The aim of this ontology is to be used in the text extraction of pharmacogenomics relationships. It enables the comparison, standardization and integration of relations expressed in an heterogeneous manner in natural langage. Developed by the Helix Group, Department of Genetics, Stanford University, and by the Orpailleur Group, LORIA - INRIA Nancy. This is a modification of version 100318. It takes care of: (1) passive and active verb issue such that X metabolized Y and X is metabolized by Y are properly converted. (2) at end, will also manually change owl file to include inverses for all pairs of inverse relations. This ontology is developed for and in English. We added a prefix to the ontology. contact: Adrien Coulet coulet --no spam-- AT --no spam-- stanford --no spam-- DOT --no spam-- edu version id: 110114 accept accepted accepting receive received receiving tolerate tolerated tolerating account accounted activate activated initiate initiated start started trigger triggered administer administered inject injected prescribe prescribed recommend recommended affect affected affecting affection cause caused lead provide provided provoke provoked alter altered change changed convert converted modified modify transform transformed combine combined correct corrected alleviate attenuate attenuated decrease decreases diminish diminished limit lower reduce relieve worsen worsened delay delayed retard retarded slow slowed confirm confirmed demonstrate demonstrated determine determined elicit elicited establish established explain explained find found prove proved resolve resolved reveal revealed show showed sustain sustained eliminate eliminated assess assessed characterize characterized detect detected estimate estimated evaluate evaluated identified identify measure measured express expressed effective function functioned operate serve work exhibit expose had has have offer present include included accelerate accelerated aggravate aggravated ameliorate ameliorated augment augmented elevate elevated enhance enhanced exacerbate exacerbated gain gained greater higher highered improve improved increase increased promote raised raises catalyse catalysed catalyze catalyzed induce induced stimulate stimulated contribute contributed depend depended dependence effect effected exert exerted influence influenced interfere interfered play played antagonize antagonized depress depressed depresses inhibit inhibited repress repressed represses is$$accepted is$$received is$$tolerated is$$activated is$$initiated is$$started is$$triggered is$$administered is$$injected is$$prescribed is$$recommended is$$affected association correlate correlated correletion implicate implicated interact interacted interaction involve involved is$$associated is$$correlated is$$implicated is$$involved is$$linked is$$related link linked relate related relation relationship is$$caused is$$provided is$$provoked led result resulted is$$altered is$$changed is$$converted is$$modified is$$transformed is$$combined comparable compare compared is$$compared is$$corrected is$$alleviated is$$attenuated is$$decreased is$$diminished is$$limited is$$lowered is$$reduced is$$relieved is$$worsened reduction is$$delayed is$$retarded is$$slowed is$$slown slown is$$confirmed is$$demonstrated is$$determined is$$elicited is$$established is$$explained is$$found is$$proved is$$proven is$$resolved is$$revealed is$$showed is$$shown is$$sustained proven is$$eliminated is$$assessed is$$characterized is$$detected is$$estimated is$$evaluated is$$identified is$$measured expression is$$expressed is$$included augmentation improvement is$$accelerated is$$aggravated is$$ameliorated is$$augmented is$$elevated is$$enhanced is$$exacerbated is$$gained is$$highered is$$improved is$$increased is$$promoted is$$raised induction is$$catalysed is$$catalyzed is$$induced is$$stimulated depend on depended on depends on exerted influenced interfered is$$contributed is$$dependent is$$effected is$$influenced is$$played inhibition is$$antagonized is$$depressed is$$inhibited is$$repressed is$$assisted is$$facilitated is$$helped is$$mediated is$$metabolised is$$metabolized is$$predisposed is$$prevented prevention is$$achieved is$$developed is$$generated is$$obtained is$$performed is$$produced is$$controlled is$$managed is$$modulated is$$potentiated is$$regulated modulation is$$reflected is$$represented is$$reversed is$$considered is$$examined is$$experienced is$$investigated is$$observed is$$reported is$$studied is$$tested is$$evoked is$$indicated is$$suggested is$$abolished is$$avoided is$$blocked is$$stopped is$$suppressed is$$terminated is$$targeted is$$carried is$$transported is$$treated is$$applied is$$required is$$used assist assisted facilitate facilitated help helped mediate mediated metabolise metabolised metabolization metabolize metabolized metabolizing NEVER EVER EVER remove this!!! It represents quantifiers (eg. dose modifies Drug in DrugDose -- warfarin dose modifies dose) occur occurred occurs predispose predisposed prevent prevented achieve achieved develop developed generate generated obtain obtained perform performed produce produced control controlled manage managed modulate modulated potentiate potentiated regulate regulated reflect reflected represent represented reverse reversed consider considered examine examined experience experienced investigate investigated observe observed report reported studied study test tested evoke evoked indicate indicated suggest suggested abolish abolished avoid avoided block blocked stop stopped suppress suprpressed terminate terminated target targeted carried carries carry transport transported treat treated treatment applied apply applying require required requiring use used useful using the text of a text has DrugBank accession has Entrez Gene ID has PharmGKB accession has ID has accession has phenotype concept id phare:AbsenceOfDrugTreatment absence cessation discontinuation removal suppression withdrawal phare:AbsenceOfGeneProductActivity absence phare:Aerosol aerosol phare:Analysis phare:Antibody antibody phare:Antidepressant antidepressant phare:Antihistamine antihistamine histamine antagonist phare:Antipsychotic antipsychotic phare:Anxiety anxiety phare:Apoptosis apoptosis phare:Aspirin aspirin phare:BetaBlocker beta-blocker phare:Bleeding bleeding hemorrhage phare:Blood blood phare:Cancer carcinoma melanoma metastasis neoplasm neoplasms neoplastic process tumor phare:CanisLupus dog phare:Capsule capsule phare:Carboxylation carboxylation phare:Cell cell cell line line phare:ChemicalModification modification phare:Chimera chimera phare:Cisplatin cisplatin phare:Cream cream phare:Dealkylation dealkylation n-dealkylation o-dealkylation phare:Death death necrosis phare:Demethylation demethylation n-demethylation o-demethylation phare:Depression depression phare:Derivative derivative phare:Disease admission appearance diagnosis disease diseases disorder episode event experience form formation impairment incidence injury lesion maintenance model observation occurence onset pathogenesis pathology patophysiology period presence sequela syndrome type phare:DiseaseAbsence absence phare:DiseaseCause assessment cause etiology factor phare:DiseaseDuration day duration hour length minute phare:DiseaseEffect disturbance effect implication response result phare:DiseaseExacerbation complication development exacerbation extent growth increase progression prolongation refractory stimulation phare:DiseaseRelapse recurrence relapse phare:DiseaseRelief alleviation amelioration disappearance healing improvement inhibition reduction relief remission reversal suppression termination phare:DiseaseSensitivity perception resistance sensitivity tolerance vulnerability phare:DiseaseSeverity acute amount amplitude crisis degree grade intensity level magnitude morbidity range scale severity size phare:DiseaseSideEffect side effect side-effect phare:DiseaseSurvival disease-free disease-free survival survival phare:Drug class content drug group molecule prodrug type phare:DrugAbsorption absorption phare:DrugAbuse abuse excess overdosage overdose phare:DrugAccumulation accumulation phare:DrugActivation activation phare:DrugActivity activity bioactivity phare:DrugAddict abuser addict addicted phare:DrugAdverseReaction adverse effect adverse reaction harmful effect secondary effect side