# REAL COMPLETED EXAMPLE
# This file is based on the ESM2-v1.1 embedding processed in this
# project. Do not upload it unchanged. Copy submission.yaml and
# describe your own embedding.

schema_version: 1
embedding_id: esm2_v1_1
display_name: ESM2-v1.1

contributor:
  name: Daniel Tabares Lopez
  affiliation: ETH Zurich

scientific:
  category: Protein
  modality: Protein sequence
  description: Human gene-level protein-sequence embeddings generated by Zhong et al. from UniProt human protein sequences using the ESM-2 650M checkpoint and mean pooling, then standardized to the project's Ensembl gene universe.
  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