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
+
- Go back to [[POC_Meetings_Minutes]] main page
  
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=Vascular tissues and cell types=
+
- All new terms and changes should be listed here: [[Release_21]]
  
−
These terms will need to be fixed before the Wood Ontology meeting in February.
 
  
−
See POC conf call [[POC_Conf._Call_1-24-12]]
 
  
−
==[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3476728&group_id=76834 phloem and its children]==
 
−
See POC conf call [[POC_Conf._Call_1-24-12]]
 
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3476729&group_id=76834&atid=835555 xylem]==
+
=Annotation Guidelines=
−
See [[POC Conf. Call 1-31-12]]
+
Comments from PJ from previous meeting (9-27-11):
 +
Ask MS if she can write up a small blurb on how she created the Maize annotations.  Maize probe ids => gene ids  methods and cut-offs, a guide for other collaborators and  a page for the info.
 +
Maybe co-author it with SR
 +
 
 +
-This will also be helpful when applying for new grants
 +
 
 +
-it would be helpful to have a detailed guide on our wiki for collaborators
 +
 
 +
* Need to update the [[Annotation_Association_File_Format]] page
 +
 
 +
=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.
 +
 
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/596/ link to #596]
 +
 
 +
[http://www.sciencedirect.com/science/article/pii/S2090447912000524 structure and properties of sorghum stalks]
 +
 
 +
 
 +
Propsed new terms:
 +
 
 +
=='''Abscission Zones'''==
 +
June 2014
 +
 
 +
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).
 +
 
 +
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)
 +
 
 +
===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.
 +
 
 +
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: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/589/ 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.''
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3476730&group_id=76834&atid=835555 leaf vein, mid vein]==
+
==caryopsis hull (PO:0006000)==
−
See [[POC Conf. Call 1-31-12]]
+
* [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.''
  
−
==Primary and secondary growth, etc.==
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/575/ founder cells]==
−
===proposed terms for GO===
+
New terms:
−
'''primary growth (new term):'''
+
phyllome founder cell (PO:0025586)]: A plant cell (PO:0009002) that is part of the phyllome anlagen (PO:0025430).
  
−
'''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)
+
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.
  
−
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.
+
PMID:12610522
  
−
is_a growth (GO:0040007)
+
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.
  
−
'''secondary or lateral growth'''
+
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).
  
−
GO currently defines secondary growth as: Increase in plant girth due to the activity of lateral meristems (vascular and cork cambium). Source: PMID:19074290 
+
==Revisions to cortex (PO:0005708) and other portion of ground tissue (PO:0025059) children==
  
−
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.
+
See notes from discussion on POC call [[POC_Conf._Call_9-24-13]]
  
−
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.
+
Issue is that some cortex terms are children of cortex (PO:0005708) and others are is_a portion of ground tissue (PO:0025059)
  
 +
[[File:Cortex terms.png]]
  
−
'''lateral growth (GO:new term):''' Growth of a plant axis (shoot axis or root) that originates from a lateral meristem (PO:0020145).
 
  
−
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).  
+
Fill in details here.....
  
  
−
'''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)
+
==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.
  
−
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.  
+
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.
  
−
Add synonym "cambial secondary growth", which is makes the meaning clearer.
+
-Added Narrow synonyms: adnate perianth and connate perianth
  
 +
*[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
  
−
'''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).
+
*[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
  
−
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.
+
*[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.  
  
−
References: Fahn 1990, ISBN:0080374903, Rudall 1991, JSTOR:4354165
+
* [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).
  
 +
***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.
  
−
'''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)
 
  
−
comment: Occurs in shoot axes and rarely in roots in many monocotyledons.
+
*[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).  
  
−
Ref: JSTOR:4354165, Rudall 1991, and Esau ISBN:0471245208
+
*[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.
  
−
'''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.
+
==Need to look at these associated terms:==
 +
* is_a:
 +
** PO:0025324 : banner petal [0]
 +
** PO:0025326 : keel petal [0]
  
−
comment: Occurs in the stems of some Arecaceae (palms).
+
* 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]
  
−
Ref.: Fahn 1990, ISBN:0080374903
 
  
−
==PO terms for lateral meristems==
+
For corolla:
−
See [[POC Conf. Call 1-31-12]].
+
* 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]
  
−
==conductive and related cell types==
+
* fused corolla (PO:0025581): A corolla (PO:0009059) that is composed of fused petals (PO:0025583).
−
===Current parent: axial cell===
+
* calyptra corolla (PO:0025330): A fused corolla (PO:0025581) that is composed of fused petals (PO:0025583). Very similar definitions
−
'''Existing structure:'''
 
  
−
axial cell (PO:0000081)
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/98/ epicalyx] ==
  
−
>sieve tube member (PO:0000289, alt: PO:0000286)
+
* epicalyx (PO:00090630): A collective phyllome structure (PO:0025023) composed of two or more phyllomes immediately outside the calyx (PO:0009060). [source: POC:curators]
  
−
>phloem fiber (PO:0004519)
+
''Do we need a new term for epicalyx bract? - What are the individual members of the epicalyx; they are bracts.''
  
−
>xylem element (PO:0000273)
+
Existing term: flower bract (PO:0009034): A bract that subtends a perianth that is part of a flower. [source: POC:curators] 
  
−
>>tracheary element (PO:0000273)
+
''Add epicalyx bract as an exact synonym?, or make a new child of flower bract . Not every flower bract is part of an epicalyx''
  
−
>>>tracheid (PO:0000301)
+
''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.
  
−
>>>vessel member (PO:0002003)
+
''Decided that we needed to add a new term:''
  
−
>>xylem fiber (PO:0000274)
+
''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.''
  
−
>>>fiber tracheid (PO:0000355)
+
==arilloid and arillode and caruncle==
  
−
>>>libriform fiber (PO:0004520)
+
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''
  
−
>>>septate fiber (PO:0004521)
+
* '''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.
  
−
'''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]
+
Synonyms exact: ariloide (Spanish)
  
−
Comment: These cells make up the axial system, also known as vertical or longitudinal system.
+
*'''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.
  
−
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).
+
Synonyms exact: carúncula (Spanish)
  
−
Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system.
+
*aril PO:0009090: An arilloid that is an outgrowth of a seed from a seed funicle. [source: ISBN:9780881928501]
  
−
See [[Items for future meetings#other wood terms]], below.
+
Synonyms
 +
exact: arilo (Spanish)
 +
exact: 仮種皮 (Japanese)  
  
−
===New proposed hierarchy (children of plant cell):===
+
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.
  
