Datasets:

scbirlab
/

thomas-2018-spark-wt

license: cc-by-nc-4.0
task_categories:
  - text-classification
tags:
  - chemistry
  - biology
  - antibiotics
  - SMILES
pretty_name: SPARK dataset of human-curated and standardized MICs
size_categories:
  - 10K<n<100K
configs:
  - config_name: unsplit
    data_files:
      - split: train
        path: all/scaffold-split-*.csv.gz
  - config_name: all
    data_files:
      - split: train
        path: all/scaffold-split-train.csv.gz
      - split: validation
        path: all/scaffold-split-validation.csv.gz
      - split: test
        path: all/scaffold-split-test.csv.gz
  - config_name: Acinetobacter-baumannii
    data_files:
      - split: train
        path: Acinetobacter-baumannii/scaffold-split-train.csv.gz
      - split: validation
        path: Acinetobacter-baumannii/scaffold-split-validation.csv.gz
      - split: test
        path: Acinetobacter-baumannii/scaffold-split-test.csv.gz
  - config_name: Brucella-abortus
    data_files:
      - split: train
        path: Brucella-abortus/scaffold-split-train.csv.gz
      - split: validation
        path: Brucella-abortus/scaffold-split-validation.csv.gz
      - split: test
        path: Brucella-abortus/scaffold-split-test.csv.gz
  - config_name: Escherichia-coli
    data_files:
      - split: train
        path: Escherichia-coli/scaffold-split-train.csv.gz
      - split: validation
        path: Escherichia-coli/scaffold-split-validation.csv.gz
      - split: test
        path: Escherichia-coli/scaffold-split-test.csv.gz
  - config_name: Francisella-tularensis
    data_files:
      - split: train
        path: Francisella-tularensis/scaffold-split-train.csv.gz
      - split: validation
        path: Francisella-tularensis/scaffold-split-validation.csv.gz
      - split: test
        path: Francisella-tularensis/scaffold-split-test.csv.gz
  - config_name: Klebsiella-pneumoniae
    data_files:
      - split: train
        path: Klebsiella-pneumoniae/scaffold-split-train.csv.gz
      - split: validation
        path: Klebsiella-pneumoniae/scaffold-split-validation.csv.gz
      - split: test
        path: Klebsiella-pneumoniae/scaffold-split-test.csv.gz
  - config_name: Pseudomonas-aeruginosa
    data_files:
      - split: train
        path: Pseudomonas-aeruginosa/scaffold-split-train.csv.gz
      - split: validation
        path: Pseudomonas-aeruginosa/scaffold-split-validation.csv.gz
      - split: test
        path: Pseudomonas-aeruginosa/scaffold-split-test.csv.gz
  - config_name: Staphylococcus-aureus
    data_files:
      - split: train
        path: Staphylococcus-aureus/scaffold-split-train.csv.gz
      - split: validation
        path: Staphylococcus-aureus/scaffold-split-validation.csv.gz
      - split: test
        path: Staphylococcus-aureus/scaffold-split-test.csv.gz
  - config_name: Streptococcus-pneumoniae
    data_files:
      - split: train
        path: Streptococcus-pneumoniae/scaffold-split-train.csv.gz
      - split: validation
        path: Streptococcus-pneumoniae/scaffold-split-validation.csv.gz
      - split: test
        path: Streptococcus-pneumoniae/scaffold-split-test.csv.gz
  - config_name: Yersinia-enterocolitica
    data_files:
      - split: train
        path: Yersinia-enterocolitica/scaffold-split-train.csv.gz
      - split: validation
        path: Yersinia-enterocolitica/scaffold-split-validation.csv.gz
      - split: test
        path: Yersinia-enterocolitica/scaffold-split-test.csv.gz
  - config_name: Yersinia-pestis
    data_files:
      - split: train
        path: Yersinia-pestis/scaffold-split-train.csv.gz
      - split: validation
        path: Yersinia-pestis/scaffold-split-validation.csv.gz
      - split: test
        path: Yersinia-pestis/scaffold-split-test.csv.gz

SPARK (wild-type accumulator phenotype): Human-curated and standardized MICs

These data were collated by the authors of:

Joe Thomas, Marc Navre, Aileen Rubio, and Allan Coukell Shared Platform for Antibiotic Research and Knowledge: A Collaborative Tool to SPARK Antibiotic Discovery ACS Infectious Diseases 2018 4 (11), 1536-1539 DOI: 10.1021/acsinfecdis.8b00193

We cleaned the original SPARK dataset to subset the most relevant columns, remove empty values, give succint column titles, and split by species.

