Cortexa research tool·genomics·bioportal

BioPortal Annotate Text

Annotate biomedical text with ontology terms using BioPortal's Annotator (named entity recognition). Scans free text and identifies mentions of biomedical concepts from 900+ ontologies. Useful for extracting disease mentions, drug names, gene functions, phenotypes, and anatomical terms from clinical notes, papers, or abstracts. Example: annotate 'Melanoma is a malignant tumor of melanocytes' to find DOID:1909 (melanoma) and DOID:162 (cancer).

Livelast probed 2026-04-30 23:07Z· 112msCortexa

Status

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

Last probed: 1d ago
Last success: 1d ago
Last latency: 112ms

Schema

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

{
  "properties": {
    "longest_only": {
      "description": "If true (default), only return longest matching spans. Set false for all possible matches.",
      "type": [
        "boolean",
        "null"
      ]
    },
    "ontologies": {
      "description": "Comma-separated ontology acronyms to restrict annotation. If null, uses all ontologies. Common: 'DOID,HP,CHEBI,GO,NCIT,MESH'.",
      "type": [
        "string",
        "null"
      ]
    },
    "text": {
      "description": "Biomedical text to annotate. Can be a sentence, abstract, or clinical note. Maximum recommended length: 500 words.",
      "type": "string"
    }
  },
  "required": [
    "text"
  ],
  "type": "object"
}

Examples (1)

Default BioPortal Annotate Text call

public-safeinput

{
  "text": ""
}

Expected response keys: success

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

Identifiers

Catalog ID: tu_BioPortal_annotate_text
Tool name: BioPortal_annotate_text
Added: 2026-04-30 22:47Z
Tags: tooluniverse

BioPortal Annotate Text

Livelast probed 2026-04-30 23:07Z· 112msCortexa

Schema

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

{ "properties": { "longest_only": { "description": "If true (default), only return longest matching spans. Set false for all possible matches.", "type": [ "boolean", "null" ] }, "ontologies": { "description": "Comma-separated ontology acronyms to restrict annotation. If null, uses all ontologies. Common: 'DOID,HP,CHEBI,GO,NCIT,MESH'.", "type": [ "string", "null" ] }, "text": { "description": "Biomedical text to annotate. Can be a sentence, abstract, or clinical note. Maximum recommended length: 500 words.", "type": "string" } }, "required": [ "text" ], "type": "object" }