Difference between revisions of "Sunday Sept 11th, 2011"

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Back to main agenda for [[POC_Meeting_at_NYBG;_Sept_10th-11th,_2011]].
 
Back to main agenda for [[POC_Meeting_at_NYBG;_Sept_10th-11th,_2011]].
  
−
=Upcoming release and unfinished edits to PAO (9:00AM - 11:00AM)=
+
=Review of the Physcomitrella presentation:=
−
==Changes for this release==
+
There were some suggestions for changes, so those were made and the final version is linked here:  [[Moss 2011 Meeting- PO presentation]]
 +
 
 +
=Next steps for the PO:=
 +
 
 +
PJ: presented the PO at  NSF as part of the Gramene application
 +
 
 +
As part of publication process of paper authors will be encouraged/required to annotate to the PO and GO and ...?, Initially starting with Plant cell
 +
*text mining: associate to GO, PO and TO *[http://www.textpresso.org/ Textpresso]
 +
expression, phenotype, interactions
 +
 
 +
PJ: Update from NSF person, we will need a one-page description of future directions (this fall? when?)
 +
*plant phenotypes focus of interest, new directions
 +
 
 +
*Problems with lack of plant annotations coming to GO (JB), PO will be the gatekeeper and coordinate them
 +
 
 +
GO model genome and Gramene
 +
 
 +
Cathy Wu- Protein Ontology- use their pipeline?
 +
 
 +
Freelance annotators @ Plant Cell (soon Plant Physiology)
 +
 
 +
Need robust plant phenotype Ontology (TO?), Environment Ontology (EnvO), Plant Disease Ontology (PDO), GAZ, PRO
 +
 
 +
NSF: Interorganismal and Environment Systems
 +
 
 +
allergies, food, symbionts, toxins, ecology, pathogens
 +
 
 +
''BS: Need to find money for development of the Plant Disease Ontology''
 +
 
 +
Infectious Disease Ontology (IDO): human disease, need to be able to link to the PDO
 +
 
 +
Apply to USDA/NIH/NSF?  what is the best route?
 +
 
 +
PRO- no resources for plant protein ontology dev. apply for additional $$?
 +
 
 +
BS: presenting: [http://gensc.org/gc_wiki/index.php/GSC_12#Agenda Environment Ontology (EnvO)] at [http://gensc.org/gc_wiki/index.php/GSC_12 12th Genomic Standard Consortium]
 +
 
 +
==Trait Ontology==
 +
see the TO on [http://www.gramene.org/plant_ontology/ontology_browse.html#to Trait Ontology on Gramene]
 +
 
 +
=Discussion of the Pheno RCN=
 +
 
 +
''Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.
 +
 
 +
''Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".''
 +
 
 +
=Plans for upcoming Release=
  
 
See details at [[Summary_of_Changes_to_PO_September_2011]]
 
See details at [[Summary_of_Changes_to_PO_September_2011]]
Line 10: Line 56:
 
'''Major changes for this release were:'''
 
'''Major changes for this release were:'''
  
−
1. Includsion of Spanish synonyms. They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them.  Look up notes from meeting...
+
1. Inclusion of Spanish synonyms. They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them.  Look up notes from meeting...
  
 
Not clear if this is a problem with just the dev browser.
 
Not clear if this is a problem with just the dev browser.
 +
 +
''Need to follow up on this.''
  
 
2. [[Eliminating_Zea/Poaceae_terms_from_PO]]
 
2. [[Eliminating_Zea/Poaceae_terms_from_PO]]
 +
 +
''More or less complete. PGDSO may change as we go forward, but we can use as is for now.''
  
 
3. New annotation files:
 
3. New annotation files:
  
−
*Should we wait for MaizeGDB to send all their new annotations?
+
*Should we wait for MaizeGDB to send all their new annotations? ''Yes. At least get the PAO annotations in.''
  
 
*Addition of new annotations for grape (LC working on) and [[http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]]
 
*Addition of new annotations for grape (LC working on) and [[http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/po_anatomy_gene_fragaria_jaiswallab.assoc?view=log strawberry]]
Line 25: Line 75:
  
 
*Japanese synonyms?
 
*Japanese synonyms?
 +
 +
''Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.''
 +
 +
''Japanese synonyms are not currently in the editors' file. Should be added.''
  
