BioAgents Metadata Harvesting

Pipeline endpoints

Processing runs on task workers in the Eliza OS agent framework: a submission returns a task ID immediately, and a forty-page PDF never blocks a connection. Four REST endpoints cover the flow, and the Ekayana Console uses the same ones.

BioAgents endpoints sit behind the same authentication and UCAN authorization as the rest of the API, and connect to the Bio-DID-Sequencer core so that approved metadata can be written into DID documents.

Submit, poll, retrieve (JavaScript)

// 1. Send an uploaded paper through BioAgents
const res = await fetch('https://api.ekayana.com/api/bioagents/process', {
  method: 'POST',
  headers: {
    Authorization: `Bearer ${token}`,
    'Content-Type': 'application/json',
  },
  body: JSON.stringify({
    file_cid: 'QmXg9Pp2ytZ14xgK35M6iTC2Vz6jR9zYgooNp2UHPTMnPN',
    title: 'CRISPR-Cas9 Gene Editing for Neurodegenerative Diseases',
    authors: ['Jane Smith', 'John Doe'],
    doi: '10.1234/example.2026.001',
  }),
});

// 2. Processing is asynchronous. Poll the task until it completes.
const { task_id } = await res.json();
const status = await fetch(
  `https://api.ekayana.com/api/bioagents/status/${task_id}`,
  { headers: { Authorization: `Bearer ${token}` } },
);

// 3. When it completes, fetch the extracted metadata for the owner to review
const metadata = await fetch('https://api.ekayana.com/api/bioagents/metadata', {
  method: 'POST',
  headers: {
    Authorization: `Bearer ${token}`,
    'Content-Type': 'application/json',
  },
  body: JSON.stringify({ task_id }),
});