Elgar Pichler
Matthias Samwald
Susie Stephens
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.
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
1.0.2
M. Scott Marshall
Trish Whetzel
ontology, translational medicine, personalized medicine, life sciences, health care
Julia Kozlovsky
Joanne Luciano
W3C Health Care and Life Sciences Interest Group
Creative Commons - By Attribution
Michel Dumontier
Translational Medicine Ontology
Christi Denney
Colin Batchelor
A chemical substance is a material entity consisting of many chemical entities and typically has connected boundaries.
chemical substance
a DNA sequence is a sequence of characters that represents the composition and connectivity of a a DNA molecule.
DNA sequence
IAO:0000120
dcterms:AgentClass
A population is a collection of organisms.
OCRe_research:Population
population
Galen:Diagnosis
NCI thesaurus
ACGT:Diagnosis
OBI:0000075
OCRe_clinical: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.
MSH:D003933
UMLS:C0011900
FHHO:Diagnosis
NCIt:Diagnosis
diagnosis
SNOMEDCT:439401001
LNC:LP72437-4
Comparative effectiveness is a drug measure that provides information about which treatment works best, for whom, and under what circumstances.
IAO:0000121
comparative effectiveness
criterion
A role played by a material entity it being the subject of a study.
subject role
NCIt:Target
UMLS:C1521840
gene name
A chemical entity role is a role played by a chemical entity.
chemical entity role
p-value
A quantity is a quantitative measure of some feature.
quantity
A molecular structure description is a description of a molecule in terms of its composition and connectivity.
Examples: connection table, fragment, pharmacophore.
molecular structure description
Ethinicity is the quality of an organism that describes membership in a social group based on a common heritage.
ethnicity
linkedct:agency
ACGT:Institution
SNOMEDCT:385437003
BIRNLex:2085
LNC:LP76237-4
UMLS:C1272753
NCIt:Institution
dailymed:organization
An institution is an entity created by legislation or by practice which acts legally in the same way as a person.
institution
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.
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.
active ingredient role
clinical trial
HL7V3.0:CLNTRL
IAO:0000121
SNOMEDCT:110465008
A clinical trial is a study to assess the efficacy of a substance for the treatment of a condition.
MSH:D016430
NCIt:Clinical_Trial
linkedct:trials
arm of clinical study
An arm of clinical study is a population that participates in a clinical trial and is subject to some intervention.
linkedct:trial_arm_group
IAO:0000120
length value
SNOMEDCT:366925008
NCIt:Lifestyle
Lifestyle is a description about an individual`s manner of living.
SNOMEDCT:134436002
IAO:0000121
MSH:D008019
SNOMEDCT:367150003
lifestyle
UMLS:C0023676
BIRNLex:2364
Galen:patent
MSH:D020490
IAO:0000313
patent
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.
BRO:Patent
American Heritage(R) Stedman's Medical Dictionary
A genetic description is a description of the genetic composition of some entity.
genetic description
publication date
An expert role is a role played by a knowledgeable person.
expert role
A measure is an information content entity that describes or quantifies some thing.
measure
statistical quantity
A regulatory authority is an institution created by legislation which acts to control what treatments can be prescribed.
regulatory authority
organismal quality
A drug measure is a biomedical measure that describes or is a measure of drugs or their activies.
drug measure
temporal quality
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.
inactive ingredient role
CDISC glossary
sider:side_effects
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.
SNOMEDCT:406644009
MSH:D004362
adverse drug event
NCI Thesaurus
IAO:0000124
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.
treatment safety value
An absent phenotype is a phenotype that represents the notable absence of a characteristic.
absent phenotype
A pharmaceutical ingredient is a chemical substance that is part of a formulated pharmaceutical that bears a pharmaceutical ingredient role.
dailymed:ingredients
pharmaceutical ingredient
IAO:0000124
An exclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the exclusion of candidate patients.
exclusion criterion for clinical trial
Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
UMLS:C1457887
symptom
NCIt:Symptom
CPR: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.
ACGT:Symptom
comparative description
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.
age
process description
drugbank:targets
A molecular target is a molecular entity that is the target of a transformation process.
molecular target
dose
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.
IAO:0000121
UMLS:C1955886
NCIt:Biomarker
MSH:D054316
biomarker
IEV:0000001
NCI Thesaurus
NCIt: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.
