Difference between revisions of "Goal 1. Anatomical Entities"

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'''This page is under construction.'''
 
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Back to [[Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda]]
 
Back to [[Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda]]
  
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=Review existing anatomy/morphology terms and definitions=
+
=1. Review existing anatomy/morphology terms and definitions=
 
==Cell types related to wood==
 
==Cell types related to wood==
 +
===tracheary elements===
 +
*tracheary element (PO:0000290)
 +
*tracheid (PO:0000301) ''need to make it clearer that a perforation is a specific anatomical entity, not just some random hole.
 +
*vessel member (PO:0002003) ''vessel element should be primary name and vessel segment should be a related, not exact, synonym''
 +
 +
===fiber cells===
 +
*sclerenchyma cell (PO:0000077) - parent term
 +
*fiber cell (PO:0025407)
 +
*phloem fiber cell (PO:0004519)
 +
*xylem fiber cell (PO:0000274)
 +
*libriform fiber cell (PO:0004520)
 +
*fiber tracheid (PO:0000355)
 +
*gelatious fiber cell (PO:0025422)
 +
 +
===sieve elements (PO:0025406)===
 +
*sieve cell (PO:0025415)
 +
*sieve tube member (PO:0000289)
 +
====New terms for GO====
 +
These subcellular components have been added to GO:
 +
*GO:0097217 sieve area
 +
*GO:0097218 sieve plate
 +
*GO:0097219 compound sieve plate
 +
*GO:0097220 simple sieve plate
 +
*perforation plate (requested)
 +
 +
===initial cells (PO:0004011)===
 +
*cambial initial
 +
*fusiform initial (PO:0000079) (syn.: xylem initial, xylem mother cell) ''Need to work on this term. May be better as synonym of cambial initial. Xylem mother cell should not be  a synonym, but should be a separate term.''
 +
*ray initial (PO:0000082)
 +
*phloem mother cell (PO:0000400)
  
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===sieve elements===
+
===wood parenchyma cells (PO:0004525)===
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Definitions from Esau's Anatomy of Seed Plants
+
*axial wood parenchyma cell (PO:0004526)
 +
*ray wood parenchyma cell(PO:0004527)
 +
*procumbent ray wood parenchyma cell (PO:0004529) ''add synonym: procumbent cell''
 +
*upright ray wood parenchyma cell (PO:0004528) ''add synonym: upright cell''
 +
*sheath cell (PO:0004531)
 +
*tile cell (PO:0004530)
  
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'''sieve element (PO:0025406):''' A plant cell (PO:0009002) that is part of a portion of phloem (PO:0005417) tissue, has sieve areas (modified pits) in its walls, and lacks a nucleus in its mature protoplast.
+
*companion cell (PO:0000071)
 +
*albuminous cell (PO:0025412)
  
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Comment: Sieve elements function mainly in longitudinal conduction of organic solutes. Classified into sieve cells (PO:0025415) and sieve tube members (PO:0000289) based on the presence of sieve plates (GO:0097218) and specialization of sieve areas (GO:0097217) in different parts of the cell. Develops from either a cambial initial (PO:0000295) or a procambial cell (PO:0025258).
+
==Tissue types related to wood==
 +
===portion of vascular tissue (PO:0009015)===
 +
====xylem (PO:0005352)====
 +
*vessel (PO:0025417)
  
−
part_of phloem, participates_in sporophyte stage
+
*primary xylem (PO:0005849)
 +
*protoxylem (PO:0000272)
 +
*metaxylem (PO:0000372)
  
 +
*secondary xylem (PO:0005848) ''add comments that ducts are part of secondary xylem''
 +
*heartwood (PO:0004512)
 +
*sapwood (PO:0004513) ''add comment that both conduction and storage take place here''
 +
*growth ring (PO:0004514) ''add annual ring as narrow synonym''
 +
*early wood (PO:0004515)
 +
*late wood (PO:0004516)
  
−
'''sieve cell (PO:0025415):''' A sieve element in which the sieve areas are not aggregated into sieve plates.
+
*growth ring boundary (PO:0004517)
  
