

rosette leaf: A vascular leaf (PO:0009025) that is part of a collective leaf structure (PO:0025022) in which the leaves are borne on a stem base (PO:0008039) that has very short stem internodes (PO:0020142).

comment: In many species, including Arabidopsis thaliana, the sporophyte vegetative stage (PO:0007134) is characterized by the production of the rosette leaves.


cauline leaf (PO:0000013): A vascular leaf (PO:0009025) that is borne on a stem (PO:0009047) or branch (PO:0025073) that has elongated shoot internodes (PO:0005005).

comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.

Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?


Links from Lol:

http://www.arabidopsis.org/portals/education/growth.jsp

http://www.jstor.org/stable/2656849

non-vascular rosette leaves?

At the POC meeting on 6/7/11, PJ suggested that we make new general terms for rosette leaf and cauline leaf, is_a children of leaf. Then we could make specific terms for vascular rosette leaf and vascular cauline leaf.

However, I don't know if the terms rosette leaf and cauline leaf are ever used for non-vascular plants. Certainly leaves occur on a stem in mosses and liverworts, but it is not the case that the leaves first form during a rosette stage then the stem elongates. Instead, leaves are formed from the stem apex as it elongates.

If rosette leaf and cauline leaf only have one child each (vascular rosette leaf or vascular cauline leaf), is there really a point in making the general category?

Don't need these

sporocyte

Existing definitions:

sporocyte (PO:0006204): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.

microsporocyte (PO:0020047): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) microspores. [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

megasporocyte (PO:0000431): A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC


At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.

Already have:

megasporocyte develops_from female archesporial cell

microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell


Proposed definitions:

sporocyte (PO:0006204): A plant cell (PO:0009002) that develops from an archesporial cell (PO:0030056) and undergoes meiosis (GO:0007126) to produces four plant spores (PO:0025017).

Add: sporocyte develops_from archesporial cell

Should we add spore develops_from sporocyte? yes

meiosis (GO:0007126)


microsporocyte (PO:0020047): A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]

synonyms: microspore mother cell, PMC, pollen mother cell

Should we add microspore develops_from microsporocyte?

male meiosis (GO:0007140)

Better to use meiosis, rather than male meiosis.


megasporocyte (PO:0000431): A sporocyte (PO:0006204) that develops from a female archesporial cell (PO:0006015) and undergoes meiosis (GO:0007126) to produces four megaspores (PO:0020019). [source: ISBN:0471245208]

synonyms: megaspore mother cell, MMC

female meiosis (GO:0007143)

Better to use meiosis, rather than female meiosis.


Also need to address:

primary sporogenous cell (PO:0006088), current def.: It is formed by the division of the male archesporial initial. After several mitotic divisions these cells differentiate into pollen mother cells.


proposed def.: A plant cell (PO:0009002) that develops from a male archesporial cell (PO:0006014) and, after several mitotic divisions, develops into microsporocytes (PO:0020047).

okay


Note: external ontology ids should go in both the definition and as a Dbxref, because they don't work as links otherwise. They work as links okay in the comments.

spikelet

At the POC meeting on 8-30-11, we decided that this definition needs some work.

Current def.: Ultimate and congested inflorescence branch of the grasses. [source: APWeb:Glossary] Comment: It consists of one to many closely-packed flowers and associated glumes etc.

Should make it more general, because spikelets are found throughout the Poales (close relatives of grasses).


Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.

Comment: Part of a spike type inflorescence as found in grasses and other Poales.

From Ale:

spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards

spikelet: a small spike or secondary spike; the ultimate flower cluster of grasses and sedges, consisting of one to may flowers subtended by two bracts (glumes)

lamina areole

Propose new definitions:

phyllome lamina areole (PO:0025391): A cardinal organ part (PO:0025001) that is part of a phyllome lamina (PO:0025396) and is completely surrounded by phyllome lamina veins (PO:0025348) and cannot be divided into any smaller parts that are completely surrounded by phyllome lamina veins.

