Translational Medicine Ontology
type: Ontology
creator: Elgar Pichler
creator: Matthias Samwald
creator: Susie Stephens
description: 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.
imports: tmo-external.owl
comment: 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
version info: 1.0.2
creator: M. Scott Marshall
creator: Trish Whetzel
imports: owlrl-all
subject: ontology, translational medicine, personalized medicine, life sciences, health care
creator: Julia Kozlovsky
creator: Joanne Luciano
publisher: W3C Health Care and Life Sciences Interest Group
rights: Creative Commons - By Attribution
creator: Michel Dumontier
creator: Christi Denney
creator: Colin Batchelor

chemical substance
type: Class
description: A chemical substance is a material entity consisting of many chemical entities and typically has connected boundaries.
subclass of: tmo resource:arcb4cdb1
subclass of: MaterialEntity

molecular entity
type: Class
description: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
has db xref: GRO:MolecularEntity
has db xref: CHEBI:23367
subclass of: MaterialEntity

DNA sequence
type: Class
description: a DNA sequence is a sequence of characters that represents the composition and connectivity of a a DNA molecule.
disjoint with: RNA sequence
subclass of: nucleotide sequence

RNA sequence
type: Class
subclass of: nucleotide sequence

nucleotide sequence
type: Class
subclass of: sequence
description: 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
type: Class
has db xref: IAO:0000120
has db xref: dcterms:AgentClass
description: A population is a collection of organisms.
has db xref: OCRe_research:Population
subclass of: MaterialEntity

diagnosis
type: Class
has db xref: Galen:Diagnosis
IAO_0000119: NCI thesaurus
has db xref: ACGT:Diagnosis
has db xref: OBI:0000075
subclass of: study
has db xref: OCRe_clinical:Diagnosis
description: 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.
has db xref: MSH:D003933
has db xref: UMLS:C0011900
has db xref: FHHO:Diagnosis
has db xref: NCIt:Diagnosis
has db xref: SNOMEDCT:439401001
has db xref: LNC:LP72437-4

study
type: Class
has db xref: IAO:0000121
has db xref: LNC:LP74341-6
description: A study is a planned process that consists of planning, study execution, documentation and the production of conclusion(s).
has db xref: NCIt:Study
has db xref: UMLS:C0947630
subclass of: planned process
has db xref: OCRe_research:Study
has db xref: OBI:0000471
has db xref: SNOMEDCT:224699009

comparative effectiveness
type: Class
description: Comparative effectiveness is a drug measure that provides information about which treatment works best, for whom, and under what circumstances.
has db xref: IAO:0000121
subclass of: comparative description

comparative description
type: Class
subclass of: description

criterion
type: Class
subclass of: IAO_0000033

subject role
type: Class
description: A role played by a material entity it being the subject of a study.
disjoint with: diagnostic role
subclass of: Role
disjoint with: IAO_0000442
has db xref: NCIt:Target
disjoint with: expert role
disjoint with: chemical entity role
has db xref: UMLS:C1521840

diagnostic role
type: Class
subclass of: Role
disjoint with: subject role
disjoint with: chemical entity role
disjoint with: expert role
disjoint with: IAO_0000442

chemical entity role
type: Class
description: A chemical entity role is a role played by a chemical entity.
subclass of: Role
disjoint with: subject role
disjoint with: diagnostic role
disjoint with: expert role
disjoint with: IAO_0000442

expert role
type: Class
description: An expert role is a role played by a knowledgeable person.
subclass of: Role
disjoint with: subject role
disjoint with: chemical entity role
disjoint with: diagnostic role
disjoint with: IAO_0000442

gene name
type: Class
subclass of: IAO_0000009

identifier
type: Class
description: An identifier is an information content entity which consists of one or more symbols in order to identify some entity.
subclass of: IAO_0000030

p-value
type: Class
subclass of: statistical quantity

statistical quantity
type: Class
subclass of: numerical quantity selected from a continuous variable

quantity
type: Class
description: A quantity is a quantitative measure of some feature.
subclass of: IAO_0000030

molecular structure description
type: Class
description: A molecular structure description is a description of a molecule in terms of its composition and connectivity.
comment: Examples: connection table, fragment, pharmacophore.
subclass of: physical description

