File size: 4,399 Bytes
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"embedding": "string_prot",
"species": "Homo sapiens",
"shape": [
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"dtype": "float32",
"gene_identifier": "Current HGNC symbol for one-to-one mappings; original identifier for unresolved or duplicate-symbol groups",
"row_order": "genes.json[i] identifies embeddings.npy[i]; row_mapping.csv is in the same order",
"origin": {
"database": "STRING",
"version": "12.5",
"taxon_id": 9606,
"representation": "ProtT5 protein sequence embeddings",
"url": "https://stringdb-downloads.org/download/protein.sequence.embeddings.v12.5/9606.protein.sequence.embeddings.v12.5.h5",
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"citations": [
"https://doi.org/10.1093/bioinformatics/btaf496",
"https://doi.org/10.1093/nar/gkae1113"
],
"license": "CC BY 4.0",
"license_evidence": "https://string-db.org/cgi/download?species_text=Homo+sapiens"
},
"preprocessing": {
"filtering": "None; all source proteins retained",
"normalization": "None",
"pooling": "None",
"conversion": "float16 -> float32, exactly preserving the stored source values",
"row_order": "Original HDF5 protein order; differs between network and sequence files"
},
"identifier_mapping": {
"authority": "HGNC approved complete set",
"url": "https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt",
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"snapshot_retrieved_utc": "2026-10-14T20:45:19.024543+00:00",
"latest_record_date_modified": "2026-10-12",
"approved_records": 45277,
"license": "CC0",
"license_url": "https://www.genenames.org/about/license/",
"collision_policy": "Keep all rows. Use current symbols for one-to-one mappings; retain original names for all members of duplicate-symbol groups and for unresolved/ambiguous mappings.",
"case_policy": "Exact, case-sensitive identifier matching; no suffix stripping or guessed renaming",
"row_mapping": "row_mapping.csv is in embeddings.npy row order and records canonical symbols, stable IDs, evidence and publication identifiers",
"method": "Intersect nonempty HGNC-ID, Ensembl-gene-ID and Entrez-ID candidate sets from STRING aliases; unresolved conflicts stay unresolved. When no stable-ID candidates exist, try UniProt, preferred current symbol, annotated current symbol, preferred previous symbol, then preferred alias; require one candidate.",
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"verification": "Every reloaded vector exactly equals its source cast to float32; every input row retained; unique published IDs and row mapping checked; no added WT row."
}
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