README.md

---
version: 1.2.0
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.
citation: "@article{\n  Meng_A_curated_diverse_2021,\n  author = {Meng, Fanwang and\
  \ Xi, Yang and Huang, Jinfeng and Ayers, Paul W.},\n  doi = {10.1038/s41597-021-01069-5},\n\
  \  journal = {Scientific Data},\n  number = {289},\n  title = {A curated diverse\
  \ molecular database of blood-brain barrier permeability with chemical descriptors},\n\
  \  volume = {8},\n  year = {2021},\n  url = {https://www.nature.com/articles/s41597-021-01069-5},\n\
  \  publisher = {Springer Nature}\n}"
size_categories:
- 1K<n<10K
config_names:
- B3DB_classification
- B3DB_classification_extended
- B3DB_regression
- B3DB_regression_extended
configs:
- config_name: B3DB_classification
  data_files:
  - split: test
    path: B3DB_classification/test.csv
  - split: train
    path: B3DB_classification/train.csv
- config_name: B3DB_classification_extended
  data_files:
  - split: test
    path: B3DB_classification_extended/test.csv
  - split: train
    path: B3DB_classification_extended/train.csv
- config_name: B3DB_regression
  data_files:
  - split: test
    path: B3DB_regression/test.csv
  - split: train
    path: B3DB_regression/train.csv
- config_name: B3DB_regression_extended
  data_files:
  - split: train
    path: B3DB_regression_extended/train-*
  - split: test
    path: B3DB_regression_extended/test-*
dataset_info:
- config_name: B3DB_classification
  features:
  - name: B3DB_classification_index
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  - name: compound_name
    dtype: string
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  - name: MolCount
    dtype: int64
  splits:
  - name: train
    num_bytes: 656000
    num_examples: 5855
  - name: test
    num_bytes: 218640
    num_examples: 1951
- config_name: B3DB_classification_extended
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  - name: Xp-5d
    dtype: float64
  - name: Xp-6d
    dtype: float64
  - name: Xp-7d
    dtype: float64
  - name: AXp-0d
    dtype: float64
  - name: AXp-1d
    dtype: float64
  - name: AXp-2d
    dtype: float64
  - name: AXp-3d
    dtype: float64
  - name: AXp-4d
    dtype: float64
  - name: AXp-5d
    dtype: float64
  - name: AXp-6d
    dtype: float64
  - name: AXp-7d
    dtype: float64
  - name: Xp-0dv
    dtype: float64
  - name: Xp-1dv
    dtype: float64
  - name: Xp-2dv
    dtype: float64
  - name: Xp-3dv
    dtype: float64
  - name: Xp-4dv
    dtype: float64
  - name: Xp-5dv
    dtype: float64
  - name: Xp-6dv
    dtype: float64
  - name: Xp-7dv
    dtype: float64
  - name: AXp-0dv
    dtype: float64
  - name: AXp-1dv
    dtype: float64
  - name: AXp-2dv
    dtype: float64
  - name: AXp-3dv
    dtype: float64
  - name: AXp-4dv
    dtype: float64
  - name: AXp-5dv
    dtype: float64
  - name: AXp-6dv
    dtype: float64
  - name: AXp-7dv
    dtype: float64
  - name: SZ
    dtype: float64
  - name: Sm
    dtype: float64
  - name: Sv
    dtype: float64
  - name: Sse
    dtype: float64
  - name: Spe
    dtype: float64
  - name: Sare
    dtype: float64
