plain list of human cell lines
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3.1 years ago
bstrs • 0

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 • 1.6k views
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3.1 years ago
Amos Bairoch ▴ 120

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.

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Thanks Amos!

This is exactly what I was looking for!

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3.0 years ago
Amos Bairoch ▴ 120

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" } .
}
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This looks good too!

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3.1 years ago
GenoMax 141k

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

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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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