PGxO

A lightweight and simple ontology to reconcile and trace knowledge in pharmacogenomics (PGx).

PGxO is also available on http://ns.inria.fr/pgxo/ and on the NCBO BioPortal.

A full description of the motivation, implementation and instantiation of PGxO is available in [2].

When citing PGxO, please use [2].

Documentation

Documentation is available in the doc/ folder:

• widoco/doc/index.html: HTML documentation of PGxO
• pgxo-overview.pdf: Figure presenting PGxO main concepts and relations.
• MIRO.md: Minimum Information for the Reporting of an Ontology (MIRO) associated with PGxO.
• pgxo_with_instances.owl: An instantiated example of PGxO. Note that the instanciation used in PGxLOD contains additional metadata (e.g., entity spans for text extraction, ClinPGx IDs are associated with PMIDs, different namespaces and naming conventions)
• pgxo_with_instances_figure.pdf: Global figure presenting the instantiated example of PGxO.

Mappings

Mappings are available in the mappings/ folder:

• mapp1.owl: Mappings from PGxO to four ontologies related to PGx (SO-PHARM, PO, PHARE and Genomic CDS).
• mapp2.owl: Mappings from PGxO to three large spectrum ontologies (MeSH, NCIt and SNOMED CT).

License

PGxO is under Creative Commons BY NC 4.0.

References

1. Monnin, P., Jonquet, C., Legrand, J., Napoli, A., & Coulet, A. (2017, October). PGxO: A very lite ontology to reconcile pharmacogenomic knowledge units. In Methods, tools & platforms for Personalized Medicine in the Big Data Era. Link
2. Monnin, P., Legrand, J., Husson, G., Ringot, P., Tchechmedjiev, A., Jonquet, C., Napoli, A., & Coulet, A. PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison. BMC Bioinformatics 20-S(4): 139:1-139:16 (2019). Link

@Article{Monnin2019,
    author="Monnin, Pierre
    and Legrand, Jo{\"e}l
    and Husson, Graziella
    and Ringot, Patrice
    and Tchechmedjiev, Andon
    and Jonquet, Cl{\'e}ment
    and Napoli, Amedeo
    and Coulet, Adrien",
    title="PGxO and PGxLOD: a reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison",
    journal="BMC Bioinformatics",
    year="2019",
    month="Apr",
    day="18",
    volume="20-S",
    number="4",
    pages="139",
    issn="1471-2105",
    doi="10.1186/s12859-019-2693-9",
    url="https://doi.org/10.1186/s12859-019-2693-9"
}

Acknowledgments

PGxO is supported by the PractiKPharma project (http://practikpharma.loria.fr/), funded by the French National Research Agency (ANR) under grant ANR-15-CE23-0028.