  - name: Sp
    dtype: float64
  - name: Si
    dtype: float64
  - name: MZ
    dtype: float64
  - name: Mm
    dtype: float64
  - name: Mv
    dtype: float64
  - name: Mse
    dtype: float64
  - name: Mpe
    dtype: float64
  - name: Mare
    dtype: float64
  - name: Mp
    dtype: float64
  - name: Mi
    dtype: float64
  - name: SpAbs_Dt
    dtype: float64
  - name: SpMax_Dt
    dtype: float64
  - name: SpDiam_Dt
    dtype: float64
  - name: SpAD_Dt
    dtype: float64
  - name: SpMAD_Dt
    dtype: float64
  - name: LogEE_Dt
    dtype: float64
  - name: SM1_Dt
    dtype: float64
  - name: VE1_Dt
    dtype: float64
  - name: VE2_Dt
    dtype: float64
  - name: VE3_Dt
    dtype: float64
  - name: VR1_Dt
    dtype: float64
  - name: VR2_Dt
    dtype: float64
  - name: VR3_Dt
    dtype: float64
  - name: DetourIndex
    dtype: float64
  - name: SpAbs_D
    dtype: float64
  - name: SpMax_D
    dtype: float64
  - name: SpDiam_D
    dtype: float64
  - name: SpAD_D
    dtype: float64
  - name: SpMAD_D
    dtype: float64
  - name: LogEE_D
    dtype: float64
  - name: VE1_D
    dtype: float64
  - name: VE2_D
    dtype: float64
  - name: VE3_D
    dtype: float64
  - name: VR1_D
    dtype: float64
  - name: VR2_D
    dtype: float64
  - name: VR3_D
    dtype: float64
  - name: NsLi
    dtype: int64
  - name: NssBe
    dtype: int64
  - name: NssssBe
    dtype: int64
  - name: NssBH
    dtype: int64
  - name: NsssB
    dtype: int64
  - name: NssssB
    dtype: int64
  - name: NsCH3
    dtype: int64
  - name: NdCH2
    dtype: int64
  - name: NssCH2
    dtype: int64
  - name: NtCH
    dtype: int64
  - name: NdsCH
    dtype: int64
  - name: NaaCH
    dtype: int64
  - name: NsssCH
    dtype: int64
  - name: NddC
    dtype: int64
  - name: NtsC
    dtype: int64
  - name: NdssC
    dtype: int64
  - name: NaasC
    dtype: int64
  - name: NaaaC
    dtype: int64
  - name: NssssC
    dtype: int64
  - name: NsNH3
    dtype: int64
  - name: NsNH2
    dtype: int64
  - name: NssNH2
    dtype: int64
  - name: NdNH
    dtype: int64
  - name: NssNH
    dtype: int64
  - name: NaaNH
    dtype: int64
  - name: NtN
    dtype: int64
  - name: NsssNH
    dtype: int64
  - name: NdsN
    dtype: int64
  - name: NaaN
    dtype: int64
  - name: NsssN
    dtype: int64
  - name: NddsN
    dtype: int64
  - name: NaasN
    dtype: int64
  - name: NssssN
    dtype: int64
  - name: NsOH
    dtype: int64
  - name: NdO
    dtype: int64
  - name: NssO
    dtype: int64
  - name: NaaO
    dtype: int64
  - name: NsF
    dtype: int64
  - name: NsSiH3
    dtype: int64
  - name: NssSiH2
    dtype: int64
  - name: NsssSiH
    dtype: int64
  - name: NssssSi
    dtype: int64
  - name: NsPH2
    dtype: int64
  - name: NssPH
    dtype: int64
  - name: NsssP
    dtype: int64
  - name: NdsssP
    dtype: int64
  - name: NsssssP
    dtype: int64
  - name: NsSH
    dtype: int64
  - name: NdS
    dtype: int64
  - name: NssS
    dtype: int64
  - name: NaaS
    dtype: int64
  - name: NdssS
    dtype: int64
  - name: NddssS
    dtype: int64
  - name: NsCl
    dtype: int64
  - name: NsGeH3
