Cellosaurus release 50 is available on https://www.cellosaurus.org/
1) Statistics
- 159461 cell lines (118612 human, 28415 mouse, 2949 rat)
- 878 species represented
- 119844 synonyms
- 464228 cross-references to 112 resources (cell line catalogs, databases, ontologies, etc.)
- 161523 references to 28313 distinct publications (papers, patents, theses, etc.)
- 14241 web links
- 8986 human, mouse and dog cell lines with STR profiles (from 896 distinct sources)
- 2490 NCIt and 1360 ORDO (Orphanet) disease terms cited
- 840 UBERON, 265 CL and 11 PO terms cited
Since release 49 of May 2024: 5821 entries were created and 30218 entries were updated
2) Change in the CC lines
2a) Replacement of the CC "transfected with" by a new CC "Genetic integration".
The format of the "Genetic integration" CC is:
CC Genetic integration: Method=Method_name; Gene=Resource_abbrev; %s; Gene/protein_name[ (Note=Free_text)].
Where: Method_name is currently one of the following:
CRISPR/Cas9
Homologous recombination
PiggyBac transposition
TALEN
Transduction
Transfection/transduction
Transfection
Transgenic fish
Transgenic mouse
Transgenic rat
ZFN
Where: Resource_abbrev is one of the following external resource:
CGNC
FlyBase_Gene
FPbase
HGNC
MGI
RGD
UniProtKB
VGNC
Two of these resources are newly used in the Cellosaurus: CGNC the Chicken Gene Nomenclature Consortium Database and FPbase, the Fluorescent Protein database
Corresponding entries in the file cellosaurus_xrefs.txt:
Abbrev: CGNC
Name : Chicken Gene Nomenclature Consortium Database
Server: http://birdgenenames.org/cgnc/
Db_URL: http://birdgenenames.org/cgnc/GeneReport?id=%s
Term. : Yes
Cat : Organism-specific databases
//
Abbrev: FPbase
Name : Fluorescent Protein database
Server: https://www.fpbase.org/
Db_URL: https://www.fpbase.org/protein/%s/
Term. : Yes
Cat : Sequence databases
//
Examples:
CC Genetic integration: Method=CRISPR/Cas9; Gene=FPbase; BFJKS; TagBFP (Note=Blue fluorescent protein derived from eqFP578).
CC Genetic integration: Method=Transfection; Gene=CGNC; 49631; OVAL/SERPINB14.
CC Genetic integration: Method=Transduction; Gene=HGNC; 11730; TERT.
2b) Breed/subspecies
This comment topic can now optionally have references to one or more Vertebrate Breed Ontology (VBO), FlyBase strain or Rat Strain Ontology (RS) terms.
Here are the relevant descriptions from the cellosaurus_xrefs.txt file:
Topic: Breed/subspecies
Format: CC Breed/subspecies: Breed/subspecies_name[; Resource_abbrev=%s1[+%s2..+%sn]].
Where: Resource_abbrev is one of the following external resource:
FlyBase_Strain
RS
VBO
These are newly used in the Cellosaurus and correspond to the Drosophila genome database; strain entry (FlyBase_Strain), the Rat Strain Ontology (RS) and the Vertebrate Breed Ontology (VBO).
Corresponding entries in the file cellosaurus_xrefs.txt:
Abbrev: FlyBase_Strain
Name : Drosophila genome database; strain entry
Server: https://flybase.org
Db_URL: https://flybase.org/reports/%s.htm
Term. : Yes
Cat : Organism-specific databases
//
Abbrev: RS
Name : Rat Strain Ontology
Server: https://github.com/rat-genome-database/RS-Rat-Strain-Ontology
Db_URL: https://rgd.mcw.edu/rgdweb/ontology/view.html?acc_id=%s
Term : Yes
Cat : Organism-specific databases
//
Abbrev: VBO
Name : Vertebrate Breed Ontology
Server: https://monarch-initiative.github.io/vertebrate-breed-ontology/
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/vbo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252F%s
Term. : Yes
Cat : Taxonomy
//
Examples:
CC Breed/subspecies: Alaskan Malamute; VBO=VBO_0200017.
CC Breed/subspecies: Hereford x Limousin; VBO=VBO_0000232+VBO_0000274.
CC Breed/subspecies: Oregon-R; FlyBase_Strain=FBsn0000276.
CC Breed/subspecies: Berlin-Druckrey IV (BD-IV); RS=RS:0000089.
2c) Derived from site
This comment topic now accepts terms from the Plant Ontology (PO).
Corresponding entry in the file cellosaurus_xrefs.txt:
Abbrev: PO
Name : Plant Ontology
Server: https://browser.planteome.org/amigo
Db_URL: https://www.ebi.ac.uk/ols4/ontologies/po/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252%s
Term. : Yes
Cat : Anatomy/cell type resources
//
Examples:
CC Derived from site: In situ; Hypocotyl; PO=PO_0020100.
CC Derived from site: In situ; Seedling; PO=PO_0008037.
2d) Knockout cell
This comment topic now accept terms from the Chicken Gene Nomenclature Consortium Database (CGNC) described in the section 2a above.
