POC Conf. Call 6-14-11 - Revision history

Cooperl at 18:30, 24 June 2011

2011-06-24T18:30:33Z

Cooperl: /* Conductive cells and tissues for vascular and non-vascular plants */

2011-06-24T18:29:10Z

Conductive cells and tissues for vascular and non-vascular plants

Cooperl: /* conductive tissue for bryophytes and vascular plants */

2011-06-24T18:25:14Z

conductive tissue for bryophytes and vascular plants

Cooperl: /* conductive tissue for bryophytes and vascular plants */

2011-06-24T18:23:45Z

conductive tissue for bryophytes and vascular plants

Cooperl at 18:23, 24 June 2011

2011-06-24T18:23:18Z

Cooperl: /* Report from the2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM */

2011-06-24T18:10:50Z

Report from the2011 Semantic Web Workshop June 6th and 7th, Santa Fe, NM

Rwalls: /* conductive tissue for bryophytes and vascular plants */

2011-06-15T14:30:09Z

conductive tissue for bryophytes and vascular plants

Rwalls: /* User requests still open on Source Forge; PGDSO */

2011-06-15T14:29:07Z

User requests still open on Source Forge; PGDSO

Rwalls at 14:00, 15 June 2011

2011-06-15T14:00:37Z

Rwalls: /* TraitNet requests */

2011-06-15T13:58:10Z

TraitNet requests

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 '''POC meeting, Webex Conference Call; Date: Tuesday June 14th, 2011 10am (PDT)'''
 In attendance:
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+'''This week's meeting was canceled.'''

← Older revision		Revision as of 18:29, 24 June 2011
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	=Items arising from previous meetings:=		=Items arising from previous meetings:=
−
−
−	~~=Conductive cells and tissues for vascular and non-vascular plants=~~
−
−	~~THIS PART IS STILL UNDER CONSTRUCTION~~
−
−
−	~~==conductive and related cell types for bryophytes and vascular plants==~~
−
−	~~===Current parent: axial cell===~~
−
−	~~'''axial cell (PO:0000081):''' A vascular cell derived from the fusiform cambial initial and oriented with its longest diameter parallel with the main axis of stem or root. [source: ISBN:0471245208]~~
−
−	~~Comment: These cells make up the axial system, also known as vertical or longitudinal system.~~
−
−	~~'''Existing descendents of axial cell:'''~~
−
−	~~sieve tube member (PO:0000289, alt: PO:0000286)~~
−
−	~~phloem fiber (PO:0004519)~~
−
−	~~xylem element (PO:0000273)~~
−
−	~~>tracheary element (PO:0000273)~~
−
−	~~>>tracheid (PO:0000301)~~
−
−	~~>>vessel member (PO:0002003)~~
−
−	~~>xylem fiber (PO:0000274)~~
−
−	~~>>fiber tracheid (PO:0000355)~~
−
−	~~>>libriform fiber (PO:0004520)~~
−
−	~~>>septate fiber (PO:0004521)~~
−
−
−	The term axial cell, and the current definition, describe a particular type of vascular cells found in wood. This is not appropriate as the parent for xylem and phloem cells. Also, the term axial cell is not widely used. "Axial system" is widely used to describe the vascular tissue in wood (in contrast to the radial system).
−
−	~~Suggest that we obsolete this term, possibly replace with new terms for axial system and radial system~~
−
−
−	At the bryophyte term meeting on 4-25-2011 (RW and MAG present), we decided that axial cell was not the correct term to use to describe all of the elongated cells associated with conducting tissue in plants. They are different cell types and have different origins, so they should not all be grouped together.
−
−
−	~~===New proposed hierarchy (children of plant cell):===~~
−
−	~~plant cell~~
−
−	~~>hydroid~~
−
−	~~>leptoid~~
−
−	~~>vascular cell (new term)~~
−
−	~~>>sieve tube member~~
−
−	~~>>tracheary element~~
−
−	~~>>>tracheid~~
−
−	~~>>>vessel member~~
−
−	~~>>phloem fiber cell~~
−
−	~~>>xylem fiber cell~~
−
−	~~>>other kinds of fiber cells~~
−
−	~~>ground tissue cell (PO:0025030)~~
−
−	~~>>stereid~~
−
−	~~>>collenchyma cell~~
−
−	~~>>sclerenchyma cell (PO:0000077)~~
−
−	~~>>>fiber cell (new term)~~
−
−	~~>>>sclerid (new term)~~
−
−
−
−	~~'''Proposed definitions:'''~~
−
−	~~'''fiber cell:'''~~
−
−	~~'''vascular cell:'''~~