    dtype: int64
  - name: NssGeH2
    dtype: int64
  - name: NsssGeH
    dtype: int64
  - name: NssssGe
    dtype: int64
  - name: NsAsH2
    dtype: int64
  - name: NssAsH
    dtype: int64
  - name: NsssAs
    dtype: int64
  - name: NsssdAs
    dtype: int64
  - name: NsssssAs
    dtype: int64
  - name: NsSeH
    dtype: int64
  - name: NdSe
    dtype: int64
  - name: NssSe
    dtype: int64
  - name: NaaSe
    dtype: int64
  - name: NdssSe
    dtype: int64
  - name: NddssSe
    dtype: int64
  - name: NsBr
    dtype: int64
  - name: NsSnH3
    dtype: int64
  - name: NssSnH2
    dtype: int64
  - name: NsssSnH
    dtype: int64
  - name: NssssSn
    dtype: int64
  - name: NsI
    dtype: int64
  - name: NsPbH3
    dtype: int64
  - name: NssPbH2
    dtype: int64
  - name: NsssPbH
    dtype: int64
  - name: NssssPb
    dtype: int64
  - name: SsLi
    dtype: int64
  - name: SssBe
    dtype: int64
  - name: SssssBe
    dtype: int64
  - name: SssBH
    dtype: int64
  - name: SsssB
    dtype: float64
  - name: SssssB
    dtype: int64
  - name: SsCH3
    dtype: float64
  - name: SdCH2
    dtype: float64
  - name: SssCH2
    dtype: float64
  - name: StCH
    dtype: float64
  - name: SdsCH
    dtype: float64
  - name: SaaCH
    dtype: float64
  - name: SsssCH
    dtype: float64
  - name: SddC
    dtype: float64
  - name: StsC
    dtype: float64
  - name: SdssC
    dtype: float64
  - name: SaasC
    dtype: float64
  - name: SaaaC
    dtype: float64
  - name: SssssC
    dtype: float64
  - name: SsNH3
    dtype: int64
  - name: SsNH2
    dtype: float64
  - name: SssNH2
    dtype: int64
  - name: SdNH
    dtype: float64
  - name: SssNH
    dtype: float64
  - name: SaaNH
    dtype: float64
  - name: StN
    dtype: float64
  - name: SsssNH
    dtype: int64
  - name: SdsN
    dtype: float64
  - name: SaaN
    dtype: float64
  - name: SsssN
    dtype: float64
  - name: SddsN
    dtype: float64
  - name: SaasN
    dtype: float64
  - name: SssssN
    dtype: float64
  - name: SsOH
    dtype: float64
  - name: SdO
    dtype: float64
  - name: SssO
    dtype: float64
  - name: SaaO
    dtype: float64
  - name: SsF
    dtype: float64
  - name: SsSiH3
    dtype: float64
  - name: SssSiH2
    dtype: int64
  - name: SsssSiH
    dtype: int64
  - name: SssssSi
    dtype: int64
  - name: SsPH2
    dtype: int64
  - name: SssPH
    dtype: int64
  - name: SsssP
    dtype: int64
  - name: SdsssP
    dtype: float64
  - name: SsssssP
    dtype: int64
  - name: SsSH
    dtype: float64
  - name: SdS
    dtype: float64
  - name: SssS
    dtype: float64
  - name: SaaS
    dtype: float64
  - name: SdssS
    dtype: float64
  - name: SddssS
    dtype: float64
  - name: SsCl
    dtype: float64
  - name: SsGeH3
    dtype: int64
  - name: SssGeH2
    dtype: int64
  - name: SsssGeH
    dtype: int64
  - name: SssssGe
    dtype: int64
  - name: SsAsH2
    dtype: int64
  - name: SssAsH
    dtype: int64
  - name: SsssAs
    dtype: int64
  - name: SsssdAs
    dtype: int64
  - name: SsssssAs
    dtype: int64
  - name: SsSeH
    dtype: int64
  - name: SdSe
    dtype: int64
