io.github.sanjaysgk/can-immune

Tools

• database_overview

  Get the headline size of the CAN-IMMUNE database in one call. Returns total counts of mutations, genes, and unique mutant peptides, plus how many cell lines, tissues, and cancer types are covered, and the data sources (COSMIC, DepMap/CCLE, PubMed). Use this first to size the resource or to answer "how big is the database / how many X are there" questions. No parameters.

  shallow
• fetch

  Fetch the full record for an id returned by `search` (ChatGPT connector interface). Takes an id like 'gene:TP53' or 'cell_line:MDA-MB-231' and returns {id, title, text, url, metadata} where `text` is the full JSON profile (same data as get_gene / get_cell_line). Always call `search` first to obtain a valid id.

  shallow
• get_cell_line

  Get the full profile for one cancer cell line by exact name. Returns tissue of origin, cancer type, total mutations, unique mutant peptides and genes, data sources, Cellosaurus and DepMap model IDs, gender, category / cell type, and the top ~15 most-mutated genes in that line, plus a link to its page. Use after `search_cell_lines`, or when the exact name is known, for a deep dive on one line. Returns an error field if the name is not found.

  shallow
• get_gene

  Get the full profile for one gene by exact symbol. Returns total mutations and how they split between cell lines vs tissues, unique mutant peptides, sample and transcript counts, UniProt accession / name / reviewed status, the top ~15 recurrent mutations in that gene, and a link to the gene page. Use this after `search_genes` (or when you already know the symbol) to answer detailed questions about a single gene. Returns an error field if the symbol is not found.

  shallow
• get_gene_mutations

  List individual mutations in a gene (a bounded sample of rows). Each row gives the CAN-IMMUNE mutation ID (CANLIB...), the amino-acid change, the CDS change, mutation type (missense / complex substitution), data source, the sample it came from, its primary site, and the mutant peptide. Ordered by mutation ID. Capped at `limit` rows (max 100) for speed - for the complete table of a heavily-mutated gene, link the user to the gene page on the website.

  shallow
• get_mhc_binding

  Look up a CACHED MHC-I binding prediction for a peptide + HLA allele. Returns the NetMHCpan result (best binding core, %Rank_EL, binder level SB/WB/NB, and neoepitope %Rank_Neo when computed) for predictions already stored in the cache. This tool does NOT run new predictions - it only reads cached ones; if nothing is cached it returns cached=false with a note. To generate a new prediction, use the interactive button on the mutation page of the website.

  shallow
• list_cancer_types

  List cancer types (histology) ranked by mutation burden. Returns each cancer type / histology with its total mutations, unique samples, and unique genes, most-mutated first. Use to see which cancer types dominate the database or to pick one for further drill-down on the website.

  shallow
• list_tissues

  List primary tissues ranked by mutation burden. Returns each tissue (COSMIC primary-tissue samples only, kept separate from cell lines) with its total mutations, unique samples, and unique genes, most-mutated first. Use for tissue-level questions; for cell lines use `search_cell_lines`.

  shallow
• search

  Search CAN-IMMUNE for genes and cell lines (ChatGPT connector interface). Returns {results: [{id, title, url}]} combining matching genes and cell lines, each with a stable `id` (like 'gene:TP53' or 'cell_line:MDA-MB-231'). Pass that `id` to `fetch` to retrieve the full record. This is the generic search endpoint ChatGPT expects; MCP-native clients can also use the more specific `search_genes` / `search_cell_lines` tools.

  shallow
• search_cell_lines

  Find cancer cell lines by name, ranked by mutation burden. Returns each matching cell line with its tissue of origin, cancer type, total mutations, unique mutant peptides, data sources (COSMIC / DepMap-CCLE / PubMed), and Cellosaurus ID. Covers only cell-line models (kept separate from primary tissue samples). Use before `get_cell_line` or `top_genes_in_cell_line`. Ordered by mutation count (most mutated first).

  shallow
• search_genes

  Find genes by symbol or full name, ranked by how mutated they are. Matches the gene symbol OR the full gene name (partial, case-insensitive) and returns each hit with its total mutation count, unique mutant-peptide count, sample count, and UniProt accession. Use it to locate a gene before calling `get_gene`, or to rank a set of genes by mutation burden. Results are ordered by mutation count (most mutated first).

  shallow
• top_genes_in_cell_line

  Rank the most-mutated genes within one specific cell line. Answers "what is the top mutated gene in <cell line>" / "which genes are most altered in <cell line>". Returns genes with their mutation counts for that line, highest first, from precomputed per-cell-line stats (fast). For the whole profile of the line use `get_cell_line` instead.

  shallow

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