GRO:Pathway
Galen:Pathway
MI:0619
pathway
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
GRO:MolecularEntity
CHEBI:23367
molecular entity
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.
HL7V3.0:IACT
inactive ingredient
IAO:0000124
A inclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the inclusion of candidate patients.
inclusion criterion for clinical trial
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 target role
DNA
dose in milligram per week
A medical measure is a measure that describes or is a measure of medically relevant entities.
medical measure
Sex is an quality that inheres in an organism for which sexual differentiation is required for sexual reproduction.
sex
GRO:Protein
ODGI:Protein
A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain).
SNOMEDCT:88878007
ACGT:Protein
CHEBI:36080
BIRNLex:23
GO:0003675
SO:0000358
UMLS:C0033684
Galen:Protein
NCIt:Protein
PRO:000000001
FMA:Protein
protein
medical description
numerical quantity selected from a discrete variable
time elapsed
companion diagnostic role
Galen:Metabolite
CHEBI:25212
NCIt:Metabolite
A metabolite role is the role played by a material entity that is a metabolic substrate, intermediate or product.
LNC:LP20702-4
metabolite role
UMLS:C0870883
Male is a sex quality for which sex organs contain only male gametes
male
snp identifier
dcterms:AgentClass
foaf:Agent
dcterms:Agent
A clinical trial protocol is a clinical protocol about the objective(s), design, methodology, statistical considerations, and organization of a clinical trial.
clinical trial protocol
invariant nucleic acid region
A clinical trial criterion is a directive information entity which, if satisfied, contributes to the inclusion or exclusion of candidate patients.
clinical trial criterion
EFO:0000322
UMLS:C0007600
MSH:D002460
NCIt:Cell_Line
BIRNLex:11036
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.
Drug efficacy is a measure of the capabilty of a drug to produce an intended effect as a function of its concentration.
IAO:0000124
drug efficacy
mass value
three letter amino acid sequence
numerical quantity selected from a continuous variable
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.
OCRe_clinical:Clinician
medical expert role
OCRe_clinical:Subject
A clinical subject role is the role played by an organism who is the subject of a clinical procedure or assessment.
clinical subject role
Female is a sex quality for which sex organs contain only female gametes
female
drugbank:enzymes
An enzyme is a protein that catalyzes (increases the rate of) a chemical reaction.
enzyme
genetic status
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.
UMLS:C0311392
SNOMEDCT:72670004
NCIt:Sign
sign
deletion
single letter amino acid sequence
genetic variant
Galen:Gene
diseasome:genes
UMLS:C0017337
SNOMEDCT:67271001
pharmgkb:Gene
gene
MSH:D005796
SO:0000704
FMA:Structural_gene
NCIt:Gene_Object
GRO:Gene
LNC:LP32747-5
NCIt:Gene
PRO:Gene
NDFRT:C242394
A gene is a part of DNA that encodes information about other molecular entities.
NCIt:Side_Effect
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.
ACGT:Disease
LNC:LP21006-9
DOID:4
A quality of an organism which predisposes it to undergo pathological processes because of one or more disorders in that organism.
NDFRT:C2140
Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
GRO:Disease
diseasome:diseases
pharmgkb:Disease
UMLS:C0012634
OBI:0000155
BIRNLex:11013
disease
linkedct:condition
MSH:D004194
NCIt:Disease_or_Disorder
An amino acid sequence position indicates the position of an amino acid residue in relation to the start of the peptide chain.
amino acid sequence position
milligram per week
ncbi submitter snp identifier
description
pharmgkb:Association
pharmgkb:DrugGeneVariantInteraction
drugbank:drug_interactions
A drug interaction is a process in which a drug interacts with a living system in such a way that it affects its behaviour.
drug interaction
insertion
A planned process is a process in which specific objectives are realized in a plan designed by some agent.
OBI:0000011
BIRNLex:11021
planned process
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.
patient role
genotype with SNP
UMLS:C0752046
SO:0000694
NCIt:Single_Nucleotide_Polymorphism
MSH:D020641
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.
obsolete
SO:0001023
allele
An allele is a specific variant of a gene.