−
Comment: Sieve areas in sieve cells generally have narrow pores and thin connecting strands, and they are not highly specialized, but instead are fairly uniform throughout the cell wall. Typical of gymnosperms and non-seed vascular plants. Differ from sieve tube members, which have sieve plates and more pronounced specialization of sieve areas. 
+
====phloem (PO:0005417)====
 +
*sieve tube (PO:0025416)
  
 +
*primary phloem (PO:0006075)
 +
*protophloem (PO:0006077)
 +
*metaphloem (PO:0006076)
 +
*internal phloem (PO:0006216)
  
−
'''sieve tube member (PO:0000289):''' A sieve element that is part of a sieve tube and has sieve areas aggregated into sieve plates.
+
*secondary phloem (PO:0005043) ''also, inner bark. See paper by Junika 87''
 +
*included phloem (PO:0004524)
  
−
Comment: Sieve tube members have sieve areas that are specialized into those with wide pores in sieve plates and those with with narrow pores in lateral sieve areas. Sieve tube members may have inclined end walls with compound or simple sieve plates. Typical of angiosperms. Differ from sieve cells, which have less pronounced specialization of sieve areas and no sieve plates.
+
===wood parenchyma (PO:0004532)===
 +
*axial wood parenchyma (PO:0004533)
 +
*ray wood parenchyma (PO:0004534)
  
−
syn.: sieve tube element, sieve tube segment
+
===lateral meristem (PO:0020145)===
 +
*cambium (PO:0005597) ''should specifically refer to a ring of initials (actually, it does this, because it talks about a single layer of cells). Also add  term for cambial zone, as a cardinal organ part, because it is not always clear which cells are the initials and there is a gradient of differentiation.''
 +
*cork cambium (PO:0005599)
 +
*vascular cambium (PO:0005598)
 +
 
 +
===systems===
 +
*vascular system (PO:0000034) is_a plant structure
 +
*axial system (PO:0025410)
 +
*ray system (PO:0025411)
 +
 
 +
=2. Develop list of anatomy/morphology terms that are missing=
 +
Do we need only wood-related terms, or other terms for woody plants?
 +
''Will also need terms for some structures found in gymnosperms, such as reproductive structures.''
 +
 
 +
See new page for [[Wood Ontology PO and GO Term Development]].
 +
 
 +
==wood related term suggestions==
 +
===Terms for PO:===
 +
 
 +
reaction wood/tension wood/compression wood - review by Wilson and Archer
 +
 
 +
aggregate ray (also maybe homogenous, heterogenous, uniseriate, multiseriate, fusiform rays)
 +
 
 +
storied cambium and ray
 +
 
 +
non-storied cambium and ray
 +
 
 +
aggregate ray, homogenous or heterogeneous, uniseriate, multiseriate
 +
 
 +
oil cell
 +
 
 +
ray tracheid
 +
 
 +
traumatic resin
 +
 
 +
(apotracheal, paratracheal, marginal, aliform, confluent) axial parenchyma
 +
 
 +
read review of laticifer cells by Pickering
 +
 
 +
knot loose and tight
 +
 
 +
interfascicular cambium
 +
 
 +
vascular bundle types - amphicentric, vasicentric, medulary
 +
 
 +
inter- and intra-xylary phloem
 +
 
 +
successive cambium
 +
 
 +
epithelium cell
 +
 
 +
ray tracheid and subtypes
 +
 
 +
cambial zone
 +
 
 +
square cell
 +
 
 +
axial parenchyma strands
 +
 
 +
resin canal
 +
 
 +
pith flecks (maybe)
 +
 
 +
breakdown ray area
 +
 
 +
cambial zone
 +
 
 +
xylem mother cell, and work on definition of phloem mother cell and cambial initial
 +
 
 +
inner and outer bark
 +
 
 +
terms for how vessels and parenchyma are arranged in wood (e.g., vascicentric)
 +
 
 +
===Terms for GO:===
 +
 
 +
pit, pit types, torus, margo, simple, membrane types, tyloses etc.,
 +
 
 +
casparian strip
 +
 
 +
mineral inclusions: calcium oxalate, silica, druses
  
−
part_of sieve tube
 
  
−
====New terms for GO====
 
−
These subcellular components have been added to GO:
 
  
−
*GO:0097217 sieve area
+
See good description in Eames, also see Esau.
−
*GO:0097218 sieve plate
 
−
*GO:0097219 compound sieve plate
 
−
*GO:0097220 simple sieve plate
 
  
−
'''sieve area:''' A cell wall part that is a pit-like area in a plant-type cell wall of a sieve element and has as parts pores lined with callose and occupied by strands of protoplasmic material that interconnect the protoplasts of contiguous sieve elements.
 
