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cl-basic.obo
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format-version: 1.2
subsetdef: ubprop:upper_level "abstract upper-level terms not directly useful for analysis"
synonymtypedef: HUMAN_PREFERRED "preferred term when talking about an instance of this class in Homo sapiens"
synonymtypedef: LATIN "latin term"
synonymtypedef: PLURAL "plural term"
remark: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, [email protected], University at Buffalo.
ontology: cl/cl-basic
property_value: http://purl.org/dc/elements/1.1/license http://creativecommons.org/licenses/by/4.0/
[Term]
id: CL:0000000
name: cell
namespace: cell
def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [CARO:mah]
comment: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
subset: ubprop:upper_level
xref: CALOHA:TS-2035
xref: FMA:68646
xref: GO:0005623
xref: KUPO:0000002
xref: VHOG:0001533
xref: WBbt:0004017
xref: XAO:0003012
[Term]
id: CL:0000001
name: primary cultured cell
namespace: cell
def: "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." [ReO:mhb]
comment: Covers cells actively being cultured or stored in a quiescent state for future use.
synonym: "primary cell culture cell" EXACT []
synonym: "primary cell line cell" RELATED []
synonym: "unpassaged cultured cell" EXACT []
xref: BTO:0002290
is_a: CL:0000010 ! cultured cell
[Term]
id: CL:0000002
name: obsolete immortal cell line cell
namespace: cell
def: "OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line." [ReO:mhb]
comment: Obsoleted in July 2013 and replaced by the CLO 'immortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts.\n\nCovers cells actively being cultured or stored in a quiescent state for future use.
synonym: "continuous cell line cell" EXACT []
synonym: "permanent cell line cell" EXACT []
is_obsolete: true
replaced_by: CLO:0000019
[Term]
id: CL:0000003
name: native cell
namespace: cell
def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [CARO:mah]
comment: To accommodate unicellular organisms better, 'cell in vivo' has been re-labeled 'native cell' to better represent its intended meaning - that is, that it is a cell in the context of a multicellular organism or in a natural environment. 'Native' is intended to contrast with 'in vitro', which refers to cells or other biological entities that have been intentionally placed in a controlled, non-natural setting for the purpose of study or manipulation. (MAH 1.12.12).
subset: ubprop:upper_level
synonym: "cell in vivo" NARROW []
xref: CARO:0000013
is_a: CL:0000000 ! cell
[Term]
id: CL:0000004
name: obsolete cell by organism
namespace: cell
def: "OBSOLETE: A classification of cells by the organisms within which they are contained." [FB:ma]
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its species. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
is_obsolete: true
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
[Term]
id: CL:0000005
name: fibroblast neural crest derived
namespace: cell
is_a: CL:0000057 ! fibroblast
[Term]
id: CL:0000006
name: neuronal receptor cell
namespace: cell
synonym: "neuronal receptor cell (sensu Animalia)" EXACT []
is_a: CL:0000101 ! sensory neuron
is_a: CL:0000197 ! receptor cell
[Term]
id: CL:0000007
name: early embryonic cell
namespace: cell
def: "A cell found in the embryo before the formation of all the gem layers is complete." [GOC:tfm]
is_a: CL:0002321 ! embryonic cell
[Term]
id: CL:0000008
name: migratory cranial neural crest cell
namespace: cell
is_a: CL:0000333 ! migratory neural crest cell
[Term]
id: CL:0000009
name: obsolete fusiform initial
namespace: cell
alt_id: CL:0000274
def: "Obsolete. Use PO:0000079 from Plant Ontology instead. 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." [ISBN:0471245208]
comment: replaced_by: PO:0000079
synonym: "xylem initial" RELATED []
synonym: "xylem mother cell" RELATED []
is_obsolete: true
[Term]
id: CL:0000010
name: cultured cell
namespace: cell
def: "A cell in vitro that is or has been maintained or propagated as part of a cell culture." [ReO:mhb]
comment: Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture.
