Difference between revisions of "POC Conf. Call 1-4-11"

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In attendance:  
 
In attendance:  
  
−
POC members:   
+
POC members:  Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU),  Dennis Stevenson (NYBG),  Justin Preece (OSU), Justin Elser (OSU), Maire Alejandra Gandolfo; (Cornell University),
  
−
Absent:  
+
Absent: Chris Mungall (Lawrence Berkeley National Lab) Barry Smith (University at Buffalo, NY),
  
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Collaborators:  
+
Collaborators: None
  
  
−
Acceptance of the minutes from the [[POC Conf. Call 12-22-10]]?
+
Acceptance of the minutes from the [[POC Conf. Call 12-28-10]]? ''There were no additions, deletions or changes to the minutes of the last meeting.''
  
  
  
−
==Issues arising from last week's meeting==
+
==Completion of Changes for the Next Release:==
  
−
===inflorescence and infructescence branch orders, secondary inflorescence===
+
'''*Timeline and Plan for Upcoming Release:'''
  
 +
- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)
  
−
There was some debate last week about whether or not to name the sub-inflorescences that arise from the main inflorescence axis primary inflorescence or secondary inflorescence. We decided it should be consistent with how we describe branching orders.
+
*Internal review before full release:
  
−
We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.
+
- Annotations that need to be moved:
  
−
We do have terms for inflorescence branch orders:
+
- List of changes: [[Summary_of_Changes_to_PO_Jan2011]] (still under construction)
  
−
inflorescence axis (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]
+
-see also [[Jan 2011_Release_Page]]
  
−
inflorescence branch (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.
+
List of things to fix:
  
−
second order inflorescence branch (PO:0006321): Any branch forming from the primary or first order inflorescence branch.
+
''*Beta browser is not working, so everyone in the group should go over file on dev brower before the release. RW will make final changes on Wednesday, then LC will put the file up on the dev browser for viewing after Wednesday afternoon.''
  
−
third order inflorescence branch (PO:0006322): Any branch forming from the second order inflorescence branch.
+
''DWS commented that we should review whatw e planned to do in the original grant proposal, and make sure we are not forgetting anything. All agreed it was a good idea and we will put it on the agenda for next time.''
  
−
We don't have terms for first order inflorescence branch or primary inflorescence axis, so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis. This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.
+
==Issues arising from last week's meeting:==
  
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3150504&group_id=76834&atid=835555 inflorescence and infructescence branch orders], secondary inflorescence===
  
−
*Also need to add terms for infructescence axis and branches.
+
Should the sub-inflorescences that arise from the main inflorescence axis be named 'primary inflorescence' or 'secondary inflorescence'?
  
−
proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):
+
We decided it should be consistent with how we describe branching orders.
−
 
−
secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower''
 
  
−
secondary infructescence: A reproductive shoot system that is part of an infructescence and has a  second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit''
+
We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.  
  
 +
We do have terms for inflorescence branch orders:
  
−
*On a related note, because of the arrangement of develops_from and part_of relations, the annotations for Zea anthers are being carried up to inflorescence branch. This doesn't really make sense. May need to re-examine part_of relations or definition of tassel branch.
+
'''inflorescence axis''' (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]
  
−
[[File:Inflor branch annotations.jpg]]
+
'''inflorescence branch''' (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.
  
−
===sensu terms===
+
'''second order inflorescence branch''' (PO:0006321): Any branch forming from the primary or first order inflorescence branch.
  
−
RW replaced all of the ~80 term names that were ''structure (sensu Taxon)'' with ''Taxon term.'' However, there were three terms we had changed in November [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] that were obsoleted and replaced with new terms, rather than being renamed. Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. Not clear why they needed to be obsoleted for a renaming.
+
'''third order inflorescence branch''' (PO:0006322): Any branch forming from the second order inflorescence branch.
  
−
==User requests still open on Source Forge; PSO ==
+
*We don't have terms for 'first order inflorescence branch' or 'primary inflorescence axis', so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis.  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]===
 
  
−
submitted by Austin Mast
+
This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.
  
