Difference between revisions of "POC Conf. Call 5-03-11"

From Plant Ontology Wiki
Jump to navigationJump to search
 
(147 intermediate revisions by 2 users not shown)
Line 3: Line 3:
 
In attendance:  
 
In attendance:  
  
−
POC members:
+
POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)
  
−
Absent:
+
Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)?
  
−
Collaborators:  
+
Collaborators: none
  
  
−
Acceptance of the minutes from the [[POC_Conf._Call_4-26-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_4-28-11]]? ''There were no changes, additions or deletions.''
  
−
=Issues arising from last week's meeting:=
+
=Items arising from previous meetings:=
 +
 
 +
==Review of [https://sourceforge.net/tracker/?func=detail&aid=3234956&group_id=76834&atid=835555 apical cell] (PO:0030007) and its descendents==
 +
 
 +
''Postponed until [[POC_Conf._Call_5-06-11]]''
 +
 
 +
===New terms and definitions for apical cells===
 +
 
 +
''Postponed until [[POC_Conf._Call_5-06-11]]''
  
 
=New terms for Physcomitrella and related taxa (continued)=
 
=New terms for Physcomitrella and related taxa (continued)=
 +
==Plant Tissues==
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293886&group_id=76834&atid=835555 paraphyllium (PO:0030069)]===
 +
 +
Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)
 +
 +
Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."
 +
 +
Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.
 +
 +
Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.
 +
 +
'''Proposed definition:''' A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.
 +
 +
Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.
 +
 +
is_a epidermis, part_of gametophore axis
 +
 +
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
 +
 +
 +
''Remove the word "small" from the definition. Don't need it.''
 +
 +
''Accepted''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293891&group_id=76834&atid=835555 paraphysis (PO:0030070)]===
 +
 +
Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 +
 +
From Parihar: sterile, slender filaments accompanying reproductive organs.
 +
 +
From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses
 +
 +
These are a kind of trichome
 +
 +
 +
'''Proposed def.:''' A slender, usually uniseriate multicellular trichome that grows intermixed with the gametangia.
 +
 +
Comment: Found in bryophytes and pteridophytes, especially in mosses.
 +
 +
adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase
 +
 +
'''Should we add the adjacent_to relation?''' ''No. Adjacent to means they are in permanent contact, which is not appropriate here.''
 +
 +
 +
''New proposed def: A slender multicellular trichome that grows between the gametangia.''
 +
 +
''Comment: Usually multiseriate. Found in bryophytes and pteridophytes, especially in mosses.''
 +
 +
 +
 +
''Accepted''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293292&group_id=76834&atid=835555 axillary hair (PO:0030060)]===
 +
 +
Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 +
 +
This is a type of trichome. Axillary trichomes may also be found in angiosperms, but they are different, so suggest we specify that this for hairs in gametophores.
 +
 +
'''Proposed def., gametophore axillary hair:''' A multicellular trichome consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.
 +
 +
Comment: Found in pleurocarpous mosses. Form in the axils of leaf primordia, and may disappear when the gametophore is mature.
 +
 +
synonym: club-hair; part_of gametophore
 +
 +
 +
''Make a new general term for '''axillary hair:''' A mutlicellular trichome that has as parts a long terminal cell atop a basal stalk and grows in a leaf axil.''
 +
 +
''comment: Found in monocots and mosses. The basal stalk may contain one or more cells.''
 +
 +
''New proposed def. for '''gametophore axillary hair:''' An axillary hair that grows in a leaf axil of a non-vascular leaf.''
 +
 +
''Will need to double check definitions of the parts of the axillary hair (from last week's agenda) to make sure they are consistent with this.  Add new terms for axillary hair terminal cell, axillary hair base, and axillary hair basal cell.''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293893&group_id=76834&atid=835555 rhizoid (PO:0030071)]===
 +
 +
Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.
 +
 +
Rhizoids may also grow from thalli. They arise from an epidermal intial (the rhizoid initial), and so are like trichomes. Like trichomes, they may be uni- or multicellular
 +
 +
 +
'''Proposed def.:''' A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.
 +
 +
Comment: Found in bryophytes and pteridophytes growing from the epidermis of the lower surface of a gametophore or thallus. May be multicellular or unicellular. Usually serves to anchor the plant to the substrate.
 +
 +
Should we say: May also arise directly from a protonema or create a separate class for protonemal rhizoids?
 +
 +
develops_from rhizoid initial, participates_in gametophytic phase
 +
 +
''There was a discussion of how different rhizoids develop, and whether or not they could be grouped together. As rhizoid is currently defined, can't include protonemal rhizoids, because they don't develop from an epidermal initial. There are rhizoids on monocots (wurztelhalsrhizoid) that are not part of a gametophyte. Also need term for pegged rhizoids in liverworts.''
 +
 +
''We decided to make a new general class for rhizoids, a child of plant structure, that can include them all. Will put together new definitions and develops_from relations for the [[POC_Conf._Call_5-06-11]].''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293289&group_id=76834&atid=835555 tmema (PO:0030061)]===
 +
 +
Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition
 +
 +
Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells
 +
 +
'''Proposed def.:''' A portion of plant tissue that has as parts tmema cells.
 +
 +
Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.
 +
 +
participates_in gametophytic phase, has_part tmema cell (can't use tmema cell part_of tmema, because they can also occur as single cells in a protonema, next to a brachycyte)
 +
 +
''Accepted''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3293931&group_id=76834&atid=835555 antheridium jacket layer (PO:0030053)]===
 +
 +
Moss Ontology definition: A layer of cells that surrounds the spermatogenous tissue that cannot give rise to sperm.
 +
 +
The term jacket layer is also used for the outer layer of sporangia. Suggest naming this term '''antheridium wall''' or '''antheridium jacket layer'''
 +
 +
'''proposed definition:''' A portion of plant tissue that is a single layer of cells on the outside of an antheridium.
 +
 +
Comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells and do not give rise to sperm cells.
 +
 +
part_of antheridium; synonym: sterile jacket layer, antheridium wall
 +
 +
 +
''Accepted.  Will use antheridium jacket layer as primary name.''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3295055&group_id=76834&atid=835555 hydrome (PO:0030047)]===
 +
 +
'''proposed definition:''' A portion of plant tissue that has as parts hyrdoids.
 +
 +
Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in conduction of water and minerals and in support, similar to xylem in vascular plants.
 +
 +
disjoint_from xylem, participates_in gametophytic phase
 +
 +
Synonyms: hydrom, leptoxylem (Hebant)
 +
 +
 +
''There was some discussion about exact wording of the definition. BS explained that to a logical reasoner, when you say that X has parts only Ys, it does not follow that X has as parts all the parts of Y. So, for example, hydrome has as parts only hydroid cells excludes the possibility that hydrome has_part hydroid cell nucleus, which of course is wrong.''
 +
 +
 +
''Add to comment: A hydrome is composed of only hydroid cells.''
 +
 +
''Can't use participates in gametophytic phase, because it can also occur in a seta of mosses.''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3295055&group_id=76834&atid=835555 leptome (PO:0030048)]===
 +
 +
'''proposed definition:''' A portion of plant tissue that has as parts leptoids.
 +
 +
Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.
 +
 +
disjoint_from phloem, participates_in gametophytic phase
 +
 +
Synonyms: leptom, leptophloem (Hebant)
 +
 +
 +
''Leptome has the same issues as hydrome.''
 +
 +
''Add to comment: A leptome is composed of only leptoid cells.''
 +
 +
''Can't use participates in gametophytic phase, because it can also occur in a seta of mosses.''
  
