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