Downloads
Bulk-download the entire atlas as flat files. Per-protein JSON is also
available at /data/<UniProt>.json.
Sequences
| All sequences (FASTA) sequences.fasta | One record per protein in the atlas, header = `>UniProt Gene | Title`. | 3.1 MB | Download |
Predicted cleavages
| Predicted peaks — stringent peaks_stringent.csv | All predicted cleavage peaks at prominence ≥ 0.05. | 1.5 MB | Download |
| Predicted peaks — moderate peaks_moderate.csv | All predicted cleavage peaks at prominence ≥ 0.03. | 1.7 MB | Download |
| Predicted peaks — permissive peaks_permissive.csv | All predicted cleavage peaks at prominence ≥ 0.01. | 2.0 MB | Download |
Experimental cleavages
| Experimental cleavages cleavages.csv | All harmonised experimental cleavage annotations across UniProt, MEROPS, TopFIND, Schaeffer22, Weeks21. | 543.2 KB | Download |
Domains
| Domains — UniProt domains_uniprot.csv | Curated UniProt domain regions per protein. | 240.9 KB | Download |
| Domains — Pfam domains_pfam.csv | Pfam domain hits per protein (via InterPro). | 582.1 KB | Download |
| Domains — SMART domains_smart.csv | SMART domain hits per protein (via InterPro). | 414.0 KB | Download |
| Domains — CDD domains_cdd.csv | NCBI CDD domain hits per protein (via InterPro). | 104.7 KB | Download |
| Domains — InterPro (Domain entries) domains_interpro_domain.csv | InterPro entries of type "Domain" per protein. | 1.4 MB | Download |
| Domains — InterPro (Superfamily) domains_interpro_superfamily.csv | InterPro entries of type "Homologous Superfamily" per protein. | 791.2 KB | Download |
| Domains — TED (CATH) domains_ted.csv | TED-derived domain segmentation (CATH IDs); names are non-descriptive. | 421.7 KB | Download |
Indices
| Proteins index (TSV) proteins.tsv | Per-protein summary metadata (length, peak/cleavage counts, topology flags, coverage). | 486.7 KB | Download |
| Proteases index (TSV) proteases.tsv | Per-protease aggregate (substrate count, sites, MEROPS / UniProt cross-refs). | 12.2 KB | Download |
Programmatic access
All per-protein records are served as static JSON at
https://sheddome.secretomeatlas.org/data/<UniProt>.json.
Example for ADAM17:
curl https://sheddome.secretomeatlas.org/data/P78536.json | jq
The atlas index is at
/data/index.json and the
protease aggregate at
/data/proteases.json.
Citing
Manuscript in preparation. Please cite the website URL
(sheddome.secretomeatlas.org)
until a preprint is available. For collaborations or questions about
bulk-data access, email jlaffy@broadinstitute.org.