alternative term
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
PERSON:Daniel Schober
term editor
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
definition source
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
imported from
For external terms/classes, the ontology from which the term was imported
definition
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
Reference database or publication source.
example of usage
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
editor preferred term~editor preferred label
editor preferred label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.
LINCS ID
An annotation property that represents an ID used in the NIH LINCS project.
PubChem AID
An annotation property that represents a PubMed BioAssay Identifier accession number.
label
A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture
Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters
A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures.
Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak
A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line.
cell line
He, Tong-Chuan, et al., Identification of c-MYC as a target of the APC pathway. Science 281.5382 (1998): 1509-1512.: "To evaluate the transcriptional effects of APC, we studied a human colorectal cancer cell line (HT29-APC) containing a zinc-inducible APC gene and a control cell line (HT29–β-Gal) containing an analogous inducible lacZ gene". Note that common usage in the literature is often of the form "a human colorectal cancer cell line", as seen above. But such references to studies in "a line" refer to the fact that discrete populations of cells that are input into culturing or experiments, not an entire lineage of cells. It is these discrete populations that we refer to as 'cell lines'.
A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture).
In the spring of 2013, a working group comprised of domain experts and representatives from CLO, OBI, CL, and ReO worked to establish a consensus model and definitions of cultured cells across these efforts. This included a careful characterization of how the term 'cell line' should be defined and applied. Notes about this work and its outcomes can be found on the CLO wiki here: http://code.google.com/p/clo-ontology/wiki/Cell_Lines
The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history. As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use.
WEB: http://web.expasy.org/cellosaurus/CVCL_0045
WEB: https://www.atcc.org/Products/All/CRL-1573.aspx
BTO: BTO_0000007
EFO: EFO_0001182)
Human Embryonic Kidney 293
WEB: https://www.atcc.org/Products/All/CRL-11268.aspx
disease: clear cell carcinoma (kidney primary)
disease: epidermoid carcinoma (lung primary)
disease: colorectal adenocarcinoma (colon primary)
disease: carcinoma; small cell lung cancer; multidrug resistant
immortal human epithelial cell line cell that was derived from some colon epithelial cell from a human patient with the disease colon carcinoma
WEB: https://www.atcc.org/products/all/CCL-247.aspx
WEB: http://web.expasy.org/cellosaurus/CVCL_0291
WEB: http://www.atcc.org/products/all/CCL-2.aspx
WEB: https://www.ncbi.nlm.nih.gov/pubmed/12001993
an immortal human uterine cervix-derived epithelial cell line that was derived from cervical adenocarcinoma cancer cells taken on February 8, 1951 from Henrietta Lacks, a patient who died of her cancer on October 4, 1951.
WEB: https://www.atcc.org/products/all/HB-8065.aspx
WEB: http://web.expasy.org/cellosaurus/CVCL_0027
WEB: https://en.wikipedia.org/wiki/Hep_G2
disease: promyeloblast; acute promyelocytic leukemia
WEB: https://www.atcc.org/Products/All/CRL-1730.aspx
WEB: https://en.wikipedia.org/wiki/Jurkat_cells
an immortalized human T lymphocyte cell that was derived in the late 1970s from the peripheral blood of a 14-year-old boy with T cell leukemia
an immortal breast cancer cell line cell isolated in 1970 from a 69-year-old Caucasian woman.
WEB: https://en.wikipedia.org/wiki/MCF-7
WEB: http://web.expasy.org/cellosaurus/CVCL_0031
disease: adenocarcinoma (mammary gland primary)
an immortal breast cancer cell line cell derived from a human patient with breast adenocarcinoma
A model mammalian cell line cell that was genereated from the initial isolation in 1958 of epithelial cells from the kidney tubule of an adult Cocker Spaniel dog by Stewart H. Madin and Norman B. Darby, Jr..
disease: epidermoid carcinoma (cervix primary)
WEB: http://www.ncbi.nlm.nih.gov/pubmed/3121170
A melanoma cell line cell. This cell line was established in 1974 from a metastatic site (axillary lymph node) in a 24-year-old Caucasian female with malignant melanoma, expresses mutant B-Raf (V600E) and wildtype N-Ras.
WEB: http://web.expasy.org/cellosaurus/CVCL_1706
WEB: https://strap.nci.nih.gov/celline_detail.php?sample_id=56
WEB: https://www.atcc.org/Products/All/HTB-96.aspx
There is a CLO term for the cell line already: http://purl.obolibrary.org/obo/CLO_0009464
A human glioblastoma cell line cell. The cell line is part of the NCI-60 screening panel.