−
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
+
*All of the annotations for 'second order inflorescence branch' are from QTL, and most of them are for genes called "primary branch" or "primary branch length"
  
−
'''Fascicle''' The term fascicle can refer to different structures in different taxa. Suggest we use the term '''Fabaceae fascicle''' in this case.
+
*Most of the annotations for 'third order inflorescence branch' are for a gene called "secondary branch."
  
−
Suggested def: A reproductive shoot system that ...
+
This suggests that they are using our term 'second order inflorescence branch' as the first branch from the main inflorescence axis and 'third order inflorescence branch' as the second order branch from the main inflorescence.
  
−
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
+
Here is an image we can look at for discussion purposes: [[File:inflorescence branch orders.jpg]]
−
that two to several flowers are initiated in each bract axil rather than
 
−
just one as in a raceme. The cluster of flowers at each node is called a
 
−
fascicle. The order of initiation among flowers at a node (Fig. 5B,
 
−
Psoralea macrostachys DC) shows the fascicle to be a short shoot topped by
 
−
a second order inflorescence apical meristem. This meristem initiates
 
−
flowers in a bilaterally symmetrical order: a single abaxial flower, then
 
−
two lateral flowers, another median abaxial, then two more laterals. The
 
−
number of flowers per fascicle depends on the duration of the axillary
 
−
inflorescence apex of the short shoot, which ceases activity after
 
−
initiating the few flowers in the fascicle. No flowers are initiated
 
−
adaxially (toward the first order axis) on the short shoot (Tucker, 1987b;
 
−
Tucker and Stirton, 1991). The short shoot in a pseudoraceme can be
 
−
distinguished from a cyme in that every flower is bract subtended in a
 
−
pseudoraceme."
 
−
Source: Tucker, 2003, Flora
 
  
−
'''Bristle''' (used in key as "Stipules spinose or bristles"; might be thought of as a quality, rather than a structure)
+
*Also need to add terms for infructescence axis and branches, in order to add a terms for "hand of fruit" (see [https://sourceforge.net/tracker/?func=detail&aid=3147085&group_id=76834&atid=835555 Musa fruit terms]).
  
−
We added the term stipule spine. Could also add the term '''stipule bristle''': A stipule that is (?)
+
*Proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):
 +
 +
'''secondary inflorescence:''' A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower''
  
−
Alternative is to suggest bristled to PATO
+
'''secondary infructescence:''' A reproductive shoot system that is part of an infructescence and has as parts a  second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit''
  
  
−
'''Phyllode''' Suggested def: A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
+
''We agreed on the following naming convention:''
  
 +
''inflorescence axis (PO:0020122) and inflorescence branch (PO:0009081) will remain as is.''
  
−
'''Banner''' (as in a legume flower) - maybe name Fabaceae banner
+
''New term will be added for first-order inflorescence axis (syn: primary inflorescence axis). This will be the main axis of the inflorescence (A in diagram). The penduncle is A up to the point where it branches. Need to redefine peduncle as a shoot axis where the transition from vegetative to reproductive growth occurs. All subsequent branches from the peduncle are reproductive.''
  
−
Suggested def: A petal that is the top-most petal of a corolla in some flowers of the Fabaceae. Comment: The banner is usually larger than the adjacent wing petals.
+
''Old term second order inflorescence branch (PO:0006321) will be renamed "second order inflorescence axis," defined as an inflorescence branch that branches from the primary inflorescence axis.  It will have the exact synonym primary inflorescence branch, but also keep the old name secondary inflorescence branch as a related synonym, with comment that that was the old name.''
  
 +
''Old term third order inflorescence branch (PO:0006322) will be renamed "third order inflorescence axis," defined as an inflorescence branch that branches from a secondary inflorescence axis.  It will have the exact synonym secondary inflorescence branch, but also keep the old name third order inflorescence branch as a related synonym, with comment that that was the old name.''
  
−
'''Wing''' (as in a legume flower) - maybe name Fabaceae wing
+
''Inflorescence axes up to the ninth order will be named (create new terms). After the 9th order, will have a term for Nth order inflorescence axis.''
  
−
Suggested def: One of two petals that is adjacent to the banner in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner and keel.
+
''Similar terms will be created for infructescence branches.''
  