−
plant cell
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609179&group_id=76834&atid=835555 floral node]==
  
−
>sieve element (new term)
+
suggested definition: A cardinal organ part of a shoot axis where one or more flower may arise
  
−
>>sieve tube member (syn.: sieve tube element)
+
Parent/relationship: is_a shoot node (PO:0005004)
  
−
>>sieve cell (new term)
+
Submitted: Johnny Lloyd
  
−
>tracheary element
 
  
−
>>tracheid
+
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
  
−
>>vessel member
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/535/ spine petiole]==
  
−
>ground tissue cell (PO:0025030)
+
Requested by DWS: spine petiole (new PO:id)- A petiole that is sclerified and persistent.
  
−
>>sclerenchyma cell (PO:0000077)
+
The petiole abscisses longitudinally and the blade withers.
  
−
>>>sclerid (new term)
+
See the photo and description on this page: [http://waynesword.palomar.edu/ecoph30a.htm "Spines From Modified Petioles"]
  
−
>>>fiber cell (new term)
+
==[http://sourceforge.net/tracker/?func=detail&aid=3609178&group_id=76834&atid=835555 adventitious branch]==
  
−
>>>>phloem fiber cell
 
  
−
>>>>xylem fiber cell
+
Definition: A shoot axis (PO:00025029) that develops in an unusual place
  
−
>>>>other kinds of fiber cells?
+
Parent/relationship: is_a shoot axis (PO:0025029), develops from an adventitious bud
  
−
===New definitions - sieve elements===
 
−
Definitions from Esau's Anatomy of Seed Plants
 
  
−
'''sieve element (new term)'''
+
adventitious shoot axis
  
−
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.
+
==shoot-borne root (PO:0000042)==
 +
synonym: adventitious root
  
−
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.
+
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
  
−
'''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.
+
==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: 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: 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.  
  
−
part_of phloem, participates_in sporophyte stage
+
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.
  
  
−
'''sieve cell (new term)'''
+
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/521/ Ultimate Unit (UU)]==
 +
Requested by:  Corvez Adele  Created: 2013-02-01
  
−
proposed def.: A sieve element in which the sieve areas are not aggregated into sieve plates.
+
* 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
  
−
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. 
+
suggested parentage: Ultimate unit is_a cardinal organ part
  
 +
==moss capsule==
 +
need to open tracker for this: [https://sourceforge.net/tracker/?func=detail&aid=3140824&group_id=76834&atid=835555 moss capsule]
  
−
'''sieve tube member (PO:0000289)'''
+
==[http://sourceforge.net/tracker/?func=detail&aid=3597966&group_id=76834&atid=835555 prothallial cell] and prothallium ==
  
−
'''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).
+
On the POC POC call (12-11-12), we identified that we needed to add this as part of the gymnosperm pollen.
  
−
comment: Also sieve tube element and the obsolete sieve tube segment. Occurs in the sporophytic phase of a plant life cycle.
+
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.
  
−
'''proposed def.:''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
+
''should add the PO id for microgametophyte (PO:0025280) to the definition''
  
−
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.
 
  
−
syn.: sieve tube element, sieve tube segment
+
For reference about prothallial cells in gymnosperms see:  
  
−
part_of sieve tube (new term)
+
Morphology of gymnosperms, by John M. Coulter and Charles J. Chamberlain. pages 2277-278 and 339-340.
  
 +
Available online: [http://babel.hathitrust.org/cgi/pt?id=mdp.39015052524801;seq=356;view=1up;num=340 Coulter + Chamberlain, 1910]
  
−
'''See below for companion cells and other parenchyma cells found in vascular tissue.'''
 
  
−
====New term for sieve tube====
+
Note: prothallium is a synonym for thallus (PO:0030027) and ....
  
−
'''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.
+
How does prothallial cell compare to microgametophyte vegetative cell?
  
−
====New terms for GO====
+
prothallial cell (PO:0025533):
−
These subcellular components have been requested from GO.
+
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.
  
−
'''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: 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.
  
−
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
+
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)
  
−
'''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.
+
"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."
  
−
comment: Typical of angiosperms.
+
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.
  
−
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).
+
''We all agreed that this should be a PAE, rather than a development stage. Need to propose definition on SF.''
  
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3082379&group_id=76834&atid=835555 nucellar projections]==
  
 +
The current definition of nucellar projection (PO:0008007) is: A portion of plant tissue that is the morphologically distinct portion of the nucellus overlying the vascular strands in the grass caryopsis. part_of nucellus.
  
−
'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
+
''This definition is specific to grasses, and should be rephrased, so it is more general.''
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
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?
  
−
is_a sieve plate
+
''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).
  
−
'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
+
comment: Found a caryopsis in Poaceae.  
  
−
comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
part_of nucellus
  
−
===New definitions - tracheary elements===
+
==[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.
  
−
'''xylem element (PO:0000273):''' A cell making up xylem tissue.
+
'''Current definitions:'''
  
−
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.
+
'''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.
  
−
'''tracheary element (PO:0000290)'''
+
'''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.
  
−
current def.: General term for any water conducting cell, tracheid or vessel member.
+
comment: In Arabidopsis, refers to the leaves that are borne on ''the elongated inflorescence branches''.
  
−
Currently is part_of primary xylem and part_of secondary xylem.
 
  
−
proposed def.: A plant cell that has a lignified cell wall with secondary thickening and bordered pits and is dead at maturity.
+
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
  
−
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.
+
'''proposed definitions'''
  
−
participates_in sporophyte stage, part_of xylem, disjoint from hydroid
+
'''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.
  
−
'''tracheid (PO:0000301)'''
 
  
−
current def.: In the xylem, a dead elongated water-conducting cell in which at least the middle lamella of the end walls remains intact.
+
'''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 def.: A tracheary element that has no perforations.
+
comment: In species that undergo bolting, such as Arabidopsis thaliana, cauline leaves may start to develop before or after the shoot axes elongates.
  
−
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.
+
Question: Are there ever cauline leaves forming on an inflorescence axis (PO:0020122)?
  
  
−
'''vessel member (PO:0002003)'''
+
Links from Lol:
  
−
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.
+
http://www.arabidopsis.org/portals/education/growth.jsp
  
−
proposed def.: A trachary element that is part of a vessel and has as parts perforation plates.
+
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.
  
−
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.
+
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.
  
−
syn.: vessel element, vessel segment
+
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?
  
