cellwiki

name	cellwiki
description	Query CellWiki knowledge base for marker genes, cell type ontologies, and tissue-specific cell type constraints.
allowed-tools	Read, Bash, Glob
compatibility	Cell annotation evidence gathering

CellWiki Knowledge Base Query

When to Use

During cell type annotation to gather evidence for/against candidate hypotheses. Query CellWiki for known markers, cell type definitions, and biological constraints.

Data Location

CellWiki wiki files are at ~/CellWiki/wiki/ with:

• cell_types/*.md — One file per cell type with frontmatter and markers table
• marker_genes/ — (future) gene-centric marker database
• tissues/ — Tissue-specific cell type compositions
• contradictions.md — Known biologically incompatible marker combinations

Query Functions

query_cell_type(name, wiki_dir) -> dict

Reads ~/CellWiki/wiki/cell_types/{name}.md and returns:

{
    "name": str,           # standard_name from frontmatter
    "display_name": str,
    "cl_id": str,          # Cell Ontology ID
    "parent_type": str,
    "markers": [{"gene": str, "type": str, "evidence": str}],
    "tissues": list[str],
    "diseases": list[str],
}

list_cell_types(wiki_dir) -> list[str]

Lists all available cell type files in cell_types/.

query_markers_for_genes(genes, wiki_dir) -> list[dict]

Scans all cell type files, returns those whose markers overlap with the given gene list. Each result:

{"cell_type": str, "overlap": list[str], "jaccard": float, "markers_all": list[str]}

get_tissue_cell_types(tissue, wiki_dir) -> list[str]

Reads ~/CellWiki/wiki/tissues/ to find cell types plausible for a given tissue.