The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
Ontology for Biomarkers of Clinical Interest
The Ontology for Biomarkers of Clinical Interest is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/obci for details.
Use the Hermit reasoner in Protege to see the correct hierarchy.
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
definition source
Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
A relationship between a biomarker 'b' and its assessed entity 'e', whereby the level of 'e' is--to some statistically significant degree--above the range typically considered normal (for an individual or population of interest).
'Level' here can refer to raw counts, percentages, ratios, concentrations, activities, etc., that can be measured along a continuum scale.
'Range' here can be as small as a single point; that is, a threshold. In such case, being above the range would mean being greater than that threshold value.
A relationship between a biomarker 'b' and its purpose as defined by the BEST classification system.
A relationship between a biomarker 'b' and its evidence type as defined by the CIViC classification system.
A relationship between a biomarker 'b' and its assessed entity 'e', whereby the level of 'e' is--to some statistically significant degree--outside the range typically considered normal (for an individual or population of interest).
'Range' here can be as small as a single point; that is, a threshold. In such case, falling outside the range would mean above or below that threshold.
A relationship between a biomarker 'b' and its assessed entity 'e', whereby the level of 'e' is--to some statistically significant degree--below the range typically considered normal (for an individual or population of interest).
'Range' here can be as small as a single point; that is, a threshold. In such case, being below the range would mean being less than that threshold value.
A relationship between a biomarker 'b' and its assessed entity 'e', whereby 'e' is found to be present in cases where it is typically absent (in an individual or population of interest).
A relationship between a biomarker 'b' and its assessed entity 'e', whereby 'e' is found to be absent in cases where it is typically present (in an individual or population of interest).
A relationship between a biomarker 'b' and an anatomical source 'a', whereby a sample of 'a' is used to determine some quality of an assessed entity 'e'.
A relationship between a biomarker 'b' and its assessed entity 'e', whereby 'e' is found to be either present or absent (as compared to an individual or population of interest).
An "abnormal" condition would be indicated by either the presence of 'e' in cases where it is typically absent, or absence of 'e' in cases where it is typically present. A "normal" condition would be indicated by either the presence of 'e' in cases where it is typically present, or the absence of 'e' in cases where it is typically absent.
A relationship between a biomarker 'b' and its assessed entity 'e', whereby the quantity of 'e' is--to some statistically significant degree--different from the quantity typically considered normal (for an individual or population of interest).
'Quantity' here can refer to (1) raw counts, percentages, ratios, concentrations, activities, etc., that can be measured along a continuum scale; or (2) existence (presence or absence).
A relationship between a biomarker 'b' and its assessed entity 'e', whereby 'e' is--to some statistically significant degree--different in some respect from normal (for an individual or population of interest).
indicated by difference in some aspect of
A relationship between a biomarker 'b' and its assessed entity 'e', whereby the morphology of 'e' is--to some statistically significant degree--different from a morphology considered normal (for an individual or population of interest).
indicated by difference in morphology of
A relationship between a biomarker 'b' and its assessed entity 'e', whereby some quality of 'e' is--to some statistically significant degree--different from the quality typically considered normal (for an individual or population of interest).
A relationship between a biomarker 'b' and an anatomical source 'a', whereby an image of 'a' is used to determine some quality of an assessed entity 'e'.
x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed.
Connects a biological entity to its taxon of origin.
A relationship that holds via some environmental process
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.
evolutionarily related to
c is marker for d iff the presence or occurrence of d is correlated with the presence of occurrence of c, and the observation of c is used to infer the presence or occurrence of d. Note that this does not imply that c and d are in a direct causal relationship, as it may be the case that there is a third entity e that stands in a direct causal relationship with c and d.
A relationship between a ratio or proportion and its dividend.
A relationship between a ratio or proportion and its divisor.
Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
material entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
This atom is closely related to ChEBI's atom, but not exactly equivalent to.
atom
A material entity that consists of two or more atoms that are all connected via covalent bonds such that any atom can be transitively connected with any other atom.
This molecular entity is different than ChEBI's 'molecular entity'.
We would like to have cardinality restrictions on the logic, but there are some technical limitations.
molecule
A complex of two or more molecules that are not covalently bound.
complex of molecules
A disease that involving errors in metabolic processes of building or degradation of molecules.
metabolic disease
disease of metabolism
A disease that is the consequence of the presence of pathogenic microbial agents, including pathogenic viruses, pathogenic bacteria, fungi, protozoa, multicellular parasites, and aberrant proteins known as prions.
infectious disease
disease by infectious agent
A hypothyroidism that is present at birth.
Xref MGI. OMIM mapping confirmed by DO. [SN].
congenital hypothyroidism
A cancer that is classified based on the organ it starts in.
organ system cancer
An amino acid metabolic disorder that is classified by inadequate levels of the enzyme 3-methylcrotonyl-CoA carboxylase that helps break down proteins containing the amino acid leucine. This disease has_symptom muscular hypotonia (weak muscle tone), has_symptom muscular atrophy, has_symptom feeding difficulties, has_symptom recurrent episodes of vomiting and diarrhea, and has_symptom lethargy.
3-Methylcrotonylglycinuria
3MCC deficiency
BMCC deficiency
3-methylcrotonyl-CoA carboxylase deficiency
A tyrosinemia that has_material_basis_in deficiency of the enzyme fumarylacetoacetate hydrolase resulting in an increase in fumarylacetoacetate which inhibits previous steps in tyrosine degradation leading to an accumulation of tyrosine in the body.
hepatorenal tyrosinemia
tyrosinemia type I
An autosomal genetic disease that is characterized by the presence of two mutated copies of the gene, both of which must be present in order for the disease or trait to develop.
autosomal recessive disease
A cerebral creatine deficiency syndrome that is characterized by severe intellectual disability, seizures, speech problems and involuntary movements, has_material_basis_in homozygous or compound heterozygous mutation in the GAMT gene on chromosome 19p13.
