{
  "id": 419597,
  "title": "Potential missing terms in go-basic.obo file",
  "url": "/competitions/cafa-5-protein-function-prediction/discussion/419597",
  "author_name": "",
  "post_date": "2023-06-26T17:27:30.988075900Z",
  "votes": 4,
  "comment_count": 4,
  "views": 0,
  "content": "<p>I just wanted to quickly highlight the potential problem of GO terms not being present in the go-basic.obo file such as GO:0000003 which is associated with several proteins in train_terms.tsv but absent in go-basic.obo. </p>",
  "messages": [
    {
      "id": "2318934",
      "postDate": "06/26/2023 17:27:30",
      "content": "<p>I just wanted to quickly highlight the potential problem of GO terms not being present in the go-basic.obo file such as GO:0000003 which is associated with several proteins in train_terms.tsv but absent in go-basic.obo. </p>",
      "rawMarkdown": "I just wanted to quickly highlight the potential problem of GO terms not being present in the go-basic.obo file such as GO:0000003 which is associated with several proteins in train_terms.tsv but absent in go-basic.obo.",
      "votes": null
    },
    {
      "id": "2319119",
      "postDate": "06/26/2023 22:02:38",
      "content": "<p>After more careful inspection, it appears that GO:0000003 might be the only one that is missing so add it in yourself :) </p>",
      "rawMarkdown": "After more careful inspection, it appears that GO:0000003 might be the only one that is missing so add it in yourself :)",
      "votes": null
    },
    {
      "id": "2321289",
      "postDate": "06/28/2023 12:43:06",
      "content": "<p>I think it is present:<br>\ngrep \"GO:0000003\" /kaggle/input/cafa-5-protein-function-prediction/Train/go-basic.obo<br>\nid: GO:0000003<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nrelationship: part_of GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction</p>",
      "rawMarkdown": "I think it is present:\ngrep \"GO:0000003\" /kaggle/input/cafa-5-protein-function-prediction/Train/go-basic.obo\nid: GO:0000003\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nrelationship: part_of GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction",
      "votes": null
    },
    {
      "id": "2325454",
      "postDate": "07/01/2023 11:04:16",
      "content": "<p>Can someone confirm that the final evaluation score will be using the train <code>go-basic.obo</code> file ? Or will it be using the latest available <code>go-basic.obo</code> available in UniProt at the moment of evaluation ?</p>",
      "rawMarkdown": "Can someone confirm that the final evaluation score will be using the train `go-basic.obo` file ? Or will it be using the latest available `go-basic.obo` available in UniProt at the moment of evaluation ?",
      "votes": null
    },
    {
      "id": "2339943",
      "postDate": "07/11/2023 06:49:38",
      "content": "<p>Hi <a href=\"https://www.kaggle.com/optimo\" target=\"_blank\">@optimo</a>,</p>\n<p>As stated by the competition host <a href=\"https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2237487\" target=\"_blank\">here</a>,</p>\n<blockquote>\n  <p>It is important to note that in the evaluation we are only be <strong>using the GO terms in the .obo file we provided</strong>. GO terms are added and removed over time, so you may encounter GO terms in those files that do not exist in the .obo files we provided.</p>\n</blockquote>\n<p>I think the final evaluation is just based on the provided <code>go-basic.obo</code> and no changes will be made on this file.</p>\n<p>Hope this helps, thanks!</p>",
      "rawMarkdown": "Hi @optimo,\n\nAs stated by the competition host [here](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2237487),\n\n> It is important to note that in the evaluation we are only be **using the GO terms in the .obo file we provided**. GO terms are added and removed over time, so you may encounter GO terms in those files that do not exist in the .obo files we provided.\n\nI think the final evaluation is just based on the provided `go-basic.obo` and no changes will be made on this file.\n\nHope this helps, thanks!",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2319119,
      "author_name": "zmcxjt",
      "author_url": "",
      "post_date": "06/26/2023 22:02:38",
      "content": "<p>After more careful inspection, it appears that GO:0000003 might be the only one that is missing so add it in yourself :) </p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2321289,
      "author_name": "mtinti",
      "author_url": "",
      "post_date": "06/28/2023 12:43:06",
      "content": "<p>I think it is present:<br>\ngrep \"GO:0000003\" /kaggle/input/cafa-5-protein-function-prediction/Train/go-basic.obo<br>\nid: GO:0000003<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nrelationship: part_of GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction<br>\nis_a: GO:0000003 ! reproduction</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2325454,
      "author_name": "optimo",
      "author_url": "",
      "post_date": "07/01/2023 11:04:16",
      "content": "<p>Can someone confirm that the final evaluation score will be using the train <code>go-basic.obo</code> file ? Or will it be using the latest available <code>go-basic.obo</code> available in UniProt at the moment of evaluation ?</p>",
      "votes": null,
      "replies": [
        {
          "id": 2339943,
          "author_name": "abaojiang",
          "author_url": "",
          "post_date": "07/11/2023 06:49:38",
          "content": "<p>Hi <a href=\"https://www.kaggle.com/optimo\" target=\"_blank\">@optimo</a>,</p>\n<p>As stated by the competition host <a href=\"https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2237487\" target=\"_blank\">here</a>,</p>\n<blockquote>\n  <p>It is important to note that in the evaluation we are only be <strong>using the GO terms in the .obo file we provided</strong>. GO terms are added and removed over time, so you may encounter GO terms in those files that do not exist in the .obo files we provided.</p>\n</blockquote>\n<p>I think the final evaluation is just based on the provided <code>go-basic.obo</code> and no changes will be made on this file.</p>\n<p>Hope this helps, thanks!</p>",
          "votes": null,
          "replies": []
        }
      ]
    }
  ],
  "raw_markdown_by_id": {
    "2318934": "I just wanted to quickly highlight the potential problem of GO terms not being present in the go-basic.obo file such as GO:0000003 which is associated with several proteins in train_terms.tsv but absent in go-basic.obo.",
    "2319119": "After more careful inspection, it appears that GO:0000003 might be the only one that is missing so add it in yourself :)",
    "2321289": "I think it is present:\ngrep \"GO:0000003\" /kaggle/input/cafa-5-protein-function-prediction/Train/go-basic.obo\nid: GO:0000003\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nrelationship: part_of GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction\nis_a: GO:0000003 ! reproduction",
    "2325454": "Can someone confirm that the final evaluation score will be using the train `go-basic.obo` file ? Or will it be using the latest available `go-basic.obo` available in UniProt at the moment of evaluation ?",
    "2339943": "Hi @optimo,\n\nAs stated by the competition host [here](https://www.kaggle.com/competitions/cafa-5-protein-function-prediction/discussion/405362#2237487),\n\n> It is important to note that in the evaluation we are only be **using the GO terms in the .obo file we provided**. GO terms are added and removed over time, so you may encounter GO terms in those files that do not exist in the .obo files we provided.\n\nI think the final evaluation is just based on the provided `go-basic.obo` and no changes will be made on this file.\n\nHope this helps, thanks!"
  },
  "source": "meta"
}