physical description
type: Class
subclass of: description

ethnicity
type: Class
description: Ethinicity is the quality of an organism that describes membership in a social group based on a common heritage.
subclass of: organismal quality

organismal quality
type: Class
subclass of: Quality

institution
type: Class
has db xref: linkedct:agency
has db xref: ACGT:Institution
has db xref: SNOMEDCT:385437003
has db xref: BIRNLex:2085
has db xref: LNC:LP76237-4
has db xref: UMLS:C1272753
has db xref: NCIt:Institution
subclass of: organization
has db xref: dailymed:organization
description: An institution is an entity created by legislation or by practice which acts legally in the same way as a person.

organization
type: Class
subclass of: GenericallyDependentContinuant
disjoint with: IAO_0000030

sequence
type: Class
description: A sequence is an ordered list of objects of a specified type.
subclass of: description

active ingredient role
type: Class
description: 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.
subclass of: pharmaceutical ingredient role

pharmaceutical ingredient role
type: Class
description: A pharmaceutical ingredient role is a role played by a chemical substance that is part of a pharmaceutical formulation.
subclass of: chemical entity role

clinical trial
type: Class
has db xref: HL7V3.0:CLNTRL
subclass of: study
has db xref: IAO:0000121
has db xref: SNOMEDCT:110465008
description: A clinical trial is a study to assess the efficacy of a substance for the treatment of a condition.
has db xref: MSH:D016430
has db xref: NCIt:Clinical_Trial
has db xref: linkedct:trials

arm of clinical study
type: Class
description: An arm of clinical study is a population that participates in a clinical trial and is subject to some intervention.
subclass of: tmo resource:arcb4cdb2
has db xref: linkedct:trial_arm_group
disjoint with: human population
subclass of: population
has db xref: IAO:0000120
subclass of: tmo resource:arcb4cdb3
disjoint with: cell line

human
type: Class
subclass of: organism
disjoint with: mouse

human population
type: Class
description: A collection of humans
subclass of: population
disjoint with: cell line
disjoint with: arm of clinical study

clinical subject role
type: Class
has db xref: OCRe_clinical:Subject
description: A clinical subject role is the role played by an organism who is the subject of a clinical procedure or assessment.
subclass of: subject role

has role
type: ObjectProperty
sub property of: has attribute

cell line
type: Class
subclass of: population
has db xref: EFO:0000322
has db xref: UMLS:C0007600
has db xref: MSH:D002460
disjoint with: human population
has db xref: NCIt:Cell_Line
disjoint with: arm of clinical study
has db xref: BIRNLex:11036
description: 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.

length value
type: Class
subclass of: tmo resource:arcb4cdb4
subclass of: physical quantity

has value
type: FunctionalProperty
type: DatatypeProperty

physical quantity
type: Class
subclass of: numerical quantity

lifestyle
type: Class
has db xref: SNOMEDCT:366925008
has db xref: NCIt:Lifestyle
description: Lifestyle is a description about an individual`s manner of living.
has db xref: SNOMEDCT:134436002
has db xref: IAO:0000121
has db xref: MSH:D008019
has db xref: SNOMEDCT:367150003
has db xref: UMLS:C0023676
subclass of: historical description

historical description
type: Class
subclass of: description

patent
type: Class
has db xref: BIRNLex:2364
has db xref: Galen:patent
has db xref: MSH:D020490
has db xref: IAO:0000313
description: 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.
has db xref: BRO:Patent
IAO_0000119: American Heritage(R) Stedman's Medical Dictionary
subclass of: IAO_0000310

