cholestasis
type: Class
comment: investigator: Flockhart
comment: Arrest of the normal flow of bile.
subclass of: side effects adverse events

side effects adverse events
type: Class
comment: Undesirable actions of drugs on subject, of all severity.
subclass of: phenotyping methods

sudden death
type: Class
comment: An arrhythmogenic death in aortic stenosis, coronary disease, mesothelioma of the AV node, or single coronary artery.
comment: investigator: Roden
subclass of: outcomes measures

outcomes measures
type: Class
comment: Evaluation procedures that focus on both the outcome or status (outcome assessment) of the patient at the end of an episode of care - presence of symptoms, level of activity, and mortality; and the process (process assessment) - what is done for the patient diagnostically and therapeutically.
subclass of: phenotyping methods

vasculitis
type: Class
subclass of: side effects adverse events
comment: Inflammation of a vessel, angiitis.

permeability
type: Class
comment: Measurement of the rate of penetration of a substance through a barrier.
subclass of: molecular and cellular phenotyping

molecular and cellular phenotyping
type: Class
comment: Assays or measurements of molecular targets or related to the kinetics of molecular components.
comment: investigator: Weinshilboum
subclass of: phenotyping methods

liver microsomes
type: Class
subclass of: microsomes
comment: Microsomes in liver cells.
comment: investigator: Ratain, Flockhart, McLeod

microsomes
type: Class
comment: Artifactual vesicles formed from the endoplasmic reticulum when cells are disrupted. They are isolated by differential centrifugation and are composed of three structural features: rough vesicles, smooth vesicles, and ribosomes. Numerous enzyme activities are associated with the microsomal fraction.
subclass of: tissue or organ phenotyping
comment: investigator: Ratain

EKG
type: Class
subclass of: clinical measures
comment: investigator: Roden, Flockhart
comment: An recording of the electrical activity of the heart contraction.

clinical measures
type: Class
comment: Measurements applied to the whole individual or to samples from that individual.
subclass of: phenotyping methods

cognitive measures
type: Class
comment: Assessments of the mental status of a subject.
subclass of: clinical measures

receptor kinetics
type: Class
comment: The study of the rate at which a substrate binds to or acts at a receptor.
subclass of: molecular and cellular phenotyping

enzyme kinetics
type: Class
comment: investigator: Ratain, Weinshilboum, Giacomini, Flockhart, McLeod
subclass of: molecular and cellular phenotyping
comment: The study of the rate at which an enzyme or transporter functions.

T50
type: Class
comment: T50 (temperature at which 50% of the activity is obtained for an enzyme).
subclass of: Km measure
comment: investigator: Weinshilboum

Km measure
type: Class
comment: A kinetic parameter used to characterize an enzyme, defined as the concentration of substrate that permits half maximal rate of reaction.
comment: investigator: Ratain, Giacomini, Flockhart, Weinshilboum
subclass of: enzyme kinetics

protein degradation in rabbit reticulocyte lysate
type: Class
comment: A method to measure the protein half life in vitro, using radiolabeled proteins that are generated in the RRL, and radioactivity is measured on a gel which represents the remaining protein can be compared among each time points, from which half-life can be calculated.
subclass of: protein half life

protein half life
type: Class
comment: Protein half-life is a measure of the protein turn over rate of a protein in the cell.
subclass of: molecular and cellular phenotyping

electrophoresis mobility assay
type: Class
comment: Assay using a radioactively labeled DNA probe to determine whether any proteins bind to the DNA sequence of interest. Non-radioactive probes are used to determine whether protein binding is specific to the sequences or not.
subclass of: transcription factor detection

transcription factor detection
type: Class
subclass of: promoter function assessment
comment: Protein/DNA binding reaction to determine whether/which transcription factors might bind to the DNA sequence of interest. Also used to determine if a variant nucleotide disrupts protein binding.

phenotyping methods
type: Class
comment: Methods used to determine the phenotype of an organism, including assays, clinical measures, and observations.

