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+
+
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+
diff --git a/pgxo.owl b/pgxo.owl
index 92a5428..09bb8c0 100644
--- a/pgxo.owl
+++ b/pgxo.owl
@@ -1,44 +1,134 @@
- Pierre Monnin, Loria (CNRS, Inria Nancy-Grand Est, Université de Lorraine)
- Version 0.3
-
-Changelog:
-- Remove pgxo:partOf
-- Remove pgxo:confidence
-- Add pgxo:PharmacokineticPhenotype as subclass of pgxo:Phenotype
-- Add pgxo:PharmacodynamicPhenotype as subclass of pgxo:Phenotype
-- Add pgxo:qualifiedVariation
-- Add pgxo:qualifiedProxy
-- Add ro:dependsOn
-- Add ro:partOf and ro:hasPart (inverse relations)
-- Add dul:Entity
-- Add dul:Quality (subclass of dul:Entity)
-- Add dul:hasQuality (dul:Entity -> dul:Quality)
-- Add dul:hasDataValue (dul:Entity -> literal)
-- Define prov:Generation as subclass of dul:Entity
-- Update PharmacogenomicRelationship subsumption axiom
- Adrien Coulet, Loria - Inria, Université de Lorraine
- PGxO: a lite Pharmacogenomic Ontology
- PGxO aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships.
- Clément Jonquet, LIRMM, Université de Montpellier
+
+
+
+
+ https://github.com/practikpharma/PGxO
+ Ontology simple de pharmacogenomique
+ http://bioportal.bioontology.org/ontologies/PGXO
+
+ - R. Dieng, O. Corby, A. Giboin, and M. Ribiere. Methods and tools for corporate knowledge management. International journal of human-computer studies, 51(3):567–598, 1999.
+ - N. F. Noy, D. L. McGuinness, et al. Ontology development 101: A guide to creating your first ontology, 2001.
+
+ http://bioportal.bioontology.org/ontologies/PGXO/?p=classes
+ Lite Pharmacogenomics Ontology
+ 8
+ https://github.com/practikpharma/PGxO/issues
+ Pierre Monnin (pierre.monnin@loria.fr)
+ http://bioportal.bioontology.org/ontologies/PGXO
+ https://github.com/practikpharma/PGxO
+ Does PGxO enable to represent a PGx knowledge unit discovered from clinical data, along with its provenance?
+ PGxO
+ Adrien Coulet (adrien.coulet@loria.fr - https://orcid.org/0000-0002-1466-062X)
+
+ http://practikpharma.loria.fr
+ false
+ pgxo
+ Open Access (to be further determined)
+
+ Reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison
+ EU H2020 Marie Sklodowska-Curie Action (grant 701771)
+
+ 1
+
+ http://www.loria.fr/pgxo/PharmacogenomicRelationship,http://www.loria.fr/pgxo/Drug,http://www.loria.fr/pgxo/Phenotype,http://www.loria.fr/pgxo/GeneticFactor
+
+ Within ANR PracticKPharma project to reconcile PGx relationships
+ http://www.loria.fr/pgxo/
+ Change log (v0.3):
+ - Remove pgxo:partOf
+ - Remove pgxo:confidence
+ - Add pgxo:PharmacokineticPhenotype as subclass of pgxo:Phenotype
+ - Add pgxo:PharmacodynamicPhenotype as subclass of pgxo:Phenotype
+ - Add pgxo:qualifiedVariation
+ - Add pgxo:qualifiedProxy
+ - Add ro:dependsOn
+ - Add ro:partOf and ro:hasPart (inverse relations)
+ - Add dul:Entity
+ - Add dul:Quality (subclass of dul:Entity)
+ - Add dul:hasQuality (dul:Entity -> dul:Quality)
+ - Add dul:hasDataValue (dul:Entity -> literal)
+ - Define prov:Generation as subclass of dul:Entity
+ - Update PharmacogenomicRelationship subsumption axiom
+
+ 9
+
+ http://bioportal.bioontology.org/ontologies/PGXO
+
+ https://www.biorxiv.org/content/biorxiv/early/2018/08/13/390971.full.pdf
+ Simple Pharmacogenomics Ontology
+
+
+ https://raw.githubusercontent.com/practikpharma/PGxO/master/pgxo.owl
+ 1
+
+
+ 60
+ Does PGxO, coupled with its reconciliation rules, enable to decide if two knowledge units, with distinct provenances, may refer to the same thing?
+
+ - Point 1
+ - Point 2
+
+
+
+ 16
+ 2017-03
+
+ http://www.loria.fr/pgxo/
+ Agence Nationale de la Recherche (ANR-15-CE23-0028)
+ http://www.loria.fr
+
+
+ Description Logics (ALCI(D))
+ 0.3
+ Clement Jonquet (jonquet@lirmm.fr - https://orcid.org/0000-0002-2404-1582)
+ production
+ https://pgxlod.loria.fr
+
+
+ pharmacogenomics, pharmacogenomic relationship, PGx reconciliation, pharmacogenomic knowledge
+ PGxO fournie un ensemble minimal de concepts (avec leur role) pour la formalisation de relation de pharmacogénomique.
+ http://www.loria.fr
+ 2018-08
+
+ Work in progress within PractiKPharma project. Contact us for more information.
+ 23Kb
+ PGxO aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships.
+ Does PGxO enable to represent a PGx knowledge unit from the PGx state of the art (i.e., from a reference database or extracted from the biomedical literature), along with its provenance?
+
+ Bioinformaticians, knowledge engineers, clinical decision support systems
+ 18
+ IDEX Lorraine Université d’Excellence (15-IDEX-0004)
+
-
-
-
+
+
-
-
-
+
+ compose
part of
-
+
+ contient
has part
-
+
+ dépend de
depends on
-
+
+ cause
+ causes
-
+
-
-
+
+ est causé par
+ is caused by
+
+
+ intermédiaire qualifié
+ qualified proxy
-
+
+ qualified variation
+ variation qualifiée
-
+
@@ -124,12 +226,13 @@ Changelog:
+ a pour qualité
has quality
+
-
-
-
+
+ a pour valeur
has data value
+
-
-
+
+
+
+
+
+ Ontologie
+ Ontology
+
+
- Disease
+ Disease
+ Maladie
-
+
- Drug
+ Drug
+ Médicament
-
+
@@ -182,43 +297,48 @@ Changelog:
Gene
+ Gène
-
+
- Genetic factor
+ Facteur génétique
+ Genetic factor
-
+
- Genomic variation
+ Genomic variation
+ Variation génétique
-
+
- Haplotype
+ Haplotype
+ Haplotype
-
+
- Pharmacodynamic Phenotype
+ Pharmacodynamic Phenotype
+ Phénotype pharmacodynamique
-
+
@@ -315,43 +435,48 @@ Changelog:
- Pharmacogenomic relationship
+ Pharmacogenomic relationship
+ Relation pharmacogénomique
-
+
- Pharmacokinetic Phenotype
+ Pharmacokinetic Phenotype
+ Phénotype pharmacocinétique
-
+
- Phenotype
+ Phenotype
+ Phénotype
-
+
- Variant
+ Variant
+ Variant
-
+
Entity
+ Entité
-
+
@@ -359,23 +484,49 @@ Changelog:
Quality
+ Qualité
-
+
-
-
+
+ Entity
+ Entité
+
+
+ Generation
+ Génération
+
+
+
+
+
+
+
+
+
+
+
+
+
+