Cerebral creatine deficiency syndrome 2
GAMT deficiency
guanidinoacetate methyltransferase deficiency
A steroid inherited metabolic disorder that is characterized by adrenal insufficiency and variable degrees of hyper or hypo androgyny manifestations resulting from steroidogenic enzyme deficiency.
adrenal hyperplasia 1
congenital lipoid adrenal hyperplasia
lipoid CAH
Xref MGI.
congenital adrenal hyperplasia
A disease of anatomical entity that is located_in the thoracic cavity.
thoracic disease
An amino acid metabolic disorder that disrupts normal amino acid metabolism causing a building up of branched-chain amino acids.
organic acid metabolism disorder
organic aciduria
organic acidemia
A methylmalonic acidemia characterized by accumulation of methylmalonic acid in the blood that is unresponsive to vitamn B12 therapy and that has_material_basis_in mutation in the MUT gene on chromosome 6p12.3.
methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency
methylmalonic aciduria mut type
vitamin B12-unresponsive methylmalonic aciduria
methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency
A methylmalonic acidemia characterized by autosomal recessive inheritance, defects in the synthesis of AdoCbl, vitamin B12 therapy responsiveness and that has_material_basis_in homozygous or compound heterozygous mutation in the MMAB gene on chromosome 12q24.
methylmalonic aciduria cblB type
methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB complementation type
methylmalonic acidemia cblB type
An amino acid metabolic disorder characterized by metabolic acidosis without ketonuria, hypoglycemia, and a characteristic pattern of elevated urinary organic acid metabolites, including 3-hydroxy-3-methylglutaric, 3-methylglutaric, and 3-hydroxyisovaleric acids that has_material_basis_in homozygous or compound heterozygous mutation in the HMGCL gene on chromosome 1p36.11.
3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency
HMG-CoA lyase deficiency
HMGCL deficiency
HMGCLD
hydroxymethylglutaric aciduria
HL deficiency
3-hydroxy-3-methylglutaryl-CoA lyase deficiency
A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
congenital disorder
physical disorder
A lipid metabolism disorder that is characterized by deficiency of the enzyme very long chain acyl-CoA dehydrogenase that results in the inability to convert very long chain fatty acids.
VLCAD deficiency
very long chain acyl-CoA dehydrogenase deficiency
A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.
2019 Novel Coronavirus (2019-nCoV)
2019-nCoV infection
COVID19
SARS-CoV-2 infection
Wuhan coronavirus infection
Wuhan seafood market pneumonia virus infection
COVID-19
An organic acidemia characterized by impaired lysine, hydroxylysine, and tryptophan metabolism, increased urinary excretion of glutaric acid, and accumulation of 3-hydroxyglutaric and glutaric acid, resulting in striatal injury and a severe dystonic dyskinetic movement disorder that has_material_basis_in homozygous or compound heterozygous mutation in the GCDH gene on chromosome 19p13.
GA1
glutaric academia type 1
glutaric aciduria 1
glutaric aciduria type I
glutaryl-coA dehydrogenase deficiency
glutaryl-coenzyme A dehydrogenase deficiency
glutaric acidemia I
A parasitic protozoa infectious disease characterized as a vector-borne infectious disease caused by the presence of protozoan parasites of the genus Plasmodium in the red blood cells, transmitted from an infected to an uninfected individual by the bite of anopheline mosquitoes, and characterized by periodic attacks of chills and fever that coincide with mass destruction of blood cells and the release of toxic substances by the parasite at the end of each reproductive cycle.
induced malaria
malaria
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
disease of subdivision of hemolymphoid system
cardiovascular system disease
A respiratory system cancer that is located_in the lung.
lung neoplasm
lung cancer
A disease that is characterized by abnormally rapid cell division.
cell process disease
neoplasm
disease of cellular proliferation
An organic acidemia that involes a nonfunctional propionyl CoA carboxylase affecting conversion of amino acids and fats into sugar for energy.
GLYCINEMIA, KETOTIC
KETOTIC HYPERGLYCINEMIA
ketotic II glycinemia
ketotic glycinemia
propionic aciduria
propionyl-CoA carboxylase deficiency
OMIM mapping confirmed by DO. [SN].
propionic acidemia
An amino acid metabolic disorder characterized by inability to process isoleucine and ketones, has_symptom recurrent ketoacidotic attacks in infancy marked by vomiting, lethargy, dehydration, and seizures, and has_material_basis_in mutation in the ACAT1 gene of chromosome 11q22.3 responsible for producing the ACAT1 enzyme in mitochondria, which processes isoleucine and ketones.
2-methyl-3-hydroxybutyricacidemia
3-ketothiolase deficiency
3-oxothiolase deficiency
Mitochondrial acetoacetyl-CoA Thiolase deficiency
alpha-methylacetoaceticaciduria
peroxisomal thiolase deficiency
beta-ketothiolase deficiency
An organic acidemia that involves an accumulation of methylmalonic acid in the blood.
methylmalonic aciduria
methylmalonic acidemia
An organic acidemia that disrupts or prevents normal metabolism of the branched-chain amino acid leucine.
Isovaleryl-CoA dehydrogenase deficiency
isovaleric acid CoA dehydrogenase deficiency
isovaleric aciduria
isovaleric acidemia
An amino acid metabolic disorder that involves the accumulation of argininosuccinic acid (ASA) in the blood and urine.
Argininosuccinate lyase deficiency
argininