README.md

metadata

language: en
license: cc0-1.0
source_datasets: curated
task_categories:
  - tabular-classification
  - tabular-regression
tags:
  - chemistry
  - biology
  - medical
pretty_name: Blood-Brain Barrier Database (B3DB)
dataset_summary: >-
  Curation of 50 published resources of categorical and numeric measurements of
  Blood-Brain Barrier penetration.
size_categories:
  - 1K<n<10K
dataset_info:
  - config_name: B3DB_classification
    features:
      - name:
          feature_name_0: null
        dtype:
          feature_dtype_0: null
      - name:
          feature_name_1: null
        dtype:
          feature_dtype_1: null
      - name:
          feature_name_2: null
        dtype:
          feature_dtype_2: null
  - config_name: B3DB_classification_extended
    features:
      - name:
          feature_name_0: null
        dtype:
          feature_dtype_0: null
      - name:
          feature_name_1: null
        dtype:
          feature_dtype_1: null
      - name:
          feature_name_2: null
        dtype:
          feature_dtype_2: null
  - config_name: B3DB_regression
    features:
      - name:
          feature_name_0: null
        dtype:
          feature_dtype_0: null
      - name:
          feature_name_1: null
        dtype:
          feature_dtype_1: null
      - name:
          feature_name_2: null
        dtype:
          feature_dtype_2: null
  - config_name: B3DB_regression_extended
    features:
      - name:
          feature_name_0: null
        dtype:
          feature_dtype_0: null
      - name:
          feature_name_1: null
        dtype:
          feature_dtype_1: null
      - name:
          feature_name_2: null
        dtype:
          feature_dtype_2: null

Blood-Brain Barrier Database (B3DB)

The Blood-Brain Barrier Database (B3DB) is a large benchmark dataset compiled from 50 published resources (as summarized at raw_data/raw_data_summary.tsv) and categorized based on the consistency between different experimental references/measurements. This dataset was published in Scientific Data and a mirror of the theochem/B3DB the official Github repo where it is occasionally uploaded with new experimental data. Scientists who would like to contribute data should contact the database's maintainers (e.g., by creating a new Issue in the database).

A subset of the molecules in B3DB has numerical logBB values (1058 compounds), while the whole dataset has categorical (BBB+ or BBB-) BBB permeability labels (7807 compounds). Some physicochemical properties of the molecules are also provided.

Citation

Please use the following citation in any publication using our B3DB dataset:

@article{Meng_A_curated_diverse_2021,
author = {Meng, Fanwang and Xi, Yang and Huang, Jinfeng and Ayers, Paul W.},
doi = {10.1038/s41597-021-01069-5},
journal = {Scientific Data},
number = {289},
title = {A curated diverse molecular database of blood-brain barrier permeability with chemical descriptors},
volume = {8},
year = {2021},
url = {https://www.nature.com/articles/s41597-021-01069-5},
publisher = {Springer Nature}
}

Features of B3DB

1. The largest dataset with numerical and categorical values for Blood-Brain Barrier small molecules (to the best of our knowledge, as of February 25, 2021).

2. Inclusion of stereochemistry information with isomeric SMILES with chiral specifications if available. Otherwise, canonical SMILES are used.

3. Characterization of uncertainty of experimental measurements by grouping the collected molecular data records.

4. Extended datasets for numerical and categorical data with precomputed physicochemical properties using mordred.