is_a: CL:0000578 ! experimentally modified cell in vitro
[Term]
id: CL:0000011
name: migratory trunk neural crest cell
namespace: cell
is_a: CL:0000333 ! migratory neural crest cell
[Term]
id: CL:0000012
name: obsolete cell by class
namespace: cell
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
is_obsolete: true
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
[Term]
id: CL:0000013
name: obsolete dentine secreting cell
namespace: cell
is_obsolete: true
consider: CL:0000140
[Term]
id: CL:0000014
name: germ line stem cell
namespace: cell
synonym: "germline stem cell" EXACT []
is_a: CL:0000034 ! stem cell
is_a: CL:0000039 ! germ line cell
[Term]
id: CL:0000015
name: male germ cell
namespace: cell
xref: FMA:72290
xref: MA:0002765
xref: ncithesaurus:Spermatogenic_Cell
xref: VHOG:0001531
is_a: CL:0000586 ! germ cell
[Term]
id: CL:0000016
name: male germ line stem cell
namespace: cell
is_a: CL:0000014 ! germ line stem cell
is_a: CL:0000015 ! male germ cell
[Term]
id: CL:0000017
name: spermatocyte
namespace: cell
def: "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." [GOC:tfm, MESH:A05.360.490.890.880]
xref: BTO:0001275
xref: CALOHA:TS-0951
xref: EMAPA:31484
xref: FBbt:00004936
xref: FMA:84049
xref: WBbt:0006799
is_a: CL:0000015 ! male germ cell
[Term]
id: CL:0000018
name: spermatid
namespace: cell
def: "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." [MESH:A05.360.490.890.860]
synonym: "nematoblast" EXACT []
xref: BTO:0001274
xref: CALOHA:TS-0950
xref: EMAPA:31486
xref: FBbt:00004942
xref: FMA:72294
xref: WBbt:0006800
is_a: CL:0000015 ! male germ cell
is_a: CL:0000413 ! haploid cell
[Term]
id: CL:0000019
name: sperm
namespace: cell
def: "A mature male germ cell that develops from a spermatid." [GOC:tfm, MESH:A05.360.490.890]
synonym: "sperm cell" EXACT []
synonym: "spermatozoid" EXACT []
synonym: "spermatozoon" EXACT []
xref: BTO:0001277
xref: BTO:0002046
xref: CALOHA:TS-0949
xref: FBbt:00004954
xref: FMA:67338
xref: WBbt:0006798
is_a: CL:0000064 ! ciliated cell
is_a: CL:0000219 ! motile cell
is_a: CL:0000408 ! male gamete
[Term]
id: CL:0000020
name: spermatogonium
namespace: cell
def: "An euploid male germ cell of an early stage of spermatogenesis." [MESH:A05.360.490.890.900]
xref: BTO:0000958
xref: CALOHA:TS-2193
xref: EMAPA:31482
xref: FBbt:00004935
xref: FMA:72291
is_a: CL:0000015 ! male germ cell
[Term]
id: CL:0000021
name: female germ cell
namespace: cell
def: "Female germ cell is a germ cell that supports female gamete production." [GOC:tfm, PMID:11023867, PMID:20454446]
xref: MA:0000388
xref: ncithesaurus:Egg
xref: VHOG:0001530
is_a: CL:0000586 ! germ cell
[Term]
id: CL:0000022
name: female germ line stem cell
namespace: cell
is_a: CL:0000014 ! germ line stem cell
is_a: CL:0000021 ! female germ cell
[Term]
id: CL:0000023
name: oocyte
namespace: cell
def: "A female germ cell that has entered meiosis." [GOC:tfm, ISBN:0721662544]
synonym: "oogonium" RELATED []
xref: BTO:0000964
xref: CALOHA:TS-0711
xref: FBbt:00004886
xref: FMA:18644
xref: WBbt:0006797
is_a: CL:0000021 ! female germ cell
[Term]
id: CL:0000024
name: oogonial cell
namespace: cell
def: "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." [GOC:tfm, ISBN:0721662544]
xref: FMA:83673
is_a: CL:0000021 ! female germ cell
[Term]
id: CL:0000025
name: egg cell
namespace: cell
def: "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." [GOC:tfm, ISBN:0721662544]
synonym: "mature oocyte" EXACT []
synonym: "ovum" EXACT []
xref: BTO:0000369
xref: BTO:0003801
xref: CALOHA:TS-2191
xref: FBbt:00057012
xref: FMA:67343
xref: MA:0000388
is_a: CL:0000675 ! female gamete
[Term]
id: CL:0000026
name: invertebrate nurse cell
namespace: cell
def: "A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte." [GOC:tfm, PMID:15848391]
synonym: "nurse cell" RELATED []
xref: BTO:0000953
xref: FBbt:00004878
is_a: CL:0000039 ! germ line cell
is_a: CL:0000412 ! polyploid cell
[Term]
id: CL:0000027
name: smooth muscle cell neural crest derived
namespace: cell
is_a: CL:0000192 ! smooth muscle cell
[Term]
id: CL:0000028
name: CNS neuron (sensu Nematoda and Protostomia)
namespace: cell
is_a: CL:2000029 ! central nervous system neuron
[Term]
id: CL:0000029
name: neuron neural crest derived
namespace: cell
is_a: CL:0000540 ! neuron
[Term]
id: CL:0000030
name: glioblast
namespace: cell
xref: FBbt:00005145
is_a: CL:0000055 ! non-terminally differentiated cell
[Term]
id: CL:0000031
name: neuroblast
namespace: cell
def: "A cell that will develop into a neuron often after a migration phase." [http://en.wikipedia.org/wiki/Neuroblast]
xref: BTO:0000930
xref: FBbt:00005146
xref: FMA:70563
is_a: CL:0000047 ! neuronal stem cell
is_a: CL:0000055 ! non-terminally differentiated cell
[Term]
id: CL:0000032
name: neuroplacodal cell
namespace: cell
def: "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." [GOC:tfm, ISBN:0618947256]
synonym: "neural placode cell" EXACT []
is_a: CL:0002321 ! embryonic cell
[Term]
id: CL:0000033
name: apocrine cell
namespace: cell
def: "An apocrine cell is a secretory cell characterized loss of part of the cytoplasm during the process of secretion - secretions are budded off through the plasma membrane producing membrane bound vesicles containing the secreted substance." [GOC:tfm, ISBN:0721662544]
is_a: CL:0000151 ! secretory cell
[Term]
id: CL:0000034
name: stem cell
namespace: cell
def: "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." [GOC:tfm, MESH:A11.872]
xref: CALOHA:TS-2086
xref: FMA:63368
is_a: CL:0011115 ! precursor cell
[Term]
id: CL:0000035
name: single fate stem cell
namespace: cell
def: "A stem cell that self-renews as well as give rise to a single mature cell type." [GOC:tfm]
synonym: "unipotent stem cell" EXACT []
synonym: "unipotential stem cell" EXACT []
xref: FMA:70569
is_a: CL:0000723 ! somatic stem cell
[Term]
id: CL:0000036
name: epithelial fate stem cell
namespace: cell
is_a: CL:0000035 ! single fate stem cell
[Term]
id: CL:0000037
name: hematopoietic stem cell
namespace: cell
def: "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Hematopoietic_stem_cell, PMID:19022770]
comment: Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative.