 
==Target dates:==
 
==Target dates:==
 
We discussed having a release in September, 2011
 
We discussed having a release in September, 2011
  
−
*Finish all edits: 9/16/2011?
+
*Finish all edits: 9/23/2011
  
 
*Update annotation files and test on beta browser:
 
*Update annotation files and test on beta browser:
Line 35: Line 89:
 
*Other tasks?
 
*Other tasks?
  
−
*Final release:  End of September
+
*Final release:  End of September?
 +
 
 +
=Outstanding edits to finish before release=
  
 +
See [[Items_for_future_meetings]]
  
−
==Additional edits to finish before release==
+
==PGDSO==
 +
Edits requested by MS for MaizeGDB
  
−
See [[Items_for_future_meetings]]
+
===[http://wiki.plantontology.org:8080/index.php/Items_for_future_meetings#coleoptile_emergence_--_definition coleoptile emergence]===
  
−
===PGDSO edits requested by Mary for MaizeGDB===
+
From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be:
  
−
====[http://wiki.plantontology.org:8080/index.php/Items_for_future_meetings#coleoptile_emergence_--_definition coleoptile emergence]====
+
'''suggested def'n: coleoptile emergence (PO:0007045):''' Emergence of coleoptile from the seed. (rather than above ground)
  
−
From Mary at 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.  
+
This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.  
  
 
PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."
 
PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."
  
−
All of the sibling terms to cotyledon emergence (coleoptile, epidcotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.
+
*All of the sibling terms to cotyledon emergence (coleoptile, epicotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.
  
 
'''Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?'''
 
'''Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?'''
  
 +
''We will keep the existing terms that reference emergence from the soil, but rename as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.''
  
−
PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleteling the term and creating a new one.  
+
PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleting the term and creating a new one.  
  
 
Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.
 
Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.
  
  
−
Also, '''all of these terms should be renamed as stages or phases''' rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are phases, not developmental processes.
+
Also, '''all of these terms should be renamed as stages''' rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are stages, not developmental processes.
  
 
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.
 
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.
Line 68: Line 127:
 
[[File:germination_stages.jpg]]
 
[[File:germination_stages.jpg]]
  
 +
====current and proposed definitions====
  
 
'''current: seedling growth (PO:0007131):''' Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination  
 
'''current: seedling growth (PO:0007131):''' Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination  
Line 73: Line 133:
 
Seedling growth stage should begin after germination, not after imbibition. Imbibition is part of germination, and a seedling does not exist until after germination.
 
Seedling growth stage should begin after germination, not after imbibition. Imbibition is part of germination, and a seedling does not exist until after germination.
  
−
'''proposed: seedling growth phase''' A vegetative growth phase that begins with germination and ends with the development of the first adult leaves.
+
'''proposed: seedling growth stage''' A vegetative growth stage that begins with germination and ends with the development of the first adult leaves.
  
 
Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
 
Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
  
 +
''new proposed  name and def.:'' '''seedling development stage:''' A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.''
 +
 +
'''Note:''' After the PGDSO is revised, the parent of this term will be sporophyte vegetative development stage, so definition will change slightly.
 +
 +
 +
'''Note:''' all of the definitions below describe only a single point in time, when they should describe an interval. New definitions will be posted on Source Forge.
  
 
'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
 
'''current: shoot emergence (PO:0007030):''' Shoot or leaf breaks through the soil surface.
  
−
'''proposed: shoot emergence phase (new number):''' A vegetative growth phase that occurs when a part of shoot system emerges from a seed.
+
'''proposed: shoot emergence stage (new number):''' A vegetative growth stage that occurs when a part of a shoot system emerges from a seed.
  
 
Comment: This terms is used only for seed plants.
 
Comment: This terms is used only for seed plants.
 +
 +
''new proposed names and definitions:''
 +
 +
'''shoot emergence from growth medium development stage (PO:0007030):''' A seedling growth stage that occurs when a part of a shoot system emerges from the growth medium.
 +
 +
'''shoot emergence from seed coat development stage (new number):''' A seedling growth stage that occurs when a part of a shoot system emerges from a seed coat.
  
  
 
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]  
 
'''current: coleoptile emergence (PO:0007045):''' Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]  
  
−
'''proposed: coleoptile emergence phase (new number):''' A shoot emergence phase that occurs when a coleoptile emerges from a seed.
+
'''proposed: coleoptile emergence stage (new number):''' A shoot emergence stage that occurs when a coleoptile emerges from a seed.
  
