cell type node
Pankaj Jaiswal
pj37 at cornell.edu
Fri Apr 2 11:47:40 EST 2004
central cell
< polar nucleus
< primary endosperm nucleus
Are we doing subcellular strutures too in the anatomy ? If not, I guess
these children belong to the GO component ontology.
Pankaj
Katica Ilic wrote:
> 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
>
>
> --------------------------------------------------------------------------
> 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.
> --------------------------------------------------------------------------
>
>
>
> ------------------------------------------------------------------------
>
> !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
>
>
>
> ------------------------------------------------------------------------
>
> !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
--
******************************
Pankaj Jaiswal, PhD
Gramene Database
Department of Plant Breeding
G-15 Bradfield Hall
Cornell University
Ithaca, NY-14853
tel: +1-607-255-3103
fax: +1-607-255-6683
web: http://www.gramene.org
*****************************
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