human
genotype with copy number variation
A genotype of which variants with a different number of copies of a sequence identifical region exist.
has attribute
medical expert role
An medical expert role is a role played by a human in a clinical context who is involved in the assessment or administration of treatment or its results.
diagnostic exclusion criterion
A diagnostic exclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, excludes a diagnostic result.
ancestral allele
In a group of allelic variants in a population, the ancestral allele is the allele from which all other allelic variants are believed to have descended from during phylogeny.
drug-drug interaction
A drug-drug interaction is a drug interaction in which two drugs interact in such a way to produce an abnormal phenotypic event.
diagnostic role
medical finding
biomedical measure
A biomedical measure is an information content entity that describes or is a measure of biomedically relevant entities.
physical description
gene variant
A gene variant is a variant of another gene based on some difference in sequence (composition and connectivity)
age
biomarker
A biomarker is a characteristic of a material entity that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention.
time elapsed
sign
Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance.
Yoruba in Ibadan, Nigeria
A particular community in Ibadan, Nigeria, with individuals who identified themselves as having four Yoruba grandparents. The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
indicator
An indicator is an entity for which its observation/detection is used in some objective.
quantity
A quantity is a quantitative measure of some feature.
active ingredient role
An active ingredient role is a role played by a chemical substance which has the disposition to treat a certain disease and is part of a pharmaceutical formulation.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A DNA region is a part of a DNA molecule that is made up of a continous chain of deoxyribonucleotide residues.
DNA region
dose in milligram per week
absent phenotype
An absent phenotype is a phenotype that represents the notable absence of a characteristic.
snp identifier
assay
An assay is a planned process with the objective to obtain information about a material entity.
DNA sequence
a DNA sequence is a sequence of characters that represents the composition and connectivity of a a DNA molecule.
arm of clinical study
An arm of clinical study is a population that participates in a clinical trial and is subject to some intervention.
genotype with multiple nucleotide polymorphism
A genotype with a multiple-nucleotide polymorphism (MNP). An MNP is a variation of several adjacent nucleotides in the genomes of members of a species. For a variation to be considered an MNP, it must occur in at least 1% of the population.
ranged numerical quantity
clinical protocol
A clinical protocol is a directive information entity about the objective(s), design, methodology, statistical considerations, and organization of a clinical procedure.
insertion
female
Female is a sex quality for which sex organs contain only female gametes
patient record
syndrome
A syndrome is a group of signs and symptoms that characterize a particular abnormality.
temporal functional quantity
market
Maasai in Kinyawa, Kenya
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
has value
A nucleic acid region is a part of a nucleic acid that is made up of a continous chain of nucleotide residues.
nucleic acid region
Toscani in Italia
nucleotide sequence position
A nucleotide sequence position indicates the position of a nucleotide residue in relation to the start of the nucleic acid.
pharmgkb subject identifier
pharmaceutical ingredient
A pharmaceutical ingredient is a chemical substance that is part of a formulated pharmaceutical that bears a pharmaceutical ingredient role.
nucleic acid
disease progression
provides supporting evidence for
identifier
An identifier is an information content entity which consists of one or more symbols in order to identify some entity.
Examples: connection table, fragment, pharmacophore.
molecular structure description
A molecular structure description is a description of a molecule in terms of its composition and connectivity.
3D molecular structure
ethnicity
Ethinicity is the quality of an organism that describes membership in a social group based on a common heritage.
age in years
comparative effectiveness
Comparative effectiveness is a drug measure that provides information about which treatment works best, for whom, and under what circumstances.
mass value
symptom
A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease.
Population with african ancestry in Southwest USA
sequence position
A sequence position is a identifier for an item in a sequence of items and whose numeric value relates to the position of the item from the start of the sequence.
weight in kilograms
toxic
length value
inactive ingredient role
An inactive ingredient role is a role played by a chemical substance which is part of a pharmaceutical formulation but does not have the disposition to treat a certain disease.
numerical quantity selected from a continuous variable
protein
A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain).
is variant of
ratio
genetic description
A genetic description is a description of the genetic composition of some entity.
ncbi reference snp identifier
clinical trial criterion
A clinical trial criterion is a directive information entity which, if satisfied, contributes to the inclusion or exclusion of candidate patients.