Comment: Any order of phyllome lamina vein can form the sides of a phyllome lamina areole. Taken together, the phyllome lamina areoles form a contiguous field of polygons over the area of a phyllome lamina. part_of phyllome lamina


leaf lamina areole (PO:0025392): A phyllome lamina areole (PO:0025391) that is part of a leaf lamina (PO:0020039) and is completely surrounded by leaf lamina veins (PO:0020138) and cannot be divided into any smaller parts that are completely surrounded by leaf lamina veins.

Comment: Any order of leaf lamina vein can form the sides of a leaf lamina areole. Taken together, the leaf lamina areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole. part_of leaf lamina

ovuliferous scale

New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).

"Ovuliferous scale" seems to be the more commonly used name.

proposed def., ovuliferous scale: A megasporophyll (PO:0009027) that is part of a seed-scale complex (PO:id).

Comment: Has as part an ovuliferous scale ovule (PO:0025491) and is part of a ovulate cone ().

need to review this

Currently, ovuliferous scale is a narrow synonym of megasporophyll


ovulate cone, new term: A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).

synonym: female cone (related)

Move more specific synonyms form strobilus to these terms.

microsporangiate cone, new term: A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).


seed-scale complex: A reproductive shoot system (PO:0025082) that is part of an ovulate cone (PO:0025083) and has as parts a ovuliferous scale () and a ovuliferous scale sterile bract ().


ovuliferous scale sterile bract: A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().

Definitions of megasporophyll and microsporophyll

move part about angiosperms to the comment

Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.

Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.

pericarp and seed coat

What is the problem with pericarp?

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

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


pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.

Synonyms related: fruit peel, fruit rind

New def.: A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.

comment: Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.

endocarp ; PO:0009086, synonym inner epidermis of pericarp

exocarp ; PO:0009085 synonyms outer epidermis of pericarp,


seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.

Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument

Get rid of "usually" in def. of integument. From: http://en.wikipedia.org/wiki/Caryopsis

is a type of simple dry fruit — one that is monocarpelate (formed from a single carpel) and indehiscent (not opening at maturity) and resembles an achene, except that in a caryopsis the pericarp is fused with the thin seed coat.

The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.

The term grain is also used in a more general sense as synonymous with cereal (as in "cereal grains", which include some non-Gramineae). Considering that the fruit wall and the seed are intimately fused into a single unit, and the caryopsis or grain is a dry fruit, little concern is given to technically separating the terms "fruit" and "seed" in these plant structures. In many grains, the "hulls" to be separated before processing are actually flower bracts.

link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251


we also have the term:

caryopsis hull (PO:0006000): A collective phyllome structure that encloses a fruit of the Poaceae (caryopsis) and develops from a dried lemma and palea. [source: POC:Ramona_Walls]

ovary and the like

An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.

The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).


ovary wall: Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.

style: (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.

If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.

stigma: Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.

anther and filament

Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this cool picture).

It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).

Cacti terms:

spinule: word for when the spines are stipules – synonym of stipule spine

In Beentje, spinule is defined as a small spine.

Add "spinule" as narrow synonym for stipule spine and as related synonym for other kinds of spines.

cladode and phylloclade

From Beentje:

cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf

phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.

FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.

proposed definition:

cladode: A shoot axis that is flattened and expanded.

comment: Has an increased surface area for photosynthesis and may function similar to a leaf in plants that have no or small leaves, such as cacti. Consists of one to several internodes and nodes.

synonyms: phylloclade, cladophyll

Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla? This does not work. The comment also does not work. Similarily the synonyms are not so much synonyms as they are subsets.

I don't know what the problem is with Cholla. As far as I know, it does not have cladodes or phylloclades, because the axes are round.

Recent interesting paper on cladodes in Asparagus:

Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. The Plant Cell Online, 24, 929 –940.

PMID:22415273

In Asparagus, some cladodes have re-evolved a rounded shape. Are they still cladodes, or just shoot axes again at that point (given that the PO is not based on homology)?

rib

Should also add 'rib' for cacti and other plants.

Definition:

-caryopsis new child of fruit

-adventitious root nodule

Make two sub-types of tapetum

Based on the discussion on the PO conf call 4-9-13, we need to add the two types of tapetum(s). Added as a comment on tapetum for now.

See tracker at: tapetum types

Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:

Need to determine if it is more appropriate to put them as child of tapetum or anther wall tapetum.

See references in the literature to: Sporne KR (1973) A Note on the Evolutionary Status of Tapetal Types in Dicotyledons. New Phytologist 72: 1173–1174

link

link to book

link to OSU Thesis


Organizing the types of plant cells

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

In CL, they are organized by type:

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

Revisions to Plant Structure Development Stages:

POC 9-10-13: Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point

Stages of Plant Embryo Development

Currently: in Version #20, Aug 2013:

Plant Embryo Dev Stages.png

Note: Not sure where the coleoptilar stage (PO:0001094) fits in- it has no letter code and apparently never has (at least in the last 4 years). The A zygotic stage term was removed sometime in 2011. Currently the heirarchy looks quite odd as starts with "B- proembryo stage"

-Removed the letters in the names and added preceded_by to order the stages. made coleoptilar stage (PO:0001094) a subclass of bilateral stage (PO:0004507).

Revisions June-July 2014:

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

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


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



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

Sub-classes:

plant proembryo stage (PO:0001180)]

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

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


-

plant embryo globular stage (PO:0001185)

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

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

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

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

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

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


proposed definition RW:

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

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

Propose re-revised def'n LC:

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

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

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


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


Revised def'n LC:

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


--

plant embryo bilateral stage (PO:0004507)

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

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


RW: New proposed definition:

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

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

Ref: PMID:24784759


--




--

Suggested revisions from Dora Szakonyi (from 2012-06-27):

  • See Open SF tracker: #488 embryo development terms
  • At the moment B proembryo stage_PO:0001180 is a synonym for both 'eight-celled stage in Arabidopsis' and 'two-celled stage in Arabidopsis'. Maybe it would be good to introduce as child terms separately:

* B proembryo stage_PO:0001180 (= preglobular stage)

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

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

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

* For D bilateral stage_PO:0004507

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

* E expanded cotyledon stage_PO:0001078 Linear cotyledon stage embryo

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

* F mature embryo stage_PO:0001081


Older trackers:

References:

Other "To do" items:

  • Next: start working on the fruit ripening stages, leaf and and tuber development stages- see below
  • Complete edits on prothallial cell and prothallium
  • Post list of phloem terms to tracker- what needs to be done on them?
  • follow up with French fern folks about terms for ferns - email inquiry, terms on tracker
  • reopen gametophyte and sporophyte?
  • Resolve the question about axis vs stem
  • Open tracker for new term for caryopsis, other types of fruit
  • look at spikelet rachilla (PO:0009080): The axis of the spikelet, above the glumes. is_a inflorescence branch (PO:0025111). needs to be revised. tracker?
  • spikelet needs to be revised
  • ovary wall should not be a cardinal organ part as ovary is not an organ See Items_for_future_meetings#ovary_and_the_like below.
  • pappus element should not be a COP, as a pappus is not an organ- collective organ part structure. Each pappus element is a part of some organ (although there is some debate about which organ it is part of), thus pappus element is a cardinal organ part. The pappus is a collection of pappus elements, and therefor a collective organ part structure. I think the classification is correct.
  • egg apparatus- should not be a COP, as it part_of embryo sac which is_a megagametophyte which is_a whole plant This was classified back when we were looser with putting things under COP. Need to propose an alternative classification. Maybe a portion of plant tissue?
  • there are a number of parts of fruit such as the fruit septum (PO:0025268), fruit locule, fruit valve that should have dual parentage- e.g. fruit septum is_a septum (is_a col. organ part structure) and should also be is_a cardinal part of a multi-tissue plant structure.
  • Need to revisit the AISO annotations of segmented images, as some of the protoxylem terms are not in the live version yet (will be in Release #20).
  • Need to work on the development of the gametophytes in moss Moss Physcomitrella patens Reproductive Organ Development, Plant Phys, 2013
  • Add PO:id for tapetum (PO:0025313) to comment on tapetum cell (PO:0025543)
  • need to fix: paraclade cortex PO:0004721: A portion of ground tissue that is part of a cortex and part of a paraclade. - change to 'primary inflorescence branch cortex'; add PO:Ids
  • Add preceded_by to the sub-classes of floral organ formation stage (PO:0025585):
  • Need to fix: spikelet rachilla: (PO:0009080): The axis of the spikelet, above the glumes. [source: POC:curators] - Should be an inflorescence branch (primary?), add PO:Ids
  • look at caruncle (PO:0020060) again- came up in the contest of the arillode and arilloid.
  • Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.
  • should we add a costa has part hydrome and leptome, they are not always there?
  • fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  • need to revisit the portion of meristem tissue definition- about 2 dozen direct is_a children, many of which are actually determinate tissues such as the phyllome anlagen (PO:0025430) and child terms, the primordium, etc
  • Need to revisit shoot node (PO:0005004): A cardinal organ part of a shoot axis where one or more spikelet, flower, floret, branch, bud, or leaf may arise. Refer to the POC call 10-1-13 for more details.
  • Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see POC_Conf._Call_10-29-13)
  • Consider getting rid of apical meristem (PO:0020144)- it forces dual parentage on the two child terms- shoot apical meristem (PO:0020148) and root apical meristem (PO:0020147) and forms a loop/cycle.