synonym: "blood forming stem cell" EXACT []
synonym: "colony forming unit hematopoietic" RELATED []
synonym: "hemopoietic stem cell" EXACT []
synonym: "HSC" EXACT []
xref: BTO:0000725
xref: CALOHA:TS-0448
xref: FMA:70337
xref: FMA:86475
xref: VHOG:0001485
is_a: CL:0000723 ! somatic stem cell
is_a: CL:0008001 ! hematopoietic precursor cell
[Term]
id: CL:0000038
name: erythroid progenitor cell
namespace: cell
def: "A progenitor cell committed to the erythroid lineage." [GOC:add, ISBN:0721601464]
synonym: "BFU-E" RELATED []
synonym: "blast forming unit erythroid" RELATED []
synonym: "burst forming unit erythroid" RELATED []
synonym: "CFU-E" RELATED []
synonym: "colony forming unit erythroid" RELATED []
synonym: "erythroid stem cell" RELATED []
xref: BTO:0004911
is_a: CL:0000764 ! erythroid lineage cell
is_a: CL:0000839 ! myeloid lineage restricted progenitor cell
[Term]
id: CL:0000039
name: germ line cell
namespace: cell
def: "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." [GOC:tfm, ISBN:0721662544]
comment: Originally this term had some plant germ line cell children.
subset: ubprop:upper_level
is_a: CL:0000548 ! animal cell
[Term]
id: CL:0000040
name: monoblast
namespace: cell
def: "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." [GOC:add, http://en.wikipedia.org/wiki/Monoblast, http://www.copewithcytokines.de, PMID:1104740]
comment: Morphology: mononuclear cell, diameter 12-20 _M, non-granular, N/C ratio 3/1 - 4/1; markers: CD11b (shared with many other myeloid cells); location: Adult: bone marrow; fetal: liver, Yolk Sac; role or process: hematopoiesis, monocyte development; lineage: hematopoietic, myeloid.
synonym: "CFU-M" RELATED []
synonym: "colony forming unit macrophage" RELATED []
synonym: "colony forming unit monocyte" RELATED []
synonym: "monocyte stem cell" RELATED []
xref: CALOHA:TS-1195
xref: FMA:83553
is_a: CL:0000763 ! myeloid cell
is_a: CL:0002194 ! monopoietic cell
[Term]
id: CL:0000041
name: mature eosinophil
namespace: cell
def: "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464]
comment: Eosinophils are CD125-positive (IL-5R), GM-CSFR-positive, IL-3R-positive, VLA4-positive. They can also express MHC Class I & II, CD4, CD9, CD11a, CD11b, CD11c, CD13, CD15, CD16, CD17, CD18, CD24, CD25,CD28, CD29, CD32, CD33, CD35, CD37, CD39, CD43, CD44, CD45, CD45RB, CD45RO, CD46, CD47, CD48, CD49d, CD49f, CD50, CD52, CD53, CD54, CD55, CD58, CD59, CD62L, CD63, CD65, CD66, CD69, CD71, CD76, CD80, CD81, CD82, CD86, CD87, CD88, CD89, CD92, CD95, CD97, CD98, CD99, CD100, CD101, CD116, CD117, CD119, CD120, CD123, CD124, CD125, CD131, CD137, CD139, CD148, CD149, CD151, CD153, CD156, CD162, CD161, CD162, CD165, CD174, CD182, CD183, CD191, CD192, CD193, CD196, CD213, IL9R, ad integrin, beta-7 integrin, FceRI, IL13Ra1, TGFbR, PAFR, LTB4R, C3aR, CystLT1R, CystLT2R, fMLPR, CRTH2 (PGD2 receptor), histamine 4R, IDO, KYN, PAR-2, Siglec-8, Siglec-10, LIR1, LIR2, LIR3, LIR7, TLR7, TLR8, and VLA-4. Eosinophils can also secrete CXCL1, eotaxin-1, GM-CSF, IL-2, IL-3, IL-4, IL-5, IL-6, IL-8, IL-10, IL-12, IL-13, IL-16, IL-18, IFN-gamma, LTC4, MIP-1alpha, NGF, PAF, RANTES, substance P, TGF-alpha, TGF-beta, TNF-alpha, and VIP.