A pharmaceutical ingredient role is a role played by a chemical substance that is part of a pharmaceutical formulation.
pharmaceutical ingredient role
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.
chromosomal sequence position
genetic test
RNA sequence
A biomedical measure is an information content entity that describes or is a measure of biomedically relevant entities.
biomedical measure
mass per unit time
ncbi reference snp identifier
OBI:0000070
MSH:Q000032
Galen:Assay
cto_asyont:Assay
PATO:0000003
SNOMEDCT:272392009
assay
EFO:0001455
NCIt:Assay
UMLS:C1510438
BIRNLex:11025
An assay is a planned process with the objective to obtain information about a material entity.
variant DNA region
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).
NCI Thesaurus
UMLS:C0033325
NCIt:Prognosis
prognosis
A prognosis is a hypothesis about the likely course of a disease, the chance of recovery or recurrence.
MSH:D011379
Galen:Prognosis
pchr:Encounter
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.
UMLS:C0262926
NCIt:Personal_Medical_History
personal medical history
A phenotype is an observable characteristic of an organism.
phenotype
A DNA region is a part of a DNA molecule that is made up of a continous chain of deoxyribonucleotide residues.
DNA region
A genotype of which variants exist that differ though an insertion, deletion or a combination thereof.
genotype with indel variation
A multitude numerical quantity is a numerical quantity that indicates the number of individuals.
multitude numerical quantity
age
organization
drugbank:references
A nucleotide sequence position indicates the position of a nucleotide residue in relation to the start of the nucleic acid.
nucleotide sequence position
An item in a collection identifier is an identifier for an entity that is a member of a collection.
item in collection identifier
organism
A collection of humans
human population
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.
sequence position
A genotype of which variants with a different number of copies of a sequence identifical region exist.
SO:0001019
genotype with copy number variation
An indicator is an entity for which its observation/detection is used in some objective.
indicator
pharmgkb subject identifier
genotype with short tandem repeat variation
0
9
age in years
gene symbol
unit of measurement
human
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).
item in sequence identifier
genomic sequence
A genomic sequence is the collection of sequences that make up an individual's genetic matter.
mouse
year
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.
A magnitude of a genetic marker refers to the the significance of some genetic marker
magnitude of a genetic marker
pharmgkb sample identifier
3D molecular structure
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.
genotype with multiple nucleotide polymorphism
race
dsDNA
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).
ribonucleotide sequence position
An identifier is an information content entity which consists of one or more symbols in order to identify some entity.
identifier
physical quantity
spatial positional datum
nucleic acid
physical description
numerical quantity
molecular entity part
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.
A hypothesis is an information content entity that describes a possible correlation between two or more variables.
UMLS:C1512571
OBI:0000074
NCIt:Hypothesis
hypothesis
A chromosome number is an identifier for a chromosome that identifies it from a collection of chromosomes for a given organism.
chromosome number
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).
deoxyribonucleotide sequence position
medical finding
temporal quantity
ranged numerical quantity
IAO:0000121
LNC:LP74341-6
A study is a planned process that consists of planning, study execution, documentation and the production of conclusion(s).
NCIt:Study
study
UMLS:C0947630
OCRe_research:Study
OBI:0000471
SNOMEDCT:224699009
medical history
ratio
diagnostic role
A diagnostic result is a medical measure of determining the nature of a problem or illness through medical procedure.
IAO:0000124
diagnostic result
pharmacodynamic measure
centimeter
molecular complex
A pharmaceutical product is a formulated pharmaceutical that has been approved to treat patients.
UMLS:C1708062
NCIt:Finished_Pharmaceutical_Product
pharmaceutical product
A diagnostic criterion is a directive information entity for consideration during a diagnosis which, if satisfied, contributes to a diagnostic result
IAO:0000124
diagnostic criterion
amino acid residue
The mechanism of action is a description of processes and behaviour of a biologically active molecule in its administration into a living system.
NCIt:Mechanism_of_Action
mechanism of action
genotype with allele
A genotype containing one matching allele on each chromosome (e.g., CYP2C9*1/*3)
A collection of humans from a particular region.
regionally-defined human population
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.
protein sequence
amino acid sequence
ACGT:Syndrome
EFO:0000428
MSH:D013577
syndrome
UMLS:C0039082
EFO:0000716
NCIt:Syndrome
A syndrome is a group of signs and symptoms that characterize a particular abnormality.