−
=Continuing User requests: for PSO=
+
''Need to add to definition of leptoid that they are anucleate at maturity.''
  
−
- Deal with and complete the list of user requests on SourceForge-
+
===[https://sourceforge.net/tracker/?func=detail&aid=3295056&group_id=76834&atid=835555 stereome (PO:0030050)]===
  
−
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms]==
+
From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.
  
−
submitted by Austin Mast
+
'''proposed definition:''' A portion of ground tissue that has as parts stereids.
  
−
Several terms have already been dealt with (Taproot, Stem Hair, Prickles, Anther pore and anther slit)
+
Comment: Found in bryophytes in gametophore axes or non-vascular leaves. May function in support.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165981&group_id=76834&atid=835555 fascicle] The term fascicle can refer to different structures in different taxa. Suggest we use the term '''floral fascicle''' or '''flower fascicle''' in this case, to distinguish it from a "leaf fascicle," which we may want to add for describing gymnosperms.
+
participates_in gametophytic phase
  
−
From Tucker, 2003, Flora:
+
''Stereome has the same issues as hydrome.''
−
(in the Papilionoideae) "Pseudoracemes (Fig. 5B) differ from racemes in
 
−
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."
 
  
−
'''Proppsed def:''' A second order inflorescence in which the second order inflorescence branch bears two or more flowers but is not elongated.  Comment: A fascilce appears to be a cluster of flowers in an axil of a single bract of the main inflorescence. Common in some sections of the Fabaceae.
+
''Add to comment: A stereome is composed of only steroid cells.''
  
 +
''Need to check to see if we can use participates in gametophytic phase, if it occurs  in a seta or not.''
  
−
[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)
+
===[https://sourceforge.net/tracker/?func=detail&aid=3295058&group_id=76834&atid=835555 central strand (PO:0030051)]===
  
−
We added the term stipule spine. Could also add the term '''stipule bristle''': A stipule that has a brush-like appearance.
+
From Crum: a group of cells forming a central axis of some stems, usually made of small, elongated cells
  
−
Alternative is to suggest bristled to PATO
+
From Schofeld: a central strand of smaller cells in the center of stems of many mosses.
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]
+
'''proposed definition:''' A portion of plant tissue that is an axial strand in the center of a gametophore axis and has as part hydrome or leptome.  
  
−
'''Proppsed def:''' A leaf in which there is no normal lamina development, but instead the petiole or petiole plus rachis is laminar.
+
Comment: Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a root protostele in vascular plants, but this term should only be used for non-vascular plants. ''Should we add: analogous to a vein or vascular bundle in vascular plants?''
  
 +
synonyms: conducting strand, central cylinder
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3165994&group_id=76834&atid=835555 banner, wing and keel]
+
part_of gametophore axis (or can it also be part of a seta?)
  
−
'''Banner''' (as in a legume flower) - suggest using name 'banner petal'
+
''Don't use part of gametophore axis. Can also be part of seta.''
  
−
'''Proppsed 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.
+
''In defintion, say has as part '''a''' hydrome or '''a''' leptome.''' ''
  
 +
''New proposed comment: Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a protostele in vascular plants, but this ONTOLOGY CLASS should only be used for non-vascular plants. Analogous to a vein or vascular bundle in vascular plants.''
  
−
'''Wing''' (as in a legume flower) - suggest using name 'wing petal'
+
''Accepted''
  
−
'''Proppsed def:''' One of two petals that is adjacent to the banner petal in some flowers of the Fabaceae. Comment: The wing petals are usually much smaller than the banner petal and the corolla keel.
+
===[https://sourceforge.net/tracker/?func=detail&aid=3295062&group_id=76834&atid=835555 costa (PO:0030072)]===
  
 +
'''proposed definition:''' A portion of plant tissue that is a single or double strand in the center of a non-vascular leaf and has as part hydrome or leptome.
  
−
'''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 'corolla keel'
+
Comment: Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this term should only be non-vascular leaves.
  
−
Suggest three new terms:
+
part_of non-vascular leaf
  
−
'''fused petal:''' A petal that is fused to another petal.
+
synonym: phyllid costa, phyllid midvein, phyllid midrib, non-vascular leaf midvein, non-vascular leaf midrib
  
−
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).
 
  
 +
''New proposed comment: Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this ONTOLOGY CLASS should only be USED FOR non-vascular leaves.''
  
−
'''fused corolla:''' A corolla in which the petals are fused.
+
''Accepted''
  
−
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.
+
==Parts of sporangium==
  
 +
''Postponed until [[POC_Conf._Call_5-06-11]]''
  
−
'''corolla keel:''' A fused corolla that consists of the two lowest petals in some flowers of the Fabaceae.
+
=Other Issues=
 +
'''*Review for OBO Foundry Acceptance'''
  
−
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.
+
''Postponed until [[POC_Conf._Call_5-10-11]]''
  
−
==TraitNet requests==
+
=Upcoming meetings 2011:=
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080906&group_id=76834&atid=835555 corm]  
+
'''[http://www.phenotypercn.org/?page_id=458 Phenotype RCN Meeting]: June 1-3rd, Boulder CO'''
  
−
proposed def: A short, enlarged storage stem in which the internodes do not elongate. Comment: usually underground.
+
PJ will attend
  
−
child of stem (PO:0009047).
+
More details TBA
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]
 
  
−
Their comment: is synonym to Tubercle
+
'''[http://www.iplantcollaborative.org/2011/02/09/2011-semantic-web-workshop-june-6-7-santa-fe-nm 2011 Semantic Web Workshop] June 6th and 7th, Santa Fe, NM.
 +
'''
  
−
podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
+
Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.  
  
−
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).
+
-JE and JP will be attending
  
−
proposed def:
+
-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.
  