synonym: "mature eosinocyte" EXACT []
synonym: "mature eosinophil leucocyte" EXACT []
synonym: "mature eosinophil leukocyte" EXACT []
synonym: "polymorphonuclear leucocyte" BROAD []
synonym: "polymorphonuclear leukocyte" BROAD []
is_a: CL:0000771 ! eosinophil
is_a: CL:0002242 ! nucleate cell
[Term]
id: CL:0000042
name: neutrophilic myeloblast
namespace: cell
def: "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." [GOC:add, ISBN:0721601464, PMID:12560239, PMID:15514007]
comment: These cells are CD11b-negative, CD15-negative, CD16-negative, CD35-negative, CD49d-positive, CD68-positive, lactotransferrin-negative, and fMLP receptor-negative. They are found in the Band 3 fraction.
synonym: "neutrophilic granuloblast" RELATED []
is_a: CL:0000834 ! neutrophil progenitor cell
is_a: CL:0000835 ! myeloblast
[Term]
id: CL:0000043
name: mature basophil
namespace: cell
alt_id: CL:0000739
def: "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation." [GOC:add, GOC:dsd, GOC:tfm, http://www.cap.org, ISBN:0721601464, PMID:18466030, PMID:19231594, PMID:20837449]
comment: Mature basophils are also capable of producing IL-3, IL-5, IL-6, IL-8, IL-13, IL-25, CCL22, tslp, vegf, and LTC4.
synonym: "mature basophil leucocyte" EXACT []
synonym: "mature basophil leukocyte" EXACT []
synonym: "polymorphonuclear leucocyte" BROAD []
synonym: "polymorphonuclear leukocyte" BROAD []
xref: BTO:0001026
xref: CALOHA:TS-0688
is_a: CL:0000767 ! basophil
is_a: CL:0002242 ! nucleate cell
is_a: CL:0002274 ! histamine secreting cell
[Term]
id: CL:0000045
name: obsolete thymus processed stem cell
namespace: cell
def: "OBSOLETE (was not defined before being made obsolete)." []
comment: Consider using term 'pro-T cell ; CL:0000827' or the term 'thymocyte ; CL:0000893' or one of its children instead.
is_obsolete: true
[Term]
id: CL:0000046
name: obsolete bursa processed stem cell
namespace: cell
def: "OBSOLETE (was not defined before being made obsolete)." []
comment: Consider using term 'pro-B cell ; CL:0000826' or the term 'immature B cell ; CL:0000816 or one of its children instead.
is_obsolete: true
[Term]
id: CL:0000047
name: neuronal stem cell
namespace: cell
def: "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." [GOC:tfm, http://en.wikipedia.org/wiki/Neural_stem_cell, MESH:D058953, PMID:15247488]
synonym: "neural stem cell" EXACT []
synonym: "NSC" EXACT []
xref: BTO:0002881
xref: CALOHA:TS-2360
xref: FMA:86684
is_a: CL:0000048 ! multi fate stem cell
is_a: CL:0002319 ! neural cell
[Term]
id: CL:0000048
name: multi fate stem cell
namespace: cell
def: "A stem cell that can give rise to multiple lineages of cells." [GOC:add]
synonym: "multi-fate stem cell" EXACT []
synonym: "multifate stem cell" EXACT []
synonym: "multipotent cell" EXACT []
synonym: "multipotent stem cell" EXACT []
xref: FMA:84789
is_a: CL:0000034 ! stem cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000049
name: common myeloid progenitor
namespace: cell
def: "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages." [GOC:add, ISBN:0878932437, MESH:D023461]
comment: This cell type is intended to be compatible with any vertebrate common myeloid progenitor. For mammalian CMP known to be CD34-positive, please use the term 'common myeloid progenitor, CD34-positive' (CL_0001059).
synonym: "CFU-GEMM" RELATED [ISBN:0878932437]
synonym: "CFU-S" RELATED [ISBN:0878932437]
synonym: "CMP" EXACT [ISBN:0878932437]
synonym: "colony forming unit granulocyte, erythrocyte, macrophage, and megakaryocyte" RELATED [ISBN:0878932437]
synonym: "common myeloid precursor" EXACT []
synonym: "multipotential myeloid stem cell" RELATED [ISBN:0878932437]
synonym: "myeloid stem cell" RELATED [ISBN:0878932437]
synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437]
xref: BTO:0004730
is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell
[Term]
id: CL:0000050
name: megakaryocyte-erythroid progenitor cell
namespace: cell
def: "A progenitor cell committed to the megakaryocyte and erythroid lineages." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Megakaryocyte-erythroid_progenitor_cell, MESH:D055015, PMID:16647566]
comment: MEPs are reportedly CD19-negative, CD34-negative, CD45RA-negative, CD110-positive, CD117-positive, and SCA1-negative and reportedly express the transcription factors GATA-1 and NF-E2.