RNA sequence
disease
A quality of an organism which predisposes it to undergo pathological processes because of one or more disorders in that organism.
Further information can be found in the publication "The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside", published in the Journal of Biomedical Semantics: http://www.jbiomedsem.com/content/2/S2/S1
The Translational Medicine Ontology (TMO) is a high-level, patient-centric ontology that extends existing domain ontologies to integrate data across aspects of drug discovery and clinical practice. The ontology has been developed by participants in the World Wide Web Consortium’s Semantic Web for Health Care and Life Sciences Interest Group.
W3C Health Care and Life Sciences Interest Group
ontology, translational medicine, personalized medicine, life sciences, health care
A part of a molecular entity or a set of molecular entities. It can be made up of several non-connected sub-parts, potentially on separate molecular entities.
molecular entity part
scale numerical value
evidence
Evidence is a group of indicators that are relevant in some decision-making process.
deletion
description
organism
hypothesis
A hypothesis is an information content entity that describes a possible correlation between two or more variables.
pharmacokinetic measure
study
A study is a planned process that consists of planning, study execution, documentation and the production of conclusion(s).
process description
has unit
clinical subject role
A clinical subject role is the role played by an organism who is the subject of a clinical procedure or assessment.
dsDNA
intervention
An intervention is a study in which a substance is administered to a subject or group of subjects.
July 2003 human reference sequence (NCBI Build 34)
deoxyribonucleotide sequence position
A dexoyribonucleotide sequence position is an ordinal number which reflects the position of a deoxyribonucleotide in relation to the first deoxyribonucleotide of the same deoxyribonucleic acid (DNA).
active ingredient
An active ingredient is a pharmaceutical ingredient that has the disposition to treat a certain disease.
race
molecular target role
A molecular target role is a role played by a chemical entity in which it is a specific target of an intervention that aims to change it behavior.
molecular complex
mechanism of action
The mechanism of action is a description of processes and behaviour of a biologically active molecule in its administration into a living system.
attribute of
genomic sequence
A genomic sequence is the collection of sequences that make up an individual's genetic matter.
patent
American Heritage(R) Stedman's Medical Dictionary
A patent is an information entity granted by a patent office which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
genetic variant
organismal quality
lifestyle
Lifestyle is a description about an individual`s manner of living.
medical measure
A medical measure is a measure that describes or is a measure of medically relevant entities.
Chinese in Metropolitan Denver, Colorado
height in centimeters
non toxic
criterion
molecular target
A molecular target is a molecular entity that is the target of a transformation process.
numerical quantity selected from a discrete variable
cell line
A cell line is a material entity that consists of a population of cells cultured in vitro that are descended through one or more generations (and possible sub-cultures) from a single primary culture which was originally derived from part of an organism.
genetic status
International Normalized Ratio on the Therapeutic Dose of Warfarin
subject role
A role played by a material entity it being the subject of a study.
ncbi submitter snp identifier
enzyme
An enzyme is a protein that catalyzes (increases the rate of) a chemical reaction.
single letter amino acid sequence
allele
An allele is a specific variant of a gene.
genotype with allele
A genotype containing one matching allele on each chromosome (e.g., CYP2C9*1/*3)
enumerated numerical quantity
An enumerated numerical quantity is a numerical quantity selected from a discrete set of quantities.
environmental description
An environmental description is a description concerning some aspect of a physical environment.
invariant nucleic acid region
mouse
CEPH (Utah residents with ancestry from northern and western Europe)
A population of individuals living in Utah with ancestry from northern and western Europe. The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
pharmacodynamic measure
temporal quality
side effect
A side effect is an effect of an intervention, whether therapeutic or adverse, that is secondary to the intended effect of the intervention.
chromosome number
A chromosome number is an identifier for a chromosome that identifies it from a collection of chromosomes for a given organism.
diagnosis
A diagnosis is a study composed of investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.