← Older revision		Revision as of 18:25, 24 June 2011
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	=Items arising from previous meetings:=		=Items arising from previous meetings:=

−
−	~~=conductive tissue for bryophytes and vascular plants=~~

	=Conductive cells and tissues for vascular and non-vascular plants=		=Conductive cells and tissues for vascular and non-vascular plants=

← Older revision		Revision as of 18:23, 24 June 2011
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	=conductive tissue for bryophytes and vascular plants=		=conductive tissue for bryophytes and vascular plants=
−
−	~~''This is just a place holder for notes on this subject. We did not deal with it at this meeting.''~~
−
−	~~trace as possible name for category for veins, central strands, and costas~~
−
−	~~===vascular tissue===~~
−
−	~~For vascular plants, we have the class:~~
−
−	~~'''portion of vascular tissue (PO:0009015):''' A portion of plant tissue that has parts xylem and phloem. [APweb:Glossary]~~
−
−	~~Comment: Functions in conduction and support. In the stem it is often found as a stele, surrounded by the cortex and surrounding the pith.~~
−
−	~~part_of vascular bundle (which is part_of vascular system)~~
−
−	~~This is okay, but suggest that we make it a child of the new class '''portion of axial tissue''' (see below), and also change definition to include xylem '''or''' phloem.~~
−
−
−	~~'''Proposed definition:''' A portion of plant tissue that has as parts tracheary elements or sieve tube members.~~
−
−	Comment: Functions in conduction and support. In shoot axes, vascular tissue is often found as part of a stele or may occur as scattered vascular bundles. May include other types of tissue, such as fibers.
−
−	~~part_of vascular system (should add vascular system participates_in sporophytic phase)~~
−
−	~~currently part_of vascular bundle. Removed this relation, because it is not true for all plants. Also vascular bundle is now a portion of vascular tissue, so it can't be part_of.~~
−
−
−	~~'''children of vascular tissue:'''~~
−
−	'''hydathode''' (PO:0005660) - A structural modification of vascular and non-vascular tissues, usually in a leaf, that permits the release of water through a pore in the epidermis. [GR:pj, ISBN:0080374913]
−
−	~~Should be is_a cardinal organ part. Do hydathodes ever occur on stems or branches, or are they always part of phyllomes?~~
−
−	~~'''proposed definition:''' A cardinal organ part that releases water through a pore.~~
−
−	Comment: Usually found on leaves. Hydathodes may have one or more pores that appear to be incompletely developed stomata that lack the ability to open and close. Generally, hydathodes are located at the end of a minor vein. In many plants, hydathodes includes a portion of thin-walled parenchyma between the tracheary elements and the pore, known as an epithem. In some plants, hydathodes are associated with secretory tissue.
−
−
−	~~'''leaf vein''' (PO:0005417) - see more below details below~~
−
−
−	~~'''phloem''' (PO:0005417): A portion of vascular tissue whose principal function is conducting organic substances. [GR:pj]~~
−
−	~~'''proposed definition:''' A portion of vascular tissue that has as parts sieve tube members.~~
−
−	~~Comment: Functions in the conduction of organic substances in vascular plants.~~
−
−
−	~~'''metaphloem''' (PO:0006076): Part of the primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.~~
−
−	~~'''proposed definition:''' A portion of phloem tissue that is the part of a primary phloem that differentiates after the protophloem and before the secondary phloem, if any of the latter is formed.~~
−
−
−	~~'''protophloem''' (PO:0006077): The first-formed elements of the primary phloem.~~
−
−	~~'''proposed definition:''' A portion of phloem tissue that has as parts the first-formed elements of the primary phloem.~~
−
−
−	'''tracheid bar''' (PO:0019026): A distinct ring-like structure, composed of tracheid cells, which surrounds the hilum of some taxa e.g., Phaseolus, and forms a groove in the surface of the pericarp (immediately adjacent to the hilum). [ISBN:0080280293]
−
−	~~-should be is_a xylem~~
−
−
−	~~'''xylem''' (PO:0005352): A portion of vascular tissue composed of (''that has as parts'') xylem elements.~~
