Difference between revisions of "POC Conf. Call 9-10-13"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(106 intermediate revisions by 2 users not shown)
Line 1: Line 1:
−
POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PST/1pm EST
+
POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PDT/1pm EDT
  
−
In attendance:  
+
In attendance: ''Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)''
  
−
Absent:
+
Absent: none
  
 
- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting
 
- please see the [[Items_for_future_meetings]] page, will be moved here before the meeting
  
−
=NSF PI meeting Sept 4th-6th in DC=
+
=multi-tissue plant structure development stage (PO:new)=
−
* PJ and DWS attended
+
* Needs a parent term: [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/492/ multi-tissue plant structure development stage] (PO:new), then the definitions can be re-written, currently a direct child of plant structure development stage (PO:0009012).  This would also be the parent for seed development and plant organ development (see below)
−
''Any news?''
+
 
 +
''Accepted, will post proposed definition on SF tracker''
 +
 
 +
=leaf development stage (PO:0001050)=
 +
* See [https://docs.google.com/spreadsheet/ccc?key=0AuKRnUE1LrAgdFlpaU5lZ0xvRkNfVG8xV1pSRFlWSVE&usp=sharing Google Doc] for revisions in progress.
 +
* Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.
 +
 
 +
* '''leaf development stage (PO:0001050)''': A phyllome development stage (PO:0025579) that has as a primary participant a leaf (PO:0025034).
 +
 
 +
Current structure: All these will be renamed "vascular leaf...."
 +
 
 +
[[File:leaf_dev_stages.jpg]]
 +
 
 +
* Links to Relevant References
 +
** [http://www.plantcell.org/site/teachingtools/TTPB3.xhtml Genetic Control of Leaf Development- Plant Cell]
 +
** [http://www.nature.com/ng/journal/v42/n12/full/ng.703.html The developmental dynamics of the maize leaf transcriptome]
 +
** [http://link.springer.com/article/10.1007%2Fs10265-009-0248-2 Uchida et al (2010) Coordination of leaf development via regulation of KNOX1 genes. Journal of Plant Research 123: 7–14]
 +
** [http://www.nature.com/nrg/journal/v4/n3/full/nrg1002.html Comparative plant development: the time of the leaf?]
 +
** [http://www.nature.com/nature/journal/v434/n7032/abs/nature03410.html Independent recruitment of a conserved developmental mechanism during leaf evolution]
 +
==vascular leaf development stage and child terms==
 +
Proposed new term and definition:
 +
*''' [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/555/ vascular leaf development stage (new PO:0025570)]''': A leaf development stage (PO:0001050) that begins with the onset of vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).
 +
 
 +
 
 +
We will also need:
 +
'''* non-vascular leaf development stage (new PO:id)''': A leaf development stage (PO:0001050) that begins with the onset of non-vascular leaf initiation stage and ends with the termination of the non-vascular leaf senescence stage.
 +
 
 +
* Need to do more research on the development of the [http://www.plantontology.org/amigo/go.cgi?view=details&search_constraint=terms&depth=0&query=PO:0025075&session_id=5645b1377543007 non-vascular leaf]
 +
see also: [http://palaeos.com/plants/bryophyta/bryophyta.html#Leaves moss phyllides], [http://plantphys.info/plant_biology/copyright/moss.html moss info] and [[Background_info_on_Physco_biology_and_culture]].
 +
 
 +
''PJ: We should have a parallel "generic" branch of leaf development to group the stages such as leaf expansion across both non-vascular or vascular leaves.''
 +
 
 +
 
 +
''Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point''
 +
 
 +
==New/revised child terms under vascular leaf development stage (PO:0025570)==
 +
 
 +
* ''Note: Use "during which" rather than "when" and "ends with the beginning of the..."''
 +
* ''Each definition should have a consistent format (ie. begin with the termination/ends with the initiation).''
 +
* ''Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.''
 +
 
 +
==vascular leaf initiation stage (PO:0007040)==
 +
[https://sourceforge.net/p/obo/plant-ontology-po-term-requests/556/ vascular leaf initiation stage (PO:0007040)]: A vascular leaf development stage (PO:0025570) when localized cells of the peripheral zone (PO:0000225) in the shoot apical meristem (PO:0020148) transition from indeterminate growth to determinate growth and ends with the beginning of the vascular leaf expansion stage (PO:0001052).  Comment: Cells in the primordium are not yet differentiated.
 +
 
