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

PGxO is also available 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 is available in the doc/ folder:

• pgxo.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 version of PGxO.
• global-fig.pdf: Global figure presenting the instantiation of PGxO.

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).

PGxO is under Creative Commons BY NC 4.0.

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" } 

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.