Description of Cellosaurus - a knowledge resource on cell lines

Introduction

Cellosaurus is a knowledge resource on cell lines. It attempts to describe all cell lines used in biomedical research.

Its scope includes:

• Immortalized cell lines
• Naturally immortal cell lines (example: stem cell lines)
• Finite life cell lines when those are distributed and used widely
• Vertebrate cell line with an emphasis on human, mouse and rat cell lines
• Invertebrate (insects and ticks) cell lines
• Plant cell lines

Its scope does not include:

• Primary cell lines (with the exception of the finite life cell lines described above)

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Detailed content description

For each cell line we provide the following information:

• A recommended name. This is most frequently the name provided in the original publication
• A list of synonyms. We try to list all the different synonyms for the cell line, including alternative use of lower and upper cases characters. Misspellings are not included in synonyms
• A unique accession number
• The species of origin
• Structured comments. To describe:
  • contaminated/misidentified cell lines
  • misspellings
  • from which breed/subspecies a cell line is derived from
  • from which anatomical site (tissue/organ) the cell line has been sampled (with links to the UBERON ontology)
  • from which cell type the cell line belongs to (with links to the CL ontology)
  • if a cell line contains integrated genetic element(s) (by transfection, transduction or other methods)
  • if a cell line contains gene(s) that have been knocked-out
  • if a cell line has been selected for resistance to a chemical compound
  • if a cell line has been discontinued from a cell catalog
  • if a cell line is registered in an official list
  • if a cell line belongs to a specific cell panel
  • if a cell line has been the target of specific "omics" studies
  • if a cell line belongs to a specific "group" (example: fish cell lines, vaccine production cell lines, etc.)
  • for an hybridoma: the target of the produced monoclonal antibody and its isotype (example: 'IgG2b, kappa')
  • the transformant used to transform a cell line
  • the population doubling time
  • the HLA typing information
  • the microsatellite instability degree
  • important sequence variations (compared to the reference genome of the species)
  • as well as various other characteristics of a cell line
• For cell lines originating from a diseased patient/animal, we provide the NCI Thesaurus entry code for the disease(s) that the individual from which the cell line originated was suffering from. For human rare diseases we also provide the ORDO entry code of the disease
• For human, mouse and dog cell lines where this information is available, we provide the STR (short tandem repeat) profile information
• If a cell line originates from another one, we provide a link to the parent cell line
• If a cell line originates from the same individual as other cell line(s) (sister cell lines), cross-references to these sister cell line(s) are provided
• The sex of the individual from which the cell line has been derived
• The age of the individual from which the cell line has been derived (at the time of "sampling")
• The category to which a cell line belongs. Currently this can be one of the following categories:
  • Cancer cell line
  • Conditionally immortalized cell line
  • Embryonic stem cell
  • Factor-dependent cell line
  • Finite cell line
  • Hybrid cell line
  • Hybridoma
  • Induced pluripotent stem cell
  • Somatic stem cell
  • Spontaneously immortalized cell line
  • Stromal cell line
  • Telomerase immortalized cell line
  • Transformed cell line
  • Undefined cell line type
• Web links
• Publication references. We principally provide the references for publications describing the establishment of a cell line or its characterization. We do not attempt to capture all the literature that make use of a particular cell line. References can be of the type:
  • Journal articles
  • Books, Book chapters, Conferences proceedings, Technical documents
  • Patents
  • Theses (PhD, MD, MDSc, VMD, MSc or BSc)
• Cross-references to:
  • Cell line catalogs/collections: Abcam, Abeomics, ABM, AddexBio, ATCC, BCRC, BCRJ, BEI Resources, CancerTools, CBA, CCLV, CCTCC, Cell Biolabs, CLS, Coriell, DGRC, DiscoverX, DSHB, DSMZ, ECACC, FCDI, GeneCopoeia, Genomeditech, Horizon Discovery, Hysigen, IBRC, ICLC, Imanis, Innoprot, IZSLER, JCRB, KCB, KCLB, Kerafast, KYinno, Millipore, MMRRC, NCBI_Iran, NCI-DTP, NHCDR, NIHhESC, NISES, NRFC, PerkinElmer, RCB (Riken), RIKEN_BRC_EPD, Rockland, RSCB, Sigma-Aldrich, TKG, TNGB, Ubigene, WiCell and Ximbio
  • Ontologies: BCGO, BTO, CLO, EFO, MCCL, MeSH and Wikidata
  • Cell line databases/resources: cancercelllines, CCRID, Cell_Model_Passport, CGH-DB, CLDB, ColonAtlas, Cosmic-CLP, dbMHC, DepMap, DSMZCellDive, ESTDAB, FCS-Free, FlyBase_Cell_line, GDSC, hPSCreg, ICLDB, IGRhCellID, IHW, IPD-IMGT/HLA, LIMORE, LINCS_HMS, LINCS_LDP, Lonza, SKIP, SKY/M-FISH/CGH, SLKBase and TOKU-E
  • Resources that list cell lines as samples: 4DN, ABCD, ArrayExpress, BioGrid_ORCS_Cell_line, BioSample, BioSamples, ChEMBL (cells and targets), Cosmic, dbGAP, EGA, ENCODE, GEO, IARC_TP53, IGSR, LiGeA, MetaboLights, PharmacoDB, PRIDE, Progenetix and PubChem_Cell_line
• Information on when a Cellosaurus entry was created, when it was last updated and which version of the entry is currently available

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Some background information

Cellosaurus is developed by Amos Bairoch of the CALIPHO group at the SIB - Swiss Institute of Bioinformatics. It was initiated to be used as a cell line controlled vocabulary in the context of the neXtProt knowledgebase, but it quickly become apparent that there was a need for a cell line knowledge resource that would serve the needs of individual researchers, cell line distributors and bioinformatic resources. This leads to an increase of the scope and depth of the content of Cellosaurus.

Cellosaurus is:

• A participant of the Resource Identification Initiative (RII)
• An active contributor to the work of the International Cell Line Authentication Committee (ICLAC)
• An Global Core Biodata Resource
• An ELIXIR Core Data Resource
• An IRDiRC Recognized Resource

Reference for Cellosaurus:
Bairoch A.
The Cellosaurus, a cell line knowledge resource.
J. Biomol. Tech. 29:25-38(2018)
DOI: 10.7171/jbt.18-2902-002; PMID: 29805321

We have chosen to apply to Cellosaurus the Creative Commons Attribution 4.0 International Licence (CC BY 4.0).