 +
''DWS: Should omit transition from indeterminate growth -> determinate growth. The peripheral meristem is always in the shoot apical meristem.
 +
 
 +
''The cells in the SAM transition from anticlinal divisions to periclinal divisions, leading to a leaf primordium or bump. Usually in L2 or L3, rarely in L1.''
 +
 
 +
''Later mitosis ceases leaving the marginal or submarginal meristems and the leaf expansion stage is mainly cell expansion''
 +
 
 +
''Leaf development in Monocots need to be looked at as they have a basal intercalary meristem.''
 +
 
 +
''What are "localized cells"? The cell divisions are localized ''
 +
 
 +
'''''revised Def'n: vascular leaf initiation stage:''' A vascular leaf development stage (PO:0025570) which begins with the onset of localized periclinal division in the peripheral zone (PO:0000225) and ends with the beginning of the vascular leaf primordium formation stage (PO:0001019).''
 +
 
 +
''PJ- we should add a note that the concentration of auxin is highest under the spot where the primordium will form- the vascular leaf anlagen (PO:0025431). 
 +
 
 +
''Note that this comment is already there on the vascular leaf anlagen (PO:0025431) term''
 +
 
 +
''can we leave out "in the SAM"?
 +
 
 +
''This is when the analagen forms- later develops into the primordium''
 +
 
 +
''Create a 'vascular leaf primordium development stage'- move existing term 
 +
 
 +
followed by a stage called 'vascular leaf surface polarity determination stage (synonym "pre-expansion stage)'''
 +
 
 +
''DWS: Need to look at the organization of the SAM in ferns- Do they have the equivalent of a peripheral zone?: cup-shaped zone, runs from protoderm to protoderm, under the apical cell.  DWS will look into it.''
 +
 
 +
''DWS: Need to look at the development of phyllode leaves (PO:0025335), such as those in Acacia and other desert plants. They expand perpendicularly to the pattern of normal leave, have strong adaxial meristems, rather than marginal meristem. Flattened in a proximal -
 +
 
 +
This might go under the new 'vascular leaf surface polarity determination stage'
 +
 
 +
Def'n: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane, throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in development. [source: PMID:18978364, PO_REF:00006, PO_REF:00007]
 +
 
 +
Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:0025336, transition phyllode leaf). Phyllodes are generally xeromorphic.
 +
 
 +
''DWS will send us a diagram; need to think about how to encompass them.  Also in some moss plants''
 +
 
 +
[[File:Leaf dev new.png]]
 +
 
 +
 
 +
Note: Will have the new preceded_by relation added to order them
 +
 
 +
===Children of vascular leaf initiation stage (PO:0007040)===
  
−
=OBO Foundry Review of Plant Ontology=
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/560/ formation of vascular leaf founder cells (PO:0001003)]: A vascular leaf initiation stage (PO:0007040) when the cells of the shoot apical meristem (PO:0020148) form a vascular leaf anlagen (PO:0025431).
  
−
*''' Principle 1: The Ontology is Open'''
+
Comment: The leaf primordium is not yet distinguishable.
  
−
''Some improvement desirable''
+
==vascular leaf expansion stage (PO:0001052)==
  
−
"The self-review states that the PO is released under a Creative Commons license. However, it is not specified which Creative Commons license has been chosen. The ontology file does not contain a statement about the license or the policy for reuse of the ontology. However, the information is available on the website e.g. at http://plantontology.org/docs/otherdocs/principles_rationales.html: Plant Ontology by Plantontology.org is licensed under a Creative Commons Attribution-NoDerivs 3.0 United States License."
+
*  [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/557/ vascular leaf expansion stage (PO:0001052)]: A vascular leaf development stage (PO:0025570)  that begins with cell differentiation and cell expansion forming the leaf lamina (PO:0020039) and ends with the onset of the leaf fully expanded stage (PO:0001053).
 +
**new comment: The majority of leaf expansion is due to cell enlargement. The leaves of some plants may not have a conspicuous midrib or rachis.  
  