syncope
type: Class
comment: Abrupt loss of consciousness, often due to an abnormal rhythm.
comment: investigator: Roden
subclass of: side effects adverse events

cytosols
type: Class
comment: Phenotyping methods using cytosolic preparations of tissues (i.e. liver), used in genotype to phenotype (or phenotype to genotype) studies.
subclass of: tissue or organ phenotyping
comment: investigator: Weinshilboum

tissue or organ phenotyping
type: Class
subclass of: phenotyping methods
comment: All tissue-based methods used to determine the phenotype of an organism.

angioedema
type: Class
comment: A vascular reaction involving the deep dermis or subcutaneous or submucal tissues, representing localized oedema caused by dilatation and increased permeability of the capillaries and characterized by development of giant wheals.
subclass of: side effects adverse events

promoter function assessment
type: Class
comment: investigator: Weiss, Weinshilboum
subclass of: molecular and cellular phenotyping
comment: This is a general category of experiments related to assessment of the activity of a promoter.

bleeding
type: Class
comment: Emission of blood from anywhere in the body.
subclass of: side effects adverse events

thrombosis
type: Class
subclass of: side effects adverse events
comment: Abnormal clotting of blood in a blood vessel, which often results in occlusion of the vessel.

neurotoxicity
type: Class
comment: Damage, injury, or symptoms related to neural tissues, or abnormal neurological symptoms, often because of drug side-effects.
subclass of: side effects adverse events

hamilton depression scale
type: Class
subclass of: cognitive measures
comment: A 17-point screening instrument designed to measure the severity of depression.
comment: investigator: Licinio, Giacomini

western blot
type: Class
comment: investigator: Ratain, Weinshilboum
comment: An antibody-based method for detecting specific proteins.
subclass of: molecular and cellular phenotyping

yeast expression
type: Class
comment: investigator: Giacomini
subclass of: heterologous expression
comment: Refers to expression of a protein of interest in a yeast expression system.

heterologous expression
type: Class
comment: The introduction of a protein into a cell that does not normally express that protein.
subclass of: molecular and cellular phenotyping
comment: investigator: Weinshilboum

plasma drug concentrations
type: Class
subclass of: pharmacokinetics measures
comment: The quantity or amount of drug in the blood plasma.

pharmacokinetics measures
type: Class
subclass of: phenotyping methods
comment: The science and study of the factors which determine the amount of chemical agents at their sites of biological effect at various times after the application of an agent or drug to biological systems. Pharmacokinetics includes study of drug absorption and distribution (biotranslocation), study of the chemical alterations a drug may undergo in the body, (biotransformation), and study of the means by which drugs are stored in the body and eliminated from it.
comment: investigator: Ratain, Relling, Flockhart, McLeod, Giacomini, Roden

luciferase reporter utilization
type: Class
comment: A method for assaying quantitative gene expression.
comment: investigator: Ratain, Flockhart, McLeod, Weiss, Weinshilboum
subclass of: promoter function assessment

daily BP
type: Class
subclass of: blood pressure
comment: The blood pressure, measured daily.
comment: investigator: O'Connor

blood pressure
type: Class
subclass of: physical measures
comment: investigator: O'Connor, Krauss, Roden
comment: Measurement is divided into systolic (pressure during contraction of the heart) and diastolic (pressure during relaxation phase).

relapse rate
type: Class
comment: investigator: Ratain, McLeod
comment: The rate of recurrence of a disease.
subclass of: outcomes measures

antibody based arrays
type: Class
subclass of: protein arrays
comment: Microarrays containing antibodies used to assay proteins.

protein arrays
type: Class
comment: These are microarrays used to detect proteins, monitor their expression levels, and investigate protein interactions and functions.
subclass of: molecular and cellular phenotyping

second cancers
type: Class
comment: A cancer different from a cancer originally diagnosed in a patient.
comment: investigator: Ratain, Relling
subclass of: outcomes measures

genotyping methods
type: Class
comment: Methods used to determine the genotype of an organism, including sequencing assays and polymorphism detection methods.

organism phenotyping
type: Class
comment: Whole-organism methods used to determine the phenotype of an organism.
subclass of: phenotyping methods

pulmonary function tests
type: Class
comment: investigator: Roden, Flockhart
comment: Measures of how well the lungs take in and exhale air and how efficiently they transfer oxygen into the blood.
subclass of: pulmonary measures

pulmonary measures
type: Class
comment: These are laboratory tests related to lung function.
subclass of: clinical measures