effect side-effect phare:DrugAnalog 5-fluorouracil acid analog chloride magnesium quinidine similar phare:DrugAnalysis analysis assay clinical trial evaluation study test testing trial phare:DrugConsumer consumer user phare:DrugDependence addiction dependence dependency phare:DrugDisposition availability bioavailability disposition phare:DrugDistribution distribution system systemic phare:DrugDose reference 10mg 1mg 2mg abundance amount cl concentration dosage dose dosing drop g g\/kg gram high-dose kg level low-dose mass mg mg\/d mg\/kg mg\/m2 microg microg\/ml microgram microm milligram mixture mole ng parameter pg prescription quantity ratio reduction requirement tds titration volume weight phare:DrugDoseDecrease decrease drop lowering reduction restriction phare:DrugDoseIncrease augmentation increase phare:DrugDoseVariation change difference variability variation phare:DrugEffect action conclusion course effect endpoint feedback impact influence intervention mechanism outcome potency potential profile reaction response responsiveness result phare:DrugEfficacy ability auc benefit capacity characteristic defect deficiency dysregulation effectiveness efficaciousness efficacy efficiency failure favor function ineffectiveness ineffectual inefficacious inefficaciousness inefficacity inefficacy inefficiency property role usefulness value phare:DrugElimination clearance deactivation degradation elimination excretion half life half-life inactivation liberation turn over turnover phare:DrugFormulation form formulary formulation pharmaceutical formulation preparation phare:DrugGene dna gene phare:DrugInducer agonist inducer stimulator phare:DrugInfiltration infiltration phare:DrugInhibition inhibition limitation phare:DrugInhibitor antagonist blocker inhibitor phare:DrugInteraction interaction phare:DrugIsoform enantiomer isoform phare:DrugIsomer isomer phare:DrugMedia media medium phare:DrugMetabolism metabolic profile metabolism phare:DrugMetabolite component compound extract metabolite product phare:DrugModulator modulator phare:DrugPharmacodynamics dynamics pharmacodynamics phare:DrugPharmacogenomics pharmacogenetics pharmacogenomics phare:DrugPharmacokinetics cycle disposition pathway pharmacokinetic profile pharmacokinetics phare:DrugPrescription prescription phare:DrugRelatedAnalgesia analgesia phare:DrugRelatedAnticoagulation anticoagulation phare:DrugRelatedComplication complication phare:DrugRelatedImmunosuppression immunosuppression phare:DrugRelatedStress stress phare:DrugSalt acetate benzoate citrate decanoate enanthate hypochloride maleate mesylate nitrate phosphate salicylate salt sodium sulfate topiramate valerate valproate phare:DrugSecretion hypersecretion hyposecretion secretion phare:DrugSensitivity desensitization hypersensitivity hyposensitivity resistance sensitivity sensitization susceptibilty tolerability tolerance phare:DrugSolution solution phare:DrugSolvent solvent phare:DrugStimulation induction overactivity stimulation phare:DrugTarget binding site receptor recipient site target phare:DrugToxicity cytotoxicity intolerance intoxication lethality neurotoxicity poisoning safety toxicity phare:DrugTransformation biotransformation change conversion modification transformation phare:DrugTransport flux transport phare:DrugTransporter transporter phare:DrugTreatment addition adjunct adjunction administration application association bolus chemotherapy co-administration co-infusion coadministration coinfusion combination consumption exposure guideline indication infusion ingestion inhalation injection instillation intake introduction irradiation maintenance management medication microinjection monotherapy orally perfusion pharmacotherapy presence regime regimen release reuptake supplementation therapy treatment uptake usage use phare:DrugTreatmentByDelivery delivered delivery phare:DrugUptakeRate b.i.d. bid daily i\/d mg/day q.i.d. qid rate release rate t.i.d. tid uptake rate phare:Enzyme allozyme enzyme isoenzyme isoform enzyme isozyme metabolizer phare:Etoposide etoposide phare:Exon exon exonic region phare:ExonicVariant exonic variant phare:Expression abundance amount concentration content expression