v1.0.0 — Surfaceome 1.0

First tagged release of accessible-surfaceome — the pipeline, agents, and web viewer behind surfaceome.deliverome.org.

Version 1.0.0 corresponds to Surfaceome 1.0 as described in the accompanying manuscript.

What this is

Five public surface-protein resources — UniProt, GO Cellular Component, the Human Protein Atlas, the Cell Surface Protein Atlas, and SURFY — disagree substantially about which proteins reach the cell surface, agreeing on only 188. This repository builds a reconciled atlas:

• a tool-free triage agent classifies every protein-coding human gene for surface accessibility, rescuing 960 candidates absent from all five source databases;
• a literature-anchored deep-dive pipeline turns each candidate into a structured, evidence-cited record with per-claim citations;
• deterministic feature builders cover orthology, paralogs, isoforms, membrane topology, AlphaFold structure, candidate binding sites, and homo-oligomerization;
• a Cloudflare Worker + public API and a React viewer make the whole thing queryable, with full LLM reasoning exposed rather than hidden.

The deep-dived cohort (N = 5,130) resolves to roughly 1,782 canonical and 1,243 likely surface calls.

Citing

Cite the concept DOI when you mean the software in general; cite this release's version DOI when you mean the exact snapshot you ran against. CITATION.cff carries the machine-readable form.

Underlying data are deposited separately at 10.5281/zenodo.20805383 (CC BY 4.0). Code is MIT.

Acknowledgements

Supported by the Astera Institute and Anthropic. Deliverome Bio received API credits through the Claude AI for Science program for this project.