BJeLR cell
PubChem probe report: http://www.ncbi.nlm.nih.gov/books/NBK98919/
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/18355723
BJeLR cell is BJ fibroblast cell line cell transformed with hTERT, genomic SV40 LT and ST oncoproteins, and oncogenic HRASV12.
BJeH cell
BJeH=BJ derivative transformed only with hTERT (BJ fibroblasts were derived from primary human cells by transformation with hTERT, genomic SV40 Large T (LT) and Ssmall T (ST))
RS-11846 cell
WEB: http://cellfinder.org/ontology?id=CELDA_00012667
CHO-S cell
A derivative of the CHO cell line that is adapted to high-density, serum-free suspension culture
WEB: https://www.thermofisher.com/order/catalog/product/R80007
DRD cell
DRD=BJ fibroblasts expressing hTERT, SV40 small T oncoprotein, dominant negative p53, cyclin D1, a mutant form of CDK4, along with the oncogene HRASV12
WEB: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683762/
HL2/3
WEB: https://www.aidsreagent.org/reagentdetail.cfm?t=cell_lines&id=83
WEB: https://www.ncbi.nlm.nih.gov/pubmed/?term=2078409
HL2/3 is a derivative of HeLa cells and contains a stably integrated copies of the HIV-1 molecular clone HXB2/3gpt.
HeLa-MAGI-CCR5
HeLa-MAGI-CCR5 cells are derived from HeLa cells and express human CD4, CXCR4 and CCR5, and an integrated gene encoding the b-galactosidase gene expressed from the HIV long terminal repeat.
WEB: http://web.expasy.org/cellosaurus/CVCL_D260
MAGI-CCR5 cells; HeLa-R5-16, engineered to express the Envelope protein (Env) from the CCR5-tropic HIV-1 clinical isolate 92US715, and also to express the Tat protein from HIV-1 NL4 3
HeLa-R5-16
WEB: http://www.ncbi.nlm.nih.gov/pubmed/?term=16314403
HeLa-R5-16 (gift from Roche Palo Alto, LLC) is a derivative of HeLa cells, engineered to express the Envelope protein (Env) from the CCR5-tropic HIV-1 clinical isolate 92US715, and also to express the Tat protein from HIV-1 NL43
RD-HGA16
RD-HGA16 is derivative of CHO cells stably transfected with the promiscuous G-protein Gα16 gene and hygromycin-resistant. RD-HGA16 is from FLIPR LiveWare Cells (Molecular Devices, Sunnyvale CA), a series of cells and expression vectors successfully used in drug discovery, based on G-protein chimeras developed by Bruce Conklin and colleagues at the Gladstone Institute, UCSF.
WEB: http://go.pardot.com/l/83942/2015-06-17/njr/83942/4464/Data_Sheet__FLIPR_LiveWare_G_protein_Cells_and_Plasmids.pdf
Sufu-KO-LIGHT cell
WEB: https://www.google.com/patents/WO2013192301A1?cl=en
Sufu-KO-LIGHT cells were derived from Sufu knockout mouse embryonic fibroblasts according to the method of Chen et al. [Genes Dev. 2009;23(16): 1910-28.] The cells were co-transfected with the zeocin resistance vector (pVgRXR, Invitrogen) and a firefly luciferase reporter driven by eight Gli binding sites and a γ-crystallin basal promoter (8XGHBS-FL). Sufu-KO-LIGHT lacks Sufu and exhibits constitutive Hh target gene expression in response to endogenous Gli activators.
Ub-G76V-GFP/HeLa
A Hela-derived cell line cell that expresses ubiquitinated GFP (Green Fluroescent Protein)
GripTite 293 MSR cell
The GripTite™ 293 MSR Cell Line is a genetically engineered Human Embryonic Kidney (HEK 293) cell line that expresses the human macrophage scavenger receptor and strongly adheres to standard tissue culture plates for dependable results.
2B4/BCL-2 cell
A mouse T-cell hybridoma cell line cell that is derived from the murine hybridoma cell line 2B4, stably transfected to overexpress the human protein BCL-2.
2B4/MCL-1 cell
A mouse T-cell hybridoma cell line cell that is derived from the murine hybridoma cell line 2B4, stably transfected to overexpress the human protein MCL-1.
AVA5 cell
AVA5 cells are derived from the Huh-7 human hepatoma cell line, stably-expressing the HCV replicon (sub-genomic [CON1], genotype 1b); http://www.apath.com/index.html. See also PMID: 27013634, 1110665, 10390360
BCL-2 1863 cell
A murine leukemia cell line driven by the overexpression of Myc and BCL-2.
C17.2 cell
An immortalised mouse neural progenitor cell line cell that is capable of differentiation in vitro and is established by retorviral-mediated transduction of the avian myc oncogene into mitotic progenitor cells of neonatal mouse cerrebellum. Mouse strain CD1 x C57BL/6.
