scbirlab/thomas-2018-spark-wt

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 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