Cellosaurus

{{Short description|On-line knowledge resource on cell lines}}

{{COI|date=July 2018}}

{{infobox biodatabase

|title = Cellosaurus

|logo =

|description = Cellosaurus: a knowledge resource on cell lines

|scope = Cell lines

|organism = Vertebrate, Insect, Tick

|center = Swiss Institute of Bioinformatics

|laboratory = CALIPHO

|author = Amos Bairoch

|pmid =

|released =

|standard =

|format = Flat file database, OBO and XML

|url = {{URL|https://www.cellosaurus.org/}}

|download = ftp://ftp.expasy.org/databases/cellosaurus

|webservice = API https://api.cellosaurus.org/

|sql =

|sparql =

|webapp = Search

|standalone =

|license = Creative Commons CC BY 4.0

|versioning = Yes

|frequency = 4 to 6 releases per year

|curation = Yes - manual

|bookmark = Yes - individual cell line entries

|version =

}}

Cellosaurus is an online knowledge base on cell lines, which attempts to document all cell lines used in biomedical research.{{cite journal |author=Bairoch Amos|title=The Cellosaurus, a cell-line knowledge resource |journal=Journal of Biomolecular Techniques |volume=29 |pages=1–14 |year=2018 |pmid=29805321 |doi=10.7171/jbt.18-2902-002 |issue=[Epub ahead of print |pmc=5945021}} It is provided by the Swiss Institute of Bioinformatics (SIB). It is an ELIXIR Core Data Resource{{Cite web|last=Dubar|first=Elsa|title=Cellosaurus and Rhea join the portfolio of ELIXIR Core Data Resources|url=https://www.sib.swiss/about-sib/news/10817-cellosaurus-and-rhea-join-elixir-core-data-resources|access-date=2021-10-19|website=www.sib.swiss|language=en-gb}}{{Cite web|date=2020-12-24|title=Rhea, Reactome and Cellosaurus acquire ELIXIR's highest quality label for databases|url=https://elixir-europe.org/news/rhea-reactome-cellosaurus-CDRs|access-date=2021-10-19|website=ELIXIR|language=en}} as well as an IRDiRC's Recognized Resource.{{Cite web|title=New IRDiRC Recognized Resource: Cellosaurus|url=https://irdirc.org/new-irdirc-recognized-resource-cellosaurus/|access-date=2021-11-02|website=irdirc.org}} It is the contributing resource for cell lines on the Resource Identification Portal.{{Cite web|url=https://scicrunch.org/resources/Cell%20Lines/source/SCR_013869-1/search?q=%2A&l=|title = RRID | Searching in Cell Lines}} As of December 2022, it contains information for more than 144,000 cell lines.{{Cite web|title=Expasy - Cellosaurus|url=https://web.expasy.org/cellosaurus/|access-date=2021-10-19|website=web.expasy.org}}

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.{{Cite web|url=https://web.expasy.org/cellosaurus/description.html|title=Description of the Cellosaurus - a knowledge resource on cell lines|website=web.expasy.org|access-date=2020-04-13}}

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){{Cite web|title=Database of Cross-Contaminated or Misidentified Cell Lines|url=http://iclac.org/wp-content/uploads/Cross-Contaminations-v8_0.pdf|url-status=live|archive-url=https://web.archive.org/web/20161220074209/http://iclac.org/wp-content/uploads/Cross-Contaminations-v8_0.pdf |archive-date=2016-12-20 }} 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. In March 2020, the Cellosaurus created a page containing cell line information relevant to SARS-CoV-2 in response to the COVID-19 pandemic.{{Cite web|url=https://www.cellosaurus.org/sars-cov-2.html|title=Cellosaurus - SARS-CoV-2 relevant information|website=www.cellosaurus.org|language=en-US|access-date=2022-09-01}}

The Cellosaurus encyclopedia is widely recognized as an authoritative source for cell line information, providing unique identifiers {{Cite web|date=2017-05-11|title=RRIDs: How did we get here and where are we going?|url=https://elifesciences.org/inside-elife/ff683ecc/rrids-how-did-we-get-here-and-where-are-we-going|access-date=2021-10-19|website=eLife|language=en}}{{Cite journal|date=2018-11-01|editor-last=Groll|editor-first=Helga|editor2-last=Rodgers|editor2-first=Peter A|title=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|doi-access=free}} and as source of curated information.{{Cite journal|last1=Horbach|first1=Serge P. J. M.|last2=Halffman|first2=Willem|date=2017-10-12|title=The ghosts of HeLa: How cell line misidentification contaminates the scientific literature|journal=PLOS ONE|volume=12|issue=10|pages=e0186281| pmid=29023500| doi=10.1371/journal.pone.0186281|pmc=5638414|bibcode=2017PLoSO..1286281H|issn=1932-6203|doi-access=free}}{{Cite journal|last1=Ong|first1=Edison|last2=Sarntivijai|first2=Sirarat|last3=Jupp|first3=Simon|last4=Parkinson|first4=Helen|last5=He|first5=Yongqun|date=December 2017|title=Comparison, alignment, and synchronization of cell line information between CLO and EFO|journal=BMC Bioinformatics|volume=18|issue=S17|page=557|doi=10.1186/s12859-017-1979-z|pmid=29322915|pmc=5763470|issn=1471-2105 |doi-access=free }}{{Cite journal|last1=Hattori|first1=Emi|last2=Oyama|first2=Rieko|last3=Kondo|first3=Tadashi|date=2019-02-13|title=Systematic Review of the Current Status of Human Sarcoma Cell Lines|journal=Cells|volume=8|issue=2|pages=157|doi=10.3390/cells8020157 |pmid=30781855|pmc=6406745|issn=2073-4409|doi-access=free}}