 
Comment: This terms is used only for seed plants.
 
Comment: This terms is used only for seed plants.
 +
 +
''See SF tracker for new proposed terms and definitions.''
  
  
 
'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]  
 
'''current: cotyledon emergence (PO:0007049):''' Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]  
  
−
'''proposed: cotyledon emergence phase (new number):''' A shoot emergence phase that occurs when a cotyledon emerges from a seed.
+
'''proposed: cotyledon emergence stage (new number):''' A shoot emergence stage that occurs when a cotyledon emerges from a seed.
  
 
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
 
Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.
  
 
See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.
 
See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.
 +
 +
''See SF tracker for new proposed terms and definitions.''
  
  
 
'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]  
 
'''current: epicotyl emergence (PO:0007054):''' Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]  
  
−
'''proposed: epicotyl emergence phase (new number):''' A shoot emergence phase that occurs when a epicotyl emerges from a seed.
+
'''proposed: epicotyl emergence stage (new number):''' A shoot emergence stage that occurs when a epicotyl emerges from a seed.
  
 
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.
 
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.
 +
 +
''See SF tracker for new proposed terms and definitions.''
  
  
 
'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
 
'''current: hypocotyl emergence (PO:0007043):''' Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]
  
−
'''proposed: hypocotyl emergence phase (new number):''' A shoot emergence phase that occurs when a hypocotyl emerges from a seed.
+
'''proposed: hypocotyl emergence stage (new number):''' A shoot emergence stage that occurs when a hypocotyl emerges from a seed.
  
 
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
 
Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.
  
 
See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.
 
See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.
−
 
  
 +
''See SF tracker for new proposed terms and definitions.''
 +
 +
''Could also add terms for feeder emergence for some gymnosperms.''
  
 
===[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3374186&group_id=76834 5 fruit formation; FF.00 fruit size 10%]===
 
===[https://sourceforge.net/tracker/?func=detail&atid=835555&aid=3374186&group_id=76834 5 fruit formation; FF.00 fruit size 10%]===
Line 122: Line 202:
 
Initial Comment from MS:
 
Initial Comment from MS:
  
−
There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view.  Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size.  For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory.
+
"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view.  Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size.  For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."
  
 
[[File:fruitsize.jpg]]
 
[[File:fruitsize.jpg]]
  
−
'''current def. of FF.00 fruit size 10% (PO:0007032):''' The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]  
+
current def'n:'''FF.00 fruit size 10% (PO:0007032):''' The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]  
  
 
Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green
 
Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green
Line 134: Line 214:
 
There are actually annotations on 3 of the 5 fruit size stages.
 
There are actually annotations on 3 of the 5 fruit size stages.
  
−
'''proposed def. (based on Mary's suggestion):''' A fruit formation stage that begins with the formation of the fruit and ends when then fruit has reached 10% of its final size.
+
proposed def'n.: (based on Mary's suggestion):''' A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.
  
 
Comment: This stage can only be used when the final size of the fruit is known.
 
Comment: This stage can only be used when the final size of the fruit is known.
  
−
===[http://wiki.plantontology.org:8080/index.php/Items_for_future_meetings#Legume_terms Legume terms] requested by Austin Mast===
+
''We agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.''
−
====[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]====
+
 
 +
''RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?''
 +
 
 +
==[http://wiki.plantontology.org:8080/index.php/Items_for_future_meetings#Legume_terms Legume terms]==
 +
requested by Austin Mast
 +
 
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]===
 
reference: Lawrence, Taxonomy of Vascular Plants (1955)
 
reference: Lawrence, Taxonomy of Vascular Plants (1955)
  
Line 149: Line 235:
  
 
Synonyms vexillum (exact), standard (broad)
 
Synonyms vexillum (exact), standard (broad)
 +
 +
''Okay to add '''banner petal'''.''
  
  
Line 156: Line 244:
  
 
Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.
 
Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.
 +
 +
''Okay to add '''wing petal'''.''
  
  
Line 168: Line 258:
 
is_a collective phyllome structure, part_of corolla
 
is_a collective phyllome structure, part_of corolla
  
 +
''New proposed name: '''keel'''''
  
−
'''keel petal:''' A petal that is one of the two lowest petals of a papilionaceous corolla.
+
''We need to reword the definition of corolla (and other collective phyllome structures), because technically, the keel is a corolla (it consists of two or more petals). New definition should be the maximal set of petals or whatever in a flower.''
  