  - name: SssSe
    dtype: int64
  - name: SaaSe
    dtype: int64
  - name: SdssSe
    dtype: int64
  - name: SddssSe
    dtype: int64
  - name: SsBr
    dtype: float64
  - name: SsSnH3
    dtype: int64
  - name: SssSnH2
    dtype: int64
  - name: SsssSnH
    dtype: int64
  - name: SssssSn
    dtype: int64
  - name: SsI
    dtype: float64
  - name: SsPbH3
    dtype: int64
  - name: SssPbH2
    dtype: int64
  - name: SsssPbH
    dtype: int64
  - name: SssssPb
    dtype: int64
  - name: MAXsLi
    dtype: float64
  - name: MAXssBe
    dtype: float64
  - name: MAXssssBe
    dtype: float64
  - name: MAXssBH
    dtype: float64
  - name: MAXsssB
    dtype: float64
  - name: MAXssssB
    dtype: float64
  - name: MAXsCH3
    dtype: float64
  - name: MAXdCH2
    dtype: float64
  - name: MAXssCH2
    dtype: float64
  - name: MAXtCH
    dtype: float64
  - name: MAXdsCH
    dtype: float64
  - name: MAXaaCH
    dtype: float64
  - name: MAXsssCH
    dtype: float64
  - name: MAXddC
    dtype: float64
  - name: MAXtsC
    dtype: float64
  - name: MAXdssC
    dtype: float64
  - name: MAXaasC
    dtype: float64
  - name: MAXaaaC
    dtype: float64
  - name: MAXssssC
    dtype: float64
  - name: MAXsNH3
    dtype: float64
  - name: MAXsNH2
    dtype: float64
  - name: MAXssNH2
    dtype: float64
  - name: MAXdNH
    dtype: float64
  - name: MAXssNH
    dtype: float64
  - name: MAXaaNH
    dtype: float64
  - name: MAXtN
    dtype: float64
  - name: MAXsssNH
    dtype: float64
  - name: MAXdsN
    dtype: float64
  - name: MAXaaN
    dtype: float64
  - name: MAXsssN
    dtype: float64
  - name: MAXddsN
    dtype: float64
  - name: MAXaasN
    dtype: float64
  - name: MAXssssN
    dtype: float64
  - name: MAXsOH
    dtype: float64
  - name: MAXdO
    dtype: float64
  - name: MAXssO
    dtype: float64
  - name: MAXaaO
    dtype: float64
  - name: MAXsF
    dtype: float64
  - name: MAXsSiH3
    dtype: float64
  - name: MAXssSiH2
    dtype: float64
  - name: MAXsssSiH
    dtype: float64
  - name: MAXssssSi
    dtype: float64
  - name: MAXsPH2
    dtype: float64
  - name: MAXssPH
    dtype: float64
  - name: MAXsssP
    dtype: float64
  - name: MAXdsssP
    dtype: float64
  - name: MAXsssssP
    dtype: float64
  - name: MAXsSH
    dtype: float64
  - name: MAXdS
    dtype: float64
  - name: MAXssS
    dtype: float64
  - name: MAXaaS
    dtype: float64
  - name: MAXdssS
    dtype: float64
  - name: MAXddssS
    dtype: float64
  - name: MAXsCl
    dtype: float64
  - name: MAXsGeH3
    dtype: float64
  - name: MAXssGeH2
    dtype: float64
  - name: MAXsssGeH
    dtype: float64
  - name: MAXssssGe
    dtype: float64
  - name: MAXsAsH2
    dtype: float64
  - name: MAXssAsH
    dtype: float64
  - name: MAXsssAs
    dtype: float64
  - name: MAXsssdAs
    dtype: float64
  - name: MAXsssssAs
    dtype: float64
  - name: MAXsSeH
    dtype: float64
  - name: MAXdSe
    dtype: float64
  - name: MAXssSe
    dtype: float64
  - name: MAXaaSe
    dtype: float64
  - name: MAXdssSe
    dtype: float64
  - name: MAXddssSe
    dtype: float64
  - name: MAXsBr
    dtype: float64
