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Route B — DOME Copilot

Upload a PDF, get a structured draft in about two minutes, then review every field.

Overview

Questions:

  • How do I actually run DOME Copilot on a paper?
  • What do I get back, and in what format?
  • Which fields should I check hardest before trusting the output?

Learning Objectives

By the end of this chapter, you will be able to:

  1. Log in to the workshop DOME Copilot instance and generate an annotation
  2. Download the resulting JSON and read it against the paper
  3. Identify and correct the fields most likely to need human amendment
  4. Move a reviewed annotation into the DOME Registry

Time: 35 minutes (hands-on exercise)

Prerequisite: Chapter 3 · a publication PDF · a browser

Access

Field Value
URL https://dome-copilot.ifca.es/
User admin
Password 6yKG7b5p

Shared workshop account

This instance does not yet have federated authentication (AAI) in place, so a single shared account is provided for the tutorial. Everyone in the room is logged into the same service — do not upload confidential or unpublished material you would not be comfortable others seeing.

Step by step

  1. Go to the DOME Copilot web URL — https://dome-copilot.ifca.es/
  2. Log in with the details above
  3. Upload the publication’s primary PDF, plus any supplementary materials (also PDF). Supplementary files are worth including: several DOME fields — data splits, hyperparameters, evaluation details — are usually only stated there
  4. Provide the DOI (optional) to pull in bibliographic metadata via external APIs. Do this if you have it; it means the publication fields come from a lookup rather than from the model reading a title page
  5. Click the orange “Generate annotations” button
  6. Wait for the annotation to complete — typically around two minutes, varying with document size
  7. Download the JSON of the annotation, for refinement and sharing — for example by depositing it in the DOME Registry

If your browser warns about the certificate

The DOME Copilot server currently sends only its leaf TLS certificate without the intermediate chain. Most browsers fetch the missing intermediate automatically and connect without complaint, but some strict clients and corporate networks will show a certificate warning. The certificate itself is valid — issued to dome-copilot.ifca.es by the GEANT/HARICA academic CA. If you are blocked, try a different browser or network, or use Route A or Route C for the hands-on exercise.

Now review it — this is the actual work

The download is a draft, not a finished report. Read it against the paper, paying most attention to these:

The highest-value check. Copilot works from the manuscript text, and a plausible-sounding sentence in a field the paper is silent about is exactly what human review is for.

Watch particularly for 1.3 Redundancy between data splits and 4.3 Comparison — both are commonly under-reported in papers, and both are fields where a confident-sounding draft can paper over a real gap.

Dataset sizes (N~pos~/N~neg~), parameter counts, feature counts, metric values. Check each against the source. Numbers are cheap to verify and expensive to get wrong.

1.4 (data), 2.8 (configuration), 3.4 (software), 4.5 (evaluation files). Verify that each URL resolves and that the licence stated is the licence actually there. A dead link is a DOME finding.

If a field would alter how a reader judges the method, read the paper’s own words for it before accepting the draft.

Do not deposit an unreviewed annotation

Never upload an unchecked machine-drafted entry to the DOME Registry.

When to choose this route

Good fit: many papers; building registry coverage for a subfield; a fast first pass you will then correct; nothing installable on your machine; cost matters.

Poor fit: you want OSAI recommendations as well as DOME (use Route C); or the material is confidential — this is a shared instance.

Sources

Next: Route C — Agent Skills

  1. Gavin Farrell, Omar Abdelghani Attafi, Styliani-Christina Fragkouli, Ignacio Heredia, Saul Fernández Tobías, Melissa Harrison, Henning Hermjakob, Matt Jeffryes, Marta Obregón Ruiz, Matt Pearce, Nikos Pechlivanis, Alvaro López García, Fotis Psomopoulos, and Silvio C. E. Tosatto. DOME copilot: making transparency and reproducibility for artificial intelligence methods simple. bioRxiv, 2026. Preprint, posted 19 April 2026. doi:10.64898/2026.04.16.718888. ↩