−
Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other.
 
−
Each petal is shaped like half a boat and projects toward the front of the flower.
 
  
−
====[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]====
+
'''keel petal:''' A petal that is one of the two lowest petals of a papilionaceous corolla.
−
 
 
−
Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.
 
−
 
 
−
=====Background:=====
 
−
 
 
−
Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:
 
−
 
 
−
"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."
 
−
 
 
−
 
 
−
The main reference people cite for phyllodes is: '''D.R. Kaplan 1980''', Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.
 
−
 
 
−
Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."
 
−
 
 
−
 
 
−
'''Some more contemporary uses of the term phyllode:'''
 
−
 
 
−
'''Gardner et al. 2005''' (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):
 
−
 
 
−
"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), '''the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles'''."
 
−
 
 
−
and later in the paper:
 
−
 
 
−
"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.
 
−
 
 
−
"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."
 
−
 
 
−
 
 
−
'''Leroy and Heuret 2007''' (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by '''a type of foliar organ''' called a phyllode."  and "...the different transitional forms range from pinnate leaves to phyllodes..." 
 
−
 
 
−
'''See fig. 1 in this paper.''' They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.
 
−
 
 
−
 
 
−
'''Yang et al. 2008''' (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.
 
−
 
 
−
 
 
−
'''Forster and Bonser 2009''', Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."
 
−
 
 
−
 
 
−
RW did not find any contemporary papers that said that a phyllode is a petiole.
 
−
 
 
−
Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.
 
−
 
 
−
'''Unifacial leaf''' as synonym? No- not exactly the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311).  Might be better to make a parent term '''ensiform leaf''' which has children phyllode and unifacial leaf.
 
−
 
 
−
=====Proposed terms and definitions:=====
 
−
 
 
−
vascular leaf
 
−
 
 
−
>unifacial leaf
 
−
 
 
−
>>terete leaf (round in cross section)
 
−
 
 
−
>>ensiform leaf (flat in cross section)
 
−
 
 
−
>>>phyllode
 
−
 
 
−
 
 
−
'''unifacial leaf''': A vascular leaf that has increased activity of either the adaxial or abaxial meristem early in development, leading to abscense of the opposite surface on the leaf. (ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)
 
−
 
 
−
Comment: A unifacial leaf may be round in cross-section (terete) or it may be laminar (ensiform), in which case lamina development is in a median plane  (perpendicular to the axis), rather than a transverse plane (tangent to the axis). Unifacial leaves may be bifacial at the leaf base. Many unifacial leaves develop by reduced (or absent) activity of the marginal meristems and increased activity of the adaxial meristem early in development, leading to mature leaves with only an adaxial surface (e.g., Acacia, most monocots?). However, some develop by increased activity of the abaxial meristem early in development, leading to mature leaves with only an abaxial surface.
 
−
 
 
−
'''RW: need to check and add references for all of these'''
 
−
 
 
−
 
 
−
'''terete leaf''': A unifacial leaf that is round in cross section due throughout all of part of the length of the leaf.
 
−
 
 
−
Comment: The surface of a terete leaf correspond to either the adaxial or abaxial surface of a normal leaf.
 
−
 
 
−
 
 
−
'''ensiform leaf''': A unifacial leaf that is flat in cross section due to a lamina that develops in a median plane  (perpendicular to the axis), rather a transverse plane (tangent to the axis) throughout all of part of the length of the leaf.(ref: Lawrence, Kaplan 1970 fig. 1, Sajo and Rudall 1999)
 
−
 
 
−
Comment: Common in many monocots and some dicots. Both sides of an ensiform leaf correspond to only one of either the adaxial or abaxial surface of a normal leaf.
 
−
 
 
−
 
 
−
'''RW: Maybe phyllode should just be a narrow synonym of ensiform leaf.'''
 
−
 
 
−
'''phyllode:''' 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 develop.
 
−
 
 
−
Comment: Common in legumes of the genus Acacia. Similar development occurs in some monocot leaves (ensiform leaves), 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:xxxxxxx, phyllode-type transition leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.
 
−
 
 
−
is_a ensiform leaf, is_a adult leaf
 
−
 
 
−
 
 
−
'''phyllode-type transition leaf:''' A transitional vascular leaf in which the basal portion of the leaf has lamina development is a median plane, similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.
 
