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Define "other ..." category terms in term lookup #2

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dustine32 opened this issue Dec 14, 2023 · 1 comment
Open

Define "other ..." category terms in term lookup #2

dustine32 opened this issue Dec 14, 2023 · 1 comment
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@dustine32
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dustine32 commented Dec 14, 2023

Currently, the plan is to make up term IDs for the "other" categories. Ex:

    {
        "term_id": "OTHER:0002",
        "term_label": "other cellular process"
    },

Since these categories are derived from a mutable file level_one_terms.txt, these IDs will have to be dynamically assigned during each data conversion "build," which will inextricably tie the term lookup file to the BP modules file. For example, if the "cellular process" GO term is dropped from level_one_terms.txt then another "other" term might inherit its ID. Or if another term is added, the ID of its "other" category term may change from OTHER:0002 to OTHER:0003 or something else.

Tagging @tmushayahama

@dustine32
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Handled (AFAIK) in d1960bd. The dataflow works like:

  1. The level_one_terms.txt file is parsed in mint_other_terms.py to create a JSON lookup with an OTHER: term minted for each level 1 term. The "other biological process" term is also added.
  2. This JSON is then input into organize_bp_modules_from_slim.py so that the correct OTHER: IDs are used.
  3. The ibd_modules_organized.json and level_one_terms.json files are then used to create go_term_info.json.

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