whole plant flowering stage PO:0007016

  • Now that we have revived the flowering stages, we need to revisit the whole plant flowering stages:

whole plant flowering stage (PO:0007016): A sporophyte reproductive stage (PO:0007130) during which a flower (PO:0009046) on a whole plant (PO:0000003) is open.

This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants

  • child terms need to be revised and the synonyms need to be reviewed, compare synonyms and stages
    • PO:0007026 : FL.00 first flower(s) open stage [24,868]
    • PO:0007034 : FL.01 1/4 of flowers open stage
    • PO:0007053 : FL.02 1/2 of flowers open stage [0]
    • PO:0007052 : FL.03 3/4 of flowers open stage [0]
    • PO:0007024 : FL.04 end of flowering stage [2]

Why are there ~25,000 associations on the first one and none on the rest? They look like they are all from Zea Mays, and 1 from SGN.


fruit development stages (PO:0001002)

  • To avoid confusion, the whole plant fruit development stages (PO:0025500) were renamed in Release_19 to make it clear that they apply to whole plants.
  • The plant phenotype pilot project needs terms for grain (fruit) development stages such as milk stage (as synonym for more general term) and mature or dry stage.
  • We currently have terms for two sub-classes:
    • fruit formation stage PO:0025501 [145]
      • PO:0025503 : fruit initiation stage [0]
      • PO:0025505 : fruit size 10 to 30% stage [0]
      • PO:0025506 : fruit size 30 to 50% stage [0]
      • PO:0025507 : fruit size 50 to 70% stage [0]
      • PO:0025508 : fruit size 70% to final size stage [0]
      • PO:0025504 : fruit size up to 10% stage [0]
    • PO:0025502 : fruit ripening stage [118]

fruit ripening stage PO:0025502 and sub-classes

New terms are needed to describe the stages of ripening for individual fruits. Have a revised parent term; need the sub-classes.

fruit ripening stage: A fruit development stage (PO:0001002) during which a single fruit (PO:0009001) participates in the process of fruit ripening (GO:0009835).

Comment: Succeeds a fruit formation stage (PO:0025501). This stage is to be used for an individual fruit. Fruit ripening (GO:0009835) is defined as: an aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal. For the development stage of a whole plant (PO:0000003), use whole plant fruit ripening stage (PO:0007010).


fruit ripening (GO:0009835): An aging process that has as participant a fruit. Ripening causes changes in one or more characteristics of a fruit (color, aroma, flavor, texture, hardness, cell wall structure) and may make it more attractive to animals and aid in seed dispersal.

related synonyms: fruit maturation; fruit senescence

PO:0001170 : seed development stage [33916]

  • PO:0004506 : developing seed stage [10]
  • PO:0001040 : dry seed stage [19]
  • PO:0007633 : endosperm development stage [33495]
  • PO:0004505 : fertilized ovule stage [4]
  • PO:0025374 : seed dormant stage [23]
  • PO:0007632 : seed maturation stage [12]

plant organ development stage (PO:0025339) and child terms:

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

Phyllome snap shot.jpg

Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.

reproductive shoot system development stage (PO:0025530)