−
"We recommend that the exact license chosen be included in an additional ontology annotation '''in the ontology file'''."
+
''May be due to cell division or cell enlargement. During vascular leaf expansion stage the vasculature is forming as well- need to encompass that as well.''  
  
−
"According to the OBO Foundry principle 1 documentation, this should make use of two annotations using the following properties:
+
===Children of vascular leaf expansion stage (PO:0001052)- revised names and definitions:===
−
* dc:license
 
−
* rdfs:comment
 
−
The license type goes in the dc:license field. The mode of attribution goes in the rdfs:comment field. "
 
  
−
"While 'Creative Commons 3.0 CC-by license' is recommended, this is not mandatory and therefore the chosen attribution-noderivs license is also compatible with the Open principle. However, we urge you to consider weakening the license to one that encourages sharing and reuse without constraint to further the adoption by the community and the value of the resource for the community."
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/561/ formation of vascular leaf primordium stage (PO:0001019)]: A vascular leaf expansion stage (PO:0001052) when the shoot apical meristem (PO:0020148) forms a vascular leaf primordium (PO:0000017) on the peripheral zone (PO:0000225).
 +
''this term should move up to be a child of vascular leaf initiation stage- how does this fit in with the 'formation of vascular leaf founder cells" stage''
  
−
'''* Principle 2: Common Format'''
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/562/ formation of vascular leaflet primordia stage (PO:0004500)]: A vascular leaf expansion stage (PO:0001052) at which a leaflet primordium (PO:0025481) is initiated on the leaf rachis (PO:0020055) of a compound leaf (PO:0020043). 
  
−
''Pass''
+
'' need to review this in terms of leaflet discussion, should move up to VL initiation stage as well, most likely''
  
−
The ontology is available in both OBO and OWL formats. It should be noted that the OBO form of the ontology contains semantics which are not yet available in the OWL form (i.e. the treat-xrefs-as-isa and treat-xrefs-as-genus-differentiae constructs). These are supported by the Oort release manager and can be instantiated in OWL versions of the ontology. See https://code.google.com/p/owltools/wiki/OortOptions
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/563/ formation of ligule primordium stage (PO:0001021)]: A vascular leaf expansion stage (PO:0001052) when conical P3 leaf completely encloses SAM, and the ligule (PO:0020105) primordium is visible.
  
 +
''check "ligule (PO:0020105) primordium"- PO:id should be after the term, need to create a term ligule primordium''
 +
'' ligule PO:0020105 is not a leaf- it is a cardinal organ part, formation of ligule primordium stage would be part of leaf development, not is_a''
  
−
'''* e 5: Clearly Delineated Content'''
+
'''''Discussion on these terms were tabled for the next meeting:'''''  
−
''Some improvement desirable''
 
  
−
"There are several sub-issues that are contained in this principle.  
+
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/564/ hood-shaped primordium stage (PO:0001020]: A vascular leaf expansion stage (PO:0001052) when a hood-shaped primordium is formed, partially enclosing P1 and SAM, as in Poaceae.
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/565/ rapid elongation of vascular leaf lamina stage (PO:0001023)]: A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf lamina (PO:0020039) occurs.
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/566/ rapid elongation of leaf sheath stage (PO:0001024)]: A vascular leaf expansion stage (PO:0001052) during which a rapid elongation of the leaf sheath (PO:0020104) occurs.
  
−
Firstly, the ontology needs to have a clearly delineated scope as expressed in a statement of scope. PO does have a clearly delineated scope, and this scope does not substantially duplicate the scope of any other OBO Library ontology.  
+
==vascular leaf post-expansion stage (PO:0001053)==
 +
* [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/558/ vascular leaf post-expansion stage (PO:0001053)]: A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and cell expansion has ceased and ends with the onset of the vascular leaf senescence stage (PO:0001054).
  