IAO_0000310
type: Class
has db xref: drugbank:references

genetic description
type: Class
description: A genetic description is a description of the genetic composition of some entity.
subclass of: description

description
type: Class
subclass of: IAO_0000030

publication date
type: Class
subclass of: date

date
type: Class
subclass of: temporal quantity

measure
type: Class
description: A measure is an information content entity that describes or quantifies some thing.
subclass of: obsolete

obsolete
type: Class

numerical quantity selected from a continuous variable
type: Class
subclass of: numerical quantity

regulatory authority
type: Class
description: A regulatory authority is an institution created by legislation which acts to control what treatments can be prescribed.
subclass of: institution

drug measure
type: Class
description: A drug measure is a biomedical measure that describes or is a measure of drugs or their activies.
subclass of: biomedical measure

biomedical measure
type: Class
description: A biomedical measure is an information content entity that describes or is a measure of biomedically relevant entities.
subclass of: measure

temporal quality
type: Class
subclass of: obsolete

inactive ingredient role
type: Class
description: 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.
subclass of: pharmaceutical ingredient role

adverse drug event
type: Class
IAO_0000119: CDISC glossary
has db xref: sider:side_effects
description: 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.
has db xref: SNOMEDCT:406644009
has db xref: MSH:D004362
subclass of: side effect

side effect
type: Class
subclass of: ProcessualEntity
has db xref: NCIt:Side_Effect
description: A side effect is an effect of an intervention, whether therapeutic or adverse, that is secondary to the intended effect of the intervention.

treatment safety value
type: Class
IAO_0000119: NCI Thesaurus
has db xref: IAO:0000124
description: 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.
subclass of: functional quantity

functional quantity
type: Class
description: A functional quantity is a quantity obtained as a result of a function involving one or more parameters.
subclass of: numerical quantity selected from a continuous variable

absent phenotype
type: Class
description: An absent phenotype is a phenotype that represents the notable absence of a characteristic.
subclass of: phenotype

phenotype
type: Class
description: A phenotype is an observable characteristic of an organism.
subclass of: organismal quality

pharmaceutical ingredient
type: Class
description: A pharmaceutical ingredient is a chemical substance that is part of a formulated pharmaceutical that bears a pharmaceutical ingredient role.
has db xref: dailymed:ingredients
subclass of: tmo resource:arcb4cdb5
subclass of: chemical substance
equivalent class: tmo resource:arcb4cdb6

formulated pharmaceutical
type: Class
has db xref: medicare:drugs
has db xref: UMLS:C1705957
description: 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.
has db xref: sider:drugs
has db xref: NCIt:Pharmaceutical_Formulation
has db xref: pharmgkb:Drug
subclass of: chemical substance
has db xref: drugbank:drugs
has db xref: dailymed:drugs
subclass of: tmo resource:arcb4cdb43

exclusion criterion for clinical trial
type: Class
has db xref: IAO:0000124
description: An exclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the exclusion of candidate patients.
subclass of: clinical trial criterion

clinical trial criterion
type: Class
description: A clinical trial criterion is a directive information entity which, if satisfied, contributes to the inclusion or exclusion of candidate patients.
subclass of: criterion

symptom
type: Class
IAO_0000119: Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
has db xref: UMLS:C1457887
has db xref: NCIt:Symptom
has db xref: CPR:symptom
description: 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.
has db xref: ACGT:Symptom
subclass of: phenotype

age
type: Class
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.
subclass of: organismal quality

process description
type: Class
subclass of: description

molecular target
type: Class
has db xref: drugbank:targets
description: A molecular target is a molecular entity that is the target of a transformation process.
subclass of: molecular entity
equivalent class: tmo resource:arcb4cdb10

molecular target role
type: Class
description: 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.
subclass of: chemical entity role

dose
type: Class
subclass of: temporal functional quantity

temporal functional quantity
type: Class
subclass of: functional quantity

biomarker
type: Class
description: 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.
has db xref: IAO:0000121
has db xref: UMLS:C1955886
has db xref: NCIt:Biomarker
has db xref: MSH:D054316
subclass of: phenotype

pathway
type: Class
has db xref: IEV:0000001
IAO_0000119: NCI Thesaurus
has db xref: NCIt:Pathway
description: 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.
has db xref: GRO:Pathway
subclass of: process description
has db xref: Galen:Pathway
has db xref: MI:0619

inactive ingredient
type: Class
description: 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.
has db xref: HL7V3.0:IACT
subclass of: pharmaceutical ingredient
equivalent class: tmo resource:arcb4cdb14

inclusion criterion for clinical trial
type: Class
has db xref: IAO:0000124
description: A inclusion criterion for clinical trial is a clinical trial criterion which, if satisfied, supports the inclusion of candidate patients.
subclass of: clinical trial criterion