Ki measure
type: Class
comment: investigator: Giacomini, Flockhart, Weinshilboum
comment: The dissociation constant of an inhibitor; in enzyme kinetics.
subclass of: enzyme kinetics

immunoprecipitation
type: Class
comment: Immunoprecipitation is a way to look at the protein complex or protein-protein interactions.
subclass of: detect interacting proteins

detect interacting proteins
type: Class
subclass of: protein complex
comment: Use of biological tools such as immunoprecipitation or proteomics to look at which proteins might interact with the proteins of interest.

pulse chase analysis in cultured cell
type: Class
comment: A method to measure the protein half-life in the cell system, using cells that are incubated with radiolabeled amino acid, and immunoprecipitation (IP) can be performed using antibody against the protein interested. IP lysates are then run on the gel and radioactivity of the remaining proteins can be measured and compared among each time points.
subclass of: protein half life

myalgia
type: Class
subclass of: side effects adverse events
comment: Pain in a muscle or muscles.
comment: investigator: Krauss

eosinophilia
type: Class
subclass of: side effects adverse events
comment: The formation and accumulation of an abnormally large number of eosinophils in the blood.

renin angiotensin system measure
type: Class
comment: investigator: Krauss
subclass of: laboratory measures
comment: Measurements related to the renin/angiotensin system, such as Angiotensinogen, Angiotensin I/II, plasma renin, etc.

laboratory measures
type: Class
comment: Measurements applied to samples of blood or tissue from an individual.
subclass of: clinical measures

oligonucleotide arrays
type: Class
subclass of: expression analysis
comment: Microarray experiments containing oligonucleotides.
comment: investigator: Ratain, Relling, Flockhart, McLeod, Weiss

expression analysis
type: Class
subclass of: molecular and cellular phenotyping
comment: investigator: Ratain, Flockhart, Weiss, Weinshilboum
comment: All methods that assay gene expression.

homocysteine levels
type: Class
subclass of: laboratory measures
comment: The quantity or amount of homocysteine in the in plasma, CSF, or other fluids.

ER visit rate
type: Class
comment: The frequency of patient visits the the emergency room.
subclass of: outcomes measures
comment: investigator: Weiss

GI bleeding
type: Class
comment: investigator: McLeod
comment: Emission of blood emanating from the gastrointestinal tract.
subclass of: bleeding

PET scanning
type: Class
comment: A specialized imaging technique using short lived radioactive substances.
subclass of: clinical measures

physical measures
type: Class
subclass of: clinical measures
comment: Measurements of a physical nature on an individual.

mass spectrometry
type: Class
subclass of: molecular and cellular phenotyping
comment: A technique used to determine the mass, composition, and identity of proteins.

GFP tagging
type: Class
subclass of: promoter function assessment
comment: A molecular tag for measuring the location or expression of a protein.

spotted microarrays
type: Class
comment: Microarray experiments in which spotted arrays are used.
subclass of: expression analysis
comment: investigator: Flockhart, Weiss

asthma hospitalization rate
type: Class
comment: The frequency of occurrences of hospitalizations for acute asthma attacks.
comment: investigator: Weiss
subclass of: outcomes measures

thrombocytopenia
type: Class
subclass of: side effects adverse events
comment: A decrease in the number of platelets in the blood.

quality of life
type: Class
comment: investigator: McLeod
comment: The individuals’ perceptions of their position in life, in the context of the cultural and value systems in which they live and in relation to their goals, expectations, standards and concerns.
subclass of: outcomes measures

RT PCR
type: Class
comment: A technique for mRNA detection and quantitation.
subclass of: expression analysis
comment: investigator: Ratain, Flockhart, McLeod, Weiss, Weinshilboum

enzymatic activity
type: Class
subclass of: molecular and cellular phenotyping
comment: Measurements of the catalytic action or potency of enzymes, such as measured by enzyme kinetics.

