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 full gives the entire cleaned wild-type accumulator dataset. Species specific configurations can be accessed:

configuration            n_rows
--------------------------------
Acinetobacter-baumannii    2148
Brucella-abortus           9946
Escherichia-coli          20451
Francisella-tularensis     9671
Klebsiella-pneumoniae      3920
Pseudomonas-aeruginosa    15677
Staphylococcus-aureus      2115
Streptococcus-pneumoniae   1254
Yersinia-enterocolitica    1405
Yersinia-pestis           10002

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 2x reduced or increased for "lt" or "gt"
• mic_method: Original method for meauring the MIC
• species: Bacterial species
• strain_name: Strain of bacterial species
• 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