News:Cellosaurus release 46
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11 months ago
Amos Bairoch ▴ 120

Cellosaurus release 46 is available at https://www.cellosaurus.org/

1) Statistics

  • 146062 cell lines (107991 human, 26352 mouse, 2757 rat)
  • 805 species represented
  • 106584 synonyms
  • 422419 cross-references to 103 ontologies, databases, catalogs, etc.
  • 153209 references to 26479 distinct publications (papers, patents, theses, etc.)
  • 14162 web links
  • 8566 human, mouse and dog cell lines with STR profiles (from 800 distinct sources)

Since release 45 of March 2023: 427 entries were created and 126171 entries were updated (many entries were updated due to the changes in the CC sampling lines described below).

2) Changes concerning the CC Derived from sampling/metastatic sites lines

We have completely changed the format and content of these lines and we have also introduced cross-references to two important resources: the UBERON cross-species anatomy ontology and the CL cell (type) ontology.

There is now a unique "site" CC line which is called "Derived from site:" It is in the format:

Derived from site: Site_flag; Cellosaurus_site_term[; Note=Note_text][; UBERON=Uberon_ac[+UBERON=Uberon_ac]].

Where the "Site_flag" is either "Metastatic" or "In situ".

As indicated in the format description there are now cross-references to UBERON ontology terms.

Examples:
CC   Derived from site: In situ; Eye, cornea, epithelium; UBERON=UBERON_0001772.
CC   Derived from site: In situ; Upper jaw, hypodermis; UBERON=UBERON_0001709+UBERON_0002072.
CC   Derived from site: Metastatic; Bone marrow; UBERON=UBERON_0002371.

Information on the cell type from which the cell line originate is now stored in a separate CC line: "Cell type" and is in the format:

Cell type: Cellosaurus_cell_type; CL=CL_Accession.

As indicated in the format description there are now cross-references to CL ontology terms.

Examples:
CC   Cell type: Fibroblast of skin; CL=CL_0002620.
CC   Cell type: Brain microvascular endothelial cell; CL=CL_2000044.
CC   Cell type: Epithelial cell of ovary; CL=CL_2000064.

3) Changes in the XML file

Three new element have been created: "cell-type", "derived-from-site" and "doubling-time". The first two for the annotations described in the previous section and the last one to allow a structured representation of the doubling time information which was formerly represented as a text comment.

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