 +
''New terms for sub-parts of inflorescences or infructescences will be named "second order inflorescence" or "second order infructescene," to parallel the axes names. Definitions will be as above, except the phrase "has a parts a second order inflorescence branch" will be replaced by "has a parts a second order inflorescence axis."''
  
−
'''Keel''' (as in a legume flower): The keel consists of two fused petals, and is analogous to the fused collective tepal structure we made for Musa. Maybe name Fabaceae keel
 
  
−
Suggest three new terms:
+
''Comment from RW after meeting: pedicel and paraclade should be moved from children of branch to children of inflorescence branch.  Peduncle should be a child of shoot axis, not branch.  Need to work on definition of peduncle.''
  
−
fused petal: A petal that is fused to another petal. Comment: May be fused to two petals (one on either side). This is a phenotype that is a cross-product of PO:0009032 (petal) and PATO:0000642 (fused with).
 
  
−
fused corolla: A corolla in which the petals are fused. Comment: This is a phenotype that is a cross-product of PO:0025023 (collective phyllome structure) and PATO:0000642 (fused with). A corolla may consist of a combination of fused and free petals, in which case fused corolla only refers to those petals that are fused.
+
''Comment from Justin Preece (from chat):''
 +
''something to chew on: just have a single inflorescence branch term, and perhaps use a PATO xref term to represent DEGREE of ordinality (1st, 2nd, 3rd...Nth), and use that to characterize any annotations. what you lose with this approach is the ability to reason up and down the PO on the basis of ordinality parentage, but it's a cleaner way to represent an infinite number of ordinal inflorescence branches. it depends on whether the priority is annotative accuracy or reasoning capacity.''
  
−
keel: A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae. Comment: The two petals of the keel may be fused at the apex but free at the base. The remaining three petals (banner and two wings) are free. The keel is boat shaped.
+
===sensu terms===
−
 
 
−
 
 
−
'''Locule''' The term locule can be used to refer to the cavity in an carpel (an embryo sac and the carpel tissue that surrounds it) or in an anther (a pollen sac and the stamen tissue that surrounds it.  In the PGDSO, we have the term PO:0001026 locules established, which is an anther development stage. For clarity, we may want to add two terms: anther locule and carpel locule .
 
−
 
 
−
anther locule: A cardinal organ part that is part of an anther and has as parts a single pollen sac and the layers of anther tissue that surround it.
 
−
 
 
−
carpel locule: A cardinal organ part that is part of a carpel and has as parts an embryo sac and the layers of anther tissue that surround it and contains at least one ovule. Comment: The embryo sac may have one or more ovules in one locule or may be divided into mutliple locules, each containing an ovule. (needs work)
 
−
 
 
−
===TraitNet requests===
 
−
 
 
−
[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]
 
−
 
 
−
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
 
  
−
child of stem (PO:0009047).
+
* RW replaced all of the ~80 term names that were ''structure (sensu Taxon)'' with ''Taxon structure.'' However, there were three terms that were obsoleted and replaced with new terms in November, rather than being renamed:
  
 +
-[https://sourceforge.net/tracker/?func=detail&aid=3097528&group_id=76834&atid=835555 floret (sensu Poaceae)], [https://sourceforge.net/tracker/?func=detail&aid=3097539&group_id=76834&atid=835555 floret meristem (sensu Poaceae)] and [https://sourceforge.net/tracker/?func=detail&aid=3097525&group_id=76834&atid=835555 gynoecium (sensu Poaceae)]
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
+
Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. BS suggested that we obsolete and rename at the 10-26-10 meeting, but with ~80 terms, this might not be the best solution.
  
−
Their comment: is synonym to Tubercle
+
Also, as a test, [https://sourceforge.net/tracker/?func=detail&aid=3097534&group_id=76834&atid=835555 gynoecium (sensu Zea)] was made obsolete, because it is not different from gynoecium (sensu Poaceae). Perhaps it should be merged with gynoecium (sensu Poaceae instead).
  
−
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
+
Action:
  
−
tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are elnarge modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
+
''We decided that there should be a page on the PO wiki (under developers guidelines) with "SOPs" or guidelines on when terms should be obsoleted, destroyed, or merged and the steps to take in each case. ''
  
−
proposed def:
+
''Old terms [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] should be unobsoleted, then new terms (Poaceae floret, Poaceae floret meristem, and Poaceae gynoecium) should be merged with the old terms, so old number is primary number. Primary name will be changed to new names.''
  