May 2004 human reference sequence (NCBI Build 35)
ribonucleotide sequence position
A ribonucleotide sequence position is an ordinal number which reflects the position of a ribonucleotide in relation to the first ribonucleotide of the same ribonucleic acid (RNA).
formulated pharmaceutical
A formulated pharmaceutical is a chemical substance whose granular parts include an active ingredient, an excipient, and possibly a stability regulator for the active ingredient.
HapMap population name abbreviation
A short acronym identifying a sample population that was examined by the HapMap project.
chemical entity role
A chemical entity role is a role played by a chemical entity.
date
adverse drug event
An adverse drug event is a any untoward medical occurrence in a patient or clinical investigation subject administered a pharmaceutical product and which does not necessarily have a causal relationship with this treatment. An adverse event (AE) can therefore be any unintended sign (including an abnormal laboratory finding), symptom,or disease temporally associated with the use of a medicinal (investigational) product, whether or not related to the medicinal (investigational) product.
is described by
human population
A collection of humans
exclusion criterion for clinical trial
An exclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the exclusion of candidate patients.
obsolete
publication date
Age is the temporal quality of an organism that refers to the length of time elapsed since it came into existence. For most animals and humans, age refers to the length of time elapsed since birth.
regionally-defined human population
A collection of humans from a particular region.
health outcome
A health outcome is a medical measure of health or loss of health.
statistical quantity
institution
An institution is an entity created by legislation or by practice which acts legally in the same way as a person.
Gujarati Indians in Houston, Texas
centimeter
historical description
chromosome
protein target
chromosomal sequence position
A chromosomal nucleotide sequence position is an ordinal number which reflects the position of a nucleotide in relation to the first nucleotide of the same chromosome.
gene
A gene is a part of DNA that encodes information about other molecular entities.
companion diagnostic role
medical descriptor
prognosis
A prognosis is a hypothesis about the likely course of a disease, the chance of recovery or recurrence.
organization
in relation to
three letter amino acid sequence
metabolite role
A metabolite role is the role played by a material entity that is a metabolic substrate, intermediate or product.
unit of measurement
phenotype
A phenotype is an observable characteristic of an organism.
genotype
In this context, a genotype is a material entity made up of two DNA regions on two homologous chromosomes in a diploid cell. One chromosome is derived from the father and one is derived from the mother. The two DNA regions are located at the same genetic locus on each of the two chromosomes.
pharmgkb sample identifier
drug efficacy
Drug efficacy is a measure of the capabilty of a drug to produce an intended effect as a function of its concentration.
physical quantity
personal medical history
A personal medical history is a medical record consisting of a collection of information obtained from the patient and from other sources concerning the patient's health.
Han Chinese in Beijing, China
A population of individuals living in the residential community at Beijing Normal University who were self-identified as having at least three out of four Han Chinese grandparents. Although individuals of Beijing Normal University were from many different parts of China, this set of samples was not drawn to be representative of all Han Chinese people. The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
spatial positional datum
comparative description
mass per unit time
pharmaceutical ingredient role
A pharmaceutical ingredient role is a role played by a chemical substance that is part of a pharmaceutical formulation.
item in collection identifier
An item in a collection identifier is an identifier for an entity that is a member of a collection.
clinical trial
A clinical trial is a study to assess the efficacy of a substance for the treatment of a condition.
March 2006 human reference sequence (NCBI Build 36.1)
sequence
A sequence is an ordered list of objects of a specified type.
pharmaceutical product
A pharmaceutical product is a formulated pharmaceutical that has been approved to treat patients.
expert role
An expert role is a role played by a knowledgeable person.
pathway
A pathway is a representation of a set or series of interactions, often forming a network, which biologists have found useful to group together for organizational, historic, biophysical, or other reasons.
genotype with indel variation
A genotype of which variants exist that differ though an insertion, deletion or a combination thereof.
inclusion criterion for clinical trial
A inclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the inclusion of candidate patients.
gene name
sex
Sex is an quality that inheres in an organism for which sexual differentiation is required for sexual reproduction.
reference genomic sequence
A reference genomic sequence is a genomic sequence that serves as a standard or reference, and may be composed by the consensus of the genomes of a number of individuals or parts thereof.
toxicity
Toxicity is a quality of a chemical substance which indicates the capacity to cause injury to an organism in a dose dependent manner.
p-value
regulatory authority
A regulatory authority is an institution created by legislation which acts to control what treatments can be prescribed.