Example:
CC Knockout cell: Method=Targeted integration; CGNC; 9044; XRCC6.
3) Changes in the DR lines
3a) Cross-references were added to the cell lines entries from the Abeomics cell line collection.
Corresponding entry in the file cellosaurus_xrefs.txt:
Abbrev: Abeomics
Name : Abeomics cell line products
https://www.abeomics.com/
https://www.abeomics.com/advanced-search-result?keywords=%s
Term. : No
Cat : Cell line collections (Providers)
//
Example:
DR Abeomics; 14-145ACL
3b) Cross-references were added to the cell lines products from Genomeditech.
Corresponding entry in the file cellosaurus_xrefs.txt:
Abbrev: Genomeditech
Name : Genomeditech cell line products
Server: https://en.genomeditech.com/product?id=9
Db_URL: https://en.genomeditech.com/search?kwd=%s
Term. : No
Cat : Cell line collections (Providers)
//
Example:
DR Genomeditech; GM-C16925
3c) Cross-references were added to the cell lines products from Sigma-Aldrich.
Prevously web links were provided to this resources, but we upgraded them to cross-references.
Corresponding entry in the file cellosaurus_xrefs.txt:
Abbrev: Sigma-Aldrich
Name : Sigma-Aldrich cell line products
Server: https://www.sigmaaldrich.com
Db_URL: https://www.sigmaaldrich.com/catalog/product/sigma/%s
Term. : No
Cat : Cell line collections (Providers)
//
Example:
DR Sigma-Aldrich; CLL1219
3d) HIVReagentProgram cross-references have been merged into BEI_Resources
As indicated on the web site of the HIV Reagent Program: "effective January 14th 2024, the NIH HIV Reagent Program has transitioned into the Biological and Emerging Infections Research Resources Program (BEI-RRP), NIAID's centralized research reagent repository known as BEI Resources. As a result of this transition, HIV reagents are now available through BEI Resources". Thus we have changed the "HIVReagentProgram" cross-references to point to "BEI_Resources".
Example:
DR HIVReagentProgram; ARP-11411
is now:
DR BEI_Resources; ARP-11411
3e) ISCR cross-references have been discontinued
Because the International Stem Cell Registry (ISCR) no longer exists and is no longer archived on the WWW, we have removed the cross-references to this resource.
4) Changes in the cellosaurus_refs.txt file
4a) In the RX line, we have added, when it is available the PubMed Central identifier (PMCID).
Example: RX PubMed=16146350; DOI=10.1208/aapsj070102; PMCID=PMC2751492;
4b) We used to either have references with an authors list (RA line) or with a consortium/group (RG line). We now accept:
- More than 1 RG line per reference
- References with both RA and RG line(s)
Example: RA Worrall D., Ayoubi R., Fotouhi M., McPherson P.S., Southern K., RA Laflamme C.; RG ABIF Consortium; RG NeuroSGC/YCharOS collaborative group;
4c) For consistency with reference resources such as PubMed. We have changed author suffixes "II", "III" and "IV" to respectively "2nd", "3rd" and "4th".
Examples:
RA Wagner L.E. 2nd, Groom L.A., Dirksen R.T., Yule D.I.;
RA Yarosh D.B., Foote R.S., Mitra S., Day R.S. 3rd;
RA Yachnis A.T., Neubauer D.R., Muir D.F. 4th;
4d) For all references to books, book chapters, conference proceedings, technical documents and other miscellaneous type of documents, we used to have the RL line in the following format:
RL (In) Title; Editors; page-range; Publisher; City (Year).
We now have five different styles to cater for the specificity of the corresponding category of documents.
-1 Books
RL (In book) Title_of_book; ISBN; page-range; Publisher; City; Country (Year).
Example:
RL (In book) ISBN 9780122219702; pp.1-733; Academic Press; London; United Kingdom (2001).
-2 Book chapters
RL (In book chapter) Title_of_chapter; Editors; page-range; Publisher; City; Country (Year).
Example:
RL (In book chapter) Cancer treatment an update; Banzet P., Holland J.F., Khayat D., Weil M. (eds.); pp.179-184; Springer; Paris; France (1994).
-3 Conference/congress abstracts or posters
RL (In conference) Title_of_conference; page-range; Conference_institution; City; Country (Year).
Example:
RL (In conference) Proceedings of the Vth international workshop on multiple myeloma; pp.3.83-3.83; International Myeloma Foundation; La Baule; France (1995).
-4 Technical documents
RL (In technical document) Title_of_document_series; page-range; institution_name; City; Country (Year).
Example:
RL (In technical document) ATCC application note 17; pp.1-4; ATCC; Manassas; USA (2016).
-5 Miscellanous documents
RL (In misc. document) Document_title; page-range; institution_name; City; Country (Year).
Example:
RL (In misc. document) Annual report 2003. Federal Research Centre for Virus Diseases of Animals; pp.41-48; BFAV; Insel Riem; Germany (2004).
5) Changes in the XML file
Many changes were carried out in the XML file to reflect the changes decribed in the sections 2a to 2d and 4d.