−
 
 
−
Comment: Common in seedlings of legumes of the genus Acacia. May also occur later, after the plant has begun to produce phyllodes.
 
−
 
 
−
is_a transitional leaf, is_a vascular leaf
 
−
 
 
−
====[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]====
 
−
 
 
−
(used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
 
−
 
 
−
''Meeting of RW, MAG and DWS on 8/29/11: we felt this would be better left as a phenotypic descriptor. Should request terms needed to PATO.''
 
−
 
 
−
See more details at [[Items_for_future_meetings#bristle]]
 
−
 
 
−
===[http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_8-30-11#New_children_of_calyptra_perianth Calyptra perianth types]===
 
−
This was raised at the POC meeting [[POC_Conf._Call_8-23-11]]
 
−
 
 
−
Existing terms:
 
−
*'''fruit operculum''' (PO:0025298): A collective organ part structure that is the apical part of a circumsessile capsular fruit that separates from the rest of the capsule during dehiscence. [source: POC:curators]
 
−
 
 
−
Comment: Develops from the apical portion of a gynoecium. Found in Eucalyptus and other Myrtaceae.
 
−
 
 
−
and
 
−
 
 
−
*'''calyptra perianth''' (PO:0025299): A perianth that is composed of fused perianth parts and located on top of a gynoecium that contains an inferior ovary. [source: POC:curators]
 
−
 
 
−
Comment: May be composed of fused petals, sepals or tepals, but is generally formed from fused petals in Eucalyptus and other Myrtaceae. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra.
 
−
 
 
−
Synonyms: related: floral operculum; exact: angiosperm calyptra; exact: floral calyptra (suggest we add flower operculum as related and flower calyptra as exact)
 
−
 
 
−
===Proposed changes: More specific terms for calyptra===
 
−
At least week's meeting, there was a request for more specific terms for calyptras formed of fused petals or fused sepals.
 
−
 
 
−
In Eucalyptus, there may be one or two calyptras: an inner operculum or calyptra composed of fused petals and an outer operculum or calyptra composed of fused sepals. In many species, the sepals to do not fuse, and there is no outer operculum.
 
−
 
 
−
Our current definition of calyptra perianth includes fused tepals, which would encompass the existing term "fused collective tepal structure" (PO:0025138), but to my knowledge, tepals are not present in Eucalyptus. (The ANBG provides [http://www.anbg.gov.au/cpbr/cd-keys/euclid3/euclidsample/html/learn.htm EUCLID], an excellent resource for description of Eucatypus morphology.)
 
−
 
 
−
Suggest adding a new term "'''fused perianth'''", that is consistent with our other terms such as "fused collective tepal structure". This would be a more general term, and could include perianths that are partially fused.
 
−
 
 
−
===Proposed new terms and ontology structure:===
 
−
*need to open a SF tracker for these
 
−
 
 
−
perianth
 
−
 
 
−
> fused perianth (new)
 
−
 
 
−
>> fused collective tepal structure (PO:0025138)
 
−
 
 
−
>> calyptra perianth (flower operculum) (PO:0025299)
 
−
 
 
−
>>> calyptra calyx (outer operculum) (new)
 
−
 
 
−
>>> calyptra corolla (inner operculum) (new)
 
−
 
 
−
* Should we also add terms for fused petal and fused sepal (already have fused tepal)?
 
−
 
 
−
===terms and definitions===
 
  
−
*'''fused perianth:''' A perianth that is composed of two or more fused perianth parts (sepals, petals or tepals).
+
Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.
  
−
Comment: Perianth parts may be partially or wholly fused.
+
''Okay to add '''keel petal'''.''
  
