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