 +
For more Workshop details: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080913&group_id=76834&atid=835555 pneumatophore]
 
  
−
definition from Beentje (2010): erect (breathing) root protruding above the soil, encountered especially in mangroves
+
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30, 2011
 +
Buffalo, New York
  
−
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.
+
[http://icbo.buffalo.edu ICBO]
  
 +
LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability"
 +
along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
  
 +
'''Full-Day Workshops Schedule:'''
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]
+
'''July 26 9am-6pm'''  The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies
  
−
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.
+
'''July 27 8.30am-4pm''' Facilitating Anatomy Ontology Interoperability
  
−
We could add this term as a kind of upper level bin term (similar to trichome)
+
'''July 26 6.30pm-9pm'''  Evening Workshop: Common Logic
  
 +
'''July 27 4pm-8pm''' Evening Workshop: Doctoral and Post-Doctoral Consortium
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]
+
- LC will attend and represent the PO. Invite other plant people?
  
−
Should probably be a synonym of strobilus (PO:0025083). Narrow or exact?
 
  
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080922&group_id=76834&atid=835555 sorus]
+
'''*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
from Crum (2001): a cluster of fern sporangia
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
−
from Beentje (2010): (of pteridophytes) structure bearing or containing groups of sporangia.
 
  
−
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.  
+
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
  
−
Part_of vascular leaf, has_part sporangium
+
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
 +
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
−
Defintion from Beentje (2010): a slender, coiling structure derived from a branch, leaf or inflorescence and used for climbing.
 
  
−
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.
+
'''* International Botanical Congress (IBC2011)'''
  
−
leaf tendril (child of leaf): A leaf that is slender and coiling and lacks a lamina. Comment: Aids plant in climbing.
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
leaflet tendril (child of leaflet): A leaflet that is slender and coiling. Comment: Aids plant in climbing.
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]
  
−
leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.
+
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.  
  
−
Can add other types of tendrils if they come up or users need them.
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.  
  
−
==[https://sourceforge.net/tracker/index.php?func=detail&aid=2899934&group_id=76834&atid=835555 root terms]==
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
−
submitted by Rich Zobel (Nov 2009)
+
=Next meeting scheduled for Friday, May 6th, 2011 at 10am PDT/1pm EDT=

Latest revision as of 12:36, 5 May 2011

POC meeting, Webex Conference Call; Date: Tuesday May 3rd, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Justin Preece (OSU), Pankaj Jaiswal (OSU), Dennis Stevenson (NYBG), Barry Smith (University at Buffalo, NY), Marie Alejandra Gandolfo (Cornell University)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)?

Collaborators: none


Acceptance of the minutes from the POC_Conf._Call_4-28-11? There were no changes, additions or deletions.

Items arising from previous meetings:

Review of apical cell (PO:0030007) and its descendents

Postponed until POC_Conf._Call_5-06-11

New terms and definitions for apical cells

Postponed until POC_Conf._Call_5-06-11

New terms for Physcomitrella and related taxa (continued)

Plant Tissues

paraphyllium (PO:0030069)

Tiny filaments, scales or leaf-like structures scattered on the stems of some leafy bryophytes. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition (MO definition)

Crum defines them as "Small green outgrowths formed between the leaves on stems and branches of some pleurocarps (mosses that produce archegonia and sporophytes laterally, rather than on the tips of their axes) and a very few leafy liverworts."

Schofield describes paraphyllia as outgrowths of the epidermis, but he also describes leaves that way.

Moss Ontology has paraphyllium listed as a plant organ, but they do not arise from the SAM as phyllomes do.

Proposed definition: A portion of epidermal tissue that is a small outgrowth from the epidermis between the leaves of a gametophore axis.

Comment: Paraphyllia are much smaller than leaves and may be filamentous, scale-like, or leaf-like. Found in pleurocarpous mosses and a few leafy liverworts.

is_a epidermis, part_of gametophore axis

Paraphyllia.jpg The paraphyllia are the small, dark structures between the leaves.


Remove the word "small" from the definition. Don't need it.

Accepted

paraphysis (PO:0030070)

Moss Ontology definition: Sterile, septate, usually uniseriate hairs intermixed with sex organs. Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

From Parihar: sterile, slender filaments accompanying reproductive organs.

From Schofeld: filamentous sterile structures intermixed with the sex organs of most mosses

These are a kind of trichome


Proposed def.: A slender, usually uniseriate multicellular trichome that grows intermixed with the gametangia.