DNA
type: Class
subclass of: molecular entity
disjoint with: protein
disjoint with: molecular complex

protein
type: Class
has db xref: GRO:Protein
has db xref: ODGI:Protein
description: A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain).
has db xref: SNOMEDCT:88878007
disjoint with: nucleic acid
disjoint with: DNA
has db xref: ACGT:Protein
subclass of: molecular entity
has db xref: CHEBI:36080
has db xref: BIRNLex:23
has db xref: GO:0003675
has db xref: SO:0000358
disjoint with: molecular complex
has db xref: UMLS:C0033684
has db xref: Galen:Protein
has db xref: NCIt:Protein
has db xref: PRO:000000001
has db xref: FMA:Protein

molecular complex
type: Class
subclass of: molecular entity
disjoint with: protein
disjoint with: DNA

dose in milligram per week
type: Class
subclass of: tmo resource:arcb4cdb20
subclass of: tmo resource:arcb4cdb21
subclass of: dose

milligram per week
type: Class
subclass of: mass per unit time

has unit
type: FunctionalProperty
range: unit of measurement
domain: quantity
type: ObjectProperty

medical measure
type: Class
description: A medical measure is a measure that describes or is a measure of medically relevant entities.
subclass of: biomedical measure

sex
type: Class
description: Sex is an quality that inheres in an organism for which sexual differentiation is required for sexual reproduction.
subclass of: organismal quality

nucleic acid
type: Class
subclass of: obsolete

medical description
type: Class
subclass of: description

numerical quantity selected from a discrete variable
type: Class
subclass of: numerical quantity

numerical quantity
type: Class
subclass of: quantity

time elapsed
type: Class
subclass of: temporal quantity

temporal quantity
type: Class
subclass of: physical quantity

companion diagnostic role
type: Class
subclass of: diagnostic role

metabolite role
type: Class
has db xref: Galen:Metabolite
has db xref: CHEBI:25212
has db xref: NCIt:Metabolite
description: A metabolite role is the role played by a material entity that is a metabolic substrate, intermediate or product.
subclass of: chemical entity role
has db xref: LNC:LP20702-4
has db xref: UMLS:C0870883

male
type: Class
description: Male is a sex quality for which sex organs contain only male gametes
disjoint with: female
subclass of: sex

female
type: Class
description: Female is a sex quality for which sex organs contain only female gametes
subclass of: sex

snp identifier
type: Class
subclass of: item in sequence identifier

item in sequence identifier
type: Class
description: 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).
subclass of: item in collection identifier

Continuant
type: Class
has db xref: dcterms:AgentClass
has db xref: foaf:Agent
has db xref: dcterms:Agent

clinical trial protocol
type: Class
description: A clinical trial protocol is a clinical protocol about the objective(s), design, methodology, statistical considerations, and organization of a clinical trial.
subclass of: clinical protocol

clinical protocol
type: Class
has db xref: IAO:0000124
description: A clinical protocol is a directive information entity about the objective(s), design, methodology, statistical considerations, and organization of a clinical procedure.
subclass of: IAO_0000033

invariant nucleic acid region
type: Class
subclass of: obsolete

drug efficacy
type: Class
description: Drug efficacy is a measure of the capabilty of a drug to produce an intended effect as a function of its concentration.
has db xref: IAO:0000124
subclass of: functional quantity

mass value
type: Class
subclass of: tmo resource:arcb4cdb22
subclass of: physical quantity

three letter amino acid sequence
type: Class
subclass of: protein sequence

protein sequence
type: Class
description: 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.
disjoint with: nucleotide sequence
subclass of: sequence
label: amino acid sequence

medical expert role
type: Class
description: 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.
has db xref: OCRe_clinical:Clinician
subclass of: expert role

enzyme
type: Class
has db xref: drugbank:enzymes
description: An enzyme is a protein that catalyzes (increases the rate of) a chemical reaction.
subclass of: protein

genetic status
type: Class
subclass of: obsolete

sign
type: Class
IAO_0000119: Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
description: 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.
has db xref: UMLS:C0311392
has db xref: SNOMEDCT:72670004
has db xref: NCIt:Sign
subclass of: phenotype

