# getEuropePmcAnnotations

**Identifier:** `europepmc_getEuropePmcAnnotations`

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

List the genes/proteins, diseases, chemicals, organisms, GO terms, accession numbers and Open Targets gene-disease-drug links that Europe PMC text-mined from up to 5 articles (full text when open access, else abstract), with ontology ids (UniProt, CHEBI, UMLS, NCBITaxon, Ensembl, ChEMBL) and mention counts. Text mining is noisy: trust entities with several mentions, and read genes from mentionedAs (the symbol as written), as the UniProt match is often another species.

## Run it with the CLI

```bash
kirha tools run europepmc_getEuropePmcAnnotations \
  --input '{
    "ids": [
      "<ids>"
    ]
  }'
```

`--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_getEuropePmcAnnotations",
  "input": {
    "ids": [
      "<ids>"
    ]
  }
}'
```

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"
    },
    "types": {
      "default": [
        "genes",
        "diseases",
        "chemicals"
      ],
      "items": {
        "enum": [
          "genes",
          "diseases",
          "chemicals",
          "organisms",
          "gene_ontology",
          "accession_numbers",
          "experimental_methods",
          "gene_disease_links",
          "gene_drug_links",
          "disease_drug_links"
        ],
        "type": "string"
      },
      "minItems": 1,
      "type": "array"
    }
  },
  "required": [
    "ids"
  ],
  "type": "object"
}
```

## Output schema

```json
{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "additionalProperties": false,
  "properties": {
    "articles": {
      "items": {
        "additionalProperties": false,
        "properties": {
          "entities": {
            "items": {
              "additionalProperties": false,
              "properties": {
                "identifier": {
                  "type": "string"
                },
                "mentionedAs": {
                  "description": "Text spans as written in the article",
                  "items": {
                    "type": "string"
                  },
                  "type": "array"
                },
                "mentions": {
                  "type": "number"
                },
                "name": {
                  "description": "Normalised name; 'A + B' for a gene-disease or drug link",
                  "type": "string"
                },
                "type": {
                  "type": "string"
                }
              },
              "required": [
                "type",
                "name",
                "identifier",
                "mentions",
                "mentionedAs"
              ],
              "type": "object"
            },
            "type": "array"
          },
          "id": {
            "description": "Id for getArticle (PMID for MEDLINE)",
            "type": "string"
          },
          "pmcid": {
            "type": "string"
          }
        },
        "required": [
          "id",
          "entities"
        ],
        "type": "object"
      },
      "type": "array"
    },
    "context": {
      "type": "string"
    }
  },
  "required": [
    "context",
    "articles"
  ],
  "type": "object"
}
```

## Related tools

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

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

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