# getBioassaySummary

**Identifier:** `pubchem_getBioassaySummary`

**Provider:** [PubChem](https://kirha.com/providers/pubchem.md)

Summarise PubChem BioAssay results for a compound CID: assay counts by outcome, the protein targets it is most often active against (NCBI Gene IDs and protein accessions, mappable with UniProt), and the most potent active assays with AIDs and PubMed IDs. Returns empty counts when the compound was never tested.

## Run it with the CLI

```bash
kirha tools run pubchem_getBioassaySummary \
  --input '{
    "cid": 1
  }'
```

`--input` takes a JSON object that matches the input schema. Pass `--input -` to read it from stdin.

## Call it over HTTP

```bash
curl https://api.kirha.com/tools/v1/execute \
  --request POST \
  --header 'Content-Type: application/json' \
  --header 'Authorization: **********' \
  --data '{
  "tool_name": "pubchem_getBioassaySummary",
  "input": {
    "cid": 1
  }
}'
```

Replace the stars with an API key from https://app.kirha.com/api-keys.

## Input schema

```json
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "properties": {
    "cid": {
      "description": "PubChem CID (from findCompound)",
      "exclusiveMinimum": 0,
      "maximum": 9007199254740991,
      "type": "integer"
    },
    "limit": {
      "default": 20,
      "description": "Max active assays returned",
      "maximum": 100,
      "minimum": 1,
      "type": "number"
    }
  },
  "required": [
    "cid"
  ],
  "type": "object"
}
```

## Output schema

```json
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false,
  "properties": {
    "activeAssayCount": {
      "type": "number"
    },
    "activeAssays": {
      "items": {
        "additionalProperties": false,
        "properties": {
          "activityName": {
            "description": "e.g. IC50, Ki, Potency",
            "type": "string"
          },
          "activityValueUm": {
            "description": "µM, lower is more potent",
            "type": "number"
          },
          "aid": {
            "type": "number"
          },
          "assayName": {
            "type": "string"
          },
          "assayType": {
            "type": "string"
          },
          "pmid": {
            "type": "string"
          },
          "targetAccession": {
            "type": "string"
          },
          "targetGeneId": {
            "type": "string"
          }
        },
        "required": [
          "aid"
        ],
        "type": "object"
      },
      "type": "array"
    },
    "aids": {
      "description": "PubChem AIDs of the returned active assays",
      "items": {
        "type": "number"
      },
      "type": "array"
    },
    "cid": {
      "type": "number"
    },
    "context": {
      "type": "string"
    },
    "inactiveAssayCount": {
      "type": "number"
    },
    "inconclusiveAssayCount": {
      "type": "number"
    },
    "pmids": {
      "description": "PubMed IDs cited by the returned active assays",
      "items": {
        "type": "string"
      },
      "type": "array"
    },
    "testedAssayCount": {
      "type": "number"
    },
    "topTargets": {
      "items": {
        "additionalProperties": false,
        "properties": {
          "activeAssayCount": {
            "type": "number"
          },
          "bestActivityValueUm": {
            "type": "number"
          },
          "targetAccession": {
            "description": "UniProt or NCBI protein accession",
            "type": "string"
          },
          "targetGeneId": {
            "description": "NCBI Gene ID",
            "type": "string"
          }
        },
        "required": [
          "activeAssayCount"
        ],
        "type": "object"
      },
      "type": "array"
    }
  },
  "required": [
    "context",
    "cid",
    "testedAssayCount",
    "activeAssayCount",
    "inactiveAssayCount",
    "inconclusiveAssayCount",
    "activeAssays",
    "aids"
  ],
  "type": "object"
}
```

## Related tools

Other PubChem tools that this tool refers to, or that refer to it.

- [`findCompound`](https://kirha.com/providers/pubchem/findCompound.md)

-----

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