deletion
type: Class
subclass of: obsolete

single letter amino acid sequence
type: Class
subclass of: protein sequence

genetic variant
type: Class
subclass of: obsolete

gene
type: Class
has db xref: Galen:Gene
has db xref: diseasome:genes
has db xref: UMLS:C0017337
has db xref: SNOMEDCT:67271001
has db xref: pharmgkb:Gene
has db xref: MSH:D005796
has db xref: SO:0000704
has db xref: FMA:Structural_gene
has db xref: NCIt:Gene_Object
has db xref: GRO:Gene
has db xref: LNC:LP32747-5
has db xref: NCIt:Gene
subclass of: DNA region
has db xref: PRO:Gene
has db xref: NDFRT:C242394
description: A gene is a part of DNA that encodes information about other molecular entities.

DNA region
type: Class
comment: A DNA region is a part of a DNA molecule that is made up of a continous chain of deoxyribonucleotide residues.
subclass of: molecular entity part

disease
type: Class
has db xref: ACGT:Disease
has db xref: LNC:LP21006-9
has db xref: DOID:4
description: A quality of an organism which predisposes it to undergo pathological processes because of one or more disorders in that organism.
has db xref: NDFRT:C2140
IAO_0000119: Richard Scheuermann, Werner Ceusters, Barry Smith in "Toward an Ontological Treatment of Disease and Diagnosis"
has db xref: GRO:Disease
has db xref: diseasome:diseases
has db xref: pharmgkb:Disease
has db xref: UMLS:C0012634
has db xref: OBI:0000155
has db xref: BIRNLex:11013
has db xref: linkedct:condition
has db xref: MSH:D004194
subclass of: organismal quality
has db xref: NCIt:Disease_or_Disorder

amino acid sequence position
type: Class
description: An amino acid sequence position indicates the position of an amino acid residue in relation to the start of the peptide chain.
subclass of: sequence position

sequence position
type: Class
description: 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.
subclass of: item in sequence identifier

mass per unit time
type: Class
subclass of: unit of measurement

ncbi submitter snp identifier
type: Class
subclass of: snp identifier

drug interaction
type: Class
has db xref: pharmgkb:Association
has db xref: pharmgkb:DrugGeneVariantInteraction
has db xref: drugbank:drug_interactions
description: A drug interaction is a process in which a drug interacts with a living system in such a way that it affects its behaviour.
subclass of: ProcessualEntity

insertion
type: Class
subclass of: obsolete

planned process
type: Class
description: A planned process is a process in which specific objectives are realized in a plan designed by some agent.
has db xref: OBI:0000011
has db xref: BIRNLex:11021
subclass of: ProcessualEntity

patient role
type: Class
description: 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.
subclass of: clinical subject role

genotype with SNP
type: Class
has db xref: UMLS:C0752046
has db xref: SO:0000694
has db xref: NCIt:Single_Nucleotide_Polymorphism
has db xref: MSH:D020641
description: 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.
subclass of: genotype

genotype
type: Class
description: 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.
subclass of: molecular entity part

allele
type: Class
has db xref: SO:0001023
subclass of: variant DNA region
description: An allele is a specific variant of a gene.
equivalent class: tmo resource:arcb4cdb23

variant DNA region
type: Class
equivalent class: tmo resource:arcb4cdb27
subclass of: DNA region
subclass of: tmo resource:arcb4cdb31
comment: 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).

is variant of
type: SymmetricProperty

chromosomal sequence position
type: Class
description: 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.
subclass of: deoxyribonucleotide sequence position

deoxyribonucleotide sequence position
type: Class
description: 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).
subclass of: nucleotide sequence position

genetic test
type: Class
subclass of: assay

assay
type: Class
subclass of: planned process
has db xref: OBI:0000070
has db xref: MSH:Q000032
has db xref: Galen:Assay
has db xref: cto_asyont:Assay
has db xref: PATO:0000003
has db xref: SNOMEDCT:272392009
has db xref: EFO:0001455
has db xref: NCIt:Assay
has db xref: UMLS:C1510438
has db xref: BIRNLex:11025
description: An assay is a planned process with the objective to obtain information about a material entity.

