Pathogens data set

This data set has been generated for the annotation of pathogens from the scientific literature using the readbiomed-ncbi-pathogen-dataset-generation package.

NCBI taxonomy pathogen data set (ncbi folder)

National Center for Biotechnology Information (NCBI) data sources have been used to automatically collect information about pathogens from NCBI database resources. The folder ncbi has the files for taxonomic pathogens, PrPSc prions and toxins and a description of the content of each folder.

The information for each pathogen is in XML format and includes meta-data about the pathogen, information about subspecies and PubMed and PubMed Central identifiers that can be used to recover information about these pathogens from the scientific literature.

Manually annotated data set (manual-set folder)

The manual-set folder contains manual annotation for the characterisation of actively research pathogens from the scientific literature.

More information about the manually annotated data set is available here.

References

If you use this work in your research, remember to cite it. The publication below contains additional information about the creation of this data set.

@article{jimeno2023classifying,
  title={Classifying literature mentions of biological pathogens as experimentally studied using natural language processing},
  author={Jimeno Yepes, Antonio and Verspoor, Karin},
  journal={Journal of Biomedical Semantics},
  year={2023},
  volume={14},
  number={1},
  doi={10.1186/s13326-023-00282-y},
  url={https://doi.org/10.1186/s13326-023-00282-y}
}