synonym: "CFU-EM" EXACT []
synonym: "CFU-MegE" EXACT []
synonym: "colony forming unit erythroid megakaryocyte" EXACT []
synonym: "Meg/E progenitor" EXACT []
synonym: "megakaryocyte/erythrocyte progenitor" EXACT []
synonym: "megakaryocyte/erythroid progenitor cell" EXACT []
synonym: "MEP" EXACT []
is_a: CL:0000763 ! myeloid cell
is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell
is_a: CL:0011115 ! precursor cell
[Term]
id: CL:0000051
name: common lymphoid progenitor
namespace: cell
alt_id: CL:0000044
def: "A oligopotent progenitor cell committed to the lymphoid lineage." [GOC:add, GOC:dsd, GOC:tfm, PMID:10407577, PMID:16551251]
comment: CLP are CD7-positive, CD10-positive, CD19-negative, CD34-positive, CD45RA-positive, CD79a-negative, CD127-positive, AA4.1-positive, RAG-negative, Sca-1-low, sIgM-negative, sIgD-negative, TdT-negative, Vpre-B-negative, and pre-BCR-negative. Expression of transcription factors include E2A-positive, EBF-positive, Ikaros-negative, PU.1-negative, and Pax5-negative.
synonym: "CLP" EXACT []
synonym: "committed lymphopoietic stem cell" RELATED []
synonym: "common lymphocyte precursor" EXACT []
synonym: "common lymphocyte progenitor" EXACT []
synonym: "common lymphoid precursor" EXACT []
synonym: "early lymphocyte progenitor" RELATED []
synonym: "ELP" RELATED []
synonym: "lymphoid stem cell" RELATED []
synonym: "lymphopoietic stem cell" RELATED []
is_a: CL:0002032 ! hematopoietic oligopotent progenitor cell
is_a: CL:0011115 ! precursor cell
[Term]
id: CL:0000052
name: totipotent stem cell
namespace: cell
def: "A stem cell from which all cells of the body can form." [GOC:add, GOC:tfm]
synonym: "totipotential stem cell" EXACT []
xref: FMA:84790
is_a: CL:0000723 ! somatic stem cell
[Term]
id: CL:0000054
name: bone matrix secreting cell
namespace: cell
is_a: CL:0000151 ! secretory cell
[Term]
id: CL:0000055
name: non-terminally differentiated cell
namespace: cell
def: "A precursor cell with a limited number of potential fates." [SANBI:mhl]
comment: define using PATO mulit-potent or oligopotent?
synonym: "blast cell" EXACT []
xref: BTO:0000125
xref: FMA:84782
is_a: CL:0011115 ! precursor cell
[Term]
id: CL:0000056
name: myoblast
namespace: cell
def: "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." [GOC:tfm, MESH:A11.635, PMID:21849021]
xref: BTO:0000222
xref: CALOHA:TS-0650
xref: FBbt:00005083
xref: FMA:70335
xref: VHOG:0001529
is_a: CL:0000680 ! muscle precursor cell
[Term]
id: CL:0000057
name: fibroblast
namespace: cell
def: "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [http://en.wikipedia.org/wiki/Fibroblast, ISBN:0517223651, MESH:A11.329.228, MESH:D005347]
comment: These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative.
xref: BTO:0000452
xref: CALOHA:TS-0362
xref: FMA:63877
xref: VHOG:0001482
is_a: CL:0002320 ! connective tissue cell
[Term]
id: CL:0000058
name: chondroblast
namespace: cell
def: "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." [GO_REF:0000034, GOC:tfm, ISBN:0618947256]
synonym: "chrondoplast" EXACT []
xref: BTO:0003607
xref: FMA:66783
is_a: CL:0000055 ! non-terminally differentiated cell
is_a: CL:0002320 ! connective tissue cell
[Term]
id: CL:0000059
name: ameloblast
namespace: cell
alt_id: CL:0000053
alt_id: CL:0000139
def: "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." [GO_REF:0000034, GOC:tfm, MESH:A11.436.107]
comment: non-encoded relationship from VSAO produces VSAO:0000066
synonym: "amelocyte" EXACT []
synonym: "enamel secreting cell" EXACT []
xref: BTO:0001663
xref: FMA:70576
is_a: CL:0000146 ! simple columnar epithelial cell
is_a: CL:0000151 ! secretory cell
is_a: CL:0002077 ! ecto-epithelial cell
[Term]
id: CL:0000060
name: odontoblast
namespace: cell
def: "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." [GO_REF:0000034, ISBN:0618947256]
comment: legacy def: One of the cells forming the outer surface of dental pulp that produces tooth dentin.
