From ec596d35ae690d85e7cf91a9671863b8d39d8e22 Mon Sep 17 00:00:00 2001 From: Clement Jonquet Date: Mon, 10 Sep 2018 11:46:34 +0200 Subject: [PATCH 1/2] First round of metadata edits for review --- .DS_Store | Bin 0 -> 6148 bytes pgxo.owl | 162 +++++++++++++++++++++++++++++++++++++++++++++--------- 2 files changed, 137 insertions(+), 25 deletions(-) create mode 100644 .DS_Store diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..5008ddfcf53c02e82d7eee2e57c38e5672ef89f6 GIT binary patch literal 6148 zcmeH~Jr2S!425mzP>H1@V-^m;4Wg<&0T*E43hX&L&p$$qDprKhvt+--jT7}7np#A3 zem<@ulZcFPQ@L2!n>{z**++&mCkOWA81W14cNZlEfg7;MkzE(HCqgga^y>{tEnwC%0;vJ&^%eQ zLs35+`xjp>T0 - - 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 - + xmlns:omv="http://omv.ontoware.org/2005/05/ontology#" + xmlns:dcterms="http://purl.org/dc/terms/" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:door="http://kannel.open.ac.uk/ontology#" + xmlns:lexvo="http://lexvo.org/ontology#" + xmlns:void="http://rdfs.org/ns/void#" + xmlns:vann="http://purl.org/vocab/vann/" + xmlns:adms="http://www.w3.org/ns/adms#" + xmlns:voaf="http://purl.org/vocommons/voaf#" + xmlns:doap="http://usefulinc.com/ns/doap#" + xmlns:mod="http://www.isibang.ac.in/ns/mod#" + xmlns:sd="http://www.w3.org/ns/sparql-service-description#" + > + + + + + + + Simple Pharmacogenomics Ontology + Ontology simple de pharmacogenomique + Lite Pharmacogenomics Ontology + PGxO + http://www.loria.fr/pgxo/ + Work in progress within PractiKPharma project. Contact us for more information. + + 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 + + 0.3 + + - Point 1 + - Point 2 + + + + https://github.com/practikpharma/PGxO + http://bioportal.bioontology.org/ontologies/PGXO + https://raw.githubusercontent.com/practikpharma/PGxO/master/pgxo.owl + https://github.com/practikpharma/PGxO + https://github.com/practikpharma/PGxO/issues + https://pgxlod.loria.fr + + + + + false + production + Open Access (to be further determined) + http://www.loria.fr/pgxo/ + pgxo + http://bioportal.bioontology.org/ontologies/PGXO + http://bioportal.bioontology.org/ontologies/PGXO + http://bioportal.bioontology.org/ontologies/PGXO/?p=classes + + + PGxO aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships. + http://www.loria.fr/pgxo/PharmacogenomicRelationship,http://www.loria.fr/pgxo/Drug,http://www.loria.fr/pgxo/Phenotype,http://www.loria.fr/pgxo/GeneticFactor + pharmacogenomics, pharmacogenomic relationship, PGx reconciliation, pharmacogenomic knowledge + + + https://www.biorxiv.org/content/biorxiv/early/2018/08/13/390971.full.pdf + + + Reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison + 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? + Does PGxO enable to represent a PGx knowledge unit discovered from clinical data, along with its provenance? + Does PGxO, coupled with its reconciliation rules, enable to decide if two knowledge units, with distinct provenances, may refer to the same thing? + Within ANR PracticKPharma project to reconcile PGx relationships + http://practikpharma.loria.fr + + - 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. + + + Description Logics (ALCI(D)) + Bioinformaticians, knowledge engineers, clinical decision support systems + Agence Nationale de la Recherche (ANR-15-CE23-0028) + IDEX Lorraine Université d’Excellence (15-IDEX-0004) + EU H2020 Marie Sklodowska-Curie Action (grant 701771) + + + Pierre Monnin (pierre.monnin@loria.fr) + Adrien Coulet (adrien.coulet@loria.fr - https://orcid.org/0000-0002-1466-062X) + Clement Jonquet (jonquet@lirmm.fr - https://orcid.org/0000-0002-2404-1582) + http://www.loria.fr + http://www.loria.fr + + + 2017-03 + 2018-08 + + + + + + + 16 + 1 + 9 + 60 + 18 + 8 + 1 + 23Kb + + + + + + + + + + + + + + + + + + + - + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:dc="http://purl.org/dc/elements/1.1/"> - - - - Simple Pharmacogenomics Ontology - Ontology simple de pharmacogenomique - Lite Pharmacogenomics Ontology - PGxO - http://www.loria.fr/pgxo/ - Work in progress within PractiKPharma project. Contact us for more information. - - Change log (v0.3): + + + + + 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 @@ -51,106 +74,61 @@ - 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 - - 0.3 - + - 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 - - - https://github.com/practikpharma/PGxO - http://bioportal.bioontology.org/ontologies/PGXO - https://raw.githubusercontent.com/practikpharma/PGxO/master/pgxo.owl - https://github.com/practikpharma/PGxO - https://github.com/practikpharma/PGxO/issues - https://pgxlod.loria.fr - - - - - false - production - Open Access (to be further determined) - http://www.loria.fr/pgxo/ - pgxo - http://bioportal.bioontology.org/ontologies/PGXO - http://bioportal.bioontology.org/ontologies/PGXO - http://bioportal.bioontology.org/ontologies/PGXO/?p=classes - - - PGxO aims at providing a small set of concepts and roles that may type elements of pharmacogenomic relationships. - http://www.loria.fr/pgxo/PharmacogenomicRelationship,http://www.loria.fr/pgxo/Drug,http://www.loria.fr/pgxo/Phenotype,http://www.loria.fr/pgxo/GeneticFactor - pharmacogenomics, pharmacogenomic relationship, PGx reconciliation, pharmacogenomic knowledge - - - https://www.biorxiv.org/content/biorxiv/early/2018/08/13/390971.full.pdf - - - Reconciliation of pharmacogenomic knowledge of various provenances, enabling further comparison - 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? - Does PGxO enable to represent a PGx knowledge unit discovered from clinical data, along with its provenance? - Does PGxO, coupled with its reconciliation rules, enable to decide if two knowledge units, with distinct provenances, may refer to the same thing? - Within ANR PracticKPharma project to reconcile PGx relationships - http://practikpharma.loria.fr - - - 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. - - - Description Logics (ALCI(D)) - Bioinformaticians, knowledge engineers, clinical decision support systems - Agence Nationale de la Recherche (ANR-15-CE23-0028) - IDEX Lorraine Université d’Excellence (15-IDEX-0004) - EU H2020 Marie Sklodowska-Curie Action (grant 701771) - - - Pierre Monnin (pierre.monnin@loria.fr) - Adrien Coulet (adrien.coulet@loria.fr - https://orcid.org/0000-0002-1466-062X) - Clement Jonquet (jonquet@lirmm.fr - https://orcid.org/0000-0002-2404-1582) - http://www.loria.fr - http://www.loria.fr - - - 2017-03 - 2018-08 - - - - - - - 16 - 1 - 9 - 60 - 18 - 8 - 1 - 23Kb - - - - - - - - - - - - - - - - - - - - - - - + + - - - + + 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 - + @@ -236,12 +226,13 @@ + a pour qualité has quality + - - - + + a pour valeur has data value + - - + + + + + + Ontologie + Ontology + + - Disease + Disease + Maladie - + - Drug + Drug + Médicament - + @@ -294,43 +297,48 @@ Gene + Gène - + - Genetic factor + Facteur génétique + Genetic factor - + - Genomic variation + Genomic variation + Variation génétique - + - Haplotype + Haplotype + Haplotype - + - Pharmacodynamic Phenotype + Pharmacodynamic Phenotype + Phénotype pharmacodynamique - + @@ -427,43 +435,48 @@ - Pharmacogenomic relationship + Pharmacogenomic relationship + Relation pharmacogénomique - + - Pharmacokinetic Phenotype + Pharmacokinetic Phenotype + Phénotype pharmacocinétique - + - Phenotype + Phenotype + Phénotype - + - Variant + Variant + Variant - + Entity + Entité - + @@ -471,23 +484,49 @@ Quality + Qualité - + - - + + Entity + Entité + + + Generation + Génération + + + + + + + + + + + + + +