Citation

How to cite POPPy.

POPPy is released under CC BY-NC 4.0. If it supports your work, please cite the platform and the primary sources it harmonizes.

About Method Team Citation
How to cite

Hewryk, O. S. I., Pan, I. T., O'Reilly, P., & Romano, J. D. (2026). POPPy: A Phyto-Ontology Platform for Pharmacology. University of Pennsylvania. 

@misc{poppy2026,
  author       = {Hewryk, Oresta S. I. and Pan, Ian Tong and O'Reilly, Patience and Romano, Joseph D.},
  title        = {POPPy: A Phyto-Ontology Platform for Pharmacology},
  year         = {2026},
  institution  = {University of Pennsylvania},
  version      = {0.1.0},
  url          = {https://poppyontology.org},
  note         = {CC BY-NC 4.0}
}
Documentation

Source code, schema overview, provenance notes, and usage guidance live on GitHub at github.com/RomanoLab/poppy. View on GitHub ↗

References

The sources POPPy is built from, and the ontologies and standards it aligns to.

Data sources
  1. i.
    COCONUT 2.0: A Comprehensive Overhaul and Curation of the Collection of Open Natural Products Database
    Chandrasekhar, V., Rajan, K., Kanakam, S. R. S., et al.
    Nucleic Acids Research · 2025 · doi: 10.1093/nar/gkae1063
    DOI
  2. ii.
    CMAUP: A Database of Collective Molecular Activities of Useful Plants
    Zeng, X., Zhang, P., Wang, Y., et al.
    Nucleic Acids Research · 2019 · doi: 10.1093/nar/gky965
    DOI
  3. iii.
    The ChEMBL Database in 2023: A Drug Discovery Platform Spanning Multiple Bioactivity Data Types and Time Periods
    Zdrazil, B., Felix, E., Hunter, F., et al.
    Nucleic Acids Research · 2024 · doi: 10.1093/nar/gkad1004
    DOI
  4. iv.
    DrugCentral 2023 Extends Human Clinical Data and Integrates Veterinary Drugs
    Avram, S., Wilson, T. B., Curpan, R., et al.
    Nucleic Acids Research · 2023 · doi: 10.1093/nar/gkac1085
    DOI
  5. v.
    Dr. Duke's Phytochemical and Ethnobotanical Databases
    U.S. Department of Agriculture, Agricultural Research Service (Duke, J. A.)
    USDA-ARS · 1992–2016 · doi: 10.15482/USDA.ADC/1239279
    DOI
  6. vi.
    NPASS: Natural Product Activity and Species Source Database for Natural Product Research, Discovery and Tool Development
    Zeng, X., Zhang, P., He, W., et al.
    Nucleic Acids Research · 2018 · doi: 10.1093/nar/gkx1026
    DOI
  7. vii.
    ComptoxAI: Automating Predictive Toxicology
    Romano, J. D., Hao, Y., Moore, J. H., & Penning, T. M.
    Chemical Research in Toxicology · 2022 · doi: 10.1021/acs.chemrestox.2c00074
    DOI
Ontologies & standards POPPy aligns to
  1. i.
    ChEBI: A Database and Ontology for Chemical Entities of Biological Interest
    Degtyarenko, K., De Matos, P., Ennis, M., et al.
    Nucleic Acids Research · 2007 · doi: 10.1093/nar/gkm791
    DOI
  2. ii.
    NCBI Taxonomy: A Comprehensive Update on Curation, Resources and Tools
    Schoch, C. L., Ciufo, S., Domrachev, M., et al.
    Database · 2020 · doi: 10.1093/database/baaa062
    DOI
  3. iii.
    The Gene Ontology (GO) Database and Informatics Resource
    Gene Ontology Consortium
    Nucleic Acids Research · 2004 · doi: 10.1093/nar/gkh036
    DOI
  4. iv.
    The OBO Foundry: Coordinated Evolution of Ontologies to Support Biomedical Data Integration
    Smith, B., Ashburner, M., Ceusters, W., et al.
    Nature Biotechnology · 2007 · doi: 10.1038/nbt1346
    DOI
  5. v.
    Plants of the World Online (POWO)
    Royal Botanic Gardens, Kew
    Taxonomic validation · powo.science.kew.org
    Site