  • Is_a: collective plant organ structure development stage (PO:0025338)
  • We need to build a hierarchy for the development of conifer cones- as they are also reproductive shoot systems
    • A conifer cone is a strobilus (PO:0025083): A reproductive shoot system consisting of a number of modified leaves (sporophylls) or ovule-bearing scales grouped terminally on a stem. [source: ISBN:0716710072, POC:curators]
      • Comment: May be simple or compound. Found in lycophytes such as Selaginella and Lycopodium, sphenophytes such as Equisetum, gymnosperms such as cycad, conifers, gnetophytes and the pollen producing structures of Gingko. The term cone is often used for strobili that are woody. Flowers are sometimes considered bisexual strobili. Some flowering plants such as Alnus have inflorescences called catkins that resemble strobili, but are not.
  • moss reproductive structures: these would both be children of plant organ development, as moss lacks a shoot system.
    • multicellular plant gametangium (PO:0025124):- antheridium (PO:0025125) and archegonium (PO:0025126)- produce the gametes
    • sporangium (PO:0025094): A plant organ in which spores are produced.


Need to look at the fern sporangia- that is the reproductive structure for those plants


  • This would parallel the two existing sub-classes:

inflorescence development stage (PO:0021004)and sub-classes

  • Currently this has two sub-classes:
    • PO:0021004 : inflorescence initiation stage [0]
    • PO:0007037 : inflorescence bifurcation stage [0]
  • Inflorescence development stage (PO:0001083):A reproductive shoot system development stage (PO:0025530) that has as primary participant a inflorescence (PO:0009049).
    • inflorescence initiation stage (PO:0021004): Stage of inflorescence development marked by the formation of the inflorescence meristem on a vegetative branch. [source: POC:Felipe_Zapata]
    • inflorescence bifurcation stage ( PO:0007037): Stage of inflorescence development marked by the formation of two, often equal-sized, inflorescence meristems from one inflorescence meristem. [source: POC:curators]

These need to be revised and additional stages need to be developed.

flower development stage:

This is mostly done- this reference might be helpful for the legume flowers and have annotations to add. Floral Development in Legumes: (Plant Physiol, March 2003, Vol. 131, pp. 911-926)

collective phyllome structure development stage (PO:0025578) and child terms

collective phyllome structure development stage (PO:0025578): A collective plant organ structure development stage (PO:0025338) that has as primary participant collective phyllome structure (PO:0025023).

  • Made these part_of floral organ differentiation stage (PO:0007600), need to work on the definitions....
    • androecium development stage (PO:0007605): A collective phyllome structure development stage (PO:0025578) that has as a primary participant an androecium (PO:0009061).
    • calyx development stage (PO:0007603):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a calyx (PO:0009060).
    • corolla development stage (PO:0007604):A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).
    • gynoecium development stage (PO:0007606): A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).

Collective phyllome snap shot.jpg

New term flower bract development stage (new po:id)

flower bract development stage (new po:id):

- will be parent to lemma development stage and palea development stage

  • lemma development stage (PO:0001047): A phyllome development stage (PO:0025579) that has as a primary participant a lemma (PO:0009037).
    • PO:0001055 : lemma primordia visible stage [1]
    • PO:0001056 : lemma differentiation and expansion stage [0]
    • PO:0001057 : fully expanded lemma stage [0]


  • palea development stage (PO:0001048): A phyllome development stage (PO:0025579) that has as a primary participant a palea (PO:0009038).
    • PO:0001058 : palea primordia visible stage [1]
    • PO:0001070 : palea differentiation and expansion stage [0]
    • PO:0001071 : fully expanded palea stage [0]

anther development stage (PO:0001004) and its child terms

  • anther development stage (PO:0001004): Stages of development of the anther defined by characteristic morphological, cytological, histological or other visible features.
  • Is_a androecium development stage (PO:0007605):
  • In Release #19, we renamed anther wall tapetum degeneration initiated stage (PO:0001032): An anther development stage during which degeneration of the anther wall tapetum (PO:0009071) is initiated, as the deposition on the surface of the microspore (PO:0020048) primexine proceeds.

Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498

tuber growth and development stages

This item has been open on SF since 6/2009, How we work these in will depend on restructuring of PSDS

We will have to differentiate between the two sub-types of tuber (PO:0025522), as they will have different development:

  • tuber (PO:0025522): A plant axis (PO:0025004) that is radially enlarged. [source: POC:curators]
  • PO:0004543: shoot axis tuber [6]
  • PO:0025476: tuberous root tuber [0]

So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)


From Naama Menda: "I have a bunch of potato genes which are expressed in different tuber developmental stages (e.g. the potato pmt gene is expressed in small sprouts only (http://www.ncbi.nlm.nih.gov/pubmed/16088399).

Suggested stages:

  • tuber initiation
  • tuber growth
  • tuber maturation

Would these be the same for the two different types of tubers? Also need: tuber dormancy

  • sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  • All the SGN annotations refer to potato, which is a subterranean tuber (PO:0004547)
    • part_of children:
      • PO:0025070 : subterranean tuber axillary bud meristem
      • PO:0025081 : subterranean tuber axillary shoot (exact synonym: tuber sprout)
      • PO:0025042 : subterranean tuber axillary vegetative bud (narrow synonym: potato eye)
      • PO:0025048 : subterranean tuber epidermis
      • PO:0025045 : subterranean tuber periderm
      • PO:0025038 : subterranean tuber storage parenchyma


Further info and references:

Potato Growth & Development

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

Growth of the Potato Tuber

xylem developmental stages:

See discussions of primary xylem on POC_Conf._Call_6-11-13

Existing definitions:

* secondary xylem development stage (PO:0025427): A xylem development stage (PO:0025425) that has as primary participant a portion of secondary xylem (PO:0005848) tissue during the interval between the beginning of a cell division stage of secondary xylem (PO:0025463) and the death of the last living cell in the secondary xylem. [source: POC:wood_curators]

  • Need: primary xylem development stage (PO:new): A xylem development stage (PO:0025425) that has as primary participant a primary xylem (PO:0005849) tissue. needs to be expanded

whole plant development stages (PO:0007033)

  • sporophyte vegetative stage (PO:0007134):

child terms need to be revised:

    • plant embryo stage (PO:0007631)
    • 0 seed germination stage (PO:0007057)
    • coleoptile emergence stage (PO:0007045)
    • 1 main shoot growth stage (PO:0007112)
    • 2 formation of axillary shoot stage (PO:0007073)
    • seedling development stage (PO:0007131)

whole plant fruit ripening stage (PO:0007010)

  • whole plant fruit ripening stage: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.

Comment: Succeeds a whole plant fruit formation stage (PO:0007042). This term is to be used for a stage of development of a whole plant. For the stages of development of an individual fruit, see fruit ripening stage (PO:0025502). Although individual fruits are undergoing fruit ripening (GO:0009835), which is a type of senescence, during this stage, the whole plant is not yet undergoing multicelluar organism senescence (GO:0010259). An iteroparous species generally will have only one fruit ripening stage in its life, while a semelparous species may have multiple fruit ripening stage in its life. A whole plant fruit ripening stage may be followed by a sporophyte senescent stage, as in case (1) or by a sporophyte dormant stage (PO:0007132), as in case (2). In evergreen species and species that fruit multiple times during a growing season, a plant may have multiple fruit development stages without entering dormancy or senescence, as in case (3). In plants with continuous (i.e., indeterminate) fruit development (GO:0010154), new fruits may continue to develop after the first fruit has begun to ripen and the whole plant fruit formation stage (PO:0007042) has ended. In some plants, fruit may continue to ripen after the whole plant has entered a sporophyte dormant stage or sporophyte senescent stage and left the whole plant fruit ripening stage. Some plants may never enter a whole plant fruit ripening stage, because fruits only begin to ripen after the plant has entered a sporophyte dormant stage or sporophyte senescent stage. Although the use of synonyms like "10-dough stage in sorghum" properly refer to the development of an individual fruit, they are used as here to extrapolate to a whole plant. 


 **Add link to this tracker from the whole plant fruit ripening stage (PO:0007010)**

See comments from BS from email:

  • On Wed, Sep 18, 2013

- A lot of this needs to go, I think:

- early, middle and late are okay, but then we need to define them non-circularly and if you want to keep whole plant f.r. complete stage' then you have to define it so that it differs from 'late ...'

