_____ _ _ / ____| | | | | | ___| | | ___ ___ __ _ _ _ _ __ _ _ ___ | | / _ \ | |/ _ \/ __|/ _` | | | | '__| | | / __| | |___| __/ | | (_) \__ \ (_| | |_| | | | |_| \__ \ \_____\___|_|_|\___/|___/\__,_|\__,_|_| \__,_|___/ This is the release notes for Cellosaurus version 50 of September 2024 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 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. Examples: 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_xrefs.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. --------------------------------------- Amos Bairoch CALIPHO group SIB - Swiss Institute of Bioinformatics Geneva; Switzerland ---------------------------------------