−
part_of vessel (new term)
+
''Don't need these''
  
 +
==[https://sourceforge.net/tracker/?func=detail&aid=3299941&group_id=76834&atid=835555 sporocyte]==
 +
'''Existing definitions:'''
  
−
'''vessel (new term)'''
+
'''sporocyte (PO:0006204):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) spores.
  
−
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.
+
'''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
  
−
'''perforation plate''' (for GO)
+
'''megasporocyte (PO:0000431):''' A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores. [source: ISBN:0471245208]
  
−
proposed def.: A cell wall part that is the part of a wall of a vessel member that bears one or more openings (perforations).
+
synonyms: megaspore mother cell, MMC
  
−
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.
 
  
−
===New definitions - ground tissue cells===
+
At the POC meeting on 5/6/11, we agreed to add sporocyte develops_from archesporial cell.
  
−
'''sclerenchyma cell (PO:0000077)'''
+
Already have:
  
−
current def.: Usually dead cell variable in form and size, with more or less thick, often lignified, secondary walls.
+
megasporocyte develops_from female archesporial cell
  
−
proposed def.: A ground tissue cell with thickened secondary cell walls that are often lignified.
+
microsporocyte dvelops_from primary sporogenous cell, which develops_from male archesporial cell
  
−
comment: May or may not be devoid of protoplast at maturity. Not always easy to distinguish from xylem tissue or sclerified parenchyma cells.
 
  
−
Currently, sclerenchyma cell part_of sclerenchyma, but this is not always true. There can be isolated sclerenchyma cells.
+
'''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).
  
−
'''sclerid (new term)'''
+
Add: sporocyte develops_from archesporial cell
  
−
proposed def.: A sclerenchyma cell that has thick, lignified secondary walls with many pits.
+
Should we add spore develops_from sporocyte? ''yes''
  
−
comment: Usually not very elongated.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007126 meiosis (GO:0007126)]
  
−
====parenchyma cells in vascular tissue====
 
  
−
'''companion cell (PO:0000071)'''
+
'''microsporocyte (PO:0020047):''' A sporocyte (PO:0006204) that develops from a primary sporogenous celll (PO:0006088) and undergoes meiosis (GO:0007126) to produces four microspores (PO:0020048). [source: ISBN:0878934030]
  
−
'''current 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.
+
synonyms: microspore mother cell, PMC, pollen mother cell
  
−
'''proposed definition:''' A parenchyma cell that is adjacent to a sieve-tube member and arises from the same mother cell as the sieve-tube member.
+
Should we add microspore develops_from microsporocyte?
  
−
comment: Found in angiosperms. Compare to albuminous cells (PO:xxxx), which are found in gymnosperms.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007140 male meiosis (GO:0007140)]
  
−
Currently part_of primary phloem '''and''' part_of secondary phloem, which can't be true. Should change to part_of phloem.
+
''Better to use meiosis, rather than male meiosis.''
  
−
Suggest that we add relation companion cell adjacent_to sieve tube element.
 
  
 +
'''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]
  
−
'''albuminous cell (new term)'''
+
synonyms: megaspore mother cell, MMC
  
−
'''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.
+
[http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO:0007143 female meiosis (GO:0007143)]
  
−
comment: May be found in the rays and sometimes the axial system of gymnosperms. Compare to companion cells, which are found in angiosperms.
+
''Better to use meiosis, rather than female meiosis.''
  
−
is_a parenchyma cell, part_of phloem, adjacent_to sieve cell.
 
  
 +
'''Also need to address:'''
  
−
Should we have a term for phloem parenchyma cell? Could be parent of companion cell and albuminous cell.
+
'''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.
  
−
====fiber cells====
 
−
'''fiber cell (new term)'''
 
  
−
proposed def.: An elongated, tapering schlerenchyma cell with a more or less thick secondary cell wall.
+
'''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).
  
−
comment: May or may not have lignin in the secondary wall or a living protoplast at maturity. It may be difficult to distinguish fiber cells from xylem cells.
+
''okay''
  
  
−
'''phloem fiber cell (PO:0004519)''' (was called phloem fiber)
+
''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.''
  
−
current def.: A fiber in phloem.
+
==[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.
  
−
proposed def.: A fiber cell that is part of a portion of phloem tissue.
+
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).
  
−
'''xylem fiber cell (PO:0000274)''' (was called xylem fiber)
 
  
−
current def.: A fiber in xylem.
+
Proposed def.: A second order inflorescence that has as parts the glumes, a firinflorescence branches with short internodes, and a florets.
  
−
proposed def.: A fiber cell that is part of a portion of xylem tissue.
+
Comment: Part of a spike type inflorescence as found in grasses and other Poales.
  
−
comment:  
+
From Ale:
  
 +
spike: an unbranched, elongated inflorescence with sessile or subsessile flowers or spikelets maturing from the bottom upwards
  
−
'''libriform fiber (PO:0004520)'''
+
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)
  
−
current def.: A xylem fiber commonly with thick walls and simple pits.
+
==[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 lamina areole]==
 +
Propose new definitions:
  
−
proposed def.: A xylem fiber cell with simple pits.
+
'''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: Libriform fibers have unbordered pits while fiber tracheids have bordered pits. Many intermediate forms exists and are generally classified as fiber tracheids. If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Libriform fibers have a slit-like aperature toward the cell lumen, but no pit cavity.  
+
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
  
  
−
'''fiber tracheid (PO:0000355)'''
+
'''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.
  
−
current def.: A fiber-like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit-like apertures.
+
Comment: 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
  
−
Should this be is_a xylem fiber or is_a tracheid? Esau's definition says it is a tracheid, but her treatment it the book is as a fiber.
+
==ovuliferous scale==
 +
New term to add, needed for definition of ovuliferous scale ovule (PO:0025491).
  
−
proposed definition: A xylem fiber cell with bordered pits with pit cavities.
+
"Ovuliferous scale" seems to be the more commonly used name.
  
−
comment: If both libriform fibers and fiber tracheids are present, the libriform fibers usually have thicker walls. Fiber tracheids have bordered pits with smaller pit cavities than the vessels or tracheids of the same wood and a distinct pit cavity leading from the pit cavity to the cell lumen through the thick cell wall.
+
'''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 ().
  
−
'''septate fiber (PO:0004521)'''
+
''need to review this''
  
−
current def.: A fiber with thin transverse walls (septa), which are formed after the cell develops a secondary wall thickening.
+
''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]''
  
−
Septate fibers can be found in both the xylem and the phloem. PO:0004521 is_a xylem fiber, but both tracheid-type and libriform-type xylem fibers can be septate. There are no annotations on this term, so I suggest we obsolete it, and replace it with two new terms: septate fiber tracheid and septate libriform fiber. Could also add septate phloem fiber, is_a phloem fiber.
 
