PGxO: a lite Pharmacogenomic Ontology
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PGxO: a lite Pharmacogenomic Ontology

Latest version:
http://ns.inria.fr/pgxo/
Revision:
0.6
Authors:
Adrien Coulet (Inria, Inserm, Université Paris Cité, HeKA UMR1346, Paris, France)
Clément Jonquet (MISTEA, Université de Montpellier, Institut Agro, INRAE, Montpellier, France, and LIRMM, Université de Montpellier, Montpellier, France)
Pierre Monnin (Université Côte d'Azur, Inria, CNRS, I3S, Sophia-Antipolis, France)
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
https://creativecommons.org/licenses/by-nc/4.0/
Cite as:
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).
DOI:
10.1186/s12859-019-2693-9
PGxO v0.6 documentation

Abstract

This document describes the PGxO ontology, under the namespace http://ns.inria.fr/pgxo/. The preferred prefix for this namespace is pgxo.

Introduction back to ToC

PGxO is a lightweight and simple ontology to represent, trace, and reconcile knowledge in pharmacogenomics (PGx). Knowledge in PGx involves n-ary tuples representing so-called "pharmacogenomic relationships" and their components of three distinct types: drugs, genetic factors, and phenotypes. In PGxO, such tuples are reified as instances of the class PharmacogenomicRelationship. Components (drugs, genetic factors, phenotypes) are associated with pharmacogenomic tuples through the properties isAssociatedWith and isNotAssociatedWith and their sub-properties, as illustrated below:
Overview of PGxO main classes and properties
Figure 1: Overview of PGxO main classes and properties
Note that we re-use three properties of the Relation Ontology: ro:'part of', ro:'has part', and ro:'depends on'. Gene variants can be associated to their genes with ro:'part of' (and inversely using ro:'has part'). Complex phenotypes can be associated through ro:'depends on' to their sub-components (e.g., mentioned drugs, genes, or sub-phenotypes). To illustrate, 'metabolism of mercaptopurin' can be associated through ro:'depends on' to 'mercaptopurin'. An instantiated example of PGxO is displayed below, with additional metadata modeled using PROV-O:
Instantiated example of PGxO
Figure 2: Instantiated example of PGxO, available in RDF on GitHub
PGxO is also available on the [NCBO BioPortal](https://bioportal.bioontology.org/ontologies/PGXO). A full description of the motivation, implementation and instantiation of PGxO is available in [2]. When citing PGxO, please use [2].

Namespace declarations

Table 1: Namespaces used in the document
pgxo (default)<http://ns.inria.fr/pgxo/>
dc<http://purl.org/dc/terms/>
owl<http://www.w3.org/2002/07/owl#>
pgxo<http://ns.inria.fr/pgxo>
prov<http://www.w3.org/ns/prov#>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs<http://www.w3.org/2000/01/rdf-schema#>
ro<http://purl.obolibrary.org/obo/>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema#>

PGxO: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

PGxO: Description back to ToC

PGxO aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships.

Cross-reference for PGxO classes, object properties and data properties back to ToC

This section provides details for each class and property defined by PGxO.

Classes

Diseasec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Disease

has super-classes
Phenotype c

Drugc back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Drug

Genec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Gene

has super-classes
Genetic factor c

Genetic factorc back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/GeneticFactor

has sub-classes
Gene c, Genomic variation c

Genomic variationc back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/GenomicVariation

has super-classes
Genetic factor c
has sub-classes
Haplotype c, Variant c

Haplotypec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Haplotype

has super-classes
Genomic variation c

Pharmacodynamic phenotypec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/PharmacodynamicPhenotype

has super-classes
Phenotype c

Pharmacogenomic relationshipc back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/PharmacogenomicRelationship

has super-classes
Entity c
is in domain of
level of evidence in ClinPGx dp

Pharmacokinetic phenotypec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/PharmacokineticPhenotype

has super-classes
Phenotype c

Phenotypec back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Phenotype

has sub-classes
Disease c, Pharmacodynamic phenotype c, Pharmacokinetic phenotype c

Variantc back to ToC or Class ToC

IRI: http://ns.inria.fr/pgxo/Variant

has super-classes
Genomic variation c

Object Properties

causesop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/causes

has super-properties
influences op
is inverse of
is caused by op

decreasesop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/decreases

has super-properties
influences op
is inverse of
is decreased by op

decreases chance ofop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/decreasesChanceOf

has super-properties
influences op
is inverse of
has chance decreased by op

depends onop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/RO_0002502

does not causeop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotCause

has super-properties
does not influence op
is inverse of
is not caused by op

does not decreaseop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotDecrease

has super-properties
does not influence op
is inverse of
is not decreased by op

does not decrease chance ofop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotDecreaseChanceOf

has super-properties
does not influence op
is inverse of
has not chance decreased by op

