cosmic-toolkit

COSMIC annotation checks if gene symbols are in the Cancer Gene Census and retrieves properties like Tier, Hallmark, Tumour Types, and Role in Cancer. Query single genes, multiple genes, or from a file using case-insensitive symbol matching, then export results as JSON containing all census columns.

Yes, the Skill supports flexible inputs: single gene symbols, multiple genes, or file-based inputs. Load your gene list, perform case-insensitive matching against the Cancer Gene Census CSV, and retrieve annotated results with all census properties in JSON format.

The Cancer Gene Census returns Tier classification, Hallmark status, Tumour Types (both Somatic and Germline), Role in Cancer, and Cancer Syndrome information. All CSV columns are included in the JSON output for downstream research and reporting.

Pandas loads and processes the Cancer Gene Census CSV data. The Skill uses pandas for case-insensitive symbol matching, normalizing missing values, and structuring the annotated results into JSON payloads with all census columns preserved.

Yes, the Skill supports configurable census file paths so you can use custom or updated Census versions. You can also set optional output destinations to save JSON results to a specified location.

Gene annotation outputs as JSON containing all Cancer Gene Census columns for each queried gene. This structured format enables direct integration with downstream analyses, databases, or reporting pipelines.