  
−
'''proposed definition, septate fiber tracheid:''' A fiber tracheid that has as parts one or more thin internal partitions or septa.
 
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
'''ovulate cone, new term:''' A strobilus (PO:0025083) that has as parts ovuliferous scales () but no microsporophylls (PO:0009028).
  
−
'''proposed definition, septate libriform fiber:''' A libriform fiber that has as parts one or more thin internal partitions or septa.
+
synonym: female cone (related)
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
+
''Move more specific synonyms form strobilus to these terms.''
  
−
'''proposed definition, septate phloem fiber:''' A phloem fiber cell that has as parts one or more thin internal partitions or septa.
+
'''microsporangiate cone, new term:''' A strobilus (PO:0025083) that has as parts microsporophylls (PO:0009028) but no megasporophylls (PO:0009027).
  
−
comment: Septate fiber cells usually have a living protoplast at maturity. The septa form from mitosis within the lignified cell wall.
 
  
 +
'''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 ().
  
−
====other kinds of fiber cells?====
 
  
−
'''gelatinous fiber:''' A xylem fiber cell in which the inner-most layer of the secondary wall contains abundant alpha-cellulose and is poor in lignin.
+
'''ovuliferous scale sterile bract''': A bract (PO:0009055) that is part of a seed-scale complex and subtends an ovuliferous scale ().
  
−
comment: Commonly found in reaction wood in dicots. The inner layer of the cell wall, or G-layer, can absorb much water and swell and is relatively porous and less compact than the outer layers of the cell wall.
+
===Definitions of megasporophyll and microsporophyll===
 +
move part about angiosperms to the comment
  
−
ref: Fahn
+
Current def., megasporophyll: A structure upon which (or in the axil of which) one or more megasporangia are borne; in flowering plants, a carpel.
  
−
synonym: mucilaginous fiber
+
Current def., microporophyll: A structure on which one or more microsporangia are borne; in flowering plants, the stamen.
  
−
==other wood terms==
+
==pericarp and seed coat==
−
'''Wood''' is a synonym for secondary xylem (PO:0005848) -- see definition above.
+
''What is the problem with pericarp?''
  
−
===New terms===
+
* open tracker for pericarp cell types for PJ: "There are a number of pericarp components which may need PO terms".
−
''Do we want to define '''axial system''' and '''ray system''' as any portion of tissue, or the entirety of tissue in a plant structure?''
+
see: http://www.relata.info/docs/RT%202008%201.pdf
  
−
''Should these terms be part_of secondary xylem?''
 
  
  
−
'''axial system (new term):'''
+
pericarp (PO:0009084):A wall of a fruit, developed from the ovary or carpel wall.
  
−
''Does this definition distinguish axial system from primary vascular tissue?''
+
Synonyms related: fruit peel, fruit rind
  
−
'''proposed definition:''' 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.
+
New def.: ''A portion of plant tissue that develops form the ovary wall and forms the outer layer or layers of a fruit.''
  
−
comment: Includes portions of secondary xylem tissue and axial wood parenchyma tissue.  
+
comment: ''Usually has as parts an exocarp, mesocarp and endocarp. In a caryopsis, the pericarp is fused with the seed coat.''
  
−
synonyms: vertical system, longitudinal system
+
endocarp ; PO:0009086, synonym inner epidermis of pericarp
  
 +
exocarp ; PO:0009085 synonyms outer epidermis of pericarp,
  
−
'''ray system (new term):'''
 
  
−
'''proposed definition:''' A portion of plant tissue that develops from ray initials and extends radially in the secondary xylem and phloem of a plant axis and has as part ray wood parenchyma.
+
seed coat: A portion of plant tissue that is the covering of a seed derived from ovular - mainly integumentary - tissue.
  
−
comment: May include ray tracheids, as in Pinaceae and some Cupressaceae.
+
Revised: A portion of plant tissue that develops from an integument and forms the covering of a seed. develops_from integument
  
−
synonyms: radial system (exact), horizontal system (exact), ray (broad)
+
Get rid of "usually" in def. of integument.  From: http://en.wikipedia.org/wiki/Caryopsis
  
−
===Existing terms===
+
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.
−
'''wood parenchyma (PO:0004532):'''
 
  
−
Current def.: Parenchymatous tissue occurring in the wood.
+
The caryopsis is popularly called a grain and is the fruit typical of the family Poaceae (or Gramineae), such as wheat, rice, and corn.
  
−
Currently is_a secondary xylem. Should be is_a parenchyma.
+
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.
  
−
Proposed def.: A portion of parenchyma tissue that is part of a portion of secondary xylem and has as parts wood parenchyma cells.  
+
link to a more scientific source :http://www.jstor.org/stable/10.2307/2442251
  
  
−
'''axial wood parenchyma (PO:0004533):'''
+
we also have the term:  
  
−
Current def.: Parenchyma tissue in the axial system of secondary xylem.
+
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]
−
+
 
−
Proposed def.: A portion of wood parenchyma that is part of an axial system and has as parts axial wood parenchyma cells.
+
==ovary and the like==
 +
An ovary is either the basal part of a carpel (in an apocarpous gyneocium) or the basal part of a syncarpous gynoecium. This is how it is defined in Esau, Raven, Weberling, etc.  
 +
 
 +
The same can be said of a style or a stigma. Therefore, all of these can be either part_of carpel or part_of gynoecium (which means they are always part_of gynoecium).
 +
 
 +
 
 +
'''ovary wall:''' Part_of ovary, which may be part of carpel or part of gyneocium. Not a valid COP.
 +
 
 +
'''style:''' (Raven: A slender column of tissue that arises from the top of an ovary and through which the pollen tube grows). Just like ovary, it may be part of a carpel or part of a group of fused carpels. Weberling uses "monocarpellary style" for a style of a single carpel and "polycarpellary style" for the style of fused carpels.
 +
 
 +
If the styles are fused at the base but free at the top, the free portions are called "style branches" or "stylodia" (Troll), or "stigma branches" if it is only the stigma portion that is free.
 +
 
 +
'''stigma:''' Raven defines this as a part of a carpel. Esau is ambiguous about how to treat stigma in syncarpous gynoecium. Weberling refers to a single stigma for fused carpels, but also to multiple stigmas, if the carpels are fused at the base and style, but then free at the tips, where the stigmas are. Also refers to stigma lobes (e.g., a tulip, with three fused carpels, has a single stigma, with three lobes. Seem like we have to treat stigma the same as ovary and style.
 +
 
 +
'''anther and filament'''
 +
 
 +
Weberling: Although filaments are often fused, they are still referred to as individual filaments (e.g., the corona of Narcissus consists of fused filaments (not a single filament), with the anthers inserted on the inner surface). Anthers may also fuse, but it is less common. He uses the term "synanther" of a single structure made of fused anthers (e.g., Gesneriaceae, see this [http://www.flickr.com/photos/fostert/5236399328/ cool picture]).
 +
 
 +
It seems like it would be better to keep anther and filament as part of stamen, since that is the more commmon state. We can use special terminology for when they are fused (such as corona and synather).
 +
 
 +
==Cacti terms:==
 +
'''spinule:''' word for when the spines are stipules – synonym of stipule spine
  
−
part_of axial system
+
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.
  