This particular dataset retains only measurements on bacteria with wild-type accumulation phenotypes.

The SMILES strings have been canonicalized, and split into training (70%), validation (15%), and test (15%) sets by Murcko scaffold for each species with more than 1000 entries. Additional features like molecular weight and topological polar surface area have also been calculated.

Dataset Details

Configurations

The config all gives the entire cleaned wild-type accumulator dataset.

Species specific configurations can be accessed:

configuration	n_rows
Acinetobacter-baumannii	2148
Brucella-abortus	9947
Escherichia-coli	19660
Francisella-tularensis	9672
Klebsiella-pneumoniae	3713
Pseudomonas-aeruginosa	15454
Staphylococcus-aureus	1914
Streptococcus-pneumoniae	1254
Yersinia-enterocolitica	1405
Yersinia-pestis	10003

Dataset Description

Curated by: @eachanjohnson
Funded by: The Francis Crick Institute
License: CC-by-nc-4.0

Dataset Sources

Repository: https://www.collaborativedrug.com/spark-data-downloads
Paper: https://doi.org/10.1021/acsinfecdis.8b00193

Uses

Developing chemistry models for antibiotic drug discovery.

Dataset Structure

spark_compound_id: Original compound identifier
spark_SMILES: Original SMILES string of compound
spark_compound_batch_id: Original compound batch identifier
pubmed_id: Literature reference
doi: Literature reference
mic_micromolar: Minimum inhibitory concentration in µM, as in original dataset. Includes inequality symbols like ">"
mic_ineq_operator: Conversion of inequalities to "eq", "lt", "gt", "lteq", or "gteq"
plain_mic_micromolar: MIC with inequality symbols stripped
plain_pmic: pMIC based on MIC with inequality symbols stripped
pmic: pMIC if mic_ineq_operator == "eq", otherwise -1 or +1 for "lt" or "gt"
mic_method: Original method for meauring the MIC
species: Bacterial species
strain_name: Strain of bacterial species
strain_genotype: Genotype of bacterial strain
full_strain_name: Full name of bacterial strain, concatenation of species and strain_name
full_strain_name_with_genotype: Full name of bacterial strain, concatenation of species, strain_name, and strain_genotype
accumulation_phenotype: Whether efflux deficient. In this dataset, all "Wild type"
mic_condition: Original condition for measuring MIC
id: Numerical almost-unique identifier of compound
inchikey: Unique identifier for compound
smiles: RDKit-canonicalized SMILES string of compound
scaffold: Murcko scaffold of compound
mwt: Molecular weight of compound
clogp: Crippen LogP of compound
tpsa: Topological polar surface area of compound
is_train: In training split
is_test: In test split
is_validation: In validation split

Dataset Creation

Curation Rationale

To make available a high quality of MICs for various species.

Data Collection and Processing

Data were processed using schemist, a tool for processing chemical datasets.

Who are the source data producers?

Joe Thomas, Marc Navre, Aileen Rubio, and Allan Coukell

Personal and Sensitive Information

None.

Citation

BibTeX:

@article{doi:10.1021/acsinfecdis.8b00193,
  author = {Thomas, Joe and Navre, Marc and Rubio, Aileen and Coukell, Allan},
  title = {Shared Platform for Antibiotic Research and Knowledge: A Collaborative Tool to SPARK Antibiotic Discovery},
  journal = {ACS Infectious Diseases},
  volume = {4},
  number = {11},
  pages = {1536-1539},
  year = {2018},
  doi = {10.1021/acsinfecdis.8b00193},
  URL = {https://doi.org/10.1021/acsinfecdis.8b00193},
  eprint = {https://doi.org/10.1021/acsinfecdis.8b00193}
}

APA:

Joe Thomas, Marc Navre, Aileen Rubio, and Allan Coukell (2018). Shared Platform for Antibiotic Research and Knowledge: A Collaborative Tool to SPARK Antibiotic Discovery. ACS Infectious Diseases 2018 4 (11), 1536-1539. doi:10.1021/acsinfecdis.8b00193

Dataset Card Contact

@eachanjohnson