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plain list of human cell lines

Does anyone know a public available list (as text file?) of human cell lines?

A format like this would be great:

Id synonyms

MCF7 MCF-7

VCAP VCaP

SKBR3 SK-BR-3,SKBR-3

....

human cell lines

3 answers

A file that contains such information can be generated from the current version of the Cellosaurus. As I write this there are, in release 37, 95470 human cell lines.

You can generate such a list with a small script (Python, Perl or any language) from the text version which is available for download at:

https://ftp.expasy.org/databases/cellosaurus/cellosaurus.txt

The three types of lines that you need to parse are:

ID         Identifier (cell line name)     Once
SY         Synonyms                        Optional; once
OX         Species of origin               Once or more

You need the OX line to select only the human cell lines: ie: NCBI_TaxID=9606

As an example here are the ID and SY lines for SK-BR-3:

ID   SK-BR-3
SY   SK-Br-3; Sk-Br-3; SK BR 03; SKBR-3; SKBr-3; SK-BR3; SKBr3; SkBr3; SKBR3

Alternatively you can also generate such list by parsing the XML or OBO version of the Cellosaurus, all of which are available on the FTP site.

Thanks Amos!

This is exactly what I was looking for!

I thought of a second solution that does not require you to write a script: as we populate Wikidata with cell line items originating from the Cellosaurus, you can also use the Wikidata query service at:

https://query.wikidata.org/

And enter the following SPARQL query:

SELECT ?cellLinesLabel ?cellLinesAltLabel WHERE {
   ?cellLines wdt:P3289 ?cellosaurusId ;
              wdt:P9072 wd:Q15978631 .
   SERVICE wikibase:label { bd:serviceParam wikibase:language "en" } .
}

This looks good too!

Public available can be considered as something you can purchase. There are probably European suppliers but ATCC has these human cells available.

Thanks! The list looks like what I was looking for except that it looks challenging to download it automatically (or via command line) and convert it to simple text file. :-(

I guess that copyright does not apply to a list/index of cell lines.

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