−
'''ray wood parenchyma (PO:0004534):'''
+
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
 +
From Beentje:
  
−
Current def.: Radially oriented parenchyma tissue in secondary xylem.
+
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
  
−
Proposed def.: A portion of parenchyma tissue that is part of a ray system and has as parts ray wood parenchyma cells.
+
phylloclade: portion of stem or branch (several nodes and internodes) flattened and expanded to serve the functions of a leaf.
  
−
comment: Occurs in bands or rays of variable width and height that extend radially in the secondary xylem and phloem of a plant axis.
+
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
  
−
part_of ray system
+
proposed definition:
  
−
synonym: ray (broad)
+
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.
  
−
'''wood parenchyma cell (PO:0004525):'''
+
synonyms: phylloclade, cladophyll
  
−
Current def.: Parenchyma cell occurring within secondary xylem.  
+
Dennis said: A shoot axis that is flattened. expanded is redundant. What about cholla?
 +
This does not work. The comment also does not work. Similarily the
 +
synonyms are not so much synonyms as they are subsets.
  
−
Proposed def.: A parenchyma cell that is part of a portion of wood parenchyma.
+
''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.''
  
−
comment: Found in secondary xylem.
+
Recent interesting paper on cladodes in Asparagus:  
  
−
part_of wood parenchyma
+
Nakayama,H., Yamaguchi,T. and Tsukaya,H. (2012) Acquisition and Diversification of Cladodes: Leaf-Like Organs in the Genus Asparagus. [http://www.plantcell.org/content/early/2012/03/12/tpc.111.092924.abstract The Plant Cell Online, 24, 929 –940].
  
 +
PMID:22415273
  
−
'''ray wood parenchyma cell (PO:0004527):'''
+
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 def.: Parenchyma cell of a ray in secondary xylem.
+
===rib===
 +
Should also add 'rib' for cacti and other plants.
  
−
Proposed def.: A parenchyma cell that is part of a portion of ray wood parenchyma. develops from ray initials
+
Definition:
  
−
part_of ray wood parenchyma
+
-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.
  
−
'''upright wood ray parenchyma cell (PO:0004528)'''
+
See tracker at: [https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3298006&group_id=76834 tapetum types]
  
−
Current def.: Ray cell in secondary xylem oriented axially (vertically in the axis) with its longest dimension.
+
Comment from DWS: there are two types of tapetum: ameboid and secretory/glandular:  
  
−
Proposed def.: A ray wood parenchyma cell that is oriented with its longest dimension parallel to the axis in which it is found.
+
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
  
−
'''procumbent wood ray parenchyma cell (PO:0004529)'''
+
[http://onlinelibrary.wiley.com.ezproxy.proxy.library.oregonstate.edu/doi/10.1111/j.1469-8137.1973.tb02093.x/abstract link]
  
−
Suggest naming it "procumbent ray wood parenchyma cell".
+
[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]
  
−
Current def.: Ray cell within secondary xylem having its longest axis in radial direction.
+
[http://ir.library.oregonstate.edu/xmlui/handle/1957/9976 link to OSU Thesis]
  
−
Proposed def.: A ray wood parenchyma cell that is oriented with its longest dimension radial to the axis in which it is found.
 
  
 +
==Organizing the types of plant cells ==
  
−
'''axial wood parenchyma cell (PO:0004526)'''
+
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.
  
−
Current def.: Parenchyma cell in the axial system of secondary xylem.
+
In CL, they are organized by type:
 +
* absorptive cell CL:0000212 A cell that takes up and metabolizes substances.
  
−
Proposed def.: A wood parenchyma cell that is part of a portion of axial wood parenchyma.
+
* ciliated cell ID: CL:0000064 A cell that has a filiform extrusion of the cell surface.
  
−
===wood types===
+
* barrier cell ID: CL:0000215 A cell whose primary function is to prevent the transport of stuff across compartments.
−
'''sapwood (PO:0004513):'''
 
  
−
Current def.: Outer part of the wood of stem or root containing living cells and reserves and in which conduction of water takes place. Generally lighter colored than the heartwood.
+
* defensive cell  CL:0000473  A cell whose primary function is to protect the organism.
  
−
From Esau: Wood that in the living tree contains living cells and reserve materials.
+
* diploid cell ID: CL:0000415 A cell whose nucleus has two haploid genomes. xref_analog FMA:72300
  
−
Proposed def.: A portion of secondary xylem that has as parts living cells (wood parenchyma cells?) and reserve materials (ergastic substances?).
+
* haploid cell ID: CL:0000413 A cell whose nucleus contains a single haploid genome.
  
−
comment: Sapwood is where the conduction of water takes place. It is generally lighter colored than the heartwood (PO:0004512) and is found on the outside of a plant axis.
+
* 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.
  
−
'''heartwood ; PO:0004512'''
+
* secretory cell ID: CL:0000151 A cell that specializes in controlled release of one or more substances.
  
−
Current def.: The inner layers of secondary xylem that have largely ceased to function in storage and conduction and in which reserve materials have been removed or converted into heartwood substances; generally darker colored than the functioning sapwood.
+
* 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
  
−
Proposed def.: A portion of secondary xylem (wood) which lacks living wood parenchyma cells and in which the reserve materials (ergastic substances?) have been removed or converted into heartwood substances.
+
* supportive cell ID: CL:0000630 A cell whose primary function is to support other cell types.
  
−
comment: Heartwood has ceased to function in storage and conduction. It is generally darker colored than sapwood (PO:0004513) and is found in the center of a plant axis.
+
* 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.
  
−
'''early wood ; PO:0004515'''
+
* 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.
  