 +
''There was a general discussion of taxon-specific terms and subsets. We agreed that in principle they should use scientific rather than common names, and that subset names should agree with term names. This means, for example, that the subset for maize should be the subset for ''Zea mays spp. mays''.''
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
+
''Also, since terms like "Zea anther" are referring only to anthers in Zea mays, and not in all Zea species, they should have names like "Zea mays anther." However, since we have on our agenda to try to get away from terms with taxon names in them, I (RW) will not change the names until we decide on a final policy on how to deal with these terms.''
  
−
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
+
''PJ suggested that all terms that are in the subset for maize or rice should also be in the subset for Poaceae. RW asked if Justin E or Justin P could write a script to do this automatically, as doing it manually is bound to miss some terms.''
  
−
proposed def: A root that is erect and protrudes above the soil, found in trees that live in flooded habitats such as mangroves. Comment: Pneumatophores may provide oxygen to below ground roots growing in flooded soils.
+
Action:
  
 +
''We had a further discussion of the method GO uses to associated terms with taxa. That method has the advantage of automatically including any term from a sub-clade in the set of terms for a larger clade. PJ asked how this information is encoded in the obo file.''
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080915&group_id=76834&atid=835555 stele]
+
''LC posted a link to one of the GO-taxonomy papers in the chat:[http://www.biomedcentral.com/1471-2105/11/530 Deegan et al; 2010]''
  
−
We dealt with this under terms without is_a parents
+
''RW forwarded an additional paper that describes the method.[http://www.sciencedirect.com/science/article/B6WHD-4PJ04XX-2/2/e07badd44d5dec559ae7a8ff5dfafa99 Kusnierczyk, 2008]''
  
 +
* Elizabeth Arnaud confirmed we should use ''Musa'' as their terms encompass banana and plantain
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
+
==TIPS proposal==
−
 
+
An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. It was sent out to everyone by email.
−
definition from Beentje (2010): reproductive portion of a plant, such as a seed, fruit or fragment of fruit, that is dispersed and may give rise to a new plant.
 
−
 
 
−
We could add this term as a kind of upper level bin term (similar to trichome)
 
−
 
 
−
 
 
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[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
 
−
 
 
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Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
 
−
 
 
−
 
 
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[https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
 
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from Crum (2001): a cluster of fern sporangia
 
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from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
 
−
 
 
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Proposed definition: A cardinal organ part composed of a cluster of two or more adjacent sporagia on the surface of a leaf. Comment: May be enclosed by an indusium.
 
−
 
 
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Part_of vascular leaf, has_part sporangium
 
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−
 
 
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[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
 
−
 
 
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Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
 
−
 
 
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tendrils can derived from multiple types of structures. Suggest we make separate terms:
 
−
 
 
−
branch tendril (child of branch): A branch that is slender and coiling. Comment: Aids plant in climbing.
 
−
 
 
−
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
 
−
 
 
−
leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
 
−
 
 
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leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
 
−
 
 
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Can add other types of tendrils if they come up or users need them.
 
−
 
 
−
 
 
−
 
 
−
 
 
−
===Adding/modifying the [https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]===
 
−
 
 
−
submitted by Rich Zobel (Nov 2009)
 
−
 
 
−
==User requests still open on Source Forge; PGDSO ==
 
−
 
 
−
 
 
−
===[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
 
−
 
 
−
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:
 
−
 
 
−
-sprout development (does this correspond to tube axillary bud development? Should come after tuber maturation)
 
−
 
 
−
-tuber initiation
 
−
 
 
−
-tuber growth
 
−
 
 
−
-tuber maturation
 
−
 
 
−
How we work these in will depend on restructuring of PGDSO
 
−
 
 
−
l development in legumes (Plant Physiol, March 2003, Vol. 131, pp. 911-926
 
−
 
 
−
===[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed development stages]===
 
−
 
 
−
This is a fairly new request for terms for cotton
 
−
 
 
  
 
=Upcoming meetings 2011:=
 
=Upcoming meetings 2011:=
  
−
*'''Plant and Animal Genome XIX Conference'''  
+
*'''Plant and Animal Genome XIX Conference'''   January 15-19, 2011  [http://www.intl-pag.org/ PAG 2011]
  
−
January 15-19, 2011 [http://www.intl-pag.org/ PAG 2011]
+
Laurel, Ramona, DWS and Justin Preece are attending. PJ will attend for the weekend only as he is teaching. Alejandra cannot attend.  
  