−
Secondly, the ontology needs to have a clear upper level with root terms having definitions that indicate the content of the sub-ontologies included in the ontology. Here, we have some concerns as detailed below.  
+
''Use the "begins with.... and ends with..." template.  Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage".  Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahongany plants, but they are the exceptions. Could add as a comment (get names from DWS). ''
  
−
Thirdly, the ontology should not contain terminology that overlaps with other OBO ontologies except where content has been imported for reuse in specific contexts appropriate to the domain of the ontology.  
+
== vascular leaf senescence stage (PO:0001054)==
 +
*  [https://sourceforge.net/p/obo/plant-ontology-po-term-requests/559/ vascular leaf senescence stage (PO:0001054)]: A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.
  
−
Finally, the ontology should provide adequate coverage with respect to its stated domain so as to justify its use in applications.
+
''Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf.  Need to add the references to the GO terms.''
−
Concerns about the upper levels of the plant ontology:
 
  
−
"The definition of the root term ‘plant anatomical entity’ appears intended to be a plant specific subclass of the CARO term ‘anatomical entity’ and is defined as “An anatomical entity that is or was part of a plant.” The CARO class states that an anatomical entity is part of or located in an organism (or virus or viroid in the upcoming release of CARO), however here you include things that were once part of a plant. In OBI or ERO, such entities would be considered specimens or samples. Can you explain why this is needed? If it is justified, there is some cross-ontology coordination that should be performed.
+
''Need to look at this more-  abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf ''
  
−
"There is a need to define the high-level distinction between plant structure vs. portion of plant substance better: currently ‘plant structure’ is defined as anatomical entity that is or was part of a plant; but substances are also (or were also) part of a plant. This is likely because these are intended to be subclasses of the CARO classes, that have more specific differentia, however, there is no mireot or subclass assertion to these classes other than in the comment field. Explicit use of the CARO classes will help differentiate these top-level nodes, and inclusion of their logical class definitions can help with error-checking."
+
''Need to review leaf senescence- see [http://www.plantcell.org/site/teachingtools/TTPB20.xhtml plant cell resource] ''
  
−
" If you consider the above point on the definition of ‘anatomical entity’ referring to in vivo entities, you could consider moving ‘in vitro plant structure’ to be its own root outside anatomical entity, as it would technically be a derived structure and not part of or located within an organism (or are most of these simple plants cultured in vitro?). Efforts have been made recently in the CL and OBI to represent such things (e.g. “in environment” vs. “ex environment”, you could potentially leverage some of these design patterns and/or coordinate with them.
+
=OBO Foundry Review of Plant Ontology=
−
Other concerns from somewhat random sampling:
 
  
−
"‘cultured plant embryo’ has two asserted superclasses. While asserted multiple inheritance is debatable in terms of ontology maintenance or ontological rigor (GO has a lot of this), in this case the example ensues because of a lack of logical class expression on this class. For example, this class could instead leverage a class restriction that states ‘plant embryo’ and is_specified_output of some in vitro plant culturing. In this way, you would infer the second parent, ‘in vitro plant structure’ (dependent on how you define things as per above). This would mean higher quality axioms, easier ontology maintenance, and interoperability with other ontologies such as OBI."
+
Content of the review has been moved to a [https://docs.google.com/document/d/1ExBEb0qFi1sh4rTjvwqMsWdSR35zzrw0Znab7pzAXSk/edit?usp=sharing gdoc]
  
−
=leaf development stage (PO:0001050)=
+
=NSF PI meeting Sept 4th-6th in DC=
−
* See [https://docs.google.com/spreadsheet/ccc?key=0AuKRnUE1LrAgdFlpaU5lZ0xvRkNfVG8xV1pSRFlWSVE&usp=sharing Google Doc] for revisions in progress. Need to open trackers for these.
+
* PJ and DWS attended
 +
''Any news?''
  
 
=Upcoming meetings and Presentations 2013-2014:=
 
=Upcoming meetings and Presentations 2013-2014:=
Line 75: Line 163:
 
=Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern=
 
=Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern=
 
-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?
 