unit of measurement
type: Class
subclass of: numerical quantity

ncbi reference snp identifier
type: Class
disjoint with: ncbi submitter snp identifier
subclass of: snp identifier

prognosis
type: Class
IAO_0000119: NCI Thesaurus
has db xref: UMLS:C0033325
has db xref: NCIt:Prognosis
description: A prognosis is a hypothesis about the likely course of a disease, the chance of recovery or recurrence.
has db xref: MSH:D011379
subclass of: hypothesis
has db xref: Galen:Prognosis

hypothesis
type: Class
description: A hypothesis is an information content entity that describes a possible correlation between two or more variables.
has db xref: UMLS:C1512571
has db xref: OBI:0000074
has db xref: NCIt:Hypothesis
subclass of: description

personal medical history
type: Class
has db xref: pchr:Encounter
description: 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.
has db xref: UMLS:C0262926
has db xref: NCIt:Personal_Medical_History
subclass of: tmo resource:arcb4cdb32
subclass of: medical history

medical history
type: Class
subclass of: historical description

molecular entity part
type: Class
subclass of: MaterialEntity
subclass of: tmo resource:arcb4cdb42
comment: 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.

genotype with indel variation
type: Class
description: A genotype of which variants exist that differ though an insertion, deletion or a combination thereof.
subclass of: genotype

multitude numerical quantity
type: Class
description: A multitude numerical quantity is a numerical quantity that indicates the number of individuals.
subclass of: numerical quantity selected from a discrete variable

age
type: Class
subclass of: temporal quantity

nucleotide sequence position
type: Class
description: A nucleotide sequence position indicates the position of a nucleotide residue in relation to the start of the nucleic acid.
subclass of: sequence position

item in collection identifier
type: Class
description: An item in a collection identifier is an identifier for an entity that is a member of a collection.
subclass of: identifier

organism
type: Class
subclass of: MaterialEntity

genotype with copy number variation
type: Class
description: A genotype of which variants with a different number of copies of a sequence identifical region exist.
has db xref: SO:0001019
subclass of: genotype

indicator
type: Class
subclass of: obsolete
description: An indicator is an entity for which its observation/detection is used in some objective.

pharmgkb subject identifier
type: Class
subclass of: item in collection identifier

genotype with short tandem repeat variation
type: Class
subclass of: genotype

age in years
type: Class
subclass of: tmo resource:arcb4cdb33
subclass of: tmo resource:arcb4cdb39
subclass of: age

tmo resource:arcb4cdb35
min inclusive: 0

tmo resource:arcb4cdb37
max inclusive: 9

year
type: Class
subclass of: unit of measurement

gene symbol
type: Class
subclass of: IAO_0000028

mouse
type: Class
subclass of: organism
disjoint with: human

genomic sequence
type: Class
subclass of: tmo resource:arcb4cdb40
subclass of: sequence
description: A genomic sequence is the collection of sequences that make up an individual's genetic matter.

ancestral allele
type: Class
subclass of: tmo resource:arcb4cdb41
subclass of: allele
description: 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.

in relation to
type: ObjectProperty

magnitude of a genetic marker
type: Class
description: A magnitude of a genetic marker refers to the the significance of some genetic marker
subclass of: scale numerical value

scale numerical value
type: Class
subclass of: ranged numerical quantity

pharmgkb sample identifier
type: Class
subclass of: item in collection identifier

3D molecular structure
type: Class
subclass of: molecular structure description

genotype with multiple nucleotide polymorphism
type: Class
description: 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.
subclass of: genotype

race
type: Class
subclass of: organismal quality

dsDNA
type: Class
subclass of: molecular complex

ribonucleotide sequence position
type: Class
description: 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).
subclass of: nucleotide sequence position

spatial positional datum
type: Class
subclass of: identifier

chromosome number
type: Class
description: A chromosome number is an identifier for a chromosome that identifies it from a collection of chromosomes for a given organism.
subclass of: item in collection identifier

medical finding
type: Class
subclass of: medical description

ranged numerical quantity
type: Class
subclass of: numerical quantity selected from a continuous variable

ratio
type: Class
subclass of: functional quantity

diagnostic result
type: Class
description: A diagnostic result is a medical measure of determining the nature of a problem or illness through medical procedure.
has db xref: IAO:0000124
subclass of: medical finding