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505); part_of sieve element (PO:xxxx) - may have to go in comment
+
plant secondary cell wall pit: A cavity in a plant secondary cell wall with an pit membrane, open internally to the lumen.
  
 +
primary cell wall pit: An area of a primary plant cell wall is thin.
  
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'''sieve plate:''' A cell wall part that is the part of a wall of a sieve tube member that bears one or more highly specialized sieve areas.
+
The primary wall of the adjacent cell is also thin in the same place.
  
−
comment: Typical of angiosperms.
 
  
−
is_a cell wall part (GO:0044426), part_of plant-type cell wall (GO:0009505), has_part sieve area (GO:xxxx); part_of sieve tube member (PO:xxxx).
+
Except blind pit, which is only on one side.
  
−
Could add the relation callose deposition in phloem sieve plate (GO:0080165) inheres_in sieve plate.
 
  
 +
pit membrane
  
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'''compound sieve plate:''' A sieve plate that has as parts several specialized sieve areas in either a scalariform or reticulate arrangement.
+
simple pit
  
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comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
bordered pit
  
−
is_a sieve plate
+
primary pit field
  
  
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'''simple sieve plate:''' A sieve plate that has as part a single specialized sieve area.
+
perforation: the opening between two vessel elements
  
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comment: Often located on an end wall of a sieve tube member. Unspecialized sieve areas may occur on other parts of the cell.
+
intrusive growth
  
−
==Vascular tissues==
+
cambial dormancy (or just add stage)
  
−
==Cambia==
+
==other suggestions==
 +
Add term '''xylem cell''' and '''phloem cell'''  -- XP of cell and part_of xylem of phloem. Can't create terms for secondary xylem or secondary phloem cells, because most of the cell types can appear in both primary and secondary vascular tissue.
  
−
=Develop list of anatomy/morphology terms that are missing=
+
Xylem cell should be linked to the definition of pulp and paper (useful for TO)
−
Do we need only wood-related terms, or other terms for woody plants?
 
  
−
=Work on definitions of new terms=
+
Terms for gum/latex/resin? Too broadly defined. Could look up specific definitions in ethnobotanical literature, but people may not use them consistently.

Latest revision as of 15:18, 1 May 2012

Back to Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda

1. Review existing anatomy/morphology terms and definitions

Cell types related to wood

tracheary elements

  • tracheary element (PO:0000290)
  • tracheid (PO:0000301) need to make it clearer that a perforation is a specific anatomical entity, not just some random hole.
  • vessel member (PO:0002003) vessel element should be primary name and vessel segment should be a related, not exact, synonym

fiber cells

  • sclerenchyma cell (PO:0000077) - parent term
  • fiber cell (PO:0025407)
  • phloem fiber cell (PO:0004519)
  • xylem fiber cell (PO:0000274)
  • libriform fiber cell (PO:0004520)
  • fiber tracheid (PO:0000355)
  • gelatious fiber cell (PO:0025422)

sieve elements (PO:0025406)

  • sieve cell (PO:0025415)
  • sieve tube member (PO:0000289)

New terms for GO

These subcellular components have been added to GO:

  • GO:0097217 sieve area
  • GO:0097218 sieve plate
  • GO:0097219 compound sieve plate
  • GO:0097220 simple sieve plate
  • perforation plate (requested)

initial cells (PO:0004011)

  • cambial initial
  • fusiform initial (PO:0000079) (syn.: xylem initial, xylem mother cell) Need to work on this term. May be better as synonym of cambial initial. Xylem mother cell should not be a synonym, but should be a separate term.
  • ray initial (PO:0000082)
  • phloem mother cell (PO:0000400)

wood parenchyma cells (PO:0004525)