−
−
−	~~'''vascular bundle (PO:0005020):''' A unit strand of the vascular system containing the vascular tissues, xylem and phloem. In addition vascular cambium is often present. [GR:pj]~~
−
−	~~This currently is_a portion of plant tissue. Should be is_a portion of vascular tissue.~~
−
−	~~'''proposed definition:''' A portion of vascular tissue that is a unit strand of the vascular system and has as part xylem or phloem.~~
−
−	~~Comment: Usually contains both xylem or phloem. May also contain other types of tissue such as plant fibers or vascular cambium. May also contain portions of ground tissue.~~
−
−	~~part_of vascular system~~
−
−
−	~~====New children of plant tissue:====~~
−
−	~~'''hydrome:''' A portion of axial tissue that has as parts hyrdoids.~~
−
−	Comment: Found in bryophytes, in the center of a non-vascular shoot axis such as a gametophore or seta, or in the midrib of a non-vascular leaf. Often surrounded by leptome. May function in water conduction and support, similar to xylem in vascular plants.
−
−	~~Synonyms: hydrom, leptoxylem (Hebant)~~
−
−
−	~~'''leptome:''' A portion of axial tissue that has as parts leptoids.~~
−
−	Comment: Found in bryophytes, in non-vascular shoot axes such as a gametophore 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.
−
−	~~Synonyms: leptom, leptophloem (Hebant)~~
−
−
−	~~'''central strand:''' A unit strand of axial tissue that has as part hydrome or leptome.~~
−
−	~~Comment: Often contains both hydrome and leptome. Found in bryophytes located in the center of non-vascular shoot axes such as a gametophore axis or seta, or in the costa of a non-vascular leaf.~~
−
−	~~synonyms: conducting strand, central cylinder~~
−
−
−	~~'''stereome:''' A portion of axial tissue that has as parts stereids.~~
−
−	~~Comment: Found in bryophytes.~~
−
−	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.
−
−
−	~~'''portion of plant fiber:''' Currently fibers are plant cell types, but they should also be a tissue type.~~
−
−	~~''Proposed definition: A portion axial tissue that has as parts fiber cells.~~
−
−	~~Comment: Contains elongated, lignified fiber cells that are dead at maturity.~~
−
−	~~'''phloem fiber:''' A portion of plant fiber that has as parts phloem fiber cells.~~
−
−	~~'''xylem fiber:''' A portion of plant fiber that has as parts xylem fiber cells.~~
−
−	~~===leaf vein, midrib, costa===~~
−
−	*'''leaf vein (PO:0020138):''' A strand of vascular tissue in the leaf blade.
−
−	~~is_a portion of vascular tissue; part_of leaf vascular system~~
−
−	~~This term only applies to vascular leaves, and should be renamed vascular leaf vein.~~
−
−	~~'''proposed definition, vascular leaf vein (PO:0020138):''' A strand of vascular tissue that is part of a leaf lamina in a vascular leaf.~~
−
−	~~part_of leaf vascular system, part_of leaf lamina~~
−
−
−	*Suggest new term '''primary leaf vein''': A vascular leaf vein that originates from the base of a leaf lamina where it attaches to the petiole or to the shoot axis if no petiole is present.
−
−	~~Comment: A leaf may have more than one primary vein. The central primary vein is the midvein.~~
−
−
−	*'''midvein (PO:0020139):''' The central, and usually the most prominent, vein of a leaf or leaf-like organ. [source: APWeb:Glossary]
−
−	~~Since midvein is_a leaf vein, it should say just "leaf" instead of "leaf or leaf-like organ". Suggest we rename it '''vascular leaf midvein''' to distinguish it from '''costa'''.~~
−
−	~~'''proposed definition of vascular leaf midvein:''' A primary leaf vein that is the central vein of a leaf lamina in a vascular leaf.~~
−
−	~~Comment: Often the most prominent vein of a vascular leaf.~~
−
−	~~broad synonyms: mid rib, midrib, mid-rib~~
−
−	~~related synonym: costa, Hickey and Peterson 1978 doi:10.1139/b78-128~~
−
−
−	*Moss Ontology has requested the term '''midrib''' for bryophytes. It is often called a '''costa'''.
−
−	~~''Proposed definition for costa:''' A central strand that is part of a non-vascular leaf.~~
−
−	~~Comment: Found in bryophytes, especially mosses.~~
−
−	~~part_of non-vascular leaf~~
−
−	~~broad synonyms: mid rib, midrib, mid-rib~~
−
−	~~====Refs:====~~
−
−	~~Sperry 2003, IJPS; Hebant 1977;~~