-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?
 +
 +
''Works for most, BS may have a conflict once a month''

Latest revision as of 17:54, 23 October 2013

POC meeting, Skype Conference Call; Date: Tuesday Sept 10th, 2013 10am PDT/1pm EDT

In attendance: Laurel Cooper (OSU), Justin Elser (OSU), Justin Preece (OSU), Brian Atkinson (OSU), Dennis W Stevenson (NYBG), Pankaj Jaiswal (OSU), Barry Smith, Marie Alejandra Gandolfo (Cornell)

Absent: none

- please see the Items_for_future_meetings page, will be moved here before the meeting

multi-tissue plant structure development stage (PO:new)

  • Needs a parent term: multi-tissue plant structure development stage (PO:new), then the definitions can be re-written, currently a direct child of plant structure development stage (PO:0009012). This would also be the parent for seed development and plant organ development (see below)

Accepted, will post proposed definition on SF tracker

leaf development stage (PO:0001050)

  • See Google Doc for revisions in progress.
  • Need to look into non-vascular leaf development and see if it applies there as well, or if we will need separate terms for vascular and non-vascular leaves.
  • leaf development stage (PO:0001050): A phyllome development stage (PO:0025579) that has as a primary participant a leaf (PO:0025034).

Current structure: All these will be renamed "vascular leaf...."

Leaf dev stages.jpg

vascular leaf development stage and child terms

Proposed new term and definition:

  • vascular leaf development stage (new PO:0025570): A leaf development stage (PO:0001050) that begins with the onset of vascular leaf initiation stage (PO:0001051) and ends with the termination of the vascular leaf senescence stage (PO:0001054).


We will also need: * non-vascular leaf development stage (new PO:id): A leaf development stage (PO:0001050) that begins with the onset of non-vascular leaf initiation stage and ends with the termination of the non-vascular leaf senescence stage.

see also: moss phyllides, moss info and Background_info_on_Physco_biology_and_culture.

PJ: We should have a parallel "generic" branch of leaf development to group the stages such as leaf expansion across both non-vascular or vascular leaves.


Add comment on how every stage can end in accidental death. Also mention something death being the canonical end point

New/revised child terms under vascular leaf development stage (PO:0025570)

  • Note: Use "during which" rather than "when" and "ends with the beginning of the..."
  • Each definition should have a consistent format (ie. begin with the termination/ends with the initiation).
  • Add a comment on the top level term about how all PSDS's may be terminated before reaching senescence stage.

vascular leaf initiation stage (PO:0007040)

vascular leaf initiation stage (PO:0007040): A vascular leaf development stage (PO:0025570) when localized cells of the peripheral zone (PO:0000225) in the shoot apical meristem (PO:0020148) transition from indeterminate growth to determinate growth and ends with the beginning of the vascular leaf expansion stage (PO:0001052). Comment: Cells in the primordium are not yet differentiated.

DWS: Should omit transition from indeterminate growth -> determinate growth. The peripheral meristem is always in the shoot apical meristem.

The cells in the SAM transition from anticlinal divisions to periclinal divisions, leading to a leaf primordium or bump. Usually in L2 or L3, rarely in L1.

Later mitosis ceases leaving the marginal or submarginal meristems and the leaf expansion stage is mainly cell expansion

Leaf development in Monocots need to be looked at as they have a basal intercalary meristem.

What are "localized cells"? The cell divisions are localized

revised Def'n: vascular leaf initiation stage: A vascular leaf development stage (PO:0025570) which begins with the onset of localized periclinal division in the peripheral zone (PO:0000225) and ends with the beginning of the vascular leaf primordium formation stage (PO:0001019).

PJ- we should add a note that the concentration of auxin is highest under the spot where the primordium will form- the vascular leaf anlagen (PO:0025431).

Note that this comment is already there on the vascular leaf anlagen (PO:0025431) term

can we leave out "in the SAM"?

This is when the analagen forms- later develops into the primordium

Create a 'vascular leaf primordium development stage'- move existing term

followed by a stage called 'vascular leaf surface polarity determination stage (synonym "pre-expansion stage)

DWS: Need to look at the organization of the SAM in ferns- Do they have the equivalent of a peripheral zone?: cup-shaped zone, runs from protoderm to protoderm, under the apical cell. DWS will look into it.

