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

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'''POC meeting, Webex Conference Call; Date: Thursday April 28th, 2011 10am (PDT)'''
+
'''POC meeting, Webex Conference Call; Date: Tuesday May 3rd, 2011 10am (PDT)'''
  
 
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_4-28-11]]?
+
Acceptance of the minutes from the [[POC_Conf._Call_4-28-11]]? ''There were no changes, additions or deletions.''
  
 
=Items arising from previous meetings:=
 
=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)=
Line 35: Line 43:
 
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
 
[[File:Paraphyllia.jpg]] The paraphyllia are the small, dark structures between the leaves.
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3293891&group_id=76834&atid=835555 paraphysis]===
+
 
 +
''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
 
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
Line 51: Line 64:
  
 
adjacent_to gametangium, plural: paraphyses; particpates_in gametophytic phase
 
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)]===
 
===[https://sourceforge.net/tracker/?func=detail&aid=3293292&group_id=76834&atid=835555 axillary hair (PO:0030060)]===
Line 64: Line 88:
 
synonym: club-hair; part_of gametophore
 
synonym: club-hair; part_of gametophore
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3293893&group_id=76834&atid=835555 rhizoid]===
+
 
 +
''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.  
 
Moss Ontology definition: Filamentous tissue protruding from the gametophore stem with a rooting function.  
Line 73: Line 106:
 
'''Proposed def.:''' A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.
 
'''Proposed def.:''' A trichome that is part of a plant in the gametophytic phase and has positive gravitropism.
  
−
Comment: Found in bryophytes and pteridopytes growing from the epidermis of the lower surface of a gametophore or thallus. May also arise directly from a protonema. May be muticellular or unicellur. Usually serves to anchor the plant to the substrate.
+
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
 
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)]===
 
===[https://sourceforge.net/tracker/?func=detail&aid=3293289&group_id=76834&atid=835555 tmema (PO:0030061)]===
Line 87: Line 126:
 
Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.
 
Comment: Found in bryophytes at the base of a gemma. Participates in abscission of the gemma.
  
−
participates_in gametophytic phase, has_part tmema cell
+
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)]===
 
===[https://sourceforge.net/tracker/?func=detail&aid=3293931&group_id=76834&atid=835555 antheridium jacket layer (PO:0030053)]===
Line 100: Line 141:
  
 
part_of antheridium; synonym: sterile jacket layer, antheridium wall
 
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.''
 +
 +
''Need to add to definition of leptoid that they are anucleate at maturity.''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3295056&group_id=76834&atid=835555 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.''
 +
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3295058&group_id=76834&atid=835555 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''
 +
 +
===[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.
 +
 +
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==
 
==Parts of sporangium==
  
−
This is continued from our discussion at the [[POC_Conf._Call_3-8-11]]
+
''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:=
 +
 
 +
'''[http://www.phenotypercn.org/?page_id=458 Phenotype RCN Meeting]: June 1-3rd, Boulder CO'''
 +
 
 +
PJ will attend
 +
 
 +
More details TBA
 +
 
 +
 
 +
 
 +
'''[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.
 +
'''
 +
 
 +
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: [http://www.iplantcollaborative.org/Communities/Developers/SemanticWeb Semantic web].
 +
 
 +
 
 +
'''* ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York
 +
 
 +
[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:'''
 +
 
 +
'''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'''
 +
 
 +
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
 +
 
 +
Early-bird [http://www.aspb.org/meetings/pb-2011/registration.cfm registration] ends May 13.
 +
 
 +
Gramene will be putting together a workshop again, focusing on pathways.  PJ will present a PO poster.
  
−
Moss Ontology has requested the terms archesporium, amphithecium, and endothecium.
+
TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.
  
−
For background, see [[Summary of sporangium development]] in various non-angiosperm taxa.
+
For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.
  
  
−
Currently classes like exothecium, endothecium, primary parietal cell layer and tapetum are part of anther wall (PO:0000002). However, these layers and their constituent cell types can be part of any sporangium, not just an anther. Proposed making them part of a general class sporangium wall (as we did for parts of leaf). Tissues that are in all sporangia can be a child of this class. We could make specific children for anther exothecium, anther endothecium, etc.
 
  
 +
'''* International Botanical Congress (IBC2011)'''
  
−
*At the [[POC_Conf._Call_3-8-11]], we agree that [https://sourceforge.net/tracker/?func=detail&aid=3195056&group_id=76834&atid=835555 anther lobe] should be narrow synonym of pollen sac.
+
July 23rd-30th 2011, Melbourne, Australia'''
  
−
*At the [[POC_Conf._Call_4-28-11]] we agree to rename [https://sourceforge.net/tracker/?func=detail&aid=3195060&group_id=76834&atid=835555 theca] anther theca.
+
Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]  
  
−
*At the [[POC_Conf._Call_3-8-11]], we agree that [https://sourceforge.net/tracker/?func=detail&aid=3195060&group_id=76834&atid=835555 anther theca] (PO:0009069) should be is_a collective organ part structure, part of anther, has_part pollen sac.
+
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.  
  
−
*At the [[POC_Conf._Call_4-28-11]] we discussed making anther theca a child of sporangium theca.
+
Dennis, Alejandra, Pankaj and Ramona are planning to attend.  
  
−
*At the [[POC_Conf._Call_3-8-11]], we agree that [https://sourceforge.net/tracker/?func=detail&aid=3195067&group_id=76834&atid=835555 microsporocyte] (PO:0020047) should be part_of microsporangium instead of part_of pollen sac, so it is more general.
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
−
Also agreed to add a new term "sporocyte", parent to megasporocyte and microsporocyte, and also as a class for the sporocytes in homosporous plants like mosses. [We already have the term sporocyte, but the definitions of the sporocyte terms need a little work.]
+
=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

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