{
  "id": 403503,
  "title": "Pretrained embeddings for all SwissProt proteins (Dataset)",
  "url": "/competitions/cafa-5-protein-function-prediction/discussion/403503",
  "author_name": "",
  "post_date": "2023-04-23T13:53:44.876394700Z",
  "votes": 10,
  "comment_count": 1,
  "views": 0,
  "content": "<p>I've uploaded a dataset of pretrained (T5) embeddings per protein (whole protein level) for all the Swissprot proteins (this should include all the proteins in this challenge). </p>\n<p><a href=\"https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings\" target=\"_blank\">https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings</a></p>\n<p>Data is from <a href=\"https://www.uniprot.org/help/embeddings\" target=\"_blank\">UniProt</a>.</p>",
  "messages": [
    {
      "id": "2231640",
      "postDate": "04/23/2023 13:53:44",
      "content": "<p>I've uploaded a dataset of pretrained (T5) embeddings per protein (whole protein level) for all the Swissprot proteins (this should include all the proteins in this challenge). </p>\n<p><a href=\"https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings\" target=\"_blank\">https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings</a></p>\n<p>Data is from <a href=\"https://www.uniprot.org/help/embeddings\" target=\"_blank\">UniProt</a>.</p>",
      "rawMarkdown": "I've uploaded a dataset of pretrained (T5) embeddings per protein (whole protein level) for all the Swissprot proteins (this should include all the proteins in this challenge). \n\n[https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings](https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings)\n\nData is from [UniProt](https://www.uniprot.org/help/embeddings).",
      "votes": null
    },
    {
      "id": "2234984",
      "postDate": "04/25/2023 16:07:58",
      "content": "<p>Dan, thank you for sharing. <br>\nYou wrote</p>\n<blockquote>\n  <p>this should include all the proteins in this challenge</p>\n</blockquote>\n<p>As you can see, the dataset you've shared covers only part of the train set - among 142246 proteins in the train set, 58283 belong to TrEMBL, not  to SwissProt. As such they were not included in <a href=\"https://www.uniprot.org/help/embeddings\" target=\"_blank\">https://www.uniprot.org/help/embeddings</a><br>\nSimilarily, among 141865 proteins in Test \"superset\", 70 are from TrEMBL.<br>\nTypical examples:</p>\n<ul>\n<li><a href=\"https://www.uniprot.org/uniprotkb/P0DN89/entry\" target=\"_blank\">https://www.uniprot.org/uniprotkb/P0DN89/entry</a> (from Test \"superset\")</li>\n<li><a href=\"https://www.uniprot.org/uniprotkb/Q19523/entry\" target=\"_blank\">https://www.uniprot.org/uniprotkb/Q19523/entry</a> (from Train)</li>\n</ul>",
      "rawMarkdown": "Dan, thank you for sharing. \nYou wrote\n\n>this should include all the proteins in this challenge\n\nAs you can see, the dataset you've shared covers only part of the train set - among 142246 proteins in the train set, 58283 belong to TrEMBL, not  to SwissProt. As such they were not included in https://www.uniprot.org/help/embeddings\nSimilarily, among 141865 proteins in Test \"superset\", 70 are from TrEMBL.\nTypical examples:\n- https://www.uniprot.org/uniprotkb/P0DN89/entry (from Test \"superset\")\n- https://www.uniprot.org/uniprotkb/Q19523/entry (from Train)",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2234984,
      "author_name": "igorrrr",
      "author_url": "",
      "post_date": "04/25/2023 16:07:58",
      "content": "<p>Dan, thank you for sharing. <br>\nYou wrote</p>\n<blockquote>\n  <p>this should include all the proteins in this challenge</p>\n</blockquote>\n<p>As you can see, the dataset you've shared covers only part of the train set - among 142246 proteins in the train set, 58283 belong to TrEMBL, not  to SwissProt. As such they were not included in <a href=\"https://www.uniprot.org/help/embeddings\" target=\"_blank\">https://www.uniprot.org/help/embeddings</a><br>\nSimilarily, among 141865 proteins in Test \"superset\", 70 are from TrEMBL.<br>\nTypical examples:</p>\n<ul>\n<li><a href=\"https://www.uniprot.org/uniprotkb/P0DN89/entry\" target=\"_blank\">https://www.uniprot.org/uniprotkb/P0DN89/entry</a> (from Test \"superset\")</li>\n<li><a href=\"https://www.uniprot.org/uniprotkb/Q19523/entry\" target=\"_blank\">https://www.uniprot.org/uniprotkb/Q19523/entry</a> (from Train)</li>\n</ul>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2231640": "I've uploaded a dataset of pretrained (T5) embeddings per protein (whole protein level) for all the Swissprot proteins (this should include all the proteins in this challenge). \n\n[https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings](https://www.kaggle.com/datasets/danofer/uniprotkbswiss-prot-protein-embeddings)\n\nData is from [UniProt](https://www.uniprot.org/help/embeddings).",
    "2234984": "Dan, thank you for sharing. \nYou wrote\n\n>this should include all the proteins in this challenge\n\nAs you can see, the dataset you've shared covers only part of the train set - among 142246 proteins in the train set, 58283 belong to TrEMBL, not  to SwissProt. As such they were not included in https://www.uniprot.org/help/embeddings\nSimilarily, among 141865 proteins in Test \"superset\", 70 are from TrEMBL.\nTypical examples:\n- https://www.uniprot.org/uniprotkb/P0DN89/entry (from Test \"superset\")\n- https://www.uniprot.org/uniprotkb/Q19523/entry (from Train)"
  },
  "source": "meta"
}