Comment: Found in bryophytes and pteridophytes, especially in mosses.

adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase

Should we add the adjacent_to relation? No. Adjacent to means they are in permanent contact, which is not appropriate here.


New proposed def: A slender multicellular trichome that grows between the gametangia.

Comment: Usually multiseriate. Found in bryophytes and pteridophytes, especially in mosses.


Accepted

axillary hair (PO:0030060)

Moss Ontology definition: A small filament in an axil consisting of one long terminal cell atop a basal stalk (also called club-hair). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

This is a type of trichome. Axillary trichomes may also be found in angiosperms, but they are different, so suggest we specify that this for hairs in gametophores.

Proposed def., gametophore axillary hair: A multicellular trichome consisting of one long terminal cell atop a basal stalk that grows in the leaf axil of a non-vascular leaf.

Comment: Found in pleurocarpous mosses. Form in the axils of leaf primordia, and may disappear when the gametophore is mature.

synonym: club-hair; part_of gametophore


Make a new general term for axillary hair: A mutlicellular trichome that has as parts a long terminal cell atop a basal stalk and grows in a leaf axil.

comment: Found in monocots and mosses. The basal stalk may contain one or more cells.

New proposed def. for gametophore axillary hair: An axillary hair that grows in a leaf axil of a non-vascular leaf.

Will need to double check definitions of the parts of the axillary hair (from last week's agenda) to make sure they are consistent with this. Add new terms for axillary hair terminal cell, axillary hair base, and axillary hair basal cell.

rhizoid (PO:0030071)

Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.

Rhizoids may also grow from thalli. They arise from an epidermal intial (the rhizoid initial), and so are like trichomes. Like trichomes, they may be uni- or multicellular


Proposed def.: A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.

Comment: Found in bryophytes and pteridophytes growing from the epidermis of the lower surface of a gametophore or thallus. May be multicellular or unicellular. Usually serves to anchor the plant to the substrate.

Should we say: May also arise directly from a protonema or create a separate class for protonemal rhizoids?

develops_from rhizoid initial, participates_in gametophytic phase

There was a discussion of how different rhizoids develop, and whether or not they could be grouped together. As rhizoid is currently defined, can't include protonemal rhizoids, because they don't develop from an epidermal initial. There are rhizoids on monocots (wurztelhalsrhizoid) that are not part of a gametophyte. Also need term for pegged rhizoids in liverworts.

We decided to make a new general class for rhizoids, a child of plant structure, that can include them all. Will put together new definitions and develops_from relations for the POC_Conf._Call_5-06-11.

tmema (PO:0030061)

Moss Ontology definition: An abscission cell at the base of a gemma (vegetative propagule). Bill and Nancy Malcolm (2006): Mosses and other Bryophytes, an illustrated glossary, second edition

Their definition defines a cell type, but they have tmema as a tissue type. It would be the tissue composed of tmema cells

Proposed def.: A portion of plant tissue that has as parts tmema cells.

Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.

participates_in gametophytic phase, has_part tmema cell (can't use tmema cell part_of tmema, because they can also occur as single cells in a protonema, next to a brachycyte)

Accepted

antheridium jacket layer (PO:0030053)

Moss Ontology definition: A layer of cells that surrounds the spermatogenous tissue that cannot give rise to sperm.

The term jacket layer is also used for the outer layer of sporangia. Suggest naming this term antheridium wall or antheridium jacket layer

proposed definition: A portion of plant tissue that is a single layer of cells on the outside of an antheridium.

Comment: Cells in the antheridium jacket layer surround the inner spermatogenous cells and do not give rise to sperm cells.

part_of antheridium; synonym: sterile jacket layer, antheridium wall


Accepted. Will use antheridium jacket layer as primary name.

hydrome (PO:0030047)

proposed definition: A portion of plant tissue that has as parts hyrdoids.

Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in conduction of water and minerals and in support, similar to xylem in vascular plants.

disjoint_from xylem, participates_in gametophytic phase

Synonyms: hydrom, leptoxylem (Hebant)


There was some discussion about exact wording of the definition. BS explained that to a logical reasoner, when you say that X has parts only Ys, it does not follow that X has as parts all the parts of Y. So, for example, hydrome has as parts only hydroid cells excludes the possibility that hydrome has_part hydroid cell nucleus, which of course is wrong.


Add to comment: A hydrome is composed of only hydroid cells.

Can't use participates in gametophytic phase, because it can also occur in a seta of mosses.

leptome (PO:0030048)

proposed definition: A portion of plant tissue that has as parts leptoids.

Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore axis or seta, or in the midrib of a non-vascular leaf. Often surrounding a central hydrome. May function in the conduction of organic substances, similar to phloem in vascular plants.

disjoint_from phloem, participates_in gametophytic phase

Synonyms: leptom, leptophloem (Hebant)


Leptome has the same issues as hydrome.

Add to comment: A leptome is composed of only leptoid cells.

Can't use participates in gametophytic phase, because it can also occur in a seta of mosses.

Need to add to definition of leptoid that they are anucleate at maturity.

stereome (PO:0030050)

From Hebant: A typical moss stem comprises, from the outside to the inside, an epidermis with a thin cuticle but no stomata, an outer cortex which frequently consists of supporting ells with thickended walls ("stereids"), an inner cortex of thin-walled conducting cells, and, in a number of species, a central strand of hydroids.

proposed definition: A portion of ground tissue that has as parts stereids.

Comment: Found in bryophytes in gametophore axes or non-vascular leaves. May function in support.

participates_in gametophytic phase

Stereome has the same issues as hydrome.

Add to comment: A stereome is composed of only steroid cells.

Need to check to see if we can use participates in gametophytic phase, if it occurs in a seta or not.

central strand (PO:0030051)

From Crum: a group of cells forming a central axis of some stems, usually made of small, elongated cells

From Schofeld: a central strand of smaller cells in the center of stems of many mosses.


proposed definition: A portion of plant tissue that is an axial strand in the center of a gametophore axis and has as part hydrome or leptome.

Comment: Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a root protostele in vascular plants, but this term should only be used for non-vascular plants. Should we add: analogous to a vein or vascular bundle in vascular plants?

synonyms: conducting strand, central cylinder

part_of gametophore axis (or can it also be part of a seta?)

Don't use part of gametophore axis. Can also be part of seta.

In defintion, say has as part a hydrome or a leptome.

New proposed comment: Often contains both hydrome and leptome. Found in bryophytes. The term central strand is sometimes used to describe a protostele in vascular plants, but this ONTOLOGY CLASS should only be used for non-vascular plants. Analogous to a vein or vascular bundle in vascular plants.

Accepted

costa (PO:0030072)

proposed definition: A portion of plant tissue that is a single or double strand in the center of a non-vascular leaf and has as part hydrome or leptome.

Comment: Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this term should only be non-vascular leaves.

part_of non-vascular leaf

synonym: phyllid costa, phyllid midvein, phyllid midrib, non-vascular leaf midvein, non-vascular leaf midrib


New proposed comment: Found in bryophytes. Often contains both hydrome and leptome. Functions in support and conduction in a phyllid. The term costa is sometimes used for the midrib of monocot leaves, but this ONTOLOGY CLASS should only be USED FOR non-vascular leaves.

Accepted

Parts of sporangium

Postponed until POC_Conf._Call_5-06-11

Other Issues

*Review for OBO Foundry Acceptance

Postponed until POC_Conf._Call_5-10-11

Upcoming meetings 2011:

Phenotype RCN Meeting: June 1-3rd, Boulder CO

PJ will attend

More details TBA


2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM.

Hosted by Damian Gessler and the iPlant Collaborative, this two-day workshop will focus on biological applications for semantic web services.

-JE and JP will be attending

-JE has already worked with Damian to implement a SSWAP web service for PO terms, so further collaboration with him and iPlant will benefit the POC going forward.

For more Workshop details: Semantic web.


* ICBO 2011 Second International Conference on Biomedical Ontology July 26-30, 2011 Buffalo, New York

ICBO

LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating anatomy ontology interoperability" along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.

Full-Day Workshops Schedule:

July 26 9am-6pm The Ontological Representation of Adverse Events: Working with Multiple Biomedical Ontologies

July 27 8.30am-4pm Facilitating Anatomy Ontology Interoperability

July 26 6.30pm-9pm Evening Workshop: Common Logic

July 27 4pm-8pm Evening Workshop: Doctoral and Post-Doctoral Consortium

- LC will attend and represent the PO. Invite other plant people?


*Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Early-bird registration ends May 13.

Gramene will be putting together a workshop again, focusing on pathways. PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.

For inclusion on the program memory stick and in the program book, abstracts must be submitted by May 27.


* International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, wiil be held on Thursday, 27 July, from 13:30 to 15:30.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

Next meeting scheduled for Friday, May 6th, 2011 at 10am PDT/1pm EDT

Retrieved from "http://wiki.plantontology.org/index.php?title=POC_Conf._Call_5-03-11&oldid=8208"