−
Laurel, Ramona, DWS and Justin Preece are attending. PJ may attend for the weekend only as he is teaching.  Alejandra cannot attend.
 
  
 
'''PO Activities at PAG:'''
 
'''PO Activities at PAG:'''
  
−
* '''[http://intl-pag.org/19/19-demos.html Computer Demonstration]:'''
+
* '''[http://intl-pag.org/19/19-demos.html Computer Demonstration]:''' Ramona will present.
  
 
Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)
 
Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)
  
−
*'''[http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes]''' workshop and panel discussion:
+
Outline for [[PAG2011 Computer Demo]]
 +
 
 +
*'''[http://intl-pag.org/19/19-plant-pheno.html Plant Phenotypes]''' workshop and panel discussion: Laurel will present.
  
 
" The Plant Ontology: Linking phenotypes and genomics across plant taxa"
 
" The Plant Ontology: Linking phenotypes and genomics across plant taxa"
Line 251: Line 162:
 
[http://plantontology.org/db/workshop/pag_survey PO Workshop Reg'n site and Survey]
 
[http://plantontology.org/db/workshop/pag_survey PO Workshop Reg'n site and Survey]
  
−
*''' Poster:''' link to abstract TBA
+
*''' Poster:''' [http://intl-pag.org/19/abstracts/C01_PosterDemo_887.html PO Poster] Monday 3:00 pm - 4:30 pm
  
 
* '''Outreach Booth''' being organized by MaizeGBD- More info TBA
 
* '''Outreach Booth''' being organized by MaizeGBD- More info TBA
 +
 +
 +
*'''Phenotype Ontology RCN Summit'''
 +
[http://phenotypercn.org The Phenotype Ontology RCN]
 +
 +
February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,
 +
 +
Laurel and Pankaj will be attending.
 +
 +
  
  
Line 271: Line 192:
 
No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.  
 
No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.  
  
−
Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted the organizers to figure out how to nominate additional speakers, and will pass on information to the speakers. We hope to use the 6th time slot for a discussion session.
+
Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.  
  
−
''RW heard from organizers re. additional speakers. Will forward their information. Still waiting to hear about discussion session.''
+
We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.

Latest revision as of 19:30, 6 January 2011

POC meeting, Webex Conference Call; Date: Tuesday Jan 4th, 2011 10am (PST)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Justin Preece (OSU), Justin Elser (OSU), Maire Alejandra Gandolfo; (Cornell University),

Absent: Chris Mungall (Lawrence Berkeley National Lab) Barry Smith (University at Buffalo, NY),

Collaborators: None


Acceptance of the minutes from the POC Conf. Call 12-28-10? There were no additions, deletions or changes to the minutes of the last meeting.


Completion of Changes for the Next Release:

*Timeline and Plan for Upcoming Release:

- We completed all the changes discussed last week, and the merged plant_ontology.obo file was loaded on the *Beta* browser (Thanks Justin E!)

  • Internal review before full release:

- Annotations that need to be moved:

- List of changes: Summary_of_Changes_to_PO_Jan2011 (still under construction)

-see also Jan 2011_Release_Page

List of things to fix:

*Beta browser is not working, so everyone in the group should go over file on dev brower before the release. RW will make final changes on Wednesday, then LC will put the file up on the dev browser for viewing after Wednesday afternoon.

DWS commented that we should review whatw e planned to do in the original grant proposal, and make sure we are not forgetting anything. All agreed it was a good idea and we will put it on the agenda for next time.

Issues arising from last week's meeting:

inflorescence and infructescence branch orders, secondary inflorescence

Should the sub-inflorescences that arise from the main inflorescence axis be named 'primary inflorescence' or 'secondary inflorescence'?

We decided it should be consistent with how we describe branching orders.

We don't have terms for different vegetative branching orders (outside the inflorescence), but the stem is defined as the primary (not zero order) axis of the plant, which makes the first-order branches secondary axes.

