Difference between revisions of "Wood Ontology PO and GO Term Development"
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Need to look at definition. I think it can be used for primary phloem too. Also, phloem mother cell and xylem mother cell are not initial cells. | Need to look at definition. I think it can 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 | + | (''Add POid for xylem mother cell to definition of cell division stage of secondary xylem (PO:0025463) once we add it.'') |
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| + | interfascicular cambium (PO:0006201): Vascular cambium arising between vascular bundles or fascicles, in the interfascicular parenchyma or pith. [source: ISBN:047124529] | ||
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| + | fascicular cambium (PO:0006200): Vascular cambium originating from procambium within vascular bundles or fascicles. [source: ISBN:047124529] | ||
==New terms to request in PO== | ==New terms to request in PO== | ||
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knot loose and tight | knot loose and tight | ||
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vascular bundle types - amphicentric, vasicentric, medulary | vascular bundle types - amphicentric, vasicentric, medulary | ||
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breakdown ray area | breakdown ray area | ||
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inner and outer bark | inner and outer bark | ||
Revision as of 11:53, 31 May 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
phloem mother cell
Need to look at definition. I think it can 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.)
interfascicular cambium (PO:0006201): Vascular cambium arising between vascular bundles or fascicles, in the interfascicular parenchyma or pith. [source: ISBN:047124529]
fascicular cambium (PO:0006200): Vascular cambium originating from procambium within vascular bundles or fascicles. [source: ISBN:047124529]
New terms to request in 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
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.