does not increaseop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotIncrease

has super-properties
does not influence op
is inverse of
is not increased by op

does not increase chance ofop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotIncreaseChanceOf

has super-properties
does not influence op
is inverse of
has not chance increased by op

does not influenceop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotInfluence

has super-properties
is not associated with op
has sub-properties
does not cause op, does not decrease op, does not decrease chance of op, does not increase op, does not increase chance of op, does not metabolize op, does not transport op
is inverse of
is not influenced by op

does not metabolizeop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotMetabolize

has super-properties
does not influence op
is inverse of
is not metabolized by op

does not transportop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotTransport

has super-properties
does not influence op
is inverse of
is not transported by op

does not treatop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/doesNotTreat

has super-properties
is not associated with op
is inverse of
is not treated by op

has chance decreased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/hasChanceDecreasedBy

has super-properties
is influenced by op
is inverse of
decreases chance of op

has chance increased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/hasChanceIncreasedBy

has super-properties
is influenced by op
is inverse of
increases chance of op

has not chance decreased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/hasNotChanceDecreasedBy

has super-properties
is not influenced by op
is inverse of
does not decrease chance of op

has not chance increased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/hasNotChanceIncreasedBy

has super-properties
is not influenced by op
is inverse of
does not increase chance of op

has partop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000051

is inverse of
part of op

increasesop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/increases

has super-properties
influences op
is inverse of
is increased by op

increases chance ofop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/increasesChanceOf

has super-properties
influences op
is inverse of
has chance increased by op

influencesop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/influences

has super-properties
is associated with op
has sub-properties
causes op, decreases op, decreases chance of op, increases op, increases chance of op, metabolizes op, transports op
is inverse of
is influenced by op

is associated withop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isAssociatedWith

has characteristics: symmetric

has sub-properties
influences op, is influenced by op, is treated by op, treats op

is caused byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isCausedBy

has super-properties
is influenced by op
is inverse of
causes op

is decreased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isDecreasedBy

has super-properties
is influenced by op
is inverse of
decreases op

is increased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isIncreasedBy

has super-properties
is influenced by op
is inverse of
increases op

is influenced byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isInfluencedBy

has super-properties
is associated with op
has sub-properties
has chance decreased by op, has chance increased by op, is caused by op, is decreased by op, is increased by op, is metabolized by op, is transported by op
is inverse of
influences op

is metabolized byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isMetabolizedBy

has super-properties
is influenced by op
is inverse of
metabolizes op

is not associated withop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotAssociatedWith

has characteristics: symmetric

has sub-properties
does not influence op, does not treat op, is not influenced by op, is not treated by op

is not caused byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotCausedBy

has super-properties
is not influenced by op
is inverse of
does not cause op

is not decreased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotDecreasedBy

has super-properties
is not influenced by op
is inverse of
does not decrease op

is not increased byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotIncreasedBy

has super-properties
is not influenced by op
is inverse of
does not increase op

is not influenced byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotInfluencedBy

has super-properties
is not associated with op
has sub-properties
has not chance decreased by op, has not chance increased by op, is not caused by op, is not decreased by op, is not increased by op, is not metabolized by op, is not transported by op
is inverse of
does not influence op

is not metabolized byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotMetabolizedBy

has super-properties
is not influenced by op
is inverse of
does not metabolize op

is not transported byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotTransportedBy

has super-properties
is not influenced by op
is inverse of
does not transport op

is not treated byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isNotTreatedBy

has super-properties
is not associated with op
is inverse of
does not treat op

is transported byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isTransportedBy

has super-properties
is influenced by op
is inverse of
transports op

is treated byop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/isTreatedBy

has super-properties
is associated with op
is inverse of
treats op

metabolizesop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/metabolizes

has super-properties
influences op
is inverse of
is metabolized by op

part ofop back to ToC or Object Property ToC

IRI: http://purl.obolibrary.org/obo/BFO_0000050

is inverse of
has part op

qualified proxyop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/qualifiedProxy

qualified variationop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/qualifiedVariation

transportsop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/transports

has super-properties
influences op
is inverse of
is transported by op

treatsop back to ToC or Object Property ToC

IRI: http://ns.inria.fr/pgxo/treats

has super-properties
is associated with op
is inverse of
is treated by op

Data Properties

level of evidence in ClinPGxdp back to ToC or Data Property ToC

IRI: http://ns.inria.fr/pgxo/clinPGxLevelOfEvidence

has characteristics: functional

has domain
Pharmacogenomic relationship c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

References back to ToC

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](https://hal.inria.fr/hal-01593184/document) 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](https://doi.org/10.1186/s12859-019-2693-9)

Acknowledgments back to ToC

PGxO is supported by the PractiKPharma project, funded by the French National Research Agency (ANR) under grant ANR-15-CE23-0028.

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.