xref: BTO:0001769
xref: CALOHA:TS-0696
xref: FMA:62999
is_a: CL:0000055 ! non-terminally differentiated cell
is_a: CL:0000710 ! neurecto-epithelial cell
is_a: CL:0002159 ! general ecto-epithelial cell
[Term]
id: CL:0000061
name: cementoblast
namespace: cell
alt_id: CL:0000859
def: "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell." [GO_REF:0000034, ISBN:0781733901]
comment: Legacy def: A cell of ectomesenchymal origin that aids in the formation the cementum layer on the roots of teeth.
synonym: "cementum secreting cell" EXACT []
xref: CALOHA:TS-1164
xref: FMA:63002
is_a: CL:0000062 ! osteoblast
is_a: CL:0000151 ! secretory cell
[Term]
id: CL:0000062
name: osteoblast
namespace: cell
def: "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." [GO_REF:0000034, MESH:A11.329.629]
comment: non-encoded relationships from VSAO - capable_of_producing VSAO:0000020
xref: BTO:0001593
xref: CALOHA:TS-0720
xref: FMA:66780
is_a: CL:0000055 ! non-terminally differentiated cell
is_a: CL:0002320 ! connective tissue cell
[Term]
id: CL:0000063
name: obsolete cell by histology
namespace: cell
def: "OBSOLETE: A classification of cells by their microscopic appearance." [FB:ma, GOC:tfm]
comment: This term was made obsolete because there is no difference in meaning between it and 'cell', as any cell can be classified by its microscopic appearance. If you have used this term in annotation, please replace it with cell (CL:0000000), native cell (CL:0000003), or cell in vitro (CL:0001034) as appropriate.
is_obsolete: true
consider: CL:0000000
consider: CL:0000003
consider: CL:0001034
[Term]
id: CL:0000064
name: ciliated cell
namespace: cell
def: "A cell that has a filiform extrusion of the cell surface." [GOC:tfm]
xref: VHOG:0001532
xref: XAO:0000031
is_a: CL:0000003 ! native cell
[Term]
id: CL:0000065
name: ependymal cell
namespace: cell
def: "A neurectoderm derived cell that lines the neural lumen." [GOC:tfm, JB:jb, PMID:9550134]
synonym: "ependymocyte" EXACT []
xref: BTO:0001724
xref: FMA:70550
is_a: CL:0000067 ! ciliated epithelial cell
is_a: CL:0000710 ! neurecto-epithelial cell
[Term]
id: CL:0000066
name: epithelial cell
namespace: cell
def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [FB:ma, GOC:tfm, MESH:A11.436]
synonym: "epitheliocyte" EXACT []
xref: BTO:0000414
xref: CALOHA:TS-2026
xref: CARO:0000077
xref: FBbt:00000124
xref: FMA:66768
xref: WBbt:0003672
is_a: CL:0000548 ! animal cell
[Term]
id: CL:0000067
name: ciliated epithelial cell
namespace: cell
def: "An epithelial cell that has a cillia." [GOC:tfm]
xref: FMA:70605
is_a: CL:0000064 ! ciliated cell
is_a: CL:0000075 ! columnar/cuboidal epithelial cell
[Term]
id: CL:0000068
name: duct epithelial cell
namespace: cell
is_a: CL:0000066 ! epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000069
name: branched duct epithelial cell
namespace: cell
is_a: CL:0000068 ! duct epithelial cell
[Term]
id: CL:0000070
name: obsolete epithelial cell of gland
namespace: cell
is_obsolete: true
[Term]
id: CL:0000071
name: blood vessel endothelial cell
namespace: cell
def: "An endothelial cell that lines the vasculature." [GOC:tfm]
synonym: "cuboidal endothelial cell of vascular tree" EXACT []
is_a: CL:0000076 ! squamous epithelial cell
is_a: CL:0002139 ! endothelial cell of vascular tree
[Term]
id: CL:0000072
name: non-branched duct epithelial cell
namespace: cell
is_a: CL:0000068 ! duct epithelial cell
is_a: CL:0002078 ! meso-epithelial cell
[Term]
id: CL:0000073
name: barrier epithelial cell
namespace: cell
is_a: CL:0000066 ! epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000074
name: obsolete epithem cell
namespace: cell
def: "Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap." [ISBN:0471245208, PMID:12662305]
comment: replaced_by: PO:0000066
is_obsolete: true
[Term]
id: CL:0000075
name: columnar/cuboidal epithelial cell
namespace: cell
is_a: CL:0000066 ! epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000076
name: squamous epithelial cell
namespace: cell
xref: CALOHA:TS-1249
is_a: CL:0000066 ! epithelial cell
[Term]
id: CL:0000077
name: mesothelial cell
namespace: cell
def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544]
synonym: "mesotheliocyte" EXACT []
xref: FMA:66773
