News:Cellosaurus release 40 is available
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11 months ago
Amos Bairoch ▴ 110

Cellosaurus release 40 is available on the ExPASy server:

https://web.expasy.org/cellosaurus/

1) Statistics

  • 134839 cell lines (101276 human, 22999 mouse, 2498 rat)
  • 747 species represented
  • 96745 synonyms
  • 396097 cross-references to 97 ontologies, databases, catalogs, etc.
  • 138234 references to 23257 distinct publications (papers, patents, theses, etc.)
  • 13484 web links
  • 8032 human, mouse and dog cell lines with STR profiles (from 669 distinct sources)

Since release 39 of September 2021: 3890 entries were created and 16818 entries were updated

2) Changes concerning cross-references

2a) Change in the file cellosaurus_xref.txt

We have changed the format of the description of resources to which the Cellosaurus cross-reference to. We have added a new field "Term." (for "Terminology") that can either have the value "Yes" or "No". This field allows to distinguish between resources that are used in the context of the Cellosaurus as a source of a terminology (examples: gene names, chemical compounds, species, etc) to those that are not.

Examples of both type of cross-references:

Abbrev: ATCC
Name  : American Type Culture Collection
Server: https://www.atcc.org/
Db_URL: https://www.atcc.org/Products/%s
Term. : No
Cat   : Cell line collections

Abbrev: NCBI_TaxID
Name  : NCBI taxonomy database
Server: https://www.ncbi.nlm.nih.gov/taxonomy
Db_URL: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=%s&lvl=3
Term. : Yes
Cat   : Taxonomy

2b) Changes in the cross-references to FlyBase

We have cross references to FlyBase for two types of "objects": cell lines and genes. In the first case we are cross-referencing to FlyBase as if it was a cell line database/resource and in the other case as a terminology resource for gene names and their associated information. We therefore decided to use distinct cross-references for FlyBase cell lines and genes so as to clear up any semantic confusion.

Thus what was formerly:

Abbrev: FlyBase
Name  : Drosophila genome database
Server: https://flybase.org
Db_URL: https://flybase.org/reports/%s.html
Cat   : Organism-specific databases

is now split into:

Abbrev: FlyBase_Cell_line
Name  : Drosophila genome database; cell line entry
Server: https://flybase.org/cgi-bin/cvreport.pl?id=FBbt%3A00005329
Db_URL: https://flybase.org/reports/%s.html
Term. : No
Cat   : Cell line databases/resources

Example: DR FlyBase; FBtc9000017

Abbrev: FlyBase_Gene
Name  : Drosophila genome database; gene entry
Server: https://flybase.org
Db_URL: https://flybase.org/reports/%s.html
Term. : Yes
Cat   : Organism-specific databases

Example: CC Transfected with: FlyBase_Gene; FBgn0000546; EcR.

2c) Cross-references were added to the Abcam cell line products.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: Abcam
Name  : Abcam cell line products
Server: https://www.abcam.com/nav/cell-lines-and-lysates
Db_URL: https://www.abcam.com/%s.html
Term. : No
Cat   : Cell line collections

Example: DR Abcam; ab266619

2d) Cross-references were added to the European Genome-phenome Archive (EGA).

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: EGA
Name  : European Genome-Phenome Archive
Server: https://ega-archive.org/
Db_URL: https://ega-archive.org/studies/%s
Term. : No
Cat   : Sequence databases

Example: DR EGA; EGAS00000000056

2e) Cross-references were added to the National Repository of Fish Cell line (NRFC) in Lucknow (India). Prevously web links were provided to this resources, but we upgraded them to cross-references.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: NRFC
Name  : National Repository of Fish Cell Line
Server: https://mail.nbfgr.res.in/nrfc/
Db_URL: https://mail.nbfgr.res.in/nrfc/celldetail.php?id=%s
Term. : No
Cat   : Cell line collections

Example: DR NRFC; 16

2f) CCLE cross references have been removed

Because the data of the Cancer Cell Line Encyclopedia (CCLE) is now completely integrated in the Cancer Dependency Map (DepMap) portal and that links that go to the original CCLE web site are now redirected to DepMap we have removed these extraenous cross-references.

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