−
Current def.: The wood formed in first part of a growth ring and characterized by a lower density and larger cells than the late wood.
+
* stuff accumulating cell ID: CL:0000325 A cell that is specialised to accumulate a particular substance(s).
  
−
Proposed def.: A portion of secondary xylem (wood) that is formed in the first part of a growing season and is characterized by a lower density and larger cells than late wood.
+
=Revisions to Plant Structure Development Stages:=
 +
''POC 9-10-13: Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point''
  
 +
==[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ Stages of Plant Embryo Development]==
  
−
'''late wood ; PO:0004516'''
+
Currently: in Version #20, Aug 2013:
  
−
Current def.: The secondary xylem formed in the later part of a growth ring; denser and composed of smaller cells than the early wood.
+
[[File:Plant Embryo Dev Stages.png]]
  
−
Proposed def.: A portion of secondary xylem (wood) that is formed in the later part of a growing season and is characterized by a higher density and smaller cells than early wood.
+
Note: Not sure where the coleoptilar stage (PO:0001094) fits in- it has no letter code and apparently never has (at least in the last 4 years). The A zygotic stage term was removed sometime in 2011. Currently the heirarchy looks quite odd as starts with "B- proembryo stage"
  
 +
''-Removed the letters in the names and added preceded_by to order the stages. made coleoptilar stage (PO:0001094) a subclass of  bilateral stage (PO:0004507). ''
  
 +
===Revisions June-July 2014:===
 +
[[File:Screen Shot 2014-07-14 at 2.33.52 PM.png]]
  
−
'''ergastic substances''' (from Esau): Passive products of protoplasm, such as starch grains, fat droplets, crystals, and fluids. Occur in cytoplasm, vacules, and cell walls.
+
* '''[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/?limit=10&page=1#fde8 plant embryo development stage (PO:0007631)]''': A sporophyte vegetative stage (PO:0007134) that occurs during the interval between the '''first cell division of a plant zygote (PO:0000423)''' and one of the following:
 +
** the beginning of the seed germination stage (PO:0007057) in seed plants,  
 +
** the beginning of the formation of a plant organ (PO:0009008) such as a root (PO:0009005), shoot axis (PO:0025029), or vascular leaf (PO:0009025) in a cultured plant embryo (PO:0000010).
 +
** formation of the first vascular leaf (PO:0009025) in pteridophytes, the beginning of development of a sporangium (PO:0025094) in bryophytes,  
  
−
=Unfinished items from older agendas and user requests=
+
−
==[https://sourceforge.net/tracker/?func=detail&aid=3474999&group_id=76834&atid=835555 lobe and tooth]==
+
''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. ''
−
On 1-10-12, we added the term "sinus" and agreed to add the related terms for tooth and lobe, all part_of some margin.
 
  
−
We currently have organ margin (PO:0025005), phyllome margin (PO:0025018) without part of relations. Suggest that we add organ margin is part_of lamina, phyllome margin part_of phyllome lamina.
 
  
−
Leaf margin (PO:0020128) is already part of leaf and leaf lamina margin (PO:0025009) is part_of leaf lamina.
 
  
  
−
'''proposed definition, lobe:''' A cardinal organ part that is a rounded projection on the margin of an organ.
+
** 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 organ margin
+
===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)).
  
−
'''proposed definition, phyllome lobe:''' A lobe that is a rounded projection on the margin of a phyllome.
 
  
−
part_of leaf phyllome margin
+
-
  
 +
====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.
  
−
'''proposed definition, leaf lamina lobe:''' A phyllome lobe that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
+
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."''
  
−
part_of leaf lamina margin
+
''"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?)''
  
−
can add other types of lobes as we want, or wait until they are requested.
+
''"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, plant organ tooth:''' A cardinal organ part that is a pointed projection on the margin of an organ.
 
  
−
part_of organ margin
+
''proposed definition RW:''
 +
* '''plant embryo globular stage (PO:0001185)''': A plant embryo development stage (PO:0007631) that occurs during the interval between when a protoderm (PO:0006210) is first recognizable in a plant embryo (PO:0009009) and the onset of a plant embryo bilateral stage (PO:0004507).
  
 +
New comment: During the plant embryo globular stage, a plant embryo proper (PO:0000001) increases in diameter through cell division but retains radial symmetry, and differentiation of the three main tissue systems (vascular system (PO:0000034), epidermis (PO:0005679), and the portion of ground tissue (PO:0025059)) begins. During a plant embryo bilateral stage, the embryo begins to develop bilateral symmetry. Preceded by a plant proembryo stage (PO:0001180).
  
−
'''proposed definition, phyllom tooth:''' A plant organ tooth that is a pointed projection on the margin of a phyllome.
+
''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 leaf phyllome margin
+
comment: During the plant globular embryo stage, differentiation of the three main tissue systems (vascular system (PO:0000034); epidermis (PO:0005679); and the portion of ground tissue (PO:0025059)) occurs.
  
 +
I would avoid describing the plant embryo bilateral stage here as it is confusing to the user. Could also mention the development of the embryo hypophysis (PO:0020109).
  
−
'''proposed definition, leaf lamina tooth:''' A phyllome tooth that is a rounded projection on the margin of a leaf lamina. (Is this in vascular leaf only?)
 
  
−
part_of leaf lamina margin
+
[http://www.sciencemag.org/content/266/5185/605.abstract?sid=b709ed1b-8241-480e-82d2-17a5d62dfbce Goldberg et al, 1994 Science]:
 +
""Two critical events must occur after the embryo proper forms: (i) regions along the longitudinal apical-basal axis must differentiate from each other and generate embryonic organ systems, and (ii) the three primordial tissue layers of the embryo need to be specified. Both of these events take place during the globular-heart transition phase (Fig. 2 and Table 1). The embryo proper has a spherical shape during the proembryo and globular stages (Fig. 2). The first visible cell differentiation events occur at the 16-cell stage when the protoderm, or outer cell layer of the embryo proper, is produced and the hypophysis forms at the top of the suspensor (Fig. 2). Subsequent cell differentiation events within the embryo proper result in the production of an inner procambium tissue layer and a middle layer of ground meristem cells (Fig. 2)."
  
−
can add other types of teeth as we want, or wait until they are requested.
 
  
−
Be sure to add "teeth" as exact plural synonym to all.
 
  
−
Ref.: Harris and Harris, ISBN:0964022168.
+
''Revised def'n LC:''
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=3438986&group_id=76834&atid=835555 bud areole and lamina areole]==
+
'''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).
  