is_a: CL:0000076 ! squamous epithelial cell
is_a: CL:0000213 ! lining cell
is_a: CL:0002078 ! meso-epithelial cell
[Term]
id: CL:0000078
name: peridermal cell
namespace: cell
is_a: CL:0000076 ! squamous epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000079
name: stratified epithelial cell
namespace: cell
is_a: CL:0000066 ! epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000080
name: circulating cell
namespace: cell
def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add]
is_a: CL:0000003 ! native cell
[Term]
id: CL:0000081
name: blood cell
namespace: cell
def: "A cell found predominately in the blood." [GOC:add, GOC:tfm]
xref: FMA:62844
is_a: CL:0000988 ! hematopoietic cell
[Term]
id: CL:0000082
name: epithelial cell of lung
namespace: cell
synonym: "lung epithelial cell" EXACT []
xref: BTO:0004299
is_a: CL:0000066 ! epithelial cell
[Term]
id: CL:0000083
name: epithelial cell of pancreas
namespace: cell
def: "An epithelial cell of the pancreas." [GOC:tfm]
synonym: "pancreas epithelial cell" EXACT []
synonym: "pancreatic epithelial cell" EXACT []
xref: BTO:0000028
is_a: CL:0000066 ! epithelial cell
is_a: CL:0002371 ! somatic cell
[Term]
id: CL:0000084
name: T cell
namespace: cell
alt_id: CL:0000804
alt_id: CL:0000812
def: "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [GOC:add, GOC:tfm, ISBN:0781735149]
synonym: "immature T cell" RELATED []
synonym: "mature T cell" RELATED []
synonym: "T lymphocyte" EXACT []
synonym: "T-cell" EXACT []
synonym: "T-lymphocyte" EXACT []
xref: BTO:0000782
xref: CALOHA:TS-1001
xref: FMA:62870
xref: VHOG:0001479
is_a: CL:0000542 ! lymphocyte
[Term]
id: CL:0000085
name: germ line stem cell (sensu Vertebrata)
namespace: cell
is_a: CL:0000014 ! germ line stem cell
[Term]
id: CL:0000086
name: germ line stem cell (sensu Nematoda and Protostomia)
namespace: cell
xref: FBbt:00004861
is_a: CL:0000014 ! germ line stem cell
[Term]
id: CL:0000087
name: male germ line stem cell (sensu Nematoda and Protostomia)
namespace: cell
xref: FBbt:00004929
is_a: CL:0000016 ! male germ line stem cell
is_a: CL:0000086 ! germ line stem cell (sensu Nematoda and Protostomia)
[Term]
id: CL:0000088
name: female germ line stem cell (sensu Nematoda and Protostomia)
namespace: cell
xref: FBbt:00004873
is_a: CL:0000022 ! female germ line stem cell
is_a: CL:0000086 ! germ line stem cell (sensu Nematoda and Protostomia)
[Term]
id: CL:0000089
name: male germ line stem cell (sensu Vertebrata)
namespace: cell
synonym: "spermatogonial stem cell" EXACT [PMID:19948499]
is_a: CL:0000016 ! male germ line stem cell
is_a: CL:0000085 ! germ line stem cell (sensu Vertebrata)
[Term]
id: CL:0000090
name: female germ line stem cell (sensu Vertebrata)
namespace: cell
is_a: CL:0000022 ! female germ line stem cell
is_a: CL:0000085 ! germ line stem cell (sensu Vertebrata)
[Term]
id: CL:0000091
name: Kupffer cell
namespace: cell
def: "A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0517223651, MESH:A11.329.372.588, PMID:15771589, PMID:17105582]
comment: Markers: Mouse: F4/80+, CD11b-low, CD68+, sialoadhesin+, CD163/SRCR+; role or process: immune, antigen-presentation, clearance of senescent erythrocytes, iron metabolism. Kupffer cells are also reportedly C3aR-positive, CD14-low, CD54-positive, CD88-positive, and CD284-positive. They are also capable of producing IL-1, IL-6, TNF-alpha, nitric oxide, PGD2, PGE2, PGF2alpha, and TXA2.
synonym: "hepatic macrophage" EXACT []
synonym: "littoral cell of hepatic sinusoid" EXACT []
synonym: "liver macrophage" EXACT []
synonym: "macrophagocytus stellatus" EXACT []
synonym: "stellate cell of von Kupffer" EXACT []
synonym: "von Kupffer cell" EXACT []
xref: BTO:0000685
xref: FMA:14656
is_a: CL:0000864 ! tissue-resident macrophage
[Term]
id: CL:0000092
name: osteoclast
namespace: cell
def: "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." [GO_REF:0000031, GOC:add, GOC:tfm, ISBN:0781735149, PMID:10428500, PMID:15055519, PMID:17380158]
comment: Morphology: Highly vesicular; markers: Surface: RANK, cFMS (MCSF receptor); Secreted: cathepsin K and TRAP (tartate resistant acid phosphatase); transcription factors: PU.1, cFOS, MITF, NFkB (p52); role or process: tissue remodelling: bone resorption; lineage: hematopoietic, myeloid.