pharmacodynamic measure
type: Class
subclass of: functional quantity

centimeter
type: Class
subclass of: unit of measurement

pharmaceutical product
type: Class
description: A pharmaceutical product is a formulated pharmaceutical that has been approved to treat patients.
has db xref: UMLS:C1708062
has db xref: NCIt:Finished_Pharmaceutical_Product
subclass of: formulated pharmaceutical

diagnostic criterion
type: Class
description: A diagnostic criterion is a directive information entity for consideration during a diagnosis which, if satisfied, contributes to a diagnostic result
has db xref: IAO:0000124
subclass of: criterion

amino acid residue
type: Class
subclass of: obsolete

mechanism of action
type: Class
description: The mechanism of action is a description of processes and behaviour of a biologically active molecule in its administration into a living system.
has db xref: NCIt:Mechanism_of_Action
subclass of: process description

genotype with allele
type: Class
subclass of: genotype
description: A genotype containing one matching allele on each chromosome (e.g., CYP2C9*1/*3)

regionally-defined human population
type: Class
description: A collection of humans from a particular region.
subclass of: human population

syndrome
type: Class
has db xref: ACGT:Syndrome
has db xref: EFO:0000428
has db xref: MSH:D013577
has db xref: UMLS:C0039082
has db xref: EFO:0000716
has db xref: NCIt:Syndrome
description: A syndrome is a group of signs and symptoms that characterize a particular abnormality.
has db xref: DOID:225
subclass of: organismal quality

International Normalized Ratio on the Therapeutic Dose of Warfarin
type: Class
subclass of: ratio

kilogram
type: Class
subclass of: unit of measurement

diagnostic exclusion criterion
type: Class
description: A diagnostic exclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, excludes a diagnostic result.
has db xref: IAO:0000124
subclass of: diagnostic criterion

pharmacokinetic measure
type: Class
subclass of: functional quantity

protein target
type: Class
subclass of: protein
equivalent class: tmo resource:arcb4cdb44

disease progression
type: Class
has db xref: NDFRT:C7812
has db xref: UMLS:C0242656
has db xref: MSH:D018450
has db xref: NCIt:Disease_Progression
has db xref: OBI:0000354
has db xref: IAO:0000124
subclass of: ProcessualEntity

dosage
type: Class
has db xref: NCIt:Dose
has db xref: EFO:0000428
has db xref: SNOMEDCT:260911001
description: 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).
has db xref: LNC:LP6801-7
subclass of: temporal functional quantity
has db xref: UMLS:C0178602

nucleic acid region
type: Class
subclass of: tmo resource:arcb4cdb48
subclass of: obsolete
comment: A nucleic acid region is a part of a nucleic acid that is made up of a continous chain of nucleotide residues.

reference genomic sequence
type: Class
description: 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.
subclass of: genomic sequence

haplotype
type: Class
description: A haplotype a variant DNA region which contains several smaller variant DNA regions which tend to be inherited together.
subclass of: variant DNA region

medical descriptor
type: Class
subclass of: medical description

non toxic
type: Class
subclass of: toxicity

toxicity
type: Class
description: Toxicity is a quality of a chemical substance which indicates the capacity to cause injury to an organism in a dose dependent manner.
has db xref: UMLS:C0600688
has db xref: NCIt:Toxicity
has db xref: MSH:Q000633
has db xref: ACGT:Toxicity
subclass of: Quality

active ingredient
type: Class
description: An active ingredient is a pharmaceutical ingredient that has the disposition to treat a certain disease.
has db xref: HL7V3.0:ACTI
subclass of: pharmaceutical ingredient
equivalent class: tmo resource:arcb4cdb49

institutional payer
type: Class
comment: 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
has db xref: UMLS:C2348942
has db xref: NCIt:Healthcare_Payer
subclass of: institution

enumerated numerical quantity
type: Class
description: An enumerated numerical quantity is a numerical quantity selected from a discrete set of quantities.
subclass of: numerical quantity selected from a discrete variable

evidence
type: Class
has db xref: IAO:0000123
description: Evidence is a group of indicators that are relevant in some decision-making process.
has db xref: UMLS:C0332120
has db xref: NCIt:Evidence
subclass of: obsolete

