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The Deliverome ProjectSurfaceomev1.0

Data and code availability

All code, data, and figures are distributed under open licenses with persistent, content-addressed citation handles. Code is MIT; Zenodo deposits are CC BY 4.0; per-figure gists are archived to Software Heritage so citations resolve indefinitely.

Code

The full project — data pipelines, agent prompts, build scripts, and the source for this site — lives in one repository under the MIT License.

Repository
github.com/Deliverome-Project/accessible-surfaceome
License
MIT

At publication the tagged release is deposited on Zenodo via the GitHub integration, which mints a DOI for the release archive. Zenodo issues a concept DOI that resolves to the latest version and a version DOI for each release; cite the version DOI to pin to a specific snapshot.

Data

Datasets are deposited on Zenodo under CC BY 4.0. The deposit includes:

  • SurfaceBench — the curated 147-protein benchmark with ground-truth labels, per-model verdicts, and the curation rationale.
  • Triage results — one row per human protein-coding gene with the agent's verdict, reason, and per-call metadata.
  • Deep-dive records — per-gene JSON and Markdown for every gene that received a full evidence assembly.
Concept DOI
10.5281/zenodo.20805384 (reserved draft; populates at publication)
Version DOI (v1)
minted from the concept DOI at publication
License
CC BY 4.0

The reserved Zenodo concept DOI is wired into the figure generator (scripts/embed_figure_gist_metadata.py) so every figure PDF/PNG carries the dataset citation in its metadata as soon as it's rendered. Currently in the draft deposit:

  • triage-runs-genome-with-reasoning.tsv — every triage agent call across the protein-coding genome (verdict, reason, confidence, free-text reasoning).
  • triage-benchmark-with-reasoning.tsv — the 147-protein SurfaceBench with truth labels joined to every per-model triage call.

Coming in subsequent draft updates ahead of publication: per-gene deep-dive JSON + Markdown bundle, the consolidated evidence ledger, and a pinned code-release version DOI that resolves to the exact commit a given figure was rendered against.

Per-figure reproduction

Each published figure ships with a public GitHub Gist containing a standalone reproduction script and a short README pointing to the canonical data source. Scripts declare their dependencies inline using inline script metadata so a reader can execute the figure with uv run make_<figure>.py — no environment setup, no pip install step.

Each gist is permanently archived via Software Heritage as a SWHID of the form swh:1:dir:<sha1> — a content-addressed handle that resolves indefinitely from the Software Heritage archive and survives gist deletion, GitHub outages, or repository renames.

For convenience, every figure file also carries citation handles in its metadata: PNG outputs embed the gist URL in the Source tEXt chunk and the dataset Zenodo DOI in Subject; PDF outputs use the analogous Subject + Keywords fields. The handles travel with the file across downstream contexts — slide decks, blog posts, supplementary uploads. Read with exiftool figure.png.