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Cell Line

Use cell line commands to turn any common spelling of a cell line into a Cellosaurus accession, then read its identity, its cross-references, and its curated sequence variations.

Key boundaries:

  • Cellosaurus is the only source. The CVCL accession is the join key for every other cell line dataset.
  • Search compares normalized names: lowercase, with every non-alphanumeric character dropped. MOLM13, MOLM-13, and Molm 13 are the same query.
  • BioMCP ranks candidates and picks no winner. When two lines match exactly, both rows appear.
  • The base card never fetches cross-references. Ask for xrefs when you need the join keys.
  • Every output names the Cellosaurus release and carries the CC BY 4.0 attribution line.

Search cell lines

QUERY is required. It can be a name, a synonym, or a CVCL accession.

biomcp search cell-line MOLM13
biomcp search cell-line "MV4;11"
biomcp search cell-line KG1 --limit 5
biomcp search cell-line CVCL_2119

Each row carries match (exact or partial) and, on exact rows, matched_on (name or synonym). Exact identifier matches sort first, then exact synonym-only matches, then partial matches. Human lines come first within each group.

A hyphenated query runs twice, once as typed and once with the hyphens removed, and the two windows merge by accession. KG-1 and KG1 therefore return the same set.

When Cellosaurus fills its 1000-row window, the total is unknown and the output carries a note. Use a more specific name or the accession.

Get cell line records

biomcp get cell-line CVCL_2119
biomcp get cell-line CVCL_0064

The card carries the accession, the RRID, the identifier name, synonyms, species, disease, category, sex, and age.

A source ID also works. BioMCP resolves it to the accession first and prints the ID it resolved from.

biomcp get cell-line ACH-000362      # DepMap
biomcp get cell-line SIDM00437       # Cell Model Passports
biomcp get cell-line CHEMBL3706573   # ChEMBL
biomcp get cell-line MOLM13_950_2019 # PharmacoDB

Request cell line sections

Cross-references, the join keys other datasets use:

biomcp get cell-line CVCL_2119 xrefs

Every key is printed. A line with no link to a resource shows an empty list, so biomcp get cell-line CVCL_0007 xrefs prints gdsc and cosmic_clp as empty.

Curated sequence variations:

biomcp get cell-line CVCL_1844 variants

Rows appear as Cellosaurus published them, with the HGVS description, the HGNC link, zygosity, and the PubMed sources. BioMCP adds no interpretation.

Both sections:

biomcp get cell-line CVCL_2119 all

Helper commands

Cell line has no separate helper family. Drug response and dependency data arrive as their own sections in later work; today every command is search cell-line or get cell-line.

JSON mode

biomcp search cell-line KG1 --json
biomcp get cell-line CVCL_2119 xrefs --json

JSON carries data_as_of and data_as_of_kind at the top level. data_as_of_kind is release when BioMCP read the Cellosaurus release, and retrieved when that read failed and the value is a retrieval time instead. A filled provider window appears in _meta.notes, and pagination.total is null.

Practical tips

Two names that look alike are often two lines. HL-60 is CVCL_0002; the NCI-60 line HL-60(TB) is CVCL_A794, a separate record. The NCI-DCTD link on HL-60(TB) carries the name HL-60, so a name-based join from NCI-60 lands on the wrong line. Join on the accession, not the name.

NB4 is the identifier of CVCL_0005 and also a synonym of the neuroblastoma line SJNB-4 (CVCL_8821). Both rows are exact matches. The matched_on column tells them apart.

KG1 matches three records, two of them mouse lines. Read the species column before you pick.