cell type node
Katica Ilic
katica at acoma.Stanford.EDU
Wed Mar 31 22:00:25 EST 2004
Hello all,
Here is my cell type node (anatomy and definition file). So far, 70 terms,
with definitions mostly from K Esau. Please take a look, if it's good (as
I believe so), I'll import it to the anatomy ontology. IDs are temporary,
all the terms will have proper PO ID numbers once I import this node to
PO file.
Pankaj and Felipe, thanks for the earlier comments. Please, delete the old
version, this one has more hierarchy.
A short question: Are epithem cell and epithelium cell children of
secretory cell?
Katica
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Katica Ilic katica at acoma.stanford.edu
The Arabidopsis Information Resource Tel: (650) 325-1521 ext. 253
Carnegie Institution of Washington FAX: (650) 325-6857
Department of Plant Biology URL: http://arabidopsis.org/
260 Panama St.
Stanford, CA 94305
U.S.A.
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!version: $Revision: 1.24 $
!date: Wed Mar 31 18:15:51 PST 2004
!saved-by: Katica Ilic
!autogenerated-by: DAG-Edit version 1.410
!
!Gene Ontology definitions
!
term: antipodal cell
goid: TAIR:0000192
definition: cells located at the chalazal end of the mature embryo sac in angiosperms
definition_reference: ISBN:047125208
term: apical cell
goid: KI:0004000
definition: The single cell that occupies the distal position in an apical meristem of root or shoot and is usually interpreted as the initial cell in the apical meristem.
definition_reference: ISBN:0471245208
term: atrichoblast
goid: TAIR:0000263
definition: A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair
definition_reference: ISBN:0387987819
term: axial cell
goid: TAIR:0000081
definition: A secondary vascular cell derived from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system.
definition_reference: ISBN:0471245208
term: bulliform cell
goid: KI:0004001
definition: An enlarged epidermal cell present, with other similar cells, in longitudinal rows in leaves of grasses. Also called motor cell because of its presumed participation in the mechanism of rolling and unrolling of leaves.
definition_reference: ISBN:0471245208
term: cambial initial
goid: TAIR:0000295
definition: Cells so localized in the vascular cambium or phellogen that their periclinal divisions can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells).
definition_reference: ISBN:0471245208
term: central cell
goid: TAIR:0000194
definition: cell type containing the two polar nuclei which, after double fertilization, will develop into the endosperm.
definition_reference: TAIR:lr
term: chlorenchyma cell
goid: TAIR:0000076
definition: Parenchyma cells containng chloroplasts; a component of leaf mesophyll and other green parenchyma tissue.
definition_reference: ISBN:0471245208
term: collenchyma cell
goid: TAIR:0000075
definition: Elongated living cells with unevenly thickened nonlignified primary walls.
definition_reference: ISBN:0471245208
term: companion cell
goid: TAIR:0000071
definition: A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member.
definition_reference: ISBN:0879015322
term: contact cell
goid: KI:0004002
definition: An axial parenchyma or a ray cell physiologically associated with a tracheary element. Also a cell next to a stoma.
definition_reference: ISBN:0471245208
term: cork cell
goid: KI:0004003
definition: A phellem cell derived from the phellogen, nonliving at maturity, and having suberized walls; protective in function because the walls are highly impervious to water.
definition_reference: ISBN:0471245208
term: degenerate megaspore
goid: TAIR:0000245
definition: in monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis.
definition_reference: TAIR:lr
term: egg cell
goid: TAIR:0000190
definition: the female gamete
definition_reference: TAIR:lr
term: epidermal cell
goid: KI:0004013
definition: Cell that constitutes dermal tissue.
definition_reference: TAIR:KI
term: epidermal initial
goid: TAIR:0000349
definition: a relatively unspecialized cell that will give rise to specialized cell types of the epidermis.
definition_reference: TAIR:lr
term: epithelium cell
goid: KI:0004004
definition: A compact layer of cells, often secretory in function, covering a free surface or lining a cavity.
definition_reference: ISBN:0471245208
term: epithem cell
goid: TAIR:0000066
definition: Cells that constitute the mesophyll of a hydathode and are located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap.