−
*'''calyptra perianth''' (PO:0025299): A fused perianth that is composed of fused sepals or petals and located on top of a gynoecium that contains an inferior ovary.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
 +
'''This was tabled for discussion at a future meeting:'''  
  
−
Comment: Found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. Sometimes erroneously referred to as part of a fruit. Not the same structure as a spore capsule calyptra or fruit operculum. Use the more specific term (calytra corolla or calytra calyx) if possible. Species of the subgenera Monocalyptrus have only a calyptra corolla (inner operculum) while in most other species, a calyptra calyx is also present, at least early in flower development.
+
See more details at: [[Items_for_future_meetings]]
  
−
Synonyms: flower operculum, floral operculum, floral calyptra; angiosperm calyptra
+
==[http://wiki.plantontology.org:8080/index.php/POC_Conf._Call_8-30-11#New_children_of_calyptra_perianth Calyptra perianth types]==
  
−
*'''calyptra calyx''': A calyptra perianth composed of fused sepals.
+
'''This was tabled for discussion at a future meeting:'''  
  
−
Comment: Sometimes found in Eucalyptus and other Myrtaceae, covering an inner operculum or calyptra corolla. The sepals are generally completely fused.
+
See more details at: [[Items_for_future_meetings]]
  
−
Synonyms: outer operculum, calyx operculum
+
=Images in the PO=
 +
See: [http://www.plantsystematics.org/ Plantsystematics.org]
  
−
*'''calyptra corolla''': A calyptra perianth composed of fused petals.
+
from MAG (by email): "I am taking with me not only lots of "annotated" photos for Pankaj but also I will demonstrate everything we did with Plantsystematics.org and the PO photos. We are using the list I translated (the English version of course) and added them as keywords in Plantsystematics.org as a search engine as well."
  
−
Comment: Often found in Eucalyptus and other Myrtaceae. The petals are generally completely fused. If an outer operculum (calyptra calyx) is present, it covers the inner operculum (calyptra corolla).
 
  
−
Synonyms: inner operculum, corolla operculum
+
''Some slides have 8 images, some have 16. More than 3000 slides.''
  
−
* fused collective tepal structure (PO:0025138), calyptra calyx and calyptra corolla all have dual parentage (is_a fused perianth and is_a collective tepal structure, calyx, or corolla. If we were to import PATO:0000642 (fused with), we could make cross product definitions and infer one of the relations.
+
''Make each image and xml file so metadata is associated.''
  
−
=Images in the PO via [http://www.plantsystematics.org/ Plantsystematics.org] (11:00 AM - 12:30 PM)=
+
''Some discussion of copyright issues. PO material must be open access (according to grant), but users need to get credit for their photos. PJ suggested putting a watermark on the images with the credit for the photographer, then people can contact photographer for image without water mark if they want to use it.''
  
−
* from MAG (by email): "I am taking with me not only lots of "annotated" photos for Pankaj but also I will demonstrate everything we did with Plantsystematics.org and the PO photos. We are using the list I translated (the English version of course) and added them as keywords in Plantsystematics.org as a search engine as well."
+
''BS suggested contacting Phil Bourne from UCSD re. nano-publishing.''

Latest revision as of 19:07, 16 September 2011

Detailed agenda for Sunday Sept 11th, 2011

Back to main agenda for POC_Meeting_at_NYBG;_Sept_10th-11th,_2011.

Review of the Physcomitrella presentation:

There were some suggestions for changes, so those were made and the final version is linked here: Moss 2011 Meeting- PO presentation

Next steps for the PO:

PJ: presented the PO at NSF as part of the Gramene application

As part of publication process of paper authors will be encouraged/required to annotate to the PO and GO and ...?, Initially starting with Plant cell

  • text mining: associate to GO, PO and TO *Textpresso

expression, phenotype, interactions

PJ: Update from NSF person, we will need a one-page description of future directions (this fall? when?)

  • plant phenotypes focus of interest, new directions
  • Problems with lack of plant annotations coming to GO (JB), PO will be the gatekeeper and coordinate them

GO model genome and Gramene

Cathy Wu- Protein Ontology- use their pipeline?

Freelance annotators @ Plant Cell (soon Plant Physiology)

Need robust plant phenotype Ontology (TO?), Environment Ontology (EnvO), Plant Disease Ontology (PDO), GAZ, PRO

NSF: Interorganismal and Environment Systems

allergies, food, symbionts, toxins, ecology, pathogens

BS: Need to find money for development of the Plant Disease Ontology

Infectious Disease Ontology (IDO): human disease, need to be able to link to the PDO

Apply to USDA/NIH/NSF? what is the best route?

PRO- no resources for plant protein ontology dev. apply for additional $$?

BS: presenting: Environment Ontology (EnvO) at 12th Genomic Standard Consortium

Trait Ontology

see the TO on Trait Ontology on Gramene

Discussion of the Pheno RCN

Discussion of the Ellis book on leaf architecture. It is appropriate for draft ontology of leaf characters, even though it may be missing characters that are needed for non-dicot leaves.