  - name: MAXsSnH3
    dtype: float64
  - name: MAXssSnH2
    dtype: float64
  - name: MAXsssSnH
    dtype: float64
  - name: MAXssssSn
    dtype: float64
  - name: MAXsI
    dtype: float64
  - name: MAXsPbH3
    dtype: float64
  - name: MAXssPbH2
    dtype: float64
  - name: MAXsssPbH
    dtype: float64
  - name: MAXssssPb
    dtype: float64
  - name: MINsLi
    dtype: float64
  - name: MINssBe
    dtype: float64
  - name: MINssssBe
    dtype: float64
  - name: MINssBH
    dtype: float64
  - name: MINsssB
    dtype: float64
  - name: MINssssB
    dtype: float64
  - name: MINsCH3
    dtype: float64
  - name: MINdCH2
    dtype: float64
  - name: MINssCH2
    dtype: float64
  - name: MINtCH
    dtype: float64
  - name: MINdsCH
    dtype: float64
  - name: MINaaCH
    dtype: float64
  - name: MINsssCH
    dtype: float64
  - name: MINddC
    dtype: float64
  - name: MINtsC
    dtype: float64
  - name: MINdssC
    dtype: float64
  - name: MINaasC
    dtype: float64
  - name: MINaaaC
    dtype: float64
  - name: MINssssC
    dtype: float64
  - name: MINsNH3
    dtype: float64
  - name: MINsNH2
    dtype: float64
  - name: MINssNH2
    dtype: float64
  - name: MINdNH
    dtype: float64
  - name: MINssNH
    dtype: float64
  - name: MINaaNH
    dtype: float64
  - name: MINtN
    dtype: float64
  - name: MINsssNH
    dtype: float64
  - name: MINdsN
    dtype: float64
  - name: MINaaN
    dtype: float64
  - name: MINsssN
    dtype: float64
  - name: MINddsN
    dtype: float64
  - name: MINaasN
    dtype: float64
  - name: MINssssN
    dtype: float64
  - name: MINsOH
    dtype: float64
  - name: MINdO
    dtype: float64
  - name: MINssO
    dtype: float64
  - name: MINaaO
    dtype: float64
  - name: MINsF
    dtype: float64
  - name: MINsSiH3
    dtype: float64
  - name: MINssSiH2
    dtype: float64
  - name: MINsssSiH
    dtype: float64
  - name: MINssssSi
    dtype: float64
  - name: MINsPH2
    dtype: float64
  - name: MINssPH
    dtype: float64
  - name: MINsssP
    dtype: float64
  - name: MINdsssP
    dtype: float64
  - name: MINsssssP
    dtype: float64
  - name: MINsSH
    dtype: float64
  - name: MINdS
    dtype: float64
  - name: MINssS
    dtype: float64
  - name: MINaaS
    dtype: float64
  - name: MINdssS
    dtype: float64
  - name: MINddssS
    dtype: float64
  - name: MINsCl
    dtype: float64
  - name: MINsGeH3
    dtype: float64
  - name: MINssGeH2
    dtype: float64
  - name: MINsssGeH
    dtype: float64
  - name: MINssssGe
    dtype: float64
  - name: MINsAsH2
    dtype: float64
  - name: MINssAsH
    dtype: float64
  - name: MINsssAs
    dtype: float64
  - name: MINsssdAs
    dtype: float64
  - name: MINsssssAs
    dtype: float64
  - name: MINsSeH
    dtype: float64
  - name: MINdSe
    dtype: float64
  - name: MINssSe
    dtype: float64
  - name: MINaaSe
    dtype: float64
  - name: MINdssSe
    dtype: float64
  - name: MINddssSe
    dtype: float64
  - name: MINsBr
    dtype: float64
  - name: MINsSnH3
    dtype: float64
  - name: MINssSnH2
    dtype: float64
  - name: MINsssSnH
    dtype: float64