definition_reference: PMID:12662305
definition_reference: ISBN:0471245208
term: fiber tracheid
goid: TAIR:0000355
definition: A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures.
definition_reference: ISBN:0471245208
term: filliform apparatus
goid: TAIR:0000193
definition: A complex of cell wall invaginations in a synergid cell similar to those in transfer cells.
definition_reference: ISBN:0471245208
term: functional megaspore
goid: TAIR:0000244
definition: in monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis.
definition_reference: TAIR:lr
term: fusiform initial
goid: TAIR:0000079
definition: An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues.
definition_reference: ISBN:0471245208
term: generative cell
goid: TAIR:0000168
definition: The cell that will give rise to two sperm cells which will participate in double fertilization.
definition_reference: TAIR:KI
term: guard cell
goid: TAIR:0000293
definition: one of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor.
definition_reference: ISBN:0471245208
term: guard mother cell
goid: TAIR:0000351
definition: epidermal cell that that divides to produce the guard cells.
definition_reference: ISBN:0471245208
term: idioblast
goid: TAIR:0000283
definition: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue.
definition_reference: ISBN:0471245208
term: initial cell
goid: KI:0004011
definition: Cell in a meristem that by division gives rise to two cells one of which remains in the meristem, the other is added to the plant body
definition_reference: ISBN:0471245208
term: laticiferous cell
goid: KI:0004005
definition: A specialized cells or ducts resembling vessels; they form branched networks of latex-secreting cells in the phloem and other parts of plants.
definition_reference: :http://academic.kellogg.edu/herbrandsonc/bio111/glossary/glossary.htm
term: megaspore
goid: TAIR:0000243
definition: A haploid (1n) spore developing into a female gametophyte in heterosporous plants.
definition_reference: ISBN:0471245208
term: megasporocyte
goid: TAIR:0000431
definition: A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell.
definition_reference: ISBN:0471245208
term: meristematic cell
goid: KI:0004010
definition: A cell synthesizing protoplasm and producing new cells by division; varies in form, size, wall thickness, and degree of vacuolation, but has only a primary cell wall.
definition_reference: ISBN:0471245208
term: meristemoid
goid: TAIR:0000070
definition: A cell or a group of cells constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells.
definition_reference: TAIR:syr
definition_reference: ISBN:0471245208
term: mesophyll cell
goid: KI:0004006
definition: Cell that constitutes leaf mesophyll.
definition_reference: TAIR:KI
term: microspore
goid: TAIR:0000297
definition: A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants.
definition_reference: ISBN:0471245208
term: microsporocyte
goid: TAIR:0000160
definition: A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell.
definition_reference: ISBN:0471245208
term: mucilage cell
goid: TAIR:0000373
definition: Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water.
definition_reference: ISBN:0471245208
term: myrosin cell
goid: TAIR:0000352
definition: Cell containing glucosinolates ("mustard oil glucosides") and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae.
definition_reference: ISBN:0471245208
term: parenchyma cell
goid: TAIR:0000074
definition: Typically this is a not distinctly specialized cell with a nucleate protoplast concerned with one or more of the various physiological and biochemical activities in plants. Varies in size, form, and wall structure.
definition_reference: ISBN:0471245208
term: passage cell
goid: TAIR:0000353
definition: Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis.
definition_reference: ISBN:0471245208
term: pavement cell
goid: TAIR:0000332
definition: epidermal cells with a characteristic convoluted anticlinal cell walls that give a jigsaw like appearance to the lamina.
definition_reference: ISBN:087694289
term: phelloid cell
goid: KI:0004007
definition: A cell within the phellem (cork) but distinct from the cork cell in having no suberin in its walls.
definition_reference: ISBN:0471245208
term: phloem initial
goid: TAIR:0000400
definition: A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes. Sometimes called phloem mother cell.
definition_reference: ISBN:0471245208
term: photosynthetic cell
goid: KI:0004008
definition: A chloroplast-containing cell engaged in photosynthesis.
definition_reference: ISBN:0471245208
term: polar nucleus
goid: TAIR:0000196
definition: One of two nuclei in the central cell of a mature embryo sac. The two nuclei are derived from groups of nuclei at the two opposite poles of the eight-nucleate embryo sac.
definition_reference: ISBN:047125208
term: primary endosperm nucleus
goid: TAIR:0000195
definition: Nucleus resulting from the fusion of the male gamete and two polar nuclei in the central cell of the embryo sac.
definition_reference: ISBN:0471245208
term: ray cell
goid: TAIR:0000083
definition: A cell derived from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues.
definition_reference: ISBN:0471245208
term: ray initial
goid: TAIR:0000082
definition: A meristematic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem.
definition_reference: ISBN:0471245208
term: root hair
goid: TAIR:0000256
definition: A type of trichome on root epidermis that is a simple extension of an epidermal cell and is concerned with absorption of soil solution.
definition_reference: ISBN:0471245208
term: sclerenchyma cell
goid: TAIR:0000077
definition: Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity.
definition_reference: ISBN:0471245208
term: secretory cell
goid: KI:0004012
definition: Cell that produces secreted substances.
definition_reference: TAIR:KI
term: sieve cell
goid: TAIR:0000285
definition: A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants.
definition_reference: ISBN:0471245208
term: sieve element
goid: TAIR:0000286
definition: The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member.
definition_reference: ISBN:0471245208
term: sieve tube member
goid: TAIR:0000289
definition: One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment.
definition_reference: ISBN:0471245208
term: sillica cell
goid: KI:0004009
definition: One of two types of short cells in the epidermis of grasses, silica cells have deposits of silica in them.
definition_reference: ISBN:0471245208
term: socket cell
goid: TAIR:0000115
definition: Cell that surround a trichome and provides support for the trichome.
definition_reference: ISBN:0471245208
term: sperm cell
goid: TAIR:0000084
definition: Male gamete, part of male germ unit.
definition_reference: TAIR:KI
term: starch sheath cell
goid: TAIR:0000020
definition: Cells characterized by conspicuous and rather stable accumulation of starch.
definition_reference: ISBN:044174520
term: subsidiary cell
goid: TAIR:0000284
definition: An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue.
definition_reference: ISBN:047124520
term: synergid
goid: TAIR:0000191
definition: cells in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Play a vital role in fertilization.
definition_reference: ISBN:047125208
term: tracheary element
goid: TAIR:0000290
definition: general term for a water conducting cell, tracheid or vessel member.
definition_reference: ISBN:0471245208
term: tracheid
goid: TAIR:0000301
definition: A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements.
definition_reference: ISBN:0471245208
term: transfer cell
goid: TAIR:0000078
definition: Parenchyma cell with the wall ingrowth (or ivaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes.
definition_reference: ISBN:0471245208
term: trichoblast
goid: TAIR:0000262
definition: Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair.
definition_reference: ISBN:0471245208
term: trichome
goid: TAIR:0000282
definition: An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata.
definition_reference: ISBN:0471245208
term: vegetative cell
goid: TAIR:0000169
definition: Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus.
definition_reference: TAIR:lr
definition_reference: ISBN:0140514031
term: xylem element
goid: TAIR:0000273
definition: Cells composing the xylem
definition_reference: ISBN:0471245208
term: xylem fiber cell
goid: TAIR:0000274
definition: A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers.
definition_reference: ISBN:0471245208
term: xylem initial
goid: TAIR:0000275
definition: A cambial cell on the xylem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into xylem elements either with or without additional divisions in various planes. Sometimes called xylem mother cell.
definition_reference: ISBN:047125208
term: zygote
goid: TAIR:0000423
definition: Diploid cell produced by the fusion of sperm cell nucleus and egg cell in the process of double fertilization.
