Biology:Cellosaurus

From HandWiki
Short description: On-line knowledge resource on cell lines


Cellosaurus
Content
DescriptionCellosaurus: a knowledge resource on cell lines
Data types
captured		Cell lines
OrganismsVertebrate, Insect, Tick
Contact
Research centreSwiss Institute of Bioinformatics
LaboratoryCALIPHO
Author(s)Amos Bairoch
Access
Data formatFlat file database, OBO and XML
Websitewww.cellosaurus.org
Download URLftp://ftp.expasy.org/databases/cellosaurus
Web service URLAPI https://api.cellosaurus.org/
Tools
Web applicationSearch
Miscellaneous
Software licenseCreative Commons CC BY 4.0
Software versioningYes
Data release
frequency		4 to 6 releases per year
Curation policyYes - manual
Bookmarkable
entities		Yes - individual cell line entries

Cellosaurus is an online knowledge base on cell lines, which attempts to document all cell lines used in biomedical research.[1] It is provided by the Swiss Institute of Bioinformatics (SIB). It is an ELIXIR Core Data Resource[2][3] as well as an IRDiRC's Recognized Resource.[4] It is the contributing resource for cell lines on the Resource Identification Portal.[5] As of December 2022, it contains information for more than 144,000 cell lines.[6]

Its scope includes immortalised cell lines, naturally immortal cell lines (example: embryonic stem cells) and finite life cell lines when those are distributed and used widely. The Cellosaurus provides a wealth of manually curated information; for each cell line it lists a recommended name, synonyms and the species of origin. Other types of information include standardised disease terminology (for cancer or genetic disorder cell lines), the transformant used to immortalise a cell line, transfected or knocked-out genes, microsatellite instability, doubling time, gender and age of donor (patient or animal), important sequence variations, web links, publication references and cross-references to close to 100 different databases, ontologies, cell collections and other relevant resources.[1][7]

Since many cell lines used in research have been misidentified or contaminated, the Cellosaurus keeps track of problematic cell lines, including all those listed in the International Cell Line Authentication Committee (ICLAC)[8] tables. For human as well as some dog cell lines, it provides short tandem repeat (STR) profile information. Since July 2018, cell lines in the Cellosaurus are represented as items in Wikidata.[1] In March 2020, the Cellosaurus created a page containing cell line information relevant to SARS-CoV-2 in response to the COVID-19 pandemic.[9]

The Cellosaurus encyclopedia is widely recognized as an authoritative source for cell line information, providing unique identifiers [10][11] and as source of curated information.[12][13][14]

References

  1. ↑ 1.0 1.1 1.2 Bairoch Amos (2018). "The Cellosaurus, a cell-line knowledge resource". Journal of Biomolecular Techniques 29 ([Epub ahead of print): 1–14. doi:10.7171/jbt.18-2902-002. PMID 29805321. 
  2. ↑ Dubar, Elsa. "Cellosaurus and Rhea join the portfolio of ELIXIR Core Data Resources" (in en-gb). https://www.sib.swiss/about-sib/news/10817-cellosaurus-and-rhea-join-elixir-core-data-resources. 
  3. ↑ "Rhea, Reactome and Cellosaurus acquire ELIXIR's highest quality label for databases" (in en). 2020-12-24. https://elixir-europe.org/news/rhea-reactome-cellosaurus-CDRs. 
  4. ↑ "New IRDiRC Recognized Resource: Cellosaurus". https://irdirc.org/new-irdirc-recognized-resource-cellosaurus/. 
  5. ↑ "RRID | Searching in Cell Lines". https://scicrunch.org/resources/Cell%20Lines/source/SCR_013869-1/search?q=%2A&l=. 
  6. ↑ "Expasy - Cellosaurus". https://web.expasy.org/cellosaurus/. 
  7. ↑ "Description of the Cellosaurus - a knowledge resource on cell lines". https://web.expasy.org/cellosaurus/description.html. 
  8. ↑ "Database of Cross-Contaminated or Misidentified Cell Lines". http://iclac.org/wp-content/uploads/Cross-Contaminations-v8_0.pdf. 
  9. ↑ "Cellosaurus - SARS-CoV-2 relevant information" (in en-US). https://www.cellosaurus.org/sars-cov-2.html. 
  10. ↑ "RRIDs: How did we get here and where are we going?" (in en). 2017-05-11. https://elifesciences.org/inside-elife/ff683ecc/rrids-how-did-we-get-here-and-where-are-we-going. 
  11. ↑ Groll, Helga; Rodgers, Peter A, eds (2018-11-01). Decision letter: Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. doi:10.7554/elife.41676.020. 
  12. ↑ Horbach, Serge P. J. M.; Halffman, Willem (2017-10-12). "The ghosts of HeLa: How cell line misidentification contaminates the scientific literature". PLOS ONE 12 (10): e0186281. doi:10.1371/journal.pone.0186281. ISSN 1932-6203. PMID 29023500. Bibcode: 2017PLoSO..1286281H. 
  13. ↑ Ong, Edison; Sarntivijai, Sirarat; Jupp, Simon; Parkinson, Helen; He, Yongqun (December 2017). "Comparison, alignment, and synchronization of cell line information between CLO and EFO". BMC Bioinformatics 18 (S17): 557. doi:10.1186/s12859-017-1979-z. ISSN 1471-2105. PMID 29322915. 
  14. ↑ Hattori, Emi; Oyama, Rieko; Kondo, Tadashi (2019-02-13). "Systematic Review of the Current Status of Human Sarcoma Cell Lines". Cells 8 (2): 157. doi:10.3390/cells8020157. ISSN 2073-4409. PMID 30781855. 

External links



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