Some discussion of how to deal with continuous characters. There is no good solution with current ontology development, but one can use the general quality (character or trait), e.g., "leaf apex angle quality", with a comment "Use this term if you want to score an exact numerical value for leaf apex angle." Subtypes of general qualities (characters) are categorical character states, e.g., "leaf apex angle equal to or less than 45 degrees", with exact synonym "acute leaf apex angle".

Plans for upcoming Release

See details at Summary_of_Changes_to_PO_September_2011

Major changes for this release were:

1. Inclusion of Spanish synonyms. They seem to be working fine, except that we still should have the descriptor "(Spanish:)" preceding them. Look up notes from meeting...

Not clear if this is a problem with just the dev browser.

Need to follow up on this.

2. Eliminating_Zea/Poaceae_terms_from_PO

More or less complete. PGDSO may change as we go forward, but we can use as is for now.

3. New annotation files:

  • Should we wait for MaizeGDB to send all their new annotations? Yes. At least get the PAO annotations in.
  • Addition of new annotations for grape (LC working on) and [strawberry]

4. Other changes

  • Japanese synonyms?

Will have Japanese synonyms in obo file, but JE will strip them out before the file gets loaded on AmiGO.

Japanese synonyms are not currently in the editors' file. Should be added.

Target dates:

We discussed having a release in September, 2011

  • Finish all edits: 9/23/2011
  • Update annotation files and test on beta browser:
  • Other tasks?
  • Final release: End of September?

Outstanding edits to finish before release

See Items_for_future_meetings

PGDSO

Edits requested by MS for MaizeGDB

coleoptile emergence

From MS (MaizeGDB): It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be:

suggested def'n: coleoptile emergence (PO:0007045): 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.

PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."

  • All of the sibling terms to cotyledon emergence (coleoptile, epicotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.

Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?

We will keep the existing terms that reference emergence from the soil, but rename as stages, and add new terms for emergence from seed coat. Need to copy over list of existing synonyms to new emergence terms.

PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleting the term and creating a new one.

Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.


Also, all of these terms should be renamed as stages rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are stages, not developmental processes.

Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.

current structure:

Germination stages.jpg

current and proposed definitions

current: seedling growth (PO:0007131): Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination

Seedling growth stage should begin after germination, not after imbibition. Imbibition is part of germination, and a seedling does not exist until after germination.

proposed: seedling growth stage A vegetative growth stage that begins with germination and ends with the development of the first adult leaves.

Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.

new proposed name and def.: seedling development stage: A vegetative growth stage that has as a participant a whole plant during the interval between germination and development of the first adult leaves.

Note: After the PGDSO is revised, the parent of this term will be sporophyte vegetative development stage, so definition will change slightly.


Note: all of the definitions below describe only a single point in time, when they should describe an interval. New definitions will be posted on Source Forge.

current: shoot emergence (PO:0007030): Shoot or leaf breaks through the soil surface.

proposed: shoot emergence stage (new number): A vegetative growth stage that occurs when a part of a shoot system emerges from a seed.

Comment: This terms is used only for seed plants.

new proposed names and definitions:

shoot emergence from growth medium development stage (PO:0007030): A seedling growth stage that occurs when a part of a shoot system emerges from the growth medium.

shoot emergence from seed coat development stage (new number): A seedling growth stage that occurs when a part of a shoot system emerges from a seed coat.


current: coleoptile emergence (PO:0007045): Emergence of coleoptile above ground. [source: GR:ap, ISBN:3826331524]

proposed: coleoptile emergence stage (new number): A shoot emergence stage that occurs when a coleoptile emerges from a seed.

Comment: This terms is used only for seed plants.

See SF tracker for new proposed terms and definitions.


current: cotyledon emergence (PO:0007049): Emergence of cotyledons above ground. [source: GR:ap, ISBN:3826331524]

proposed: cotyledon emergence stage (new number): A shoot emergence stage that occurs when a cotyledon emerges from a seed.

Comment: This terms is used only for seed plants. Cannot be used in plants with hypogeal germination.

See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.

See SF tracker for new proposed terms and definitions.


current: epicotyl emergence (PO:0007054): Emergence of the epicotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: epicotyl emergence stage (new number): A shoot emergence stage that occurs when a epicotyl emerges from a seed.