	=Conductive cells and tissues for vascular and non-vascular plants=		=Conductive cells and tissues for vascular and non-vascular plants=

← Older revision		Revision as of 18:23, 24 June 2011
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	'''vascular cell:'''		'''vascular cell:'''
−
−	~~=Upcoming meetings 2011:=~~
−
−	~~'''Botany 2011 Meeting [[http://www.botanyconference.org/ Botany 2011]]''' St. Louis, MO at the Chase Park Plaza, July 9-13.~~
−
−	~~Societies participating:~~
−	~~Society for Economic Botany, the American Fern Society (AFS), the American Society of Plant Taxonomists (ASPT), and the Botanical Society of America (BSA).~~
−
−	~~Anybody going??~~
−
−
−	~~'''* 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]~~
−
−
−	~~For inclusion on the program memory stick and in the program book, abstracts must be submitted by '''May 27'''.~~
−
−	~~Gramene will be putting together a workshop again, focusing on pathways. LC and PJ will present a PO poster.~~
−
−	~~TAIR (Kate Dreher) is organizing an Outreach Booth and we are invited to take part.~~
−
−
−
−
−	~~'''* International Botanical Congress (IBC2011)'''~~
−
−	~~July 23rd-30th 2011, Melbourne, Australia'''~~
−
−	~~Registration is open [http://www.ibc2011.com/Dates.htm 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~~

← Older revision		Revision as of 18:10, 24 June 2011
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	Acceptance of the minutes from the [[POC_Conf._Call_6-7-11]]?		Acceptance of the minutes from the [[POC_Conf._Call_6-7-11]]?

−
−
−	~~==Report from the[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].~~

@@ Line 31: / Line 31: @@
-==conductive tissue for bryophytes and vascular plants==
+=conductive tissue for bryophytes and vascular plants=
 trace as possible name for category for veins, central strands, and costas
@@ Line 191: / Line 193: @@
 Sperry 2003, IJPS; Hebant 1977;
 =Conductive cells and tissues for vascular and non-vascular plants=

← Older revision		Revision as of 14:29, 15 June 2011
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	'''vascular cell:'''		'''vascular cell:'''
−
−	~~=User requests still open on Source Forge; PGDSO =~~
−	~~==[https://sourceforge.net/tracker/index.php?func=detail&aid=3035688&group_id=76834&atid=835555 terms for seed trichome development stages]==~~
−
−	~~This is a fairly new request for terms for cotton fiber development~~
−
−
−
−	~~==[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~~
−

	=Upcoming meetings 2011:=		=Upcoming meetings 2011:=

← Older revision		Revision as of 13:58, 15 June 2011
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	submitted by Rich Zobel (Nov 2009)		submitted by Rich Zobel (Nov 2009)
−
−
−	~~==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).~~
−
−
−	~~[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]~~
−
−	~~Their comment: is synonym to Tubercle~~
−
−	~~podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.~~
−
−	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).
−
−	~~proposed def:~~
−
−
−	~~[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~~
−
−	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.
−
−
−
−	~~[https://sourceforge.net/tracker/?func=detail&aid=3080916&group_id=76834&atid=835555 diaspore]~~
−
−	~~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)~~
−
−
−	~~[https://sourceforge.net/tracker/?func=detail&aid=3080919&group_id=76834&atid=835555 cone]~~
−
−	~~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]~~
−
−	~~from Crum (2001): a cluster of fern sporangia~~
−	~~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.~~
−
−	~~Part_of vascular leaf, has_part sporangium~~
−
−
−	~~[https://sourceforge.net/tracker/?func=detail&aid=3080925&group_id=76834&atid=835555 tendril]~~
−
−	~~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.~~
−
−	~~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.~~
−
−	~~leaf apex tendril (child of leaf apex): A leaf apex that is slender and coiling. Comment: Aids plant in climbing.~~
−
−	~~Can add other types of tendrils if they come up or users need them.~~
−