−
At the POC meeting on 11-8-11 we to add a term for areole, refering to a type of bud in cacti. However, this term is also used to refer to a part of a leaf (or other phyllome) lamina.
 
  
−
'''Proposed definition, bud areole (PO:0025353):''' An axillary bud that does not elongate, in which the leaves develop as spine leaves.
+
--
  
−
Comment: Found in Cactaceae. Appears as a cluster of spines. May be covered in trichomes. In species with tubercles, the areole is often found at the distal end of the tubercle. The areole originates in the axil of the leaf that becomes the tubercle but is displaced to the tip of a tubercle through adnation (fusion of two organs of different types).
+
====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 axillary bud
+
revised def'n: A plant embryo development stage (PO:0007631) during which a plant embryo proper (PO:0000001) develops bilateral symmetry.
  
−
ref.: Bell and Bryan, ISBN:9780881928501
 
  
 +
''RW: New proposed definition:''
  
−
Suggest we add a general term for lamina areole, which will cover petals, etc., and a more specific term for leaf lamina areole.
+
'''* plant embryo bilateral stage (PO:0004507)''': A plant embryo development stage (PO:0007631) that occurs during the interval between the transition from radial to bilateral symmetry in a plant embryo proper (PO:0000001) and the onset of a plant embryo expanding cotyledon stage (PO:0001078).
  
−
'''Proposed definition for lamina areole (PO:0025391):''' A cardinal organ part that is the smallest part of a lamina that is completely surrounded by veins.
+
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).
−
Comment: Any order of vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a lamina.
 
−
part_of lamina
 
  
−
'''Proposed definition for leaf lamina areole (PO:0025392):''' A lamina areole that is the smallest part of a leaf lamina that is completely surrounded by leaf veins.
+
Ref: [http://www.ncbi.nlm.nih.gov/pubmed/24784759 PMID:24784759]
−
Comment: Any order of leaf vein can form the sides of an areole. Taken together, the areoles form a contiguous field of polygons over the area of a leaf lamina. Free ending veinlets (PO:0025390) may be found within a leaf lamina areole.
+
 
−
part_of leaf lamina
+
 
 +
--
  
−
Ref: ISBN:9780801475184
 
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3463382&group_id=76834&atid=835555 colony/ramet/genet]==
 
−
This is a request from Daniel, with the Physco group.
 
  
−
"The description of moss phenotypes in many cases is at the level of (clonal) colony instead of single plant (which is IMO hard to define in this case). E.g. people measure colony area, diameter, branching etc. I want to annotate phenotypes using the EQ model by linking to PATO terms."
 
  
−
Suggest we add the following synonyms:
 
  
  
−
to "gametophore" (PO:0030018) narrow synonym: "ramet"
 
  
−
to "whole plant" (PO:0000003) related synonym: "ramet", narrow synonyms: "colony", "clonal colony", "genet"
+
--
  
 +
===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:
  
−
On a related note, Daniel added that "IMHO plant growth/life forms should be best integrated as an extension to PO. "
+
'''* 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)
  
−
=Primordia=
+
'''* Similarly, for '''C globular stage_PO:0001185''' new child terms:'''
−
These issues came up while we were working on new term requests for Agron-Omics.
+
# 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
  
−
primordium (PO:0025127): A portion of plant tissue that differentiates and develops from meristem tissue into a new plant structure. [source: POC:Curators]
+
'''* 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
  
−
Comment: The primordium is the first distinct form in the development of a plant structure.
+
'''* 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)
  
−
leaf primordium: A phyllome primordium that will develop into a leaf. [source: POC:Curators]
+
'''* F mature embryo stage_PO:0001081'''
  
−
Comment: Emerges as an outgrowth in the shoot apex (flanking the meristem).
 
  
−
I think we should modify this to say that it develops from the peripheral zone (PO:0000225) and is part of the shoot apex.
+
Older trackers:  
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/400/ #400 plant embryo stage]
  
−
''"The SAM consists of two zones. The cells of the central zone (CZ), which occupy the center of the SAM, are undifferentiated and divide to produce cells in the peripheral zone (PZ), a ring of cells below the CZ (21). Cells in the CZ are unable to form primordia. LPs (leaf primordia) only occur in the PZ."''
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/426/ #426 spore and embryo dormant stages]
  
−
General question: Do these tissues only occur in the primordium, or continue on after it becomes a young leaf? When does it stop being a primordium? If these tissues are all part of LP, then presumably the LP ends when cell stop dividing. I think usually the term primordium is used for the earliest stage of an organ's development, not all the way up until cell division ceases. Maybe better to say they develop from LP and are part_of leaf during PO:0001052 leaf expansion stage.
+
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]
  
 +
=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?
  
−
''We felt primordium should probably be an organ. All primordia have at least two types of tissue - protoderm and ground meristem(?).''
+
* fix comment on receptacle- strawberry is an accessory fruit, post on tracker
  
−
''Primordium ends and leaf begins with the formation of the different meristems (adaxial, plate) that contribute to the final form of a leaf.''
+
* 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
  
−
''Problem with having different types of primordia as organs means they will all have dual parentage (is_a primordium and is_a whatever type of organ.  We were trying to get rid of that when we made it is_a tissue.''
+
* 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.''
  
−
''promeristem as synonym of AM, not RAM''
+
* Need to revise 'root epidermis (PO:0006036)' to match the shoot system epidermis PO:0006035 (see [[POC_Conf._Call_10-29-13]])
  
−
=User requests open on Source Forge; PSDS=
+
* 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.
−
==from MaizeGDB:==
 
  
−
==[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence]==
 
−
This was discussed at the NYBG Meeting, on [[Sunday_Sept_11th,_2011]]
 
  
  
−
We don't need to deal with all of this before the release, because Mary will use radicle emergence stage instead of coleoptile emergence.
 
  
−
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)
 
  
−
This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.
+
==[https://sourceforge.net/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:
  
−
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.''
+
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.  
  
−
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.
+
''This is incorrect as in many plants, pollination occurs before the flowers open, especially self-pollinated plants''
  
−
'''current structure:'''
+
* 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]
  
−
[[File:germination_stages.jpg]]
+
''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. ''
  
−
Shoot emergence (stage) should be is_a seedling growth (stage). Seedling growth (stage) should be is_a vegetative growth stage.
 
  
−
Imbitition (stage) should be is_a germination (stage). Will deal with definitions of imbibition and germination later.
+
==fruit development stages (PO:0001002)==
 +
* See [https://docs.google.com/spreadsheet/ccc?key=0AvF6MNosp3qTdDZEMzBVdXJWZjVubkJNVlBtSmQ2WFE&usp=sharing Google Doc] for revisions in progress.
  