weight in kilograms
type: Class
subclass of: tmo resource:arcb4cdb55
subclass of: tmo resource:arcb4cdb56
subclass of: mass value

chromosome
type: Class
subclass of: tmo resource:arcb4cdb57
subclass of: molecular complex

drug-drug interaction
type: Class
has db xref: IAO:0000124
description: A drug-drug interaction is a drug interaction in which two drugs interact in such a way to produce an abnormal phenotypic event.
has db xref: SNOMEDCT:404204005
subclass of: drug interaction

medical report
type: Class
subclass of: medical description

intervention
type: Class
has db xref: IAO:0000121
description: An intervention is a study in which a substance is administered to a subject or group of subjects.
has db xref: linkedct:intervention
has db xref: OCRe_research:Intervention
has db xref: NCIt:Intervention
subclass of: study

gene variant
type: Class
subclass of: obsolete
description: A gene variant is a variant of another gene based on some difference in sequence (composition and connectivity)

market
type: Class
subclass of: institution

toxic
type: Class
subclass of: toxicity

smoker status
type: Class
description: Smoker status is a medical descriptor of the tobacco smoking behaviour of a person.
subclass of: medical descriptor

environmental description
type: Class
description: An environmental description is a description concerning some aspect of a physical environment.
has db xref: IAO:0000123
subclass of: description

e-value
type: Class
subclass of: statistical quantity

height in centimeters
type: Class
subclass of: tmo resource:arcb4cdb58
subclass of: tmo resource:arcb4cdb59
subclass of: length value

health outcome
type: Class
description: A health outcome is a medical measure of health or loss of health.
has db xref: linkedct:primary_outcomes
has db xref: IAO:0000121
has db xref: linkedct:secondary_outcomes
subclass of: medical description

nucleotide residue
type: Class
subclass of: obsolete

diagnostic inclusion criterion
type: Class
has db xref: IAO:0000124
description: A diagnostic inclusion criterion is a diagnostic criterion for consideration during a diagnosis which, if satisfied, supports a diagnostic result.
subclass of: diagnostic criterion

patient record
type: Class
subclass of: medical description

is described by
type: ObjectProperty
range: IAO_0000030

provides supporting evidence for
type: ObjectProperty
sub property of: IAO_0000136

has attribute
type: ObjectProperty
inverse of: attribute of

HapMap population name abbreviation
type: FunctionalProperty
description: A short acronym identifying a sample population that was examined by the HapMap project.
type: DatatypeProperty

Maasai in Kinyawa, Kenya
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: MKK
type: NamedIndividual

Population with mexican ancestry in Los Angeles, California
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: MXL
type: NamedIndividual

Luhya in Webuye, Kenya
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: LWK
type: NamedIndividual

Gujarati Indians in Houston, Texas
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: GIH
type: NamedIndividual

Chinese in Metropolitan Denver, Colorado
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: CHD
type: NamedIndividual

March 2006 human reference sequence (NCBI Build 36.1)
type: reference genomic sequence

February 2009 human reference sequence (GRCh37)
type: reference genomic sequence

CEPH (Utah residents with ancestry from northern and western Europe)
type: regionally-defined human population
description: 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.
HapMap population name abbreviation: CEU
type: NamedIndividual

July 2003 human reference sequence (NCBI Build 34)
type: reference genomic sequence

Han Chinese in Beijing, China
type: regionally-defined human population
description: 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.
HapMap population name abbreviation: CHB
type: NamedIndividual

May 2004 human reference sequence (NCBI Build 35)
type: reference genomic sequence

Japanese in Tokyo, Japan
type: regionally-defined human population
description: 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.
HapMap population name abbreviation: JPT
type: NamedIndividual

Yoruba in Ibadan, Nigeria
type: regionally-defined human population
description: 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.
HapMap population name abbreviation: YRI
type: NamedIndividual

Toscani in Italia
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: TSI
type: NamedIndividual

Population with african ancestry in Southwest USA
type: regionally-defined human population
description: The genetic characteristics of this population were described by the HapMap project and are used as a reference for other genetic studies.
HapMap population name abbreviation: ASW
type: NamedIndividual