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.

See SF tracker for new proposed terms and definitions.


current: hypocotyl emergence (PO:0007043): Emergence of the hypocotyl above ground. [source: GR:ap, ISBN:0306416875]

proposed: hypocotyl emergence stage (new number): A shoot emergence stage that occurs when a hypocotyl emerges from a seed.

Comment: This terms is used only for seed plants. Occurs in plants with epigeal germination.

See list of synonyms. Need to confirm that they correspond to emergence from seed, not ground.

See SF tracker for new proposed terms and definitions.

Could also add terms for feeder emergence for some gymnosperms.

5 fruit formation; FF.00 fruit size 10%

Initial Comment from MS:

"There are currently five stages based on size of final fruit, starting at 10%, etc. There is not any term for very early stage and 10% is already pretty far along from a developmental biology view. Since there seem to be no annotations for any of these stages, suggest instead of introducing new terms to change the definitions a tad. So for FF.00 fruit size 10%, define as up to 10% final size. For the case of the FF.00 fruit size term, the related term for maize would be 6.1 dilatory."

Fruitsize.jpg

current def'n:FF.00 fruit size 10% (PO:0007032): The stage when the size of the fruit is about 10% of final fruit size. [source: GR:ap, ISBN:3826331524]

Synonyms: related: 7.01 Pod 10% of final length in soybean, related: FF.00 fruit size 10% in Solanaceae, related: stage R3 in soybean, related: tomato immature green

All the other sizes are defined similarly.

There are actually annotations on 3 of the 5 fruit size stages.

proposed def'n.: (based on Mary's suggestion): A fruit formation stage that begins with the formation of a fruit and ends when the fruit has reached 10% of its final size.

Comment: This stage can only be used when the final size of the fruit is known.

We agreed that these stages could be up to and including the % size for now. Should rename terms "fruit size up to 10%", etc.

RW: When does formation of a fruit occur? Should we say fertilization of an ovary instead?

Legume terms

requested by Austin Mast

banner, wing and keel

reference: Lawrence, Taxonomy of Vascular Plants (1955)

Banner (as in a legume flower) - suggest using name banner petal

Proposed def: A petal that is the top-most petal of a papilionaceous corolla.

Comment: Usually larger than the adjacent wing petals. Found in the flowers of some Fabaceae.

Synonyms vexillum (exact), standard (broad)

Okay to add banner petal.


Wing (as in a legume flower) - suggest using name wing petal

Proposed def: One of two lateral petals that is adjacent to the banner petal of a papilionaceous corolla .

Comment: The wing petals are usually much smaller than the banner petal and the corolla keel. Found in the flowers of some Fabaceae.

Okay to add wing petal.


Keel (as in a legume flower) - suggest using name corolla keel and adding term for keel petal.

Two new terms:

corolla keel: A boat-shaped collective phyllome structure that consists of the two lowest petals of a papilionaceous corolla.

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.

is_a collective phyllome structure, part_of corolla

New proposed name: keel

We need to reword the definition of corolla (and other collective phyllome structures), because technically, the keel is a corolla (it consists of two or more petals). New definition should be the maximal set of petals or whatever in a flower.


keel petal: A petal that is one of the two lowest petals of a papilionaceous corolla.

Comment: The keel petals are usually larger than the adjacent wing petals. They are often partially fused to each other. Each petal is shaped like half a boat and projects toward the front of the flower.

Okay to add keel petal.

phyllode

This was tabled for discussion at a future meeting:

See more details at: Items_for_future_meetings

Calyptra perianth types

This was tabled for discussion at a future meeting:

See more details at: Items_for_future_meetings

Images in the PO

See: Plantsystematics.org

from MAG (by email): "I am taking with me not only lots of "annotated" photos for Pankaj but also I will demonstrate everything we did with Plantsystematics.org and the PO photos. We are using the list I translated (the English version of course) and added them as keywords in Plantsystematics.org as a search engine as well."


Some slides have 8 images, some have 16. More than 3000 slides.

Make each image and xml file so metadata is associated.

Some discussion of copyright issues. PO material must be open access (according to grant), but users need to get credit for their photos. PJ suggested putting a watermark on the images with the credit for the photographer, then people can contact photographer for image without water mark if they want to use it.

BS suggested contacting Phil Bourne from UCSD re. nano-publishing.

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