# findEuropePmcPassages

**Identifier:** `europepmc_findEuropePmcPassages`

**Provider:** [Europe PMC](https://kirha.com/providers/europepmc.md)

Find the passages of one or more open-access full texts (up to 5 articles or preprints) that best match a question, ranked by keyword relevance (BM25). Use it to answer questions whose answer sits in the methods, results, tables or figure legends rather than the abstract. Matching is lexical: phrase the question with the terms the paper would use (gene, drug, assay, cell line, numbers). Fails for articles that are not open access.

## Run it with the CLI

```bash
kirha tools run europepmc_findEuropePmcPassages \
  --input '{
    "ids": [
      "<ids>"
    ],
    "question": "what concentration of doxycycline was used to induce expression"
  }'
```

`--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": "europepmc_findEuropePmcPassages",
  "input": {
    "ids": [
      "<ids>"
    ],
    "question": "what concentration of doxycycline was used to induce expression"
  }
}'
```

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": {
    "ids": {
      "items": {
        "description": "Article id from searchArticles or getArticle, a PMID, PMCID, PPR preprint id or DOI",
        "minLength": 1,
        "type": "string"
      },
      "maxItems": 5,
      "minItems": 1,
      "type": "array"
    },
    "limit": {
      "default": 8,
      "maximum": 20,
      "minimum": 1,
      "type": "integer"
    },
    "question": {
      "description": "e.g. \"what concentration of doxycycline was used to induce expression\"",
      "minLength": 3,
      "type": "string"
    },
    "sections": {
      "description": "Search only sections whose heading contains one of these, or figures/tables by label, e.g. [\"methods\"], [\"table\"]",
      "items": {
        "type": "string"
      },
      "type": "array"
    }
  },
  "required": [
    "ids",
    "question"
  ],
  "type": "object"
}
```

## Output schema

```json
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false,
  "properties": {
    "articles": {
      "items": {
        "additionalProperties": false,
        "properties": {
          "doi": {
            "type": "string"
          },
          "id": {
            "type": "string"
          },
          "pmcid": {
            "type": "string"
          },
          "pmid": {
            "type": "string"
          },
          "title": {
            "type": "string"
          }
        },
        "required": [
          "id"
        ],
        "type": "object"
      },
      "type": "array"
    },
    "context": {
      "type": "string"
    },
    "passages": {
      "items": {
        "additionalProperties": false,
        "properties": {
          "id": {
            "description": "Article id, as in articles",
            "type": "string"
          },
          "score": {
            "type": "number"
          },
          "section": {
            "type": "string"
          },
          "text": {
            "type": "string"
          }
        },
        "required": [
          "id",
          "section",
          "text",
          "score"
        ],
        "type": "object"
      },
      "type": "array"
    },
    "unavailable": {
      "description": "Requested ids whose full text could not be read",
      "items": {
        "additionalProperties": false,
        "properties": {
          "id": {
            "type": "string"
          },
          "reason": {
            "type": "string"
          }
        },
        "required": [
          "id",
          "reason"
        ],
        "type": "object"
      },
      "type": "array"
    }
  },
  "required": [
    "context",
    "articles",
    "passages"
  ],
  "type": "object"
}
```

## Related tools

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

- [`getEuropePmcCitations`](https://kirha.com/providers/europepmc/getEuropePmcCitations.md)
- [`getArticle`](https://kirha.com/providers/europepmc/getArticle.md)
- [`searchArticles`](https://kirha.com/providers/europepmc/searchArticles.md)
- [`getEuropePmcFullText`](https://kirha.com/providers/europepmc/getEuropePmcFullText.md)

-----

[All Europe PMC tools](https://kirha.com/providers/europepmc.md) · [< Back to tools list](https://kirha.com/tools.md)