README.md

---
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](https://github.com/scbirlab/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:

```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