fainting
type: Class
comment: A form of syncope (fainting) that occurs as a part of a normal physiologic response to stress (often emotional stress). The individual becomes lightheaded, nauseated, flushed, feels warm and then may lose consciousness for several seconds.
subclass of: side effects adverse events
comment: investigator: Krauss

airways responsiveness testing with methacholine
type: Class
subclass of: pulmonary function tests
comment: A test measuring the bronchial contractility of the airways after administration of Methacholine.
comment: investigator: Weiss

supershift assay
type: Class
subclass of: transcription factor detection
comment: Assay where antibody to a protein of interest is added to see whether the protein of interest is participating in the protein binding complex.

response rate
type: Class
subclass of: outcomes measures
comment: investigator: Weiss, McLeod
comment: The rate of cure or response to a disease.

atrial fibrillation
type: Class
comment: investigator: Roden
comment: An abnormal rhythm associated with an irregular heart rate.
subclass of: outcomes measures

single channel or transport measures
type: Class
comment: investigator: Giacomini
subclass of: molecular and cellular phenotyping
comment: Kinetics of transport related to a single channel.

lipid profile
type: Class
subclass of: laboratory measures
comment: Includes total cholesterol, HDL-cholesterol (often called good cholesterol), LDL-cholesterol (often called bad cholesterol), and triglycerides, and associated computed parameters.
comment: investigator: Krauss, Flockhart

cellular uptake measure
type: Class
comment: Kinetic measures related to the uptake of a substance.
comment: investigator: Giacomini, Weinshilboum
subclass of: single channel or transport measures

metabolic measures
type: Class
subclass of: clinical measures
comment: These are measurements related to the transformation of substances in the body.

blood counts of pathogens
type: Class
subclass of: laboratory measures
comment: E.g., viremia, fungemia, etc.

insect cell expression
type: Class
comment: Refers to expression of a protein of interest in an insect cell expression system.
subclass of: heterologous expression

RFLP
type: Class
subclass of: variation discovery
comment: restriction fragment length polymorphism
comment: A convenient method for detecting SNPs is restriction fragment length polymorphism (SNP-RFLP). If one allele contains a recognition site for a restriction enzyme while the other does not, digestion of the two alleles will give rise to fragments of different length. Currently, the study of existing SNPs are most easily studied using microarrays. Microarrays allow the simultaneous testing of over a thousand separate SNPs and are quickly screened by computer. Several other ways to detect SNP's are mentioned in an article published in October 2005 in Nature by the International HapMap Consortium. [Ref: wikipedia]

hypotension
type: Class
comment: investigator: Krauss
comment: Abnormally low blood pressure, seen in shock but not necessarily indicative of it.
subclass of: side effects adverse events

pulmonary fibrosis
type: Class
comment: Scarring or thickening of tissues deep in the lung.
subclass of: side effects adverse events
comment: investigator: McLeod

erythromycin breath test
type: Class
comment: A test measuring the clearance of Erythromycin, and is an indicator of the metabolism of other drugs as well.
subclass of: metabolic measures

bone mineral density
type: Class
subclass of: clinical measures
comment: A nuclear medicine test that estimates the mineralization of bone in a subject.
comment: investigator: Flockhart

respiratory depression
type: Class
comment: A decrease in the rate or depth of respiration respiratory effort and decrease in level of alertness.
comment: investigator: Weiss
subclass of: side effects adverse events

tissue arrays
type: Class
comment: investigator: McLeod
subclass of: tissue or organ phenotyping
comment: Tissue arrays are glass slides containing spotted tissue samples, used for protein expression studies, antibody screening, tissue-type specificity studies and animal model analyses.

xenopus expression
type: Class
subclass of: heterologous expression
comment: Refers to expression of a protein of interest in the Xenopus oocytes.
comment: investigator: Giacomini

event free survival
type: Class
subclass of: outcomes measures
comment: The length of time a subject lives without having one or more complications of a disease.

event rates for myocardial infarction
type: Class
subclass of: outcomes measures
comment: The frequency of occurrences of medical events or conditions subsequent to heart attacks.

proteomics
type: Class
comment: An unbiased method can help us detect any associated proteins, using LC-MS/MS to separate the cell mixtures or lysates and run through MS/MS to detect all the possible associated proteins.
subclass of: detect interacting proteins

