Difference between revisions of "Goal 1. Anatomical Entities"
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===tracheary elements=== | ===tracheary elements=== | ||
*tracheary element (PO:0000290) | *tracheary element (PO:0000290) | ||
| − | *tracheid (PO:0000301) | + | *tracheid (PO:0000301) ''need to make it clearer that a perforation is a specific anatomical entity, not just some random hole. |
| − | *vessel member (PO:0002003) | + | *vessel member (PO:0002003) ''vessel element should be primary name and vessel segment should be a related, not exact, synonym'' |
===fiber cells=== | ===fiber cells=== | ||
| Line 30: | Line 30: | ||
===initial cells (PO:0004011)=== | ===initial cells (PO:0004011)=== | ||
*cambial initial | *cambial initial | ||
| − | *fusiform initial (PO:0000079) (syn.: xylem initial, xylem mother cell) | + | *fusiform initial (PO:0000079) (syn.: xylem initial, xylem mother cell) ''Need to work on this term. May be better as synonym of cambial initial. Xylem mother cell should not be a synonym, but should be a separate term.'' |
*ray initial (PO:0000082) | *ray initial (PO:0000082) | ||
*phloem mother cell (PO:0000400) | *phloem mother cell (PO:0000400) | ||
| Line 37: | Line 37: | ||
*axial wood parenchyma cell (PO:0004526) | *axial wood parenchyma cell (PO:0004526) | ||
*ray wood parenchyma cell(PO:0004527) | *ray wood parenchyma cell(PO:0004527) | ||
| − | *procumbent ray wood parenchyma cell (PO:0004529) | + | *procumbent ray wood parenchyma cell (PO:0004529) ''add synonym: procumbent cell'' |
| − | *upright ray wood parenchyma cell (PO:0004528) | + | *upright ray wood parenchyma cell (PO:0004528) ''add synonym: upright cell'' |
*sheath cell (PO:0004531) | *sheath cell (PO:0004531) | ||
*tile cell (PO:0004530) | *tile cell (PO:0004530) | ||
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*metaxylem (PO:0000372) | *metaxylem (PO:0000372) | ||
| − | *secondary xylem (PO:0005848) | + | *secondary xylem (PO:0005848) ''add comments that ducts are part of secondary xylem'' |
*heartwood (PO:0004512) | *heartwood (PO:0004512) | ||
| − | *sapwood (PO:0004513) | + | *sapwood (PO:0004513) ''add comment that both conduction and storage take place here'' |
| − | *growth ring (PO:0004514) | + | *growth ring (PO:0004514) ''add annual ring as narrow synonym'' |
*early wood (PO:0004515) | *early wood (PO:0004515) | ||
*late wood (PO:0004516) | *late wood (PO:0004516) | ||
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*internal phloem (PO:0006216) | *internal phloem (PO:0006216) | ||
| − | *secondary phloem (PO:0005043) | + | *secondary phloem (PO:0005043) ''also, inner bark. See paper by Junika 87'' |
*included phloem (PO:0004524) | *included phloem (PO:0004524) | ||
| Line 79: | Line 79: | ||
===lateral meristem (PO:0020145)=== | ===lateral meristem (PO:0020145)=== | ||
| − | *cambium (PO:0005597) | + | *cambium (PO:0005597) ''should specifically refer to a ring of initials (actually, it does this, because it talks about a single layer of cells). Also add term for cambial zone, as a cardinal organ part, because it is not always clear which cells are the initials and there is a gradient of differentiation.'' |
*cork cambium (PO:0005599) | *cork cambium (PO:0005599) | ||
*vascular cambium (PO:0005598) | *vascular cambium (PO:0005598) | ||
| Line 90: | Line 90: | ||
=2. Develop list of anatomy/morphology terms that are missing= | =2. Develop list of anatomy/morphology terms that are missing= | ||
Do we need only wood-related terms, or other terms for woody plants? | 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.'' | ||
| + | |||
| + | See new page for [[Wood Ontology PO and GO Term Development]]. | ||
==wood related term suggestions== | ==wood related term suggestions== | ||
===Terms for PO:=== | ===Terms for PO:=== | ||
| − | reaction wood | + | 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 | |
| − | storied cambium | + | non-storied cambium and ray |
| − | + | aggregate ray, homogenous or heterogeneous, uniseriate, multiseriate | |
oil cell | oil cell | ||
| Line 120: | Line 121: | ||
interfascicular cambium | interfascicular cambium | ||
| − | vascular bundle types | + | vascular bundle types - amphicentric, vasicentric, medulary |
inter- and intra-xylary phloem | inter- and intra-xylary phloem | ||
| Line 134: | Line 135: | ||
square cell | square cell | ||
| + | axial parenchyma strands | ||
| + | |||
| + | resin canal | ||
| + | |||
| + | pith flecks (maybe) | ||
| + | |||
| + | breakdown ray area | ||
| + | |||
| + | cambial zone | ||
| + | |||
| + | xylem mother cell, and work on definition of phloem mother cell and cambial initial | ||
| + | |||
| + | inner and outer bark | ||
| + | |||
| + | terms for how vessels and parenchyma are arranged in wood (e.g., vascicentric) | ||
===Terms for GO:=== | ===Terms for GO:=== | ||
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casparian strip | casparian strip | ||
| − | mineral inclusions: calcium oxalate, silica | + | 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. | |
Latest revision as of 15:18, 1 May 2012
Back to Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda
1. Review existing anatomy/morphology terms and definitions
tracheary elements
- tracheary element (PO:0000290)
- tracheid (PO:0000301) need to make it clearer that a perforation is a specific anatomical entity, not just some random hole.
- 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) Need to work on this term. May be better as synonym of cambial initial. Xylem mother cell should not be a synonym, but should be a separate term.
- 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) add synonym: procumbent cell
- upright ray wood parenchyma cell (PO:0004528) add synonym: upright cell
- sheath cell (PO:0004531)
- tile cell (PO:0004530)
- companion cell (PO:0000071)
- albuminous cell (PO:0025412)
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) add comments that ducts are part of secondary xylem
- heartwood (PO:0004512)
- sapwood (PO:0004513) add comment that both conduction and storage take place here
- growth ring (PO:0004514) add annual ring as narrow synonym
- 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) also, inner bark. See paper by Junika 87
- 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) should specifically refer to a ring of initials (actually, it does this, because it talks about a single layer of cells). Also add term for cambial zone, as a cardinal organ part, because it is not always clear which cells are the initials and there is a gradient of differentiation.
- 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? Will also need terms for some structures found in gymnosperms, such as reproductive structures.
See new page for Wood Ontology PO and GO Term Development.
Terms for 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
interfascicular cambium
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
cambial zone
xylem mother cell, and work on definition of phloem mother cell and cambial initial
inner and outer bark
terms for how vessels and parenchyma are arranged in wood (e.g., vascicentric)
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
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.