CEM21 cell
CEM21 (aka CEM#21 or CEM-R5Luc1#21) is derived from CEM.NKR-CCR5 by stable transfecttion of a Tet-activator responsive Luciferase reporter
DPX2 cell
DPX2 (aka DPX-2) is a HepG2-derived cell line stably integrated with a PXR (pregnane X receptor) expression vector plus a luciferase reporter, used to detect PXR activation/ CYP3A induction
FA2N-4 cell
FA2N-4 is a human hepatocyte cell line. Reference: http://web.expasy.org/cellosaurus/CVCL_0267
HBL-1 cell
HBL-1 (aka human is an EBV-negative B-cell lymphoma cell line established from the pleural effusion of a patient with malignant lymphoma, diffuse, large cell.
HMC-1-8 cell
HMC-1-8 is a human breast cancer cell line
HMLE_sh_ECAD cell
HMLE_sh_ECAD is a stable cell line mimicking a cancer stem cell (CSC), derived by knocking down E-Cadherin (via shRNA) in human breast epithelial cells to induce epithelial to mesenchymal transition (EMT)
HMLE_sh_eGFP cell
HMLE_sh_eGFP is a human breast epithelial cell line containing shRNA to GFP (green fluorescent reporter); used as an isogenic control line for HMLE_sh_ECAD
HMLE_sh_TWIST cell
HMLE_sh_TWIST is a stable cell line mimicking a cancer stem cell (CSC), derived by knocking down TWIST (via shRNA) in human breast epithelial cells to induce epithelial to mesenchymal transition (EMT); isogenic with another CSC line, HMLE_sh_ECAD
LEADING LIGHT Wnt Reporter cell line cell
An engineered 3T3 mouse fibroblast cell line, which expresses the firefly luciferase reporter gene under the control of Wnt-responsive promoters (TCF/LEF).
MCL-1 1780 cell
MCL-1 1780 is a murine leukemia cell line driven by the overexpression of Myc and MCL-1.
MG213 cell
MG213 is a subline of the BRG1/BRM-deficient cell line SW13 (http://purl.obolibrary.org/obo/CLO_0009185) that contains a stably integrated glucocorticoid-responsive MMTV-luciferase reporter.
PathHunter CHO-K1 DRD2L Beta-Arrestin cell
A PathHunter Beta-Arrestin GPCR cell line (DiscoverX), engineered to co-express the ProLink (PK) tagged GPCR (DRD2L, long form of human DRD2) and the Enzyme Acceptor (EA) tagged Beta-Arrestin. Activation of DRD2L-PK induces Beta-Arrestin-EA recruitment, forcing complementation of the two Beta-galactosidase enzyme fragments (EA and PK). The resulting functional enzyme hydrolyzes substrate to generate a chemiluminescent signal.
PathHunter CHO-K1 DRD3 Beta-Arrestin cell
A PathHunter Beta-Arrestin GPCR cell line (DiscoverX), engineered to co-express the ProLink (PK) tagged GPCR (human DRD3) and the Enzyme Acceptor (EA) tagged Beta-Arrestin. Activation of DRD3-PK induces Beta-Arrestin-EA recruitment, forcing complementation of the two Beta-galactosidase enzyme fragments (EA and PK). The resulting functional enzyme hydrolyzes substrate to generate a chemiluminescent signal.
RAW-Blue cell
RAW-Blue cells are derived from the murine RAW 264.7 macrophages with chromosomal integration of a secreted embryonic alkaline phosphatase (SEAP) reporter construct inducible by NF-κB and AP-1.
S16 cell
SW1 cell
A mouse melanoma cell line (which harbors N-Ras mutation), isolated from a small amelanotic lung metastasis in a mouse with a s.c. K-1735 tumor.
Tango cell
'Tango cell' refers to one of many stable cell lines, all based on the parental line HEK293T, designed to work in a 'Tango beta-arrestin' recruitiment assay to measure receptor activation for more than 300 GPCRs. See PMID25895059 and https://pdspdb.unc.edu/prestotango/
TMD8 cell
Human diffuse large B cell lymphoma cell line derived from a 62-year-old male patient
U87-EGFRvIII cell
U87-EGFRvIII (aka U87/vIII) is a stable cell line derived from U87MG (a human glioblastoma) to overexpress the most common mutation of epidermal growth factor receptor (EGFR) found in human glioblastomas--an in-frame deletion of an 801-bp sequence in the extracellular domain of EGFR termed EGFRvIII. (descr. in PMID 15548697).
MDCK-II cell
MDCKII-LE cell
Compared to the parent cell line, has a lower expression of endogenous ABCB1/MDR1.