−
===current and proposed terms and definitions===
+
* 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.
−
'''All of the terms below originally described a single point in time. We need to figure out when the shoot emergence stage should end.'''
 
  
−
'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
+
* 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.  
  
−
'''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 ???.
+
* 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]
  
−
Comment: This terms is used only for seed plants.
+
====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: 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 ???.
+
[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: May occur simultaneously with shoot emergence form the growth medium. This terms is used only for seed plants.
+
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).
  
  
−
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]
+
[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.
  
−
'''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 ???
+
related synonyms: fruit maturation; fruit senescence
  
−
Comment: This terms is used only for seed plants.
+
==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]
  
−
'''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 ???
+
==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 )
  
−
Comment: May occur simultaneously with coleoptile emergence form the growth medium. This terms is used only for seed plants.
+
* moved leaf development (PO:0001050) to be subclass of phyllome development stage, will be adding flower bract development (PO:new) see below.
  
 +
[[File: phyllome_snap_shot.jpg]]
  
−
'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]
+
Comment: Includes stages for the initiation, expansion, and senescence of a phyllome such as a leaf, lemma, or stamen.
  
−
'''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 ???
+
==reproductive shoot system development stage (PO:0025530)==
 +
* Is_a: collective plant organ structure development stage (PO:0025338)
  
−
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
+
* We need to build a hierarchy for the development of '''conifer cones-''' as they are also reproductive shoot systems
  
−
'''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 ???
+
** 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.
  
−
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.  
+
* 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''
  
−
'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]
 
  
−
'''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: 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.
+
* This would parallel the two existing sub-classes:
  
−
'''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 ???
+
==inflorescence development stage (PO:0021004)and sub-classes==
 +
* Currently linked to  tracker for: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/517/ shoot system development stages and child terms]
  
−
Comment: 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.
+
* 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]
  
−
'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
+
These need to be revised and additional stages need to be developed.
  
−
'''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 ???
+
==flower development stage:==
 +
This is mostly done- this reference might be helpful for the legume flowers and have annotations to add.
 +
Floral Development in Legumes: (Plant Physiol, March 2003, Vol. 131, pp. 911-926)
  
−
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
+
==collective phyllome structure development stage (PO:0025578) and child terms==
  
−
'''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/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).
  
−
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.
+
* 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).
  
−
Could also add terms for feeder emergence for some gymnosperms.
+
** '''corolla development stage (PO:0007604):'''A collective phyllome structure development stage (PO:0025578) that has as a primary participant a corolla (PO:0009059).  
  
−
For all of the above terms, need to check existing synonyms and move or copy them as needed.
+
** '''gynoecium development stage (PO:0007606):''' A collective phyllome structure development stage (PO:0025578) that has a primary participant a gynoecium (PO:0009062).
  
−
==[http://sourceforge.net/tracker/index.php?func=detail&aid=2812238&group_id=76834&atid=835555 tuber growth and development stages]==
+
[[File: collective_phyllome_snap_shot.jpg]]
  
−
This item has been open on SF since 6/2009
+
===New term flower bract development stage (new po:id)===
 +
 +
flower bract development stage (new po:id):
  
−
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).
+
- will be parent to lemma development stage and palea development stage
  
−
Suggested stages:
+
* 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]
 +
  
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
+
* 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]
  
−
-tuber initiation
+
==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):
  
−
-tuber growth
+
* 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.
  
−
-tuber maturation
+
Blackmore S, Wortley AH, Skvarla JJ, Rowley JR (2007) Pollen wall development in flowering plants. New Phytologist 174: 483–498
  
−
How we work these in will depend on restructuring of PSDS
+
==[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
  
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
+
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]
  
−
=User requests open on Source Forge: Plant Anatomical Entities=
+
So the main classes could be under: is_a plant axis development stage (PO: new) is_a plant organ development stage (PO:0025339)
−
==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
 
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3438986&group_id=76834&atid=835555 areole]===
+
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).
  
−
Proposed definition: An axillary bud that does not elongate, in which the leaves develop as spine leaves (PO:0025173).
+
Suggested stages:
 +
* tuber initiation
 +
* tuber growth
 +
* tuber maturation
  
−
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).
+
''Would these be the same for the two different types of tubers? Also need: tuber dormancy''
  
−
is_a axillary bud
+
* sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
  
−
ref.: Bell and Bryan, Plant Form
+
* 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
  
−
===glochid===
 
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3439006&group_id=76834&atid=835555 cladode and phylloclade]===
+
===Further info and references:===
−
From Beentje:
+
[http://www.cals.uidaho.edu/potatoes/potatoproductionsystems/topics/growth&development.pdf Potato Growth & Development]
  
−
cladode: single node or internode of stem or branch that is flattened and expanded to serve the functions of a leaf
+
[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]
  
−
phylloclade: portion of stem or branch (several nodes an dinternodes) flattened and expanded to serve the functions of a leaf.
+
[http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540956/pdf/plntphys00369-0069.pdf Growth of the Potato Tuber]
  
−
FNA lists cladode, phylloclade, and cladophyll as exact synonyms: A stem segment that functions as a leaf; often more or less compressed.
+
=xylem developmental stages: =
  
−
proposed definition:
+
See discussions of primary xylem on [http://wiki.plantontology.org/index.php/POC_Conf._Call_6-11-13 POC_Conf._Call_6-11-13]
  
−
cladode: A shoot axis that is flattened and expanded.
+
Existing definitions:
  
−
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.
+
'''* 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]
  
−
synonyms: phylloclade, cladophyll
+
*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''
  
−
Need to open a SF tracker for these
+
=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)
  
−
Should also add 'rib' for cacti and other plants
+
==whole plant fruit ripening stage (PO:0007010)==
 +
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3565059&group_id=76834&atid=835555 whole plant fruit ripening stage]: A whole plant fruit development stage (PO:0025500) that begins when the first fruit (PO:0009001) on a whole plant (PO:0000003) begins the process of ripening (GO:0009835) in a way which, in case there are other fruits, the majority of the other fruits start to ripen continuously therewith, and ends with earliest of the following: (1) the whole plant begins a sporophyte senescent stage (PO:0007017), (2) the whole plant begins a sporophyte dormant stage (PO:0007132), or (3) all fruits on the whole plant are finished ripening.
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
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.
  
−
Submitted by Rich Zobel (Nov 2009).
 
  
−
Still need to work on definitions for these terms.
+
  **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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