News:Cellosaurus release 45 is available
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Amos Bairoch ▴ 120

Cellosaurus release 45 is available at https://www.cellosaurus.org/

1) Statistics

  • 145368 cell lines (107864 human, 26311 mouse, 2734 rat)
  • 805 species represented
  • 106123 synonyms
  • 421462 cross-references to 103 ontologies, databases, catalogs, etc.
  • 152339 references to 26279 distinct publications (papers, patents, theses, etc.)
  • 14157 web links
  • 8520 human, mouse and dog cell lines with STR profiles (from 796 distinct sources)

Since release 44 of December 2022: 1071 entries were created and 144567 entries were updated (note: all entries were updated due to the change in the OX line described below).

2) Changes concerning the OX (species of origin) line

We have added, in between parenthesis, the species common name after the binomial nomenclature designation

For example:
OX   NCBI_TaxID=9606; ! Homo sapiens
is now:
OX   NCBI_TaxID=9606; ! Homo sapiens (Human)

3) Changes in CC lines

3a) Change in the referencing of Cellosaurus entries

In comments lines references to Cellosaurus entries used to be indicated using the accession of the entry between brackets "(CVCL_XXXX)". Accessions are now prefixed by 'Cellosaurus=' as in "(Cellosaurus=CVCL_XXXX)".

For example:
CC   Characteristics: Control cell line for 293 TRE/FLAG-POLK (CVCL_4W26).
is now:
CC   Characteristics: Control cell line for 293 TRE/FLAG-POLK (Cellosaurus=CVCL_4W26).

3b) Changes in the CC Misspelling

In the XML format information concerning the "Misspelling" comment is now structured and represented in the "misspelling-list" element.

3c) Changes in the CC Omics

We have changed the label of 4 existing "Omics" tags relevant to transcriptome studies to make them more homogenous.

CC   Omics: Deep RNAseq analysis.
is now:
CC   Omics: Transcriptome analysis by RNAseq.

CC   Omics: ESTs sequenced.
is now:
CC   Omics: Transcriptome analysis by ESTs sequencing.

CC   Omics: Single cell RNAseq analysis.
is now:
CC   Omics: Transcriptome analysis by single cell RNAseq.

CC   Omics: Transcriptome analysis.
is now:
CC   Omics: Transcriptome analysis by microarray.

And we introduced two new transcriptome studies tags:

CC   Omics: Transcriptome analysis by massively parallel signature sequencing (MPSS).
CC   Omics: Transcriptome analysis by serial analysis of gene expression (SAGE).

4) Changes concerning cross-references

Cross-references were added to the NIH Human Embryonic Stem Cell Registry. Prevously web links were provided to this resources, but we upgraded them to cross-references.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: NIHhESC
Name  : NIH Human Embryonic Stem Cell Registry
Server: https://grants.nih.gov/stem_cells/registry/current.htm
Db_URL: https://grants.nih.gov/stem_cells/registry/current.htm?ID=%s
Term. : No
Cat   : Cell line databases/resources

Example: DR NIHhESC; NIHhESC-10-0043

knowledgebase cell-line • 423 views
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