cbioportal.github.io

{
  "name": "benchmark_overview",
  "kind": "act",
  "impl": "imperative",
  "description": "Overview of the active benchmark track: genome build, published-reference source, variant & gene counts, tools compared, OncoKB oncogenic count, and whether the oncogenic-only filter is on.",
  "inputSchema": {
    "type": "object",
    "properties": {}
  },
  "page": "/cbioportal-onco-variant-annotation-bench/"
}

{
  "name": "leaderboard",
  "kind": "act",
  "impl": "imperative",
  "description": "Per-tool concordance vs the published reference — Stage 2 selection (transcript pick, protein HGVSp, variant class, consequence, HGVSc, gene) and Stage 1 annotation quality. oncogenic_only=true scores only OncoKB-oncogenic variants.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "oncogenic_only": {
        "type": "boolean"
      },
      "filter": {
        "type": "string",
        "description": "OncoKB preset id: onco, level1, level12, level123, resistance (see benchmark_overview.filters)"
      }
    }
  },
  "page": "/cbioportal-onco-variant-annotation-bench/"
}

{
  "name": "compare_tools",
  "kind": "act",
  "impl": "imperative",
  "description": "Directly compare two tools with no reference: how often they pick the same transcript / protein change / variant class, and the genes where they disagree most. Args toolA, toolB (ids from benchmark_overview).",
  "inputSchema": {
    "type": "object",
    "properties": {
      "toolA": {
        "type": "string"
      },
      "toolB": {
        "type": "string"
      }
    },
    "required": [
      "toolA",
      "toolB"
    ]
  },
  "page": "/cbioportal-onco-variant-annotation-bench/"
}

{
  "name": "gene_report",
  "kind": "act",
  "impl": "imperative",
  "description": "Per-tool transcript-pick and protein-HGVSp concordance for one gene, plus its canonical transcript from MANE/Ensembl/UniProt/MSKCC when available. Arg gene (HGNC symbol).",
  "inputSchema": {
    "type": "object",
    "properties": {
      "gene": {
        "type": "string"
      }
    },
    "required": [
      "gene"
    ]
  },
  "page": "/cbioportal-onco-variant-annotation-bench/"
}

{
  "name": "worst_genes",
  "kind": "act",
  "impl": "imperative",
  "description": "Genes where tools disagree most with the published reference on protein change (hardest genes). Arg limit (default 20).",
  "inputSchema": {
    "type": "object",
    "properties": {
      "limit": {
        "type": "number"
      }
    }
  },
  "page": "/cbioportal-onco-variant-annotation-bench/"
}