_____     _ _
   / ____|   | | |
  | |     ___| | | ___  ___  __ _ _   _ _ __ _   _ ___
  | |    / _ \ | |/ _ \/ __|/ _` | | | | '__| | | / __|
  | |___|  __/ | | (_) \__ \ (_| | |_| | |  | |_| \__ \
   \_____\___|_|_|\___/|___/\__,_|\__,_|_|   \__,_|___/


This is the release notes for Cellosaurus version 52 of April 2025

1) Statistics

163868 cell lines (121295 human, 29536 mouse, 3115 rat)
   891 species represented
124476 synonyms
468374 cross-references to 116 resources (cell line catalogs, databases, ontologies, etc.)
166137 references to 29267 distinct publications (papers, patents, theses, etc.)
 15169 web links

  9173 human, mouse and dog cell lines with STR profiles (from 941 distinct sources)

  2569 NCIt and 1384 ORDO (Orphanet) disease terms cited
   854 UBERON, 276 CL and 11 PO terms cited

Since release 51 of December 2024:
  2671 entries were created
 39770 entries were updated

2) Changes in the format of the WW lines

In previous releases, a WW line contained only a web address (URL).

Examples:
WW   https://www.thermofisher.com/ch/en/home/technical-resources/cell-lines/h/cell-lines-detail-204.html
WW   https://www.vircell.com/en/products/hep-2-cell-line
WW   https://iclac.org/wp-content/uploads/Cross-Contaminations_v13_distribution.xlsx
WW   https://es.wikipedia.org/wiki/C%C3%A9lulas_HEp-2

Starting with this release, a WW contains four distinct fields as shown here:

WW   Info|Provider; Institution/organization_name|-; Document/catalog_identifier|-; URL

- The first field ("Info" or "Provider") designates whether the associated
  web link pertains to data relevant to the cell line or pertains to
  information regarding an entity supplying the cell line.
- The name or abbreviation of the institution or organization referenced by
  the web link; if unavailable, a dash ("-") is used as a placeholder.
- The document or catalog identifier; if unavailable, a dash ("-") is used
  as a placeholder.

Examples:
WW   Info; -; -; http://hek293genome.org/v2/
WW   Info; ICLAC; -; https://iclac.org/wp-content/uploads/Cross-Contaminations_v13_distribution.xlsx
WW   Info; Wikipedia; -; https://en.wikipedia.org/wiki/KBM-7_cells
WW   Provider; BRICS; BRICS0120; http://www.brics.ac.cn/cell/template/cell/cell_detail.html?id=3924
WW   Provider; Tufts TTIC; T001034; https://viceprovost.tufts.edu/research-tool-cell-line-near-haploid-mammalian-cell-line

3) Changes in the CC omics comment

This comment is now structured in a hierarchical manner with between 1 to 4
levels.

The first level is made of 8 different categories of omics experiments:

Genomics
Glycomics
Lipidomics
Metabolomics
Phenotyping
Proteomics
Transcriptomics
Variations

The next levels allows more precise description of specific experiments.

Examples:
CC   Omics: Genomics; Whole exome sequencing.
CC   Omics: Glycomics; N-glycan profiling.
CC   Omics: Phenotyping; CRISPR screening.
CC   Omics: Proteomics; PTM; Phosphorylation; Quantitative.
CC   Omics: Proteomics; Subcellular; Mitochondrion.
CC   Omics: Transcriptomics; RNAseq; Single cell.
CC   Omics: Variations; SNP array analysis.

4) Changes in the DR lines

4a) Cross-references were added to the cell lines products from Evercyte.

Prevously web links were provided to this resources, but we upgraded them to
cross-references.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: Evercyte
Name  : Evercyte cell line products
Server: https://evercyte.com/
Db_URL: https://evercyte.com/?s=%s
Term. : No
Cat   : Cell line collections (Providers)
//

Example:
DR   Evercyte; CHT-008-0164

4b) Cross-references were added to the expression data in the Functional
Annotation of the Mammalian Genome - Samples, Transcription initiation
And Regulators (FANTOM5_SSTAR) project.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: FANTOM5_SSTAR
Name  : Functional Annotation of the Mammalian Genome - Samples, Transcription initiation And Regulators
Server: https://fantom.gsc.riken.jp/5/sstar/Main_Page
Db_URL: https://fantom.gsc.riken.jp/5/sstar/FF:%s
Term. : No
Cat   : Gene expression databases
//

Example:
DR   FANTOM5_SSTAR; 10563-108A5

4c) Cross-references were added to the cell lines products from GenScript.

Prevously web links were provided to this resources, but we upgraded them to
cross-references.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: GenScript
Name  : GenScript cell line products
Server: https://www.genscript.com/cell_lines.html
Db_URL: https://www.genscript.com/search?q=%s
Term. : No
Cat   : Cell line collections (Providers)
//

Example:
DR   GenScript; M00250

4d) Cross-references were added to the cell lines products from InvivoGen.

Prevously web links were provided to this resources, but we upgraded them to
cross-references.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: InvivoGen
Name  : InvivoGen cell line products
Server: https://www.invivogen.com/cell-lines
Db_URL: https://www.invivogen.com/search?sq=%s
Term. : No
Cat   : Cell line collections (Providers)
//

Example:
DR   InvivoGen; 293d-null

---------------------------------------
Amos Bairoch
CALIPHO group
SIB - Swiss Institute of Bioinformatics
Geneva; Switzerland
---------------------------------------