| --- |
| license: mit |
| language: |
| - en |
| tags: |
| - fluorescent proteins |
| - biology |
| pretty_name: FPbase |
| viewer: true |
| configs: |
| - config_name: default |
| data_files: |
| - split: Fpbase |
| path: data/fpbase_raw.csv |
| Citation_bibtex: |- |
| @article{Lambert2019, |
| title = {FPbase: a community-editable fluorescent protein database}, |
| volume = {16}, |
| ISSN = {1548-7105}, |
| url = {http://dx.doi.org/10.1038/s41592-019-0352-8}, |
| DOI = {10.1038/s41592-019-0352-8}, |
| number = {4}, |
| journal = {Nature Methods}, |
| publisher = {Springer Science and Business Media LLC}, |
| author = {Lambert, Talley J.}, |
| year = {2019}, |
| month = mar, |
| pages = {277–278} |
| } |
| --- |
| |
| # 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. Visit [fpbase.org](https://www.fpbase.org) for more. |
|
|
| This dataset updated on ,March 1st, 2026, collects FPbase fluorescent protein records (e.g., names, identifiers, sequences, and photophysical properties) for downstream analysis and modeling. |
|
|
| --- |
|
|
| ## Quickstart Usage |
|
|
| ### Install HuggingFace Datasets |
|
|
| Each subset can be loaded into Python using the HuggingFace [`datasets`](https://huggingface.co/docs/datasets/index) library. First, install it from the command line: |
| ```bash |
| pip install datasets |
| ``` |
|
|
| Optionally set the cache directory: |
| ```bash |
| export HF_HOME=${HOME}/.cache/huggingface/ |
| ``` |
|
|
| Then, from within Python, import the library: |
| ```python |
| import datasets |
| ``` |
|
|
| ### Load the Dataset |
|
|
| To load one of the `<DATASET ID>` subsets, use `datasets.load_dataset(...)`: |
| ```python |
| dataset_tag = "<DATASET TAG>" |
| dataset = datasets.load_dataset( |
| path="<HF PATH TO DATASET>", |
| name=f"{dataset_tag}", |
| data_dir=f"{dataset_tag}" |
| )["train"] |
| ``` |
|
|
| The dataset is loaded as a `datasets.arrow_dataset.Dataset`: |
| ```python |
| >>> dataset |
| <RESULT OF LOADING DATASET MODEL> |
| ``` |
|
|
| This column-oriented format can be accessed directly, converted to a `pandas.DataFrame`, or exported to `parquet`: |
| ```python |
| dataset.data.column("<COLUMN NAME IN DATASET>") |
| dataset.to_pandas() |
| dataset.to_parquet("dataset.parquet") |
| ``` |
|
|
| --- |
|
|
| ## Dataset Description |
|
|
| > Source: [github.com/tlambert03/FPbase](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 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 |
|
|
| Excerpts from primary literature can also be entered to store key information that is otherwise difficult to capture within the current database schema. |
|
|
| --- |
|
|
| ## Dataset Fields |
|
|
| Raw data is available at [`fpbase_raw.csv`](https://huggingface.co/datasets/RosettaCommons/FPbase/tree/main/data). |
|
|
| | Field | Description | |
| |---|---| |
| | `name` | Protein name | |
| | `fpbase_id` | ID in FPbase | |
| | `ex_max` | Excitation maximum | |
| | `em_max` | Emission maximum | |
| | `emhex` | Emission color (hex) | |
| | `exhex` | Excitation color (hex) | |
| | `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 type | |
|
|
| --- |
| ## Citation |
| ``` |
| @article{Lambert2019, |
| title = {FPbase: a community-editable fluorescent protein database}, |
| volume = {16}, |
| ISSN = {1548-7105}, |
| url = {http://dx.doi.org/10.1038/s41592-019-0352-8}, |
| DOI = {10.1038/s41592-019-0352-8}, |
| number = {4}, |
| journal = {Nature Methods}, |
| publisher = {Springer Science and Business Media LLC}, |
| author = {Lambert, Talley J.}, |
| year = {2019}, |
| month = mar, |
| pages = {277–278} |
| } |
| ``` |
|
|
| ## Licensing |
|
|
| 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. Users should attribute the original authors of the corresponding data (referenced on the relevant protein pages). |
|
|
| --- |
|
|
| ## Dataset Card Authors |
|
|
| Yijie Luo, Ming Shen, Kaley Chinoy |