definition_reference: TAIR:KI
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!autogenerated-by: DAG-Edit version 1.410
!saved-by: Katica Ilic
!date: Wed Mar 31 18:15:51 PST 2004
!version: $Revision: 1.24 $
!type: % is_a is a
!type: < part_of Part of
!type: ~ develops_from develops from
$cell type ; TAIR:0000298
%antipodal cell ; TAIR:0000192
%central cell ; TAIR:0000194
<polar nucleus ; TAIR:0000196
<primary endosperm nucleus ; TAIR:0000195
%collenchyma cell ; TAIR:0000075
%cork cell ; KI:0004003
%egg cell ; TAIR:0000190
%epidermal cell ; KI:0004013
%bulliform cell ; KI:0004001
%sillica cell ; KI:0004009
%socket cell ; TAIR:0000115 ~ epidermal initial ; TAIR:0000349
%subsidiary cell ; TAIR:0000284, TAIR:0000296 ; synonym:accessory cell
%epithelium cell ; KI:0004004
%epithem cell ; TAIR:0000066 ; CL:0000074
%generative cell ; TAIR:0000168
~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ microspore ; TAIR:0000297
%idioblast ; TAIR:0000283
%megasporocyte ; TAIR:0000431 ; synonym:archesporial cell ; synonym:megaspore mother cell
~megaspore ; TAIR:0000243
%degenerate megaspore ; TAIR:0000245
%functional megaspore ; TAIR:0000244
%meristematic cell ; KI:0004010
%apical cell ; KI:0004000
%meristemoid ; TAIR:0000070
%initial cell ; KI:0004011
%cambial initial ; TAIR:0000295, TAIR:0000080 ; synonym:cambial cell
%fusiform initial ; TAIR:0000079 ; CL:0000009
~axial cell ; TAIR:0000081 ; CL:0000363
%phloem initial ; TAIR:0000400
%ray initial ; TAIR:0000082 ; CL:0000316
~ray cell ; TAIR:0000083 ; CL:0000364
%xylem initial ; TAIR:0000275 ; synonym:xylem mother cell
~xylem element ; TAIR:0000273
~xylem fiber cell ; TAIR:0000274
%epidermal initial ; TAIR:0000349
~atrichoblast ; TAIR:0000263 ; synonym:non-hair cell
~guard mother cell ; TAIR:0000351
~guard cell ; TAIR:0000293
~pavement cell ; TAIR:0000332
~socket cell ; TAIR:0000115 % epidermal cell ; KI:0004013
~trichoblast ; TAIR:0000262 ; synonym:hair cell
~root hair ; TAIR:0000256
%microsporocyte ; TAIR:0000160 ; synonym:pollen mother cell ; synonym:primary sporogenous cell
~microspore ; TAIR:0000297
~sperm cell ; TAIR:0000084 % cell type ; TAIR:0000298 ~ generative cell ; TAIR:0000168
%parenchyma cell ; TAIR:0000074
%chlorenchyma cell ; TAIR:0000076 % photosynthetic cell ; KI:0004008
%mesophyll cell ; KI:0004006
%companion cell ; TAIR:0000071
%contact cell ; KI:0004002
%transfer cell ; TAIR:0000078
%passage cell ; TAIR:0000353
%phelloid cell ; KI:0004007
%photosynthetic cell ; KI:0004008
%chlorenchyma cell ; TAIR:0000076 % parenchyma cell ; TAIR:0000074
%mesophyll cell ; KI:0004006
%sclerenchyma cell ; TAIR:0000077
%secretory cell ; KI:0004012
%laticiferous cell ; KI:0004005
%mucilage cell ; TAIR:0000373
%myrosin cell ; TAIR:0000352
%sieve element ; TAIR:0000286
%sieve cell ; TAIR:0000285
%sieve tube member ; TAIR:0000289 ; synonym:\<new synonym> ; synonym:sieve tube element
%sperm cell ; TAIR:0000084 ~ generative cell ; TAIR:0000168 ~ microspore ; TAIR:0000297
%starch sheath cell ; TAIR:0000020
%synergid ; TAIR:0000191
<filliform apparatus ; TAIR:0000193
%tracheary element ; TAIR:0000290
%fiber tracheid ; TAIR:0000355
%tracheid ; TAIR:0000301
%trichome ; TAIR:0000282
%vegetative cell ; TAIR:0000169
%zygote ; TAIR:0000423 ; synonym:one cell stage % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374 % embryonic ; TAIR:0000374
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