  - name: MINssssSn
    dtype: float64
  - name: MINsI
    dtype: float64
  - name: MINsPbH3
    dtype: float64
  - name: MINssPbH2
    dtype: float64
  - name: MINsssPbH
    dtype: float64
  - name: MINssssPb
    dtype: float64
  - name: ECIndex
    dtype: int64
  - name: ETA_alpha
    dtype: float64
  - name: AETA_alpha
    dtype: float64
  - name: ETA_shape_p
    dtype: float64
  - name: ETA_shape_y
    dtype: float64
  - name: ETA_shape_x
    dtype: float64
  - name: ETA_beta
    dtype: float64
  - name: AETA_beta
    dtype: float64
  - name: ETA_beta_s
    dtype: float64
  - name: AETA_beta_s
    dtype: float64
  - name: ETA_beta_ns
    dtype: float64
  - name: AETA_beta_ns
    dtype: float64
  - name: ETA_beta_ns_d
    dtype: float64
  - name: AETA_beta_ns_d
    dtype: float64
  - name: ETA_eta
    dtype: float64
  - name: AETA_eta
    dtype: float64
  - name: ETA_eta_L
    dtype: float64
  - name: AETA_eta_L
    dtype: float64
  - name: ETA_eta_R
    dtype: float64
  - name: AETA_eta_R
    dtype: float64
  - name: ETA_eta_RL
    dtype: float64
  - name: AETA_eta_RL
    dtype: float64
  - name: ETA_eta_F
    dtype: float64
  - name: AETA_eta_F
    dtype: float64
  - name: ETA_eta_FL
    dtype: float64
  - name: AETA_eta_FL
    dtype: float64
  - name: ETA_eta_B
    dtype: float64
  - name: AETA_eta_B
    dtype: float64
  - name: ETA_eta_BR
    dtype: float64
  - name: AETA_eta_BR
    dtype: float64
  - name: ETA_dAlpha_A
    dtype: float64
  - name: ETA_dAlpha_B
    dtype: float64
  - name: ETA_epsilon_1
    dtype: float64
  - name: ETA_epsilon_2
    dtype: float64
  - name: ETA_epsilon_3
    dtype: float64
  - name: ETA_epsilon_4
    dtype: float64
  - name: ETA_epsilon_5
    dtype: float64
  - name: ETA_dEpsilon_A
    dtype: float64
  - name: ETA_dEpsilon_B
    dtype: float64
  - name: ETA_dEpsilon_C
    dtype: float64
  - name: ETA_dEpsilon_D
    dtype: float64
  - name: ETA_dBeta
    dtype: float64
  - name: AETA_dBeta
    dtype: float64
  - name: ETA_psi_1
    dtype: float64
  - name: ETA_dPsi_A
    dtype: float64
  - name: ETA_dPsi_B
    dtype: float64
  - name: fragCpx
    dtype: float64
  - name: fMF
    dtype: float64
  - name: nHBAcc
    dtype: int64
  - name: nHBDon
    dtype: int64
  - name: IC0
    dtype: float64
  - name: IC1
    dtype: float64
  - name: IC2
    dtype: float64
  - name: IC3
    dtype: float64
  - name: IC4
    dtype: float64
  - name: IC5
    dtype: float64
  - name: TIC0
    dtype: float64
  - name: TIC1
    dtype: float64
  - name: TIC2
    dtype: float64
  - name: TIC3
    dtype: float64
  - name: TIC4
    dtype: float64
  - name: TIC5
    dtype: float64
  - name: SIC0
    dtype: float64
  - name: SIC1
    dtype: float64
  - name: SIC2
    dtype: float64
  - name: SIC3
    dtype: float64
  - name: SIC4
    dtype: float64
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  splits:
  - name: train
    num_bytes: 10644655
    num_examples: 795
  - name: test
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    num_examples: 263
  download_size: 9687972
  dataset_size: 14179671
---