We do have terms for inflorescence branch orders:

inflorescence axis (PO:0020122): A shoot axis that is part of an inflorescence. [describes any order axis in an inflorescence]

inflorescence branch (PO:0009081): Any branch forming from the primary or the higher order inflorescence axis.

second order inflorescence branch (PO:0006321): Any branch forming from the primary or first order inflorescence branch.

third order inflorescence branch (PO:0006322): Any branch forming from the second order inflorescence branch.

  • We don't have terms for 'first order inflorescence branch' or 'primary inflorescence axis', so it is unclear if the use of the phrase "first order branch" in the definition of second order inflorescence branch refers to the main axis or a branch from this axis.

This makes all of the definitions ambiguous, but since they have annotation attached to them, we cannot change them until it is clear what they mean.

  • All of the annotations for 'second order inflorescence branch' are from QTL, and most of them are for genes called "primary branch" or "primary branch length"
  • Most of the annotations for 'third order inflorescence branch' are for a gene called "secondary branch."

This suggests that they are using our term 'second order inflorescence branch' as the first branch from the main inflorescence axis and 'third order inflorescence branch' as the second order branch from the main inflorescence.

Here is an image we can look at for discussion purposes: Inflorescence branch orders.jpg

  • Also need to add terms for infructescence axis and branches, in order to add a terms for "hand of fruit" (see Musa fruit terms).
  • Proposed term names and definitions (may change, depending on resolution of inflorescence branch order names):

secondary inflorescence: A reproductive shoot system that is part of an inflorescence and has a parts a second order inflorescence branch and any shoot axes and flowers that arise from that branch. part_of inflorescence, has_part inflorescence branch, flower

secondary infructescence: A reproductive shoot system that is part of an infructescence and has as parts a second order infructescence branch and any shoot axes and fruits that arise from that branch. part_of infructescence, has_part infructescence branch, fruit


We agreed on the following naming convention:

inflorescence axis (PO:0020122) and inflorescence branch (PO:0009081) will remain as is.

New term will be added for first-order inflorescence axis (syn: primary inflorescence axis). This will be the main axis of the inflorescence (A in diagram). The penduncle is A up to the point where it branches. Need to redefine peduncle as a shoot axis where the transition from vegetative to reproductive growth occurs. All subsequent branches from the peduncle are reproductive.

Old term second order inflorescence branch (PO:0006321) will be renamed "second order inflorescence axis," defined as an inflorescence branch that branches from the primary inflorescence axis. It will have the exact synonym primary inflorescence branch, but also keep the old name secondary inflorescence branch as a related synonym, with comment that that was the old name.

Old term third order inflorescence branch (PO:0006322) will be renamed "third order inflorescence axis," defined as an inflorescence branch that branches from a secondary inflorescence axis. It will have the exact synonym secondary inflorescence branch, but also keep the old name third order inflorescence branch as a related synonym, with comment that that was the old name.

Inflorescence axes up to the ninth order will be named (create new terms). After the 9th order, will have a term for Nth order inflorescence axis.

Similar terms will be created for infructescence branches.

New terms for sub-parts of inflorescences or infructescences will be named "second order inflorescence" or "second order infructescene," to parallel the axes names. Definitions will be as above, except the phrase "has a parts a second order inflorescence branch" will be replaced by "has a parts a second order inflorescence axis."


Comment from RW after meeting: pedicel and paraclade should be moved from children of branch to children of inflorescence branch. Peduncle should be a child of shoot axis, not branch. Need to work on definition of peduncle.


Comment from Justin Preece (from chat): something to chew on: just have a single inflorescence branch term, and perhaps use a PATO xref term to represent DEGREE of ordinality (1st, 2nd, 3rd...Nth), and use that to characterize any annotations. what you lose with this approach is the ability to reason up and down the PO on the basis of ordinality parentage, but it's a cleaner way to represent an infinite number of ordinal inflorescence branches. it depends on whether the priority is annotative accuracy or reasoning capacity.

sensu terms

  • RW replaced all of the ~80 term names that were structure (sensu Taxon) with Taxon structure. However, there were three terms that were obsoleted and replaced with new terms in November, rather than being renamed:

-floret (sensu Poaceae), floret meristem (sensu Poaceae) and gynoecium (sensu Poaceae)

Either we should unobsolete these terms and rename them or obsolete all the terms with sensu in their names. BS suggested that we obsolete and rename at the 10-26-10 meeting, but with ~80 terms, this might not be the best solution.

