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


This is the release notes for Cellosaurus version 49 of May 2024

1) Statistics

153642 cell lines (113673 human, 27737 mouse, 2887 rat)
   841 species represented
114358 synonyms
454841 cross-references to 110 resources (cell line catalogs, databases, ontologies, etc.)
160014 references to 27882 distinct publications (papers, patents, theses, etc.)
 14370 web links

  8855 human, mouse and dog cell lines with STR profiles (from 885 distinct sources)

  2443 NCIt and 1351 ORDO (Orphanet) disease terms cited
   834 UBERON and 260 CL terms cited

Since release 48 of January 2024:
  1415 entries were created
 15091 entries were updated

2) Integration of plant cell lines

We introduced a small number (30) of plant cell lines at this release. These
are the cell lines that have been (or are still) used by the community. Many
other plant cell lines have been established but seem to never have been used.
We do not plan to include them in the Cellosaurus.

The plant cell line entries have a new CC group line:

CC   Group: Plant cell line.

3) Changes in the DR lines

3a) Cross-references were added to the cell lines entries from the Hysigen
cell line collection.

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: Hysigen
Name  : Hysigen cell line collection
Server: https://hysigen.com/
Db_URL: https://hysigen.com/%s.html
Term. : No
Cat   : Cell line collections (Providers)
//

Example:
DR   Hysigen; CGKO-M2345

3b) Cross-references were added to the cell lines entries from the RIKEN BRC
Experimental Plant Division (RIKEN_BRC_EPD).

Corresponding entry in the file cellosaurus_xrefs.txt:

Abbrev: RIKEN_BRC_EPD
Name  : RIKEN BRC Experimental Plant Division cell lines
Server: https://epd.brc.riken.jp/en/
Db_URL: https://plant.rtc.riken.jp/resource/cell_line/cell_line_detail.html?brcno=%S
Term. : No
Cat   : Cell line collections (Providers)
//

Example:
DR   RIKEN_BRC_EPD; rpc00001

4) Changes in the XML file

We made a number of important changes in the XML format file, these are
accompanied by the corresponding changes in the XSD file.

- The elements <terminology-list>, <terminology> and <cv-term> are now
  obsolete.
- The <cv-term> elements are replaced with <xref> elements.
- The <xref> element has been modified: the <property-list> sub-element has
  been replaced with <label> and <discontinued> sub-elements.
- The <comment> element with category="Transfected with" now have an optional
  <xref> element instead of the previous <xref-list> element.
- In the elements <comment>, <doubling-time>, <genome-ancestry>, <hla-typing>,
  <microsatellite-instability>, <monoclonal-antibody-isotype>,
  <sequence-variation> and <str-list>, the source of the annotation, when
  available, now appears in a <source> element.
- When multiple sources are expected, <source> elements appear in a
  <source-list> element.
- As a consequence the elements <comment-sources>, <doubling-time-sources>,
  <genome-ancestry-source>, <hla-typing-source>,
  <microsatellite-instability-sources>, <monoclonal-antibody-isotype-sources>,
  <str-sources>, <variation-sources> are now obsolete.
- The <source> element can contain plain text and/or either a <xref> or a
  <reference> element.

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