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News: Cellosaurus release 30 is available
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Cellosaurus release 30 is available on the ExPASy server: https://web.expasy.org/cellosaurus/

1) Statistics

  • 112983 cell lines (84432 human, 19675 mouse, 2075 rat)
  • 625 species represented
  • 73553 synonyms
  • 331707 cross-references to 85 ontologies, databases, catalogs, etc.
  • 104057 references to 17422 distinct publications (papers, patents, theses, etc.)
  • 17769 web links
  • 6482 human, mouse and dog cell lines with STR profiles (from 434 distinct sources)

2) Addition of a date/entry history line

Starting with this release we introduced a new line type ("DT") which provides information on when a Cellosaurus entry was created, when it was last updated and which version of the entry is currently available.

In the text version of the Cellosaurus, the format of the DT line is the following:

DT Created: DD-MM-YY; Last updated: DD-MM-YY; Version: nn

Example:

DT Created: 06-06-12; Last updated: 07-09-18; Version: 5

The DT line is mandatory. It is the last line of the entry before the "//" termination line.

In the XML version of the Cellosaurus, the information on the DT line is available using the following definition:

<xs:attribute name="created" type="xs:date" use="required"/>
<xs:attribute name="last_updated" type="xs:date" use="required"/>
<xs:attribute name="entry_version" type="xs:integer" use="required"/>

In the OBO version of the Cellosaurus only the date of creation of the entry is indicated using the "creation_date" tag. Example: creation_date: 2012-10-22T00:00:00Z

3) Changes in the CC lines

3a) Genome ancestry

Julie Dutil has accepted to make available in the Cellosaurus the data from the ECLA (Estimated Cell Line Ancestry) tool (http://ecla.moffitt.org/) developed by her group. Currently ECLA computes the estimated ancestry of about 1,400 cancer cell lines. This data is stored in a new CC line termed "Genome ancestry". In the text version of the Cellosaurus, the format of this CC line is the following:

CC Genome ancestry: African=x1%; Native American=x2%; East Asian, North=x3%; East Asian, South=x4%; South Asian=x5%; European, North=x6%; European, South=x7% (Reference_or_Xref).

Example:

CC Genome ancestry: African=0.21%; Native American=0.92%; East Asian, North=1.76%; East Asian, South=0.01%; South Asian=1.21%; European, North=67.1%; European, South=28.8% (PubMed=30894373).

4) Changes in the DR lines

4a) Cross-references were added to the China Center for Type Culture Collection.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: CCTCC Name : China Center for Type Culture Collection Server: http://www.cctcc.org/ Db_URL: None Cat : Cell line collections

Example:

DR CCTCC; GDC057

4b) Cross-references were added to the Iranian Biological Research Center (IBRC) cell line collection.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: IBRC Name : Iranian Biological Research Center cell line collection Server: http://www.ibrc.ir Db_URL: None Cat : Cell line collections

Example:

DR IBRC; C10001

4c) Change in the abbreviation of a cross-reference

The IPD-IMGT/HLA database was previously abbreviated IMGT/HLA.

Example:

DR IMGT/HLA; 10074

Is now:

DR IPD-IMGT/HLA; 10074

5) Change in the ST lines: introduction of STR markers for mouse cell lines

Starting with this release we will capture STR marker information relevant to mouse cell lines. In a first instance we are introducing 19 markers: STR 1-1, STR 1-2, STR 2-1, STR 3-2, STR 4-2, STR 5-5, STR 6-4, STR 6-7, STR 7-1, STR 8-1, STR 9-2, STR 11-2, STR 12-1, STR 13-1, STR 15-3, STR 17-2, STR 18-3, STR 19-2 and STR X-1

We are prefixing these STR markers with the word "Mouse" to insure that there is no confusion with human STR markers.

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