FEV1
type: Class
comment: Forced Expiratory Volume in 1 second.
subclass of: pulmonary function tests
comment: investigator: Weiss

lipid profile Research
type: Class
subclass of: laboratory measures
comment: A panel of detailed lipid, apolipoprotein, and lipoprotein subspecies measurements used for research purposes.
comment: investigator: Krauss

hepatotoxicity
type: Class
comment: Injury and/or death of liver cells due to a drug or toxin.
subclass of: side effects adverse events
comment: investigator: Ratain, Relling, Flockhart, Krauss

electrophysiology
type: Class
subclass of: molecular and cellular phenotyping
comment: investigator: Roden, Giacomini
comment: Measurements of the electrical phenomena associated with cardiac or other physiology.

exercise response
type: Class
comment: Physiological variations that occur when a subject partakes in a defined exercise activity.
subclass of: physical measures
comment: investigator: Roden

FVC
type: Class
comment: investigator: Weiss
subclass of: pulmonary function tests
comment: Forced Vital Capacity. This is the total amount of air a subject can blow out forcefully.

protein complex
type: Class
comment: Multiple proteins interact with each other to form a complex. It can be a physical interaction, which can have no biological effects, or biological interaction which can interact indirectly. Proteins usually function as complexes rather than as a single one.
subclass of: molecular and cellular phenotyping

occurrence of neoplasm
type: Class
subclass of: outcomes measures
comment: investigator: Weinshilboum
comment: A cancer that develops in a patient.

cancer treatment related side effects
type: Class
comment: All side effects directly attributable to cancer treatment.
comment: investigator: Ratain, Relling, Flockhart
subclass of: side effects adverse events

transcript sizing
type: Class
comment: investigator: Ratain
comment: Methods that assess the length of the mRNA transcript.
subclass of: expression analysis

QT interval
type: Class
subclass of: EKG
comment: investigator: Roden, Flockhart
comment: Time from electrocardiogram Q wave to the end of the T wave corresponding to electrical systole.

protein content or level
type: Class
comment: Measurements of the quantity or amount of protein in a cell, space, or assay.
subclass of: molecular and cellular phenotyping

Kcat measure
type: Class
comment: The overall catalytic rate of an enzyme; symbol for turnover number; Vmax divided by the total enzyme concentration.
subclass of: enzyme kinetics
comment: investigator: Ratain, Giacomini

coagulation profile
type: Class
comment: investigator: Flockhart, Roden
comment: Measures the speed of blood coagulation at different steps of the coagulation pathway.
subclass of: laboratory measures

lymphocyte functional measure
type: Class
comment: These are functional measures of lymphocyte responses.
subclass of: tissue or organ phenotyping
comment: investigator: Ratain

seizure
type: Class
comment: An repetitive, uncontrollable excitation of neural tissue, usually resulting in violent muscular contractions.
subclass of: side effects adverse events

cell counts
type: Class
comment: E.g., CD4 cell counts.
subclass of: laboratory measures

survival
type: Class
comment: An organism living to or beyond a specified time. A time period during which an organism remains alive.
comment: investigator: Ratain, Relling, McLeod, Weinshilboum
subclass of: outcomes measures

serum proteomics
type: Class
subclass of: laboratory measures
comment: investigator: Relling
comment: Measurements on proteins in blood serum.

kidney microsomes
type: Class
subclass of: microsomes
comment: Microsomes in kidney cells.

Vmax measure
type: Class
comment: investigator: Ratain, Giacomini, Flockhart, Weinshilboum
comment: The maximum initial velocity of an enzyme catalyzed reaction. I.e. at saturating substrate levels.
subclass of: enzyme kinetics

24 hour BP monitoring
type: Class
comment: investigator: Krauss
subclass of: blood pressure
comment: A study recording the blood pressure at intervals during a 24-hour period.

clearance
type: Class
subclass of: pharmacokinetics measures
comment: The rate of elimination of a drug, metabolite, or other substance from the body or organ of interest.

hot flash occurrences
type: Class
subclass of: side effects adverse events
comment: The sensation of sudden flushing and sweating.
comment: investigator: Flockhart

mammalian cell expression
type: Class
comment: Refers to expression of a protein of interest in a mammalian cell expression system.
comment: investigator: Flockhart, Roden, Weinshilboum
subclass of: heterologous expression