synonym: "chondroclast" RELATED []
xref: BTO:0000968
xref: CALOHA:TS-0721
xref: FMA:66781
is_a: CL:0000766 ! myeloid leukocyte
is_a: CL:0001035 ! bone cell
[Term]
id: CL:0000093
name: obsolete osteochondroclast
namespace: cell
def: "OBSOLETE (was not defined before being made obsolete)." []
comment: Consider using 'osteoclast ; CL:0000092' instead.
is_obsolete: true
[Term]
id: CL:0000094
name: granulocyte
namespace: cell
def: "A leukocyte with abundant granules in the cytoplasm." [GOC:amm, GOC:tfm, http://en.wikipedia.org/wiki/Granulocyte, MESH:A11.118.637.415, MESH:D006098]
synonym: "granular leucocyte" EXACT []
synonym: "granular leukocyte" EXACT []
synonym: "polymorphonuclear leukocyte" EXACT []
xref: BTO:0000539
xref: BTO:0001026
xref: CALOHA:TS-0422
xref: FMA:62854
is_a: CL:0000081 ! blood cell
is_a: CL:0000766 ! myeloid leukocyte
[Term]
id: CL:0000095
name: neuron associated cell
namespace: cell
is_a: CL:0002319 ! neural cell
[Term]
id: CL:0000096
name: mature neutrophil
namespace: cell
def: "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." [GOC:add, GOC:tfm, http://www.cap.org, MESH:A11.118.637.415.583, MESH:D009504, PMID:11138776, PMID:12560239, PMID:15514007, PMID:7880385]
comment: Neutrophils are also capable of secreting GRO-alpha, IL-1beta, IL-1ra, IL-3, IL-12, IP-10, MIG, MIP-1alpha, MIP-1beta, TGF-beta, TNF-alpha, VEGF, and anti-microbial peptides. They can positively influence the chemotaxis of basophils, T-cells, monocytes, macrophages, dendritic cells, and other neutrophils. Neutrophils are also CD35-positive, CD64-positive, CD89-positive, CD184-positive, and fMLP receptor-positive Ly-6G-positive (mouse), TLR2-low, TLR4-low, and lineage-negative (CD2, CD3, CD5, CD9, CD19, CD36, CD49d, CD56, CD61, CD235a (glycophorin-A)).
synonym: "mature neutrocyte" EXACT []
synonym: "mature neutrophil leucocyte" EXACT []
synonym: "mature neutrophil leukocyte" EXACT []
synonym: "mature neutrophilic leucocyte" EXACT []
synonym: "mature neutrophilic leukocyte" EXACT []
synonym: "PMN" EXACT []
synonym: "poly" BROAD []
synonym: "polymorphonuclear leucocyte" BROAD []
synonym: "polymorphonuclear leukocyte" BROAD []
synonym: "polymorphonuclear neutrophil" EXACT []
synonym: "polynuclear neutrophilic leucocyte" EXACT []
synonym: "polynuclear neutrophilic leukocyte" EXACT []
xref: BTO:0003473
is_a: CL:0000234 ! phagocyte
is_a: CL:0000775 ! neutrophil
is_a: CL:0002242 ! nucleate cell
[Term]
id: CL:0000097
name: mast cell
namespace: cell
def: "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." [GOC:add, GOC:dsd, GOC:tfm, ISBN:068340007X, MESH:A11.329.427, MESH:D008407, PMCID:PMC1312421, PMCID:PMC2855166, PMID:15153310, PMID:16455980, PMID:19671378, PMID:212366338, PMID:9354811]
comment: Mast cells are generally integrin beta-7-negative and positive for TLR2, TLR3, TLR4, TLR5, TLR7, TLR9, C3aR, C5aR, CR3, CR4, VEGF, FGF2, and renin. They can express MHC Class I and II on their surface. Activated murine mast cells (IgE+Antigen) were capable of expressing the following co-stimulatory molecules: CD95 (Fas), CD120b, CD137 (4-1BB), CD153 (CD30L), CD154 (CD40L), GITR, ICOSL, OX40L, PD-L1, and PD-L2. Note that there was some mouse strain variation. Mast cells have also been demonstrated to produce bFGF, CCL2, CCL4, CCL5, CCL11, CCL20, CXCL2, CXCL8, CXCL10, GM-CSF, IFN-gamma, IL-1, IL-2, IL-3, IL-8, IL-10, IL-11, IL-12, IL-13, IL-16, IL-25, IL-18, MIP-1, prostaglandin D2, SCF, TGF-beta, TNF-alpha, TSLP, VEGF, and XCL1. They express the transcription factors Transcription factors AP-1, GATA1, MITF, Notch2, PIAS3, PU.1, and STAT5.
synonym: "histaminocyte" EXACT []
synonym: "labrocyte" EXACT [ISBN:0721601464]
synonym: "mastocyte" EXACT [ISBN:0721601464]
synonym: "tissue basophil" RELATED [ISBN:068340007X]
xref: BTO:0000830