A knowledge resource on cell lines - From SIB CALIPHO group - neXtProt project
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README.md
cellopub.txt
cellosaurus.obo
cellosaurus.txt
cellosaurus.xsd
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cellosaurus_faq.txt
cellosaurus_name_conflicts.txt
cellosaurus_refs.txt
cellosaurus_relnotes.txt
cellosaurus_xrefs.txt

README.md

Cellosaurus

From the CALIPHO group of the SIB - Swiss Institute of Bioinformatics; neXtProt project

##A knowledge resources on cell lines

The Cellosaurus is a knowledge resource on cell lines. It attempt to describe all cell lines used in biomedical research.

  • Immortalized cell lines
  • Naturally immortal cell lines (ie stem cell lines)
  • Finite life cell lines when those are distributed and used widely
  • Vertebrate cell lines with an emphasis on human, mouse and rat cell lines
  • Invertebrate (insects and ticks) cell lines

Its scope does not include:

  • Primary cell lines (with the exception of the finite life cell lines described above)
  • Plant cell lines

For each cell line we provide the following information:

  • A recommended name. This is most frequently the name provided in the original publication.
  • A list of synonyms. We try to list all the different synonyms for the cell line, including alternative use of lower and upper cases characters.
  • A unique accession number.
  • Structured comments that are describe a number of topics such as: contaminated cell lines, misspellings, breed/subspecies a cell line is derived from, gene transfection, metastatic or sampling site for cancer cell lines, transformant, population doubling time, sequence variations, etc.
  • For cell lines originating from a diseased patient/animal, we provide the NCI Thesaurus entry code for the disease(s) that the individual from which the cell line originated was suffering from.
  • For human and dog cell lines where this information is available, we provide the STR (short tandem repeat) profile information.
  • The species of origin.
  • If a cell line originate from another one we provide a link to the parent cell line.
  • If a cell line originate from the same individual as other cell line(s) (sister cell lines) cross-reference to these sister cell line(s) are provided.
  • The sex of the individual from which the cell line has been derived.
  • The age of the individual from which the cell line has been derived (at the time of "sampling").
  • The category to which a cell line belong. Currently this can be one of the following categories: Cancer cell line; Conditionally immortalized cell line; Embryonic stem cell; Factor-dependent cell line; Finite cell line; Hybrid cell line; Hybridoma; Induced pluripotent stem cell; Spontaneously immortalized cell line; Somatic stem cell; Stromal cell line; Telomerase immortalized cell line; Transformed cell line; Undefined cell line type
  • Web links.
  • Publication references. We principally provide the references for publications describing the establishment of a cell line or its characterization. We do not attempt to capture all the literature that make use of a particular cell line.
  • Cross-references to cell line catalogs/collections, ontologies, cell lines databases/resources and to databases that list cell lines as samples.

##Availability

The Cellosaurus is available/searchable on the web and downloadable by FTP

Home page: https://web.expasy.org/cellosaurus/

Individual entry pages: 'https://web.expasy.org/cellosaurus/%s' where %s is the accession number of the cell line

Example: https://web.expasy.org/cellosaurus/CVCL_0033

FTP: ftp://ftp.expasy.org/databases/cellosaurus

The files that are distributed by FTP and are on GitHub are:

  • cellosaurus.txt: Cellosaurus in structured flat file format

  • cellosaurus_refs.txt: Reference file: publications, patents, book chapters

  • cellosaurus_xrefs.txt: File describing how to build live links to all the resources listed in the Cellosaurus

  • cellosaurus.obo: Cellosaurus in OBO format

  • cellosaurus.xml: Cellosaurus in XML format

  • cellosaurus.xsd: XML Schema Definition (XSD) for cellosaurus.xml

  • cellosaurus_deleted_ACs.txt: List of deleted accession numbers/entries

  • cellosaurus_name_conflicts.txt: Tables of cell lines with identical names

  • cellosaurus_faq.txt: Frequently asked questions

  • cellosaurus_relnotes.txt: Release notes: statistics and description of format changes

  • cellopub.txt: Abstracts and web links for references that are not in PubMed, DOI or Patent (identifiers CLPUBnnnnn)

Important note: the cellosaurus.xml file is only available on the FTP site as it is too big to be stored in GitHub.

##Reference

Bairoch A. The Cellosaurus, a cell line knowledge resource. J. Biomol. Tech. (2018) 29:25-38 DOI: 10.7171/jbt.18-2902-002; PMID: 29805321