expression\/bioactivity level measure mrna expression presence profile quantification quantity score status transcription translation value phare:EyeDrop eye drop eyedrop phare:Gel gel phare:Gene acid class cyp3a5 dna gene probe sequence the phare:GeneAnalysis analysis assay determination evaluation measure measurement recognition screening phare:GeneInducer agonist catalyser catalyzer enhancer expresser expressor inducer phare:GeneInhibitor antagonist blocker inactivator inhibitor non-expressor repressor phare:GeneLigand ligand phare:GeneModulator modulater modulator phare:GeneOrGeneProductActivity activities activity activity difference bioactivity impact influence regulation phare:GeneOrGeneProductFunction reference action capability capacity contribution effect feedback function impact influence involvement mechanism potential process processe requirement response result role use phare:GenePathway cycle network pathway system phare:GeneProduct construct metabolite product residue sample phare:GeneProductActivation activation phare:GeneProductActivityChange Concept captures activity change, distinguished from expression change. Therefore it is cannot be under GeneProductKinetics, as this would allow the concept to be modified by some Gene or GeneProduct.(captures 'activity level' and not 'cyp2c9 expression level' or 'cyp2c9 level') augmentation change decrease difference diminution divergence elevation increase inhibition level loss lowering normalization proliferation recovery reduction regulation restoration rise stimulation suppression variation phare:GeneProductAffinity affinity phare:GeneProductAvailability availability phare:GeneProductBlockage blockage phare:GeneProductDegradation degradation phare:GeneProductDysfunction defect dysfunction knockout ko phare:GeneProductElimination elimination phare:GeneProductForm form phare:GeneProductInactivation inactivation phare:GeneProductInteraction interaction phare:GeneProductKinetics kinetic phare:GeneProductMetabolism metabolism phare:GeneProductModulation modulation phare:GeneProductProperty characteristic feature property sensitivity phare:GeneProductReaction reaction phare:GeneProductSecretion hypersecretion hyposecretion secretion phare:GeneProductStructure structure phare:GeneProductTransport transport phare:GeneRecombinant recombinant phare:GenicTherapy therapy treatment phare:GenomicRegion complex subunit component domain localization location part position region site structural component subunit zone phare:GenomicVariation change difference form genomic variation genotype genotyping haplotype\/genotype hemizygous heterozygocity heterozygous homozygocity homozygous modification present form strain test testing variability variation phare:Globulin globulin phare:Glucuronidation glucuronidation phare:Haplotype * \* haplotype phare:Headache headache phare:HomoSapiens boy child children girl human infant man men woman women phare:Hydroxylation 3-hydroxylation 5-hydroxylation alpha-hydroxylation hydroxylation n-hydroxylation phare:Hypermethylation hypermethylation phare:Immunosuppression immuno-suppression immunosuppression phare:Infection infection phare:Inhalation inhalation inhaled phare:InhalationFormulation phare:Interferon interferon phare:Intramuscular i.m. im intramuscular intramuscularly phare:Intravenous i.v. intravenous intravenously iv phare:Intron intron intronic region phare:IntronicVariant intronic variant phare:Ligand ligand phare:Lithium lithium phare:Locus locus phare:Metabolizer LM stands for low metabolizer etc. EM FM HM LM PM RM URM metabilzer metaboliser phare:Methyl-transfer methyl transfer methyl-transfer phare:Methylation methylation o-methylation phare:Modulator phare:Mrna mrna rna transcript phare:MusMusculus mice mouse phare:Mutant mutant phare:Myristoylation myristoylation phare:Ointment ointment phare:Opioid opioid phare:OralFormulation pill phare:Organism living system organism phare:OrganismLocalisation tissue phare:Overexpression augmentation elevetion increase induction overexpression stimulation up-regulation upregulation phare:Oxidation oxidation oxydation phare:Pain pain phare:Palmytoylation palmytoylation phare:Parenteral