  • axial wood parenchyma cell (PO:0004526)
  • ray wood parenchyma cell(PO:0004527)
  • procumbent ray wood parenchyma cell (PO:0004529) add synonym: procumbent cell
  • upright ray wood parenchyma cell (PO:0004528) add synonym: upright cell
  • sheath cell (PO:0004531)
  • tile cell (PO:0004530)
  • companion cell (PO:0000071)
  • albuminous cell (PO:0025412)

Tissue types related to wood

portion of vascular tissue (PO:0009015)

xylem (PO:0005352)

  • vessel (PO:0025417)
  • primary xylem (PO:0005849)
  • protoxylem (PO:0000272)
  • metaxylem (PO:0000372)
  • secondary xylem (PO:0005848) add comments that ducts are part of secondary xylem
  • heartwood (PO:0004512)
  • sapwood (PO:0004513) add comment that both conduction and storage take place here
  • growth ring (PO:0004514) add annual ring as narrow synonym
  • early wood (PO:0004515)
  • late wood (PO:0004516)
  • growth ring boundary (PO:0004517)

phloem (PO:0005417)

  • sieve tube (PO:0025416)
  • primary phloem (PO:0006075)
  • protophloem (PO:0006077)
  • metaphloem (PO:0006076)
  • internal phloem (PO:0006216)
  • secondary phloem (PO:0005043) also, inner bark. See paper by Junika 87
  • included phloem (PO:0004524)

wood parenchyma (PO:0004532)

  • axial wood parenchyma (PO:0004533)
  • ray wood parenchyma (PO:0004534)

lateral meristem (PO:0020145)

  • cambium (PO:0005597) should specifically refer to a ring of initials (actually, it does this, because it talks about a single layer of cells). Also add term for cambial zone, as a cardinal organ part, because it is not always clear which cells are the initials and there is a gradient of differentiation.
  • cork cambium (PO:0005599)
  • vascular cambium (PO:0005598)

systems

  • vascular system (PO:0000034) is_a plant structure
  • axial system (PO:0025410)
  • ray system (PO:0025411)

2. Develop list of anatomy/morphology terms that are missing

Do we need only wood-related terms, or other terms for woody plants? Will also need terms for some structures found in gymnosperms, such as reproductive structures.

See new page for Wood Ontology PO and GO Term Development.

wood related term suggestions

Terms for PO:

reaction wood/tension wood/compression wood - review by Wilson and Archer

aggregate ray (also maybe homogenous, heterogenous, uniseriate, multiseriate, fusiform rays)

storied cambium and ray

non-storied cambium and ray

aggregate ray, homogenous or heterogeneous, uniseriate, multiseriate

oil cell

ray tracheid

traumatic resin

(apotracheal, paratracheal, marginal, aliform, confluent) axial parenchyma

read review of laticifer cells by Pickering

knot loose and tight

interfascicular cambium

vascular bundle types - amphicentric, vasicentric, medulary

inter- and intra-xylary phloem

successive cambium

epithelium cell

ray tracheid and subtypes

cambial zone

square cell

axial parenchyma strands

resin canal

pith flecks (maybe)

breakdown ray area

cambial zone

xylem mother cell, and work on definition of phloem mother cell and cambial initial

inner and outer bark

terms for how vessels and parenchyma are arranged in wood (e.g., vascicentric)

Terms for GO:

pit, pit types, torus, margo, simple, membrane types, tyloses etc.,

casparian strip

mineral inclusions: calcium oxalate, silica, druses


See good description in Eames, also see Esau.


plant secondary cell wall pit: A cavity in a plant secondary cell wall with an pit membrane, open internally to the lumen.

primary cell wall pit: An area of a primary plant cell wall is thin.

The primary wall of the adjacent cell is also thin in the same place.


Except blind pit, which is only on one side.


pit membrane

simple pit

bordered pit

primary pit field


perforation: the opening between two vessel elements

intrusive growth

cambial dormancy (or just add stage)

other suggestions

Add term xylem cell and phloem cell -- XP of cell and part_of xylem of phloem. Can't create terms for secondary xylem or secondary phloem cells, because most of the cell types can appear in both primary and secondary vascular tissue.

Xylem cell should be linked to the definition of pulp and paper (useful for TO)

Terms for gum/latex/resin? Too broadly defined. Could look up specific definitions in ethnobotanical literature, but people may not use them consistently.

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