# Blood-Brain Barrier Database (B3DB)

The [Blood-Brain Barrier Database (B3DB)](https://www.nature.com/articles/s41597-021-01069-5)
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](https://www.nature.com/articles/s41597-021-01069-5) and
a mirror of the [theochem/B3DB](https://github.com/theochem/B3DB) the official Github repo where it is
occasionally uploaded with new experimental data. We used the original datasets uploaded in 2023 (regression datasets)
and 2021 (classification datasets). Scientists who would like
to contribute data should contact the database's maintainers (e.g., by creating a
[new Issue](https://github.com/theochem/B3DB/issues) 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.

[Updates 2025.08.16 -- version 1.2.0]
Removed or replaced the invalid SMILES with valid SMILES.
- Removed 'C[N+]1(C)CCC[C@H](OC(=O)[C+](O)(c2ccccc2)c2ccccc2)C1'
- Replaced 'C[N+]1(C)CCCC(OC(=O)[C+](O)(c2ccccc2)c2ccccc2)C1' with 'C/N=C(\NC#N)NCCSCc1csc(N=C(N)N)n1'


## Quickstart Usage

### Load a dataset in python
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

    $ pip install datasets

then, from within python load the datasets library

    >>> import datasets
   
and load one of the `B3DB` datasets, e.g.,

    >>> B3DB_classification = datasets.load_dataset("maomlab/B3DB", name = "B3DB_classification")
    Downloading readme: 100%|████████████████████████| 4.40k/4.40k [00:00<00:00, 1.35MB/s]
    Downloading data: 100%|██████████████████████████| 680k/680k [00:00<00:00, 946kB/s]
    Downloading data: 100%|██████████████████████████| 2.11M/2.11M [00:01<00:00, 1.28MB/s]
    Generating test split: 100%|█████████████████████| 1951/1951 [00:00<00:00, 20854.95 examples/s]
    Generating train split: 100%|████████████████████| 5855/5855 [00:00<00:00, 144260.80 examples/s]

and inspecting the loaded dataset

    >>> B3DB_classification
    B3DB_classification
    DatasetDict({
      test: Dataset({
         features: ['B3DB_classification_index', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'Y', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
         num_rows: 1951
      })
      train: Dataset({
          features: ['B3DB_classification_index', 'compound_name', 'IUPAC_name', 'SMILES', 'CID', 'logBB', 'Y', 'Inchi', 'threshold', 'reference', 'group', 'comments', 'ClusterNo', 'MolCount'],
          num_rows: 5855
      })
    })

### Use a dataset to train a model
One way to use the dataset is through the [MolFlux](https://exscientia.github.io/molflux/) package developed by Exscientia.
First, from the command line, install `MolFlux` library with `catboost` and `rdkit` support

    pip install 'molflux[catboost,rdkit]'

then load, featurize, split, fit, and evaluate the a catboost model

    import json
    from datasets import load_dataset
    from molflux.datasets import featurise_dataset
    from molflux.features import load_from_dicts as load_representations_from_dicts
    from molflux.splits import load_from_dict as load_split_from_dict
    from molflux.modelzoo import load_from_dict as load_model_from_dict
    from molflux.metrics import load_suite
    
    split_dataset = load_dataset('maomlab/B3DB', name = 'B3DB_classification')
    
    split_featurised_dataset = featurise_dataset(
      split_dataset,
      column = "SMILES",
      representations = load_representations_from_dicts([{"name": "morgan"}, {"name": "maccs_rdkit"}]))

    model = load_model_from_dict({
        "name": "cat_boost_classifier",
        "config": {
            "x_features": ['SMILES::morgan', 'SMILES::maccs_rdkit'],
            "y_features": ['Y']}})
    
    model.train(split_featurised_dataset["train"])
    preds = model.predict(split_featurised_dataset["test"])
    
    classification_suite = load_suite("classification")
    
    scores = classification_suite.compute(
        references=split_featurised_dataset["test"]['Y'],
        predictions=preds["cat_boost_classifier::Y"])


## About the DB3B

### 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](https://github.com/mordred-descriptor/mordred).


### Data splits
The original B3DB dataset does not define splits, so here we have used the `Realistic Split` method described
in [(Martin et al., 2018)](https://doi.org/10.1021/acs.jcim.7b00166).

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

```md
@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}
}
```