DWS: Need to look at the development of phyllode leaves (PO:0025335), such as those in Acacia and other desert plants. They expand perpendicularly to the pattern of normal leave, have strong adaxial meristems, rather than marginal meristem. Flattened in a proximal -

This might go under the new 'vascular leaf surface polarity determination stage'

Def'n: An adult ensiform leaf with a lamina that develops in a median plane, rather a transverse plane, throughout the length of the leaf and is a result of increased activity of the adaxial meristem early in development. [source: PMID:18978364, PO_REF:00006, PO_REF:00007]

Comment: Common in legumes of the genus Acacia. Similar development occurs in other ensiform leaves in some monocots, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:0025336, transition phyllode leaf). Phyllodes are generally xeromorphic.

DWS will send us a diagram; need to think about how to encompass them. Also in some moss plants

Leaf dev new.png


Note: Will have the new preceded_by relation added to order them

Children of vascular leaf initiation stage (PO:0007040)

Comment: The leaf primordium is not yet distinguishable.

vascular leaf expansion stage (PO:0001052)

  • vascular leaf expansion stage (PO:0001052): A vascular leaf development stage (PO:0025570) that begins with cell differentiation and cell expansion forming the leaf lamina (PO:0020039) and ends with the onset of the leaf fully expanded stage (PO:0001053).
    • new comment: The majority of leaf expansion is due to cell enlargement. The leaves of some plants may not have a conspicuous midrib or rachis.

May be due to cell division or cell enlargement. During vascular leaf expansion stage the vasculature is forming as well- need to encompass that as well.

Children of vascular leaf expansion stage (PO:0001052)- revised names and definitions:

this term should move up to be a child of vascular leaf initiation stage- how does this fit in with the 'formation of vascular leaf founder cells" stage

need to review this in terms of leaflet discussion, should move up to VL initiation stage as well, most likely

check "ligule (PO:0020105) primordium"- PO:id should be after the term, need to create a term ligule primordium ligule PO:0020105 is not a leaf- it is a cardinal organ part, formation of ligule primordium stage would be part of leaf development, not is_a

Discussion on these terms were tabled for the next meeting:

vascular leaf post-expansion stage (PO:0001053)

  • vascular leaf post-expansion stage (PO:0001053): A vascular leaf development stage (PO:0025570) that begins when the vascular leaf (PO:0009025) is fully expanded and cell expansion has ceased and ends with the onset of the vascular leaf senescence stage (PO:0001054).

Use the "begins with.... and ends with..." template. Perhaps change term to "vascular leaf mature stage", or maybe keep the "leaf fully expanded stage". Examples of leaves with indeterminate growth, ferns, viney leaves, some Mahongany plants, but they are the exceptions. Could add as a comment (get names from DWS).

vascular leaf senescence stage (PO:0001054)

  • vascular leaf senescence stage (PO:0001054): A vascular leaf development stage (PO:0025570) that begins with the formation of a abscission zone at the base of a vascular leaf (PO:0009025) and ends with leaf separation and death.

Would omit formation of a abscission zone. Perhaps say ends with death of vascular leaf. Need to add the references to the GO terms.

Need to look at this more- abscission zone (PO:0000146) starts in the petioles (are part of the leaf), starts with cell senescence, should refer to 'point of attachment'. Don't need to specify where the abscission zone forms. Note all leaves abscise, end with death of the vascular leaf

Need to review leaf senescence- see plant cell resource

OBO Foundry Review of Plant Ontology

Content of the review has been moved to a gdoc

NSF PI meeting Sept 4th-6th in DC

  • PJ and DWS attended

Any news?

Upcoming meetings and Presentations 2013-2014:

No one from PO is planning to attend

  • PAG 2014 January 11-15, 2014 - San Diego, CA, USA
    • PJ has been contacted by PAG organizers; Suggest slightly new focus "Plant Ontologies and Systems Biology"
    • Ideas for speakers- someone from GO and others?>>
    • Registration is now open: PAG 2014. Early reg'n till Nov. 1st

Next meeting scheduled for Tuesday, Sept 24th, 2013 at 10am Pacific/1pm Eastern

-MAG has requested the meeting be moved to 10:30am Pacific/1:30 pm Eastern- would that works for the others in the group?

Works for most, BS may have a conflict once a month

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_9-10-13&oldid=24883"