Luhya in Webuye, Kenya
kilogram
medical history
nucleotide residue
diagnostic criterion
A diagnostic criterion is a directive information entity for consideration during a diagnosis which, if satisfied, contributes to a diagnostic result
amino acid sequence position
An amino acid sequence position indicates the position of an amino acid residue in relation to the start of the peptide chain.
genotype with SNP
A genotype with a single-nucleotide polymorphism (SNP). A SNP is a variation at a single nucleotide locus in the genomes of members of a species. For a variation to be considered a SNP, it must occur in at least 1% of the population.
drug interaction
A drug interaction is a process in which a drug interacts with a living system in such a way that it affects its behaviour.
genetic test
patient role
A patient role is a role played a human subject that receives medical attention, care or treatment or who is registered with a medical institution with the purpose of receiving medical care when necessary.
smoker status
Smoker status is a medical descriptor of the tobacco smoking behaviour of a person.
gene symbol
DNA
medical description
multitude numerical quantity
A multitude numerical quantity is a numerical quantity that indicates the number of individuals.
haplotype
A haplotype a variant DNA region which contains several smaller variant DNA regions which tend to be inherited together.
treatment safety value
Treatment safety is a condition that refers to an absence of harmful side effects resulting from use of the product and may be assessed by laboratory testing of biological samples, special tests and procedures, psychiatric evaluation, and/or physical examination of subjects.
temporal quantity
clinical trial protocol
A clinical trial protocol is a clinical protocol about the objective(s), design, methodology, statistical considerations, and organization of a clinical trial.
Japanese in Tokyo, Japan
A population in the Tokyo metropolitan area, with people who came from (or whose ancestors came from) many different parts of Japan. Thus, this population can be viewed as representative of the majority population in Japan. The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
magnitude of a genetic marker
A magnitude of a genetic marker refers to the the significance of some genetic marker
measure
A measure is an information content entity that describes or quantifies some thing.
milligram per week
chemical substance
A chemical substance is a material entity consisting of many chemical entities and typically has connected boundaries.
item in sequence identifier
An item in a collection identifier is an identifier for an entity that is a member of an ordered sequence of items (based on some attribute).
drug measure
A drug measure is a biomedical measure that describes or is a measure of drugs or their activies.
February 2009 human reference sequence (GRCh37)
amino acid sequence
protein sequence
An amino acid sequence is a sequence of amino acids in which a word (1 more more sequence of characters) represents an amino acid and their adjacency indicates their connectivity.
inactive ingredient
An inactive ingredient is a pharmaceutical ingredient that is part of a pharmaceutical formulation but does not have the disposition to treat a certain disease.
dose
planned process
A planned process is a process in which specific objectives are realized in a plan designed by some agent.
has role
nucleotide sequence
A nucleotide sequence is a sequence of nucleotides in which a word (1 more more sequence of characters) represents a nucleotide and their adjacency indicates their connectivity.
population
A population is a collection of organisms.
genotype with short tandem repeat variation
functional quantity
A functional quantity is a quantity obtained as a result of a function involving one or more parameters.
diagnostic result
A diagnostic result is a medical measure of determining the nature of a problem or illness through medical procedure.
A variant DNA region is a DNA region of which variants with altered sequence exist in different individuals of the same species or in different samples of the same individual (e.g., genetic variation within an individual, such as mutations in a cancerous tumor). The number of nucleotide residues in different variants can differ (e.g., because of insertions and deletions).
variant DNA region
male
Male is a sex quality for which sex organs contain only male gametes
medical report
dosage
Dosage is the amount of a chemical administered to, or taken by, an organism and expressed as some function of the organism and of time (mg/kg body weight/day).
e-value
This is, at the moment, a kind of institution because the payers are typically insurance companies or government bodies. But it is possible in some jurisdictions to pay for treatment oneself. Treat by renaming to "institutional payer". --CRB
institutional payer
Population with mexican ancestry in Los Angeles, California
year
numerical quantity
amino acid residue
diagnostic inclusion criterion
A diagnostic inclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, supports a diagnostic result.