A major contributor to this article appears to have a close connection with its subject. (July 2018) |
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]
| Content | |
|---|---|
| Description | Cellosaurus: a knowledge resource on cell lines |
| Data types captured | Cell lines |
| Organisms | Vertebrate, Insect, Tick |
| Contact | |
| Research center | Swiss Institute of Bioinformatics |
| Laboratory | CALIPHO |
| Authors | Amos Bairoch |
| Access | |
| Data format | Flat file database, OBO and XML |
| Website | www |
| Download URL | ftp://ftp.expasy.org/databases/cellosaurus |
| Web service URL | API https://api.cellosaurus.org/ |
| Tools | |
| Web | Search |
| Miscellaneous | |
| License | Creative Commons CC BY 4.0 |
| Versioning | Yes |
| Data release frequency | 4 to 6 releases per year |
| Curation policy | Yes - manual |
| Bookmarkable entities | Yes - individual cell line entries |
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
edit- ^ a b c 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. PMC 5945021. PMID 29805321.
- ^ Dubar, Elsa. "Cellosaurus and Rhea join the portfolio of ELIXIR Core Data Resources". www.sib.swiss. Retrieved 2021-10-19.
- ^ "Rhea, Reactome and Cellosaurus acquire ELIXIR's highest quality label for databases". ELIXIR. 2020-12-24. Retrieved 2021-10-19.
- ^ "New IRDiRC Recognized Resource: Cellosaurus". irdirc.org. Retrieved 2021-11-02.
- ^ "RRID | Searching in Cell Lines".
- ^ "Expasy - Cellosaurus". web.expasy.org. Retrieved 2021-10-19.
- ^ "Description of the Cellosaurus - a knowledge resource on cell lines". web.expasy.org. Retrieved 2020-04-13.
- ^ "Database of Cross-Contaminated or Misidentified Cell Lines" (PDF). Archived (PDF) from the original on 2016-12-20.
- ^ "Cellosaurus - SARS-CoV-2 relevant information". www.cellosaurus.org. Retrieved 2022-09-01.
- ^ "RRIDs: How did we get here and where are we going?". eLife. 2017-05-11. Retrieved 2021-10-19.
- ^ 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. S2CID 239787612.
{{cite journal}}: Cite journal requires|journal=(help) - ^ 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. Bibcode:2017PLoSO..1286281H. doi:10.1371/journal.pone.0186281. ISSN 1932-6203. PMC 5638414. PMID 29023500.
- ^ 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. PMC 5763470. PMID 29322915.
- ^ 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. PMC 6406745. PMID 30781855.