Difference between revisions of "Wood Ontology PO and GO Term Development"
| Line 9: | Line 9: | ||
==Terms already in PO that need work== | ==Terms already in PO that need work== | ||
| − | === | + | ===[https://sourceforge.net/tracker/index.php?func=detail&aid=3314764&group_id=76834&atid=835555 fascicular and interfascicular cambium]=== |
| + | |||
| + | Part of the cambium develops from the procambium, but part of it develops from parenchyma cells in the interfascicular region. Already have separate terms for fascicular and interfascicular cambium. May need to add a term that combines the two of them for wood. | ||
| − | + | Only in shoot axes? | |
| − | |||
| − | + | '''fascicular cambium (PO:0006200):''' Vascular cambium originating from procambium within vascular bundles or fascicles. [source: ISBN:047124529] | |
| + | '''proposed def., interfascicular cambium:''' A portion of ''shoot axis'' vascular cambium that develops from a procambium in a vascular bundle. | ||
| − | + | comment: Portions of fascicular cambium may merge with the fascicular cambium from adjacent vascular bundles or the interfascular fascicular cambium to form a cylinder of cambium, or they may remain isolated. | |
| − | |||
| + | '''interfascicular cambium (PO:0006201):''' Vascular cambium arising between vascular bundles or fascicles, in the interfascicular parenchyma or pith. [source: ISBN:047124529] | ||
| − | + | Should refer to the interfascicular region (PO:0006202). | |
| + | '''proposed def., interfascicular cambium:''' A portion of ''shoot axis'' vascular cambium that develops ''from a parenchyma cell or meristematic cell'' in an interfascicular region (PO:0006202). | ||
| − | + | comment: Portions of interfascicular cambium may merge with the fascicular cambium to form a cylinder of cambium or they may remain isolated. | |
| − | |||
| + | '''other cambium terms:''' | ||
| − | + | '''included vascular cambium (PO:0004523):''' Cambium occurring within xylem. | |
| − | + | '''proposed def., included vascular cambium:''' A portion of cambium tissue that is located in a portion of ''secondary'' xylem. | |
| − | + | comment: | |
| − | + | '''outer vascular cambium (PO:0004522):''' Cambium at the outer margin of the xylem cylinder. | |
| − | |||
| − | ''' | + | See below for new term for '''storied cambium'''. |
| − | + | ===xylem and phloem mother cells=== | |
| + | '''phloem mother cell (PO:0000400), current def.:''' A cambial initial cell which is destined to differentiate into secondary phloem. | ||
| + | Comment: Phloem islands can be formed in the middle of the xylem. | ||
| − | + | is_a cambial initial cell, part_of secondary phloem | |
| − | |||
| − | + | From IAWA glossary: | |
| − | + | phloem mother cell: Cells that are cut off on the inner side by the fusform cabial initials, but which undergo further periclinal divisions before differentiating into phloem cells. | |
| − | + | xylem mother cells: A cell that is cut off on the outer side by a fusform cabial initial, but which undergoes further periclinal division before differentiating into a xylem cell. | |
| − | |||
| + | Can it be used for primary phloem too? Also, phloem mother cell and xylem mother cell are not initial cells. | ||
| − | '' | + | (''Add POid for xylem mother cell to definition of cell division stage of secondary xylem (PO:0025463) once we add it.'') |
===types of upright ray secondary xylem parenchyma cell=== | ===types of upright ray secondary xylem parenchyma cell=== | ||
Revision as of 17:16, 1 June 2012
Background
See Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda and Goal_1._Anatomical_Entities.
Also, may have a few more terms from Goal_2._Plant_Structure_Development_Stages.
Anatomy and morphology terms from PO
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.
Terms already in PO that need work
fascicular and interfascicular cambium
Part of the cambium develops from the procambium, but part of it develops from parenchyma cells in the interfascicular region. Already have separate terms for fascicular and interfascicular cambium. May need to add a term that combines the two of them for wood.
Only in shoot axes?
fascicular cambium (PO:0006200): Vascular cambium originating from procambium within vascular bundles or fascicles. [source: ISBN:047124529]
proposed def., interfascicular cambium: A portion of shoot axis vascular cambium that develops from a procambium in a vascular bundle.
comment: Portions of fascicular cambium may merge with the fascicular cambium from adjacent vascular bundles or the interfascular fascicular cambium to form a cylinder of cambium, or they may remain isolated.
interfascicular cambium (PO:0006201): Vascular cambium arising between vascular bundles or fascicles, in the interfascicular parenchyma or pith. [source: ISBN:047124529]
Should refer to the interfascicular region (PO:0006202).
proposed def., interfascicular cambium: A portion of shoot axis vascular cambium that develops from a parenchyma cell or meristematic cell in an interfascicular region (PO:0006202).
comment: Portions of interfascicular cambium may merge with the fascicular cambium to form a cylinder of cambium or they may remain isolated.
other cambium terms:
included vascular cambium (PO:0004523): Cambium occurring within xylem.
proposed def., included vascular cambium: A portion of cambium tissue that is located in a portion of secondary xylem.
comment:
outer vascular cambium (PO:0004522): Cambium at the outer margin of the xylem cylinder.
See below for new term for storied cambium.
xylem and phloem mother cells
phloem mother cell (PO:0000400), current def.: A cambial initial cell which is destined to differentiate into secondary phloem.
Comment: Phloem islands can be formed in the middle of the xylem.
is_a cambial initial cell, part_of secondary phloem
From IAWA glossary:
phloem mother cell: Cells that are cut off on the inner side by the fusform cabial initials, but which undergo further periclinal divisions before differentiating into phloem cells.
xylem mother cells: A cell that is cut off on the outer side by a fusform cabial initial, but which undergoes further periclinal division before differentiating into a xylem cell.
Can it be used for primary phloem too? Also, phloem mother cell and xylem mother cell are not initial cells.
(Add POid for xylem mother cell to definition of cell division stage of secondary xylem (PO:0025463) once we add it.)
types of upright ray secondary xylem parenchyma cell
sheath cell (PO:0004531), current def.: Cell on the margin of, and tending to form a sheath around, the procumbent cells of a multi-seriate ray as seen in tangential section.
from IAWA: One of a series of upright cells (>Ray cell, upright) on the margins of, and tending to form a sheath around, the procumbent cells of a multi-seriate ray as seen in tangential section.
tile cell (PO:0004530), current def.: Empty upright ray cell of approximately the same height as the procumbent ray cell and occurring in indeterminate horizontal series usually interspersed among the
from IAWA: A special type of apparently empty upright ray cell of approximately the same height as the procumbent ray cells and occurring in indeterminate horizontal series usually interspersed among the procumbent cells. Note: Common in certain of the Tiliales and Malvales.
New terms to request in PO
aggregate ray (also maybe homogenous, heterogenous, uniseriate, multiseriate, fusiform rays)
storied cambium and ray
storied: A term applied to the axial cells and rays in wood when these are arranged in horizontal series on tangential survaces. Note: the term is applied to particular tissues, e.g., "storied parenchyma" or used in a general sense, as in "wood with storied structure". The presence of storied structure is the cause of the ripple marks visible with the unaided eye.
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
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
inner and outer bark
terms for how vessels and parenchyma are arranged in wood (e.g., vascicentric)
Anatomy terms from GO
Terms already in GO that need work
New terms to request in 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.