WPFRS.png

Proposed Revisions to sub-classes:

Comment from RW: The current definitions are very vague and circular! For now, propose just rewording them so it is clear that they refer to whole plants, but we will need to develop some more specific boundaries for these stages at some point. 

need to open tracker for this set:

* whole plant beginning of fruit ripening stage (PO:0007036):

current name and def'n:FR.00 beginning of fruit ripening stage (PO:0007036): The stage at which fruit maturation begins.

proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant begins.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonyms:

  • BBCH principle growth stage 81; Beginning of ripening: berries begin to develop variety-specific colour
  • grape E-L stage: 35 Berries begin to colour and enlarge, beginning of veraison
  • whole plant early fruit ripening stage (PO:0007001)

current name and def'n: FR.01 early stage of fruit ripening (PO:0007001): The early stage in fruit ripening

proposed def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in an early stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

Add related synonyms:

  • middle of veraison
  • BBCH principal growth stage 83

* whole plant mid fruit ripening stage (PO:0007031): current name and def'n: FR.02 mid stage of fruit ripening (PO:0007031) The stage when fruit ripening is midway.

proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is midway.

proposed comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

* whole plant late fruit ripening stage (PO:0007050):

current name and def'n: FR.03 late stage of fruit ripening (PO:0007050): The late stage of fruit ripening.

proposed new def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of one of more fruits on the plant is in a late stage.

comment: This terms is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

* whole plant fruit ripening complete stage (PO:0007038):

current name and def'n: FR.04 fruit ripening complete stage (PO:0007038): The stage at which fruit ripening is complete.

Proposed Def'n: A fruit ripening stage of whole plant (PO:0007010) during which ripening (GO:0009835) of most of the fruits on the plant is complete.

comment: This term is best used for plant with more or less synchronous fruit development. This stage occurs only once in the life of annual plants, but may occur once for each growing season in perennial plants.

related synonyms:

  • BBCH principal growth stage 89
  • grape E-L stage: 38; Berries ripe for harvest

GO requests:

Multicellular organism senescence/aging (GO:0010259)

  • Multicellular organism senescence/aging (GO:0010259): includes loss of functions such as resistance to disease, homeostasis, and fertility, as well processes like cellular senescence, organ senescence, and wear and tear. The POC curators have requested to the GOC that they revise the definition of GO:0010259, to make it more appropriate for plants.


Link to PO tracker: gametophyte/sporophyte senescent stage


PJ Suggested revisions to leaf shaping (GO:0010358); Proposed new name: multidimensional leaf expansion: The developmental process that pertains to the organization of a leaf in three-dimensional space once the structure has initially formed.

apoplast and symplast

  • apoplast (GO:0048046): The cell membranes and intracellular regions in a plant are connected through plasmodesmata, and plants may be described as having two major compartments: the living symplast and the non-living apoplast. The apoplast is external to the plasma membrane and includes cell walls, intercellular spaces and the lumen of dead structures such as xylem vessels. Water and solutes pass freely through it.

includes tracheids

This definition needs to be modified to be similar to the one for symplast. Lots of this should go in the comment.

  • symplast (GO:0055044): The interconnected cell membranes and intracellular regions of a plant. The interconnections occur via the plasmodesmata.

- all the plasma connected, through plasmodesmata, transport through the cytoplasm

See: Link to diagram Apoplast_and_symplast_pathways

See: Apoplastic versus Symplastic Pathways in roots

  • Suggest revised GO definitions for apoplast and symplast and add transport terms

Parent term:

  • transport (GO:0006810): The directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
  • apoplastic transport (new GO term): A transport process (GO:id) that occurs in the apoplast (GO:0048046)
  • symplastic transport (new GO term): A transport process (GO:id) that occurs in the symplast (GO:0055044)

comments: symplastic transport is a diffusion process

  • Submit tracker for GO biol process term to describe callus formation

Wood ontology terms

See separate page: Wood Ontology PO and GO Term Development

root terms

Submitted by Rich Zobel (Nov 2009). Still need to work on definitions for these terms.

Growth forms

From Daniel Hiss: "IMHO plant growth/life forms should be best integrated as an extension to PO." Also need acrocarpous and pleurocarpous moss (these could be growth forms).

epidermis/epidermal cell : plant v. animal

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