parenteral parenterally phare:Paste paste phare:Patient carrier case individual patient people subject sufferer survivor phare:Peroral oral orally oros peroral perorally phare:Pharmacology pharmacology phare:Phenotype observation phenotype phare:PhenotypeAnalysis detection evaluation investigation measure study test testing trial phare:PhenotypeGene example: diabetes genes breast cancer genes dna gene phare:PhenotypeMechanism function mechanism metabolism pathway process system phare:PhenotypeRisk frequency likelihood possibility prognosis rate rating risk susceptibility phare:PhenotypeStage level stage phare:Phosphorylation phosphorylation phare:Placebo placebo phare:Plasma plasma phare:Population group number population prevalence phare:PopulationAnalysis study phare:Prenylation prenylation phare:Pretreatment pre-medication pre-treatment preadministration premedication pretreatment phare:Prodrug precursor prodrug phare:Promotor promoter promotor promotor region phare:Prophylaxis chemoprophylaxis prevention prophylaxes prophylaxis protection phare:Propranolol propranolol phare:Protease protease phare:Protein encoded isoform presence protein phare:ProteinChannel channel phare:Quinidine quinidine phare:RatusNorvegicus rat phare:Receptor receptor phare:Repression decrease deficiency depletion diminution down-regulation downregulation inhibition repression suppression phare:SelfAdministration auto medication auto-medication self administration self medication self-administration self-medication phare:Serum serum phare:Spray spray phare:Subcutaneous subcutaneous subcutaneously phare:Substrate substrate phare:Sulfation sulfation phare:Sulfoxydation sulfoxydation phare:Suppository suppository phare:Symptom characteristic component criteria evidence feature indice sign symptom phare:Synthesis biosynthesis formation production synthesis phare:Synthetase synthetase phare:Tablet caplet tab tablet phare:Tachycardia tachycardia phare:Target target phare:TherapeuticHormone hormone phare:Topical topical topically phare:TopicalFormulation phare:Trait character outcome phenotype phenotyping pigmentation trait phare:Transmucosal anal anally buccal buccally nasal nasally occular occularly sublingual sublingually transmucosal transmucosally vaginal vaginally phare:TransmucosalFormulation phare:Ubiquitination ubiquitination phare:Variant a a-allele allele c c-allele c677t d-allele deletion dimorphism duplication frame shift frame-shift g g-allele indel insertion insertion\/deletion marker mono-substitution monosubstitution mutation n1325s polymorphism polysubstitution rs2359612 s-9490-3 snp substitution t t-allele trimorphism tt ugt1a9 variant phare:Vector vector phare:Vitamin vitamin phare:_3_UTR 3'UTR phare:_5_UTR 5'UTR owl:Thing Developed by the Helix Group, Department of Genetics, Stanford University, and by the Orpailleur Group, LORIA - INRIA Nancy. This is a modification of version 100318. It takes care of: (1) passive and active verb issue such that X metabolized Y and X is metabolized by Y are properly converted. (2) at end, will also manually change owl file to include inverses for all pairs of inverse relations. This ontology is developed for and in English. We added a prefix to the ontology. contact: Adrien Coulet coulet --no spam-- AT --no spam-- stanford --no spam-- DOT --no spam-- edu version id: 110114 The aim of this ontology is to be used in the text extraction of pharmacogenomics relationships. It enables the comparison, standardization and integration of relations expressed in an heterogeneous manner in natural langage. Developed by the Helix Group, Department of Genetics, Stanford University, and by the Orpailleur Group, LORIA - INRIA Nancy. This is a modification of version 100318. It takes care of: (1) passive and active verb issue such that X metabolized Y and X is metabolized by Y are properly converted. (2) at end, will also manually change owl file to include inverses for all pairs of inverse relations. This ontology is developed for and in English. We added a prefix to the ontology. contact: Adrien Coulet coulet --no spam-- AT --no spam-- stanford --no spam-- DOT --no spam-- edu version id: 110114