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| # REAL COMPLETED EXAMPLE | |
| # This file is based on the ESM-2 embedding processed in this | |
| # project. Do not upload it unchanged. Copy submission.yaml and | |
| # describe your own embedding. The ID esm2 is already in the catalogue. | |
| schema_version: 1 | |
| embedding_id: esm2 | |
| display_name: ESM-2 | |
| contributor: | |
| name: Daniel Tabares Lopez | |
| affiliation: ETH Zurich | |
| scientific: | |
| category: Protein sequence | |
| modality: Protein sequence | |
| description: Protein sequence representation from ESM-2 650M, obtained by pooling residue-level embeddings into one vector per human protein/gene. | |
| original_method: ESM-2 protein language model | |
| model_checkpoint: esm2_t33_650M_UR50D | |
| source_publication: https://doi.org/10.1101/2025.01.29.635607 | |
| provenance: | |
| species: Homo sapiens | |
| identifier_before_mapping: Entrez Gene ID | |
| mapping_method: Source Entrez Gene IDs were mapped to the project's enriched human master gene table. Only identifiers mapping uniquely to one Ensembl gene were retained; unmapped and ambiguous identifiers were excluded, and duplicate source rows mapping to the same final gene were averaged. | |
| embedding_generated_by: Jeffrey Zhong, Lechuan Li, Ruth Dannenfelser, and Vicky Yao | |
| input_data_source: UniProt human protein sequences used in the Zhong et al. gene-embedding benchmark | |
| pooling_strategy: Mean pooling over amino-acid token embeddings | |
| licensing: | |
| redistribution_allowed: true | |
| attestations: | |
| information_is_accurate: true | |
| rights_to_redistribute: true | |
| no_sensitive_human_data: true | |
| no_patient_level_data: true | |
| source_terms_reviewed: true | |
| acceptance_of_automatic_checks: true | |