Cortexa research tool·structure·pubtator3_ext

PubTator3 Get Annotations

Extract biomedical entity annotations from PubMed articles using NCBI PubTator3. Given one or more PubMed IDs (PMIDs), returns text-mined entities including genes, diseases, chemicals, species, mutations, and cell lines with their normalized identifiers (NCBI Gene ID, MeSH, NCBI Taxonomy, etc.) and text positions. Useful for extracting structured biomedical knowledge from literature. Provide PMIDs as a comma-separated string.

Livelast probed 2026-04-30 23:07Z· 93msCortexa

Status

The most recent probe succeeded. Safe to call from the agent today.

Last probed: 1d ago
Last success: 1d ago
Last latency: 93ms

Schema

JSON Schema the agent (or your API call) must match.

{
  "properties": {
    "concepts": {
      "default": "gene,disease,chemical,species,mutation,cellline",
      "description": "Comma-separated entity types to extract: gene, disease, chemical, species, mutation, cellline (default: all types)",
      "type": "string"
    },
    "pmids": {
      "description": "Comma-separated PubMed IDs (e.g., '33205991', '33205991,34234088'). Maximum ~100 PMIDs per request.",
      "type": "string"
    }
  },
  "required": [
    "pmids"
  ],
  "type": "object"
}

Examples (1)

Default PubTator3 Get Annotations call

public-safeinput

{
  "pmids": ""
}

Expected response keys: success

Anonymous-safe example. Rate-limited; no sign-in required.

Identifiers

Catalog ID: tu_PubTator3_get_annotations
Tool name: PubTator3_get_annotations
Added: 2026-04-30 22:47Z
Tags: tooluniverse

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