Also, as a test, gynoecium (sensu Zea) was made obsolete, because it is not different from gynoecium (sensu Poaceae). Perhaps it should be merged with gynoecium (sensu Poaceae instead).

Action:

We decided that there should be a page on the PO wiki (under developers guidelines) with "SOPs" or guidelines on when terms should be obsoleted, destroyed, or merged and the steps to take in each case.

Old terms [floret (sensu Poaceae), florest meristem (sensu Poaceae), and gynoecium (sensu Poaceae)] should be unobsoleted, then new terms (Poaceae floret, Poaceae floret meristem, and Poaceae gynoecium) should be merged with the old terms, so old number is primary number. Primary name will be changed to new names.

There was a general discussion of taxon-specific terms and subsets. We agreed that in principle they should use scientific rather than common names, and that subset names should agree with term names. This means, for example, that the subset for maize should be the subset for Zea mays spp. mays.

Also, since terms like "Zea anther" are referring only to anthers in Zea mays, and not in all Zea species, they should have names like "Zea mays anther." However, since we have on our agenda to try to get away from terms with taxon names in them, I (RW) will not change the names until we decide on a final policy on how to deal with these terms.

PJ suggested that all terms that are in the subset for maize or rice should also be in the subset for Poaceae. RW asked if Justin E or Justin P could write a script to do this automatically, as doing it manually is bound to miss some terms.

Action:

We had a further discussion of the method GO uses to associated terms with taxa. That method has the advantage of automatically including any term from a sub-clade in the set of terms for a larger clade. PJ asked how this information is encoded in the obo file.

LC posted a link to one of the GO-taxonomy papers in the chat:Deegan et al; 2010

RW forwarded an additional paper that describes the method.Kusnierczyk, 2008

  • Elizabeth Arnaud confirmed we should use Musa as their terms encompass banana and plantain

TIPS proposal

An abstract/proposal was been submitted to Trends in Plant Science on Dec 31st, 2010. It was sent out to everyone by email.

Upcoming meetings 2011:

  • Plant and Animal Genome XIX Conference January 15-19, 2011 PAG 2011

Laurel, Ramona, DWS and Justin Preece are attending. PJ will attend for the weekend only as he is teaching. Alejandra cannot attend.


PO Activities at PAG:

Saturday - Early Afternoon, January 15, 2011 -- 1:30 pm - 3:00 pm (third in series of seven)

Outline for PAG2011 Computer Demo

" The Plant Ontology: Linking phenotypes and genomics across plant taxa"

Sunday Morning, 16 January 2011 -- 8:00 am - 10:10 am

Sunday Late Morning:

Time: 10:30-1:00 pm (to include lunch, will wrap up in time to get to 1:30 sessions)

PO Workshop Reg'n site and Survey

  • Outreach Booth being organized by MaizeGBD- More info TBA


  • Phenotype Ontology RCN Summit

The Phenotype Ontology RCN

February 25-27, 2010 at the National Evolutionary Synthesis Center in Durham, NC,

Laurel and Pankaj will be attending.



* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Dennis and Alejandra are planning to attend IBC2011 and speak in other symposia.

Symposium proposal was accepted, 'Bio-Ontologies for the Plant Sciences' under the genetics, genomics and bioinformatics theme.


Pankaj will give the introductory talk on general use of ontologies, GO, genomics, etc, and Ramona will present the talk on the Plant Ontology. Abstracts have been submitted.

No additional abstracts were submitted for our proposal, and Angelica does not think she will be able to attend because of lack of funds.

Dennis will speak in place of Angelica. PJ invited two other speakers. Gavin Kennedy will talk about the ontology application in large scale phenomics projects. Rudi Appels will speak on crop genomics and phenomics. Ramona has contacted these speakers to get their information and abstract; waiting for responses from them.

We received permission to use the 6th time slot for a discussion session. PJ will lead the discussion.

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