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

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.)

cambium development

From the POC meeting on 2/15/2011: Need to revisit cambium/vascular cambium. Cannot just add relation vascular cambium develops_from procambium (that is, from the procambial strands), because part of it develops from the procambium, but part of it develops from parenchyma cells in the interfascicular region. Probably need to add separate terms for fascicular and interfascicular cambium, plus a term that combines the two of them for wood.

Current terms:

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

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.