| --- |
| license: mit |
| language: en |
| --- |
| # FPbase: The Fluorescent Protein Database |
| FPbase is a free, open-source, community-editable database of fluorescent proteins and their properties, aimed at aggregating structured, searchable information useful to the imaging community and FP developers. https://www.fpbase.org. |
| This dataset packages FPbase fluorescent protein records (e.g., names, identifiers, sequences, and photophysical properties) as machine-readable files suitable for downstream analysis and modeling. |
|
|
| ## Quickstart Usage |
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| ### Install HuggingFace Datasets package |
| Each subset can be loaded into python using the HuggingFace [datasets](https://huggingface.co/docs/datasets/index) library. First, from the command line install the `datasets` library |
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| $ pip install datasets |
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| Optionally set the cache directory, e.g. |
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| $ HF\_HOME=${HOME}/.cache/huggingface/ |
| $ export HF\_HOME |
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| then, from within python load the datasets library |
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| \>\>\> import datasets |
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|
| ### fetch database information |
| Run the [pull_fpbase.py](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/blob/main/src/pull_fpbase.py) |
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| $python /src/pull_fpbase.py |
| |
| ## Output description |
| Check the [fpbase_raw.csv](https://huggingface.co/datasets/Kaleychinoy/FPbase_databazaar_2026/tree/main/data) |
| - **name: protein name** |
| - **fpbase_id: ID in FPbase** |
| - **ex_max: excitation maximum** |
| - **em_max: emission maximum** |
| - **emhex: emission color** |
| - **exhex: emission color** |
| - **ext_coeff: extinction coefficient** |
| - **qy: quantum yield** |
| - **lifetime_ns: lifetime(ns)** |
| - **pdb: PDB ID**: |
| - **genbank: genbank ID** |
| - **uniprot: Uniprot ID** |
| - **aggregation: oligomeric state** |
| - **switch_type: photo-switching types** |
| |
| ### Dataset Description |
| (https://github.com/tlambert03/FPbase) |
| FPbase is a free and open-source, community-editable database for fluorescent proteins (FPs) and their properties. |
| The primary objective is to aggregate structured and searchable FP data that is of interest to the imaging community and FP developers. |
| Each protein in the database has a dedicated page showing amino acid sequence, accession IDs (e.g. GenBank, UniProt), evolution lineages and mutations, fluorescence attributes, structural data, references that introduced or characterized the protein, |
| and more. Excerpts from primary literature can be entered to store key information about a protein that is otherwise difficult to capture within the current database schema. |
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| ## Liscensing |
| FPbase states that data in the FPbase archive are “free of all copyright restrictions” and made fully and freely available for both non-commercial and commercial use, and that users should attribute the original authors of the corresponding data (referenced on the relevant protein pages). |
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|
| ## Dataset Card Authors |
| Yijie Luo, Ming Shen |