DOID:225
A functional quantity is a quantity obtained as a result of a function involving one or more parameters.
functional quantity
historical description
International Normalized Ratio on the Therapeutic Dose of Warfarin
kilogram
A diagnostic exclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, excludes a diagnostic result.
IAO:0000124
diagnostic exclusion criterion
date
IAO:0000124
A clinical protocol is a directive information entity about the objective(s), design, methodology, statistical considerations, and organization of a clinical procedure.
clinical protocol
pharmacokinetic measure
medicare:drugs
UMLS:C1705957
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.
sider:drugs
NCIt:Pharmaceutical_Formulation
formulated pharmaceutical
pharmgkb:Drug
drugbank:drugs
dailymed:drugs
protein target
NDFRT:C7812
disease progression
UMLS:C0242656
MSH:D018450
NCIt:Disease_Progression
OBI:0000354
IAO:0000124
A sequence is an ordered list of objects of a specified type.
sequence
NCIt:Dose
EFO:0000428
SNOMEDCT:260911001
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).
LNC:LP6801-7
UMLS:C0178602
nucleic acid region
A nucleic acid region is a part of a nucleic acid that is made up of a continous chain of nucleotide residues.
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.
reference genomic sequence
A haplotype a variant DNA region which contains several smaller variant DNA regions which tend to be inherited together.
haplotype
medical descriptor
non toxic
An active ingredient is a pharmaceutical ingredient that has the disposition to treat a certain disease.
HL7V3.0:ACTI
active ingredient
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
UMLS:C2348942
NCIt:Healthcare_Payer
institutional payer
An enumerated numerical quantity is a numerical quantity selected from a discrete set of quantities.
enumerated numerical quantity
IAO:0000123
Evidence is a group of indicators that are relevant in some decision-making process.
UMLS:C0332120
NCIt:Evidence
evidence
temporal functional quantity
weight in kilograms
chromosome
IAO:0000124
A drug-drug interaction is a drug interaction in which two drugs interact in such a way to produce an abnormal phenotypic event.
SNOMEDCT:404204005
drug-drug interaction
Toxicity is a quality of a chemical substance which indicates the capacity to cause injury to an organism in a dose dependent manner.
UMLS:C0600688
NCIt:Toxicity
MSH:Q000633
ACGT:Toxicity
toxicity
medical report
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.
genotype
IAO:0000121
An intervention is a study in which a substance is administered to a subject or group of subjects.
linkedct:intervention
OCRe_research:Intervention
NCIt:Intervention
intervention
A gene variant is a variant of another gene based on some difference in sequence (composition and connectivity)
gene variant
scale numerical value
market
toxic
Smoker status is a medical descriptor of the tobacco smoking behaviour of a person.
smoker status
An environmental description is a description concerning some aspect of a physical environment.
IAO:0000123
environmental description
e-value
height in centimeters
A health outcome is a medical measure of health or loss of health.
linkedct:primary_outcomes
IAO:0000121
linkedct:secondary_outcomes
health outcome
nucleotide residue
IAO:0000124
A diagnostic inclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, supports a diagnostic result.
diagnostic inclusion criterion
patient record
is described by
provides supporting evidence for
has attribute
attribute of
in relation to
has role
is variant of
A short acronym identifying a sample population that was examined by the HapMap project.
HapMap population name abbreviation
has value
has unit
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
MKK
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.
MXL
Population with mexican ancestry in Los Angeles, California
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
LWK
Luhya in Webuye, Kenya
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
GIH
Gujarati Indians in Houston, Texas
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
CHD
Chinese in Metropolitan Denver, Colorado
March 2006 human reference sequence (NCBI Build 36.1)
February 2009 human reference sequence (GRCh37)
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.
CEU
CEPH (Utah residents with ancestry from northern and western Europe)
July 2003 human reference sequence (NCBI Build 34)
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.
CHB
Han Chinese in Beijing, China
May 2004 human reference sequence (NCBI Build 35)
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.
JPT
Japanese in Tokyo, Japan
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.
YRI
Yoruba in Ibadan, Nigeria
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
TSI
Toscani in Italia
The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
ASW
Population with african ancestry in Southwest USA