Wood Ontology PO and GO Term Development

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 and leaves.

Refs: Esau (ISBN:047124529) and Eames and McDaniels (need to add POref)

fascicular cambium (PO:0006200), current def.: Vascular cambium originating from procambium within vascular bundles or fascicles. [source: ISBN:047124529]

proposed def., fascicular cambium: A portion of vascular cambium (PO:0005598) that develops from a procambium (PO:0025275) in a vascular bundle (PO:0005020) that is part of a shoot system (PO:0009006).

comment: Found in shoot axes (PO:0025029) and vascular leaves (PO:0009025). Portions of fascicular cambium may merge with interfascular cambium (PO:0006201) or the fascicular cambium from adjacent vascular bundles to form a cylinder, or they may remain isolated.

interfascicular cambium (PO:0006201), current def.: Vascular cambium arising between vascular bundles or fascicles, in the interfascicular parenchyma or pith. [source: ISBN:047124529]

proposed def., interfascicular cambium: A portion of vascular cambium (PO:00055980) that develops from cells in an interfascicular region (PO:0006202) that is part of a shoot system (PO:0009006).

comment: Portions of interfascicular cambium may merge with fascicular cambium (PO:0006200) to form a cylinder of cambium or they may remain isolated. May develop from meristematic cells (PO:0004010) that have never differentiated into another cell type or from parenchyma cells (PO:0000074) that retain some meristematic ability.

included and outer vascular cambium

included vascular cambium (PO:0004523): Cambium occurring within xylem.

This terms is not used anywhere. Some authors use "included phloem", but even that is used incorrectly, according to Carlquist. Suggest we obsolete this term and replace it with terms such as successive cambium and interxylary phloem (see below).

outer vascular cambium (PO:0004522): Cambium at the outer margin of the xylem cylinder.

This terms is not used anywhere, and it is not clear what it means. A "normal" cambium is found at the outside of a xylem cylinder. Suggest that we obsolete this term.

See below for new term for storied cambium.

shoot lateral meristem (PO:0006344)

We need to revise our definition of shoot lateral meristem, because cambia can be found in leaves as well (often found in petioles).

current def.: A lateral meristem (PO:0020145) that is part of a shoot axis (PO:0025029).

proposed def.: A lateral meristem (PO:0020145) that is part of a shoot system (PO:0009006).

comment: Usually part of a shoot axis (PO:0025029), but also may be part of a vascular leaf (PO:0009025).

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.

currently is_a cambial initial cell, part_of secondary phloem. Should be develops_from cambial initial.

Could also have xylem or phloem mother cells in primary vascular tissue, that develop from procambium. Look into this.

From IAWA glossary:

phloem mother cell: Cells that are cut off on the inner side by the fusiform cambial 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.

Sometimes the term phloem initial is used (e.g., Esau) synonymously with phloem mother cell, but she does distinguish them in her glossary.

proposed def., phloem mother cell: A plant cell that develop from an externa division of a cambial initial cell (PO:0000295) and undergoes further divisions to form sieve elements (PO:0025406) or phloem parenchyma cells (ID) that are part of a portion of secondary phloem (PO:0005043).

Should we add relations for companion cell and sieve element develop from phloem mother cell?

Can cells of secondary phloem develop directly from VC without further division? If so, then we can't say sieve element develops from phloem mother cell.

proposed def., xylem mother cell: A plant cell that develops from an internal division of a cambial initial cell (PO:0000295) and undergoes further divisions to form tracheary elements (PO:0000290), secondary xylem parenchyma cells (PO:0004525), or xylem fiber cells (PO:0000274) that are part of a portion of secondary phloem (PO:0005043).

(Add POid for xylem mother cell to definition of cell division stage of secondary xylem (PO:0025463) once we add it.)

Subtypes of upright ray secondary xylem parenchyma cell (PO:0004528)

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.

"What does it mean, "tending to form a sheath"?

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

phloem parenchyma cell, proposed def.,: A parenchyma cell (PO:0000074) that is part of a portion of phloem tissue (PO:0005417).

• Parent to companion cell and albuminous cell, plus other phloem parenchyma cells.
• Do we want a separate term for secondary phloem parenchyma cell?

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. (From IAWA glossary).

non-storied cambium and ray

aggregate ray, homogenous or heterogeneous, uniseriate, biseriate, multiseriate, fusiform

oil cell

ray tracheid

traumatic resin resin that comes to a wound. Resin cell, traumatic resin cell.

(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

interxylary - when xylem and phloem are produced in sort of alternating strands

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

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.