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The Deliverome ProjectSurfaceomev1.0

Data and code availability

All code, data, and figures are distributed under open licenses with persistent citation handles. Code is MIT; the Zenodo data deposit is CC BY 4.0 with a DOI that resolves indefinitely; each figure ships a standalone reproduction gist archived to Software Heritage as a content-addressed SWHID.

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 — a per-gene JSON for every gene that received a full evidence assembly, each carrying its evidence chain and its deep-dive tier.
Concept DOI (all versions)
10.5281/zenodo.20805383
Version DOI (this release)
10.5281/zenodo.20805384
License
CC BY 4.0

The Zenodo 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. The published deposit contains:

  • triage-runs-genome-with-reasoning.tsv — every triage agent call across the protein-coding genome (21,950 rows: the NCBI-context sweep plus a targeted PubMed-context re-run), with verdict, reason, confidence, and free-text reasoning.
  • triage-benchmark-with-reasoning.tsv — the 147-protein SurfaceBench (4,851 rows) with truth labels joined to every per-model, per-variant triage call.
  • deep_dives_all.tar.gz — the 5,130 per-gene deep-dive JSON records, each with its full evidence chain and deep-dive classification.

A later version of the deposit will add the manuscript, against the same concept DOI.

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 archived to Software Heritage (via Save Code Now) and cited as a content-addressed swh:1:rev:<sha> of the gist's HEAD commit — recorded per figure in the repository's swhid_map.json. The revision pins the exact script + data snapshot a figure was rendered against and resolves from the SWH archive even if the gist is later deleted. The underlying dataset's durable handle is the Zenodo DOI above.

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.