{
  "id": 613299,
  "title": "FYI: T5 protein embeddings available directly from UniProt (HDF5)",
  "url": "/competitions/cafa-6-protein-function-prediction/discussion/613299",
  "author_name": "MT",
  "post_date": "2025-10-25T16:21:32.168000",
  "votes": 16,
  "comment_count": 0,
  "views": 0,
  "content": "<p>If you want to experiment with T5 embeddings for proteins, you can download the full precomputed set straight from UniProt:</p>\n<p>UniProt downloads page: <a href=\"https://www.uniprot.org/help/downloads\" target=\"_blank\">https://www.uniprot.org/help/downloads</a></p>\n<p>Direct FTP to embeddings (current release): <a href=\"https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/\" target=\"_blank\">https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/</a></p>\n<p>The download is an HDF5 (.h5) dataset containing T5 embeddings keyed by UniProt accessions.</p>\n<p><strong>Known missing IDs</strong>\nFor some reason (length quirks), \"Train\" embeddings for the following accessions are missing in the current release I checked:\nA2ASS6\nG4SLH0\nM9MRD1\nQ09165\nQ8WXI7\nQ8WZ42\nQ9H195\nQ9I7U4</p>",
  "messages": [
    {
      "id": 3306934,
      "postDate": "2025-10-25T16:21:32.170Z",
      "content": "<p>If you want to experiment with T5 embeddings for proteins, you can download the full precomputed set straight from UniProt:</p>\n<p>UniProt downloads page: <a href=\"https://www.uniprot.org/help/downloads\" target=\"_blank\">https://www.uniprot.org/help/downloads</a></p>\n<p>Direct FTP to embeddings (current release): <a href=\"https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/\" target=\"_blank\">https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/</a></p>\n<p>The download is an HDF5 (.h5) dataset containing T5 embeddings keyed by UniProt accessions.</p>\n<p><strong>Known missing IDs</strong>\nFor some reason (length quirks), \"Train\" embeddings for the following accessions are missing in the current release I checked:\nA2ASS6\nG4SLH0\nM9MRD1\nQ09165\nQ8WXI7\nQ8WZ42\nQ9H195\nQ9I7U4</p>",
      "rawMarkdown": "If you want to experiment with T5 embeddings for proteins, you can download the full precomputed set straight from UniProt:\n\nUniProt downloads page: https://www.uniprot.org/help/downloads\n\nDirect FTP to embeddings (current release): https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/\n\nThe download is an HDF5 (.h5) dataset containing T5 embeddings keyed by UniProt accessions.\n\n**Known missing IDs**\nFor some reason (length quirks), \"Train\" embeddings for the following accessions are missing in the current release I checked:\nA2ASS6\nG4SLH0\nM9MRD1\nQ09165\nQ8WXI7\nQ8WZ42\nQ9H195\nQ9I7U4\n",
      "votes": 16
    }
  ],
  "comments": [],
  "raw_markdown_by_id": {
    "3306934": "If you want to experiment with T5 embeddings for proteins, you can download the full precomputed set straight from UniProt:\n\nUniProt downloads page: https://www.uniprot.org/help/downloads\n\nDirect FTP to embeddings (current release): https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/embeddings/\n\nThe download is an HDF5 (.h5) dataset containing T5 embeddings keyed by UniProt accessions.\n\n**Known missing IDs**\nFor some reason (length quirks), \"Train\" embeddings for the following accessions are missing in the current release I checked:\nA2ASS6\nG4SLH0\nM9MRD1\nQ09165\nQ8WXI7\nQ8WZ42\nQ9H195\nQ9I7U4\n"
  }
}