Goal 1. Anatomical Entities

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)
• 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)
• 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)
• upright ray wood parenchyma cell (PO:0004528)
• 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)
• heartwood (PO:0004512)
• sapwood (PO:0004513)
• growth ring (PO:0004514)
• 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)
• 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)
• 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?

wood related term suggestions

Terms for PO:

reaction wood

tension wood

compression wood

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

storied cambium

non-storied cambium and rays

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

inter- and intra-xylary phloem

successive cambium

epithelium cell

ray tracheid and subtypes

cambial zone

square cell

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

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.