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README.md
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data_files: data/batman_formulas.csv
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sep: "\t"
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task_categories:
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language:
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- en
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- cn
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tags:
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- biology
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- life
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- chemistry
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- medical
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This dataset is a reformatted replica of [BATMAN-2.0](http://bionet.ncpsb.org.cn/batman-tcm/#/home), a database of traditional Chinese medicine (TCM) ingredients, herbs, and formulas.
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Refer to the original peer-reviewed [publication](https://doi.org/10.1093/nar/gkad926) for more detail.
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## Cite this dataset
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data_files: data/batman_formulas.csv
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sep: "\t"
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task_categories:
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- drug-discovery
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- chemical-screening
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language:
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- en
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- cn
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tags:
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- biology
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- life-sciences
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- chemistry
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- medical
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---
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This dataset is a reformatted replica of [BATMAN-2.0](http://bionet.ncpsb.org.cn/batman-tcm/#/home), a database of traditional Chinese medicine (TCM) ingredients, herbs, and formulas.
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Refer to the original peer-reviewed [publication](https://doi.org/10.1093/nar/gkad926) for more detail.
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## What can I do with this dataset?
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Check out the demo notebooks in the `demo` folder.
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BATMAN is a powerful source of data that links natural compounds and their compositions to protein targets.
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You can use this information to run drug discovery experiments or to extend the functionality of your own biomedical language models.
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For example, we used this dataset to extend the capabilities of [Precious3GPT](https://doi.org/10.57967/hf/2699) in the `demo/TCM_geroprotectors` demo project.
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While P3GPT is a transformer that can generate omics signatures for various tissues and conditions, it lacks any information on herbal medicine and TCM formulations.
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With BATMAN, we managed to remove this drawback and enable TCM screening in P3GPT.
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## Dataset structure
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- `batman_ingredients`: compounds naturally occurring in TCM herbs
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- `UID`: unique ID of an entity throughout the complete dataset;
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- `cid`: [PubChem](https://pubchem.ncbi.nlm.nih.gov/) molecule ID;
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- `pref_name`: conventional name of a compound (as mentioned in BATMAN);
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- `synonyms`: other names associated with the CID (if present in BATMAN);
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- `targets_known`: Verified human protein targets, according to BATMAN. The format is "symbol(ENTREZ_ID)"
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- `targts_pred`: All predicted protein targets, as stated in BATMAN (no significance threshold was used to filter these lists);
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- `herbs`: A list of herbs, in which the compound is encountered;
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- `formulas`: A list of TCM formulas that feature this compound.
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- `batman_herb`: herbs used in TCM
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- `UID`;
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- `pref_name`: Most commonly, the [pinyin](https://en.wikipedia.org/wiki/Pinyin) name of a herb. If not available — any other available name, e.g. latin or common English;
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- `synonyms`
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- `ingredients`: A list of all compound CIDs occurring in a herb;
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- `formulas`: A list of TCM formulas that feature thisherb.
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- `batman_formulas`: TCM formulas featured in the BATMAN dataset;
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- `UID`;
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- `pref_name`: The pinyin name of a herbal drug. Non-identical compositions sharing the same name are disambiguated using the `~X` suffix;
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- `synonyms`: The Chinese hieroglyphic spelling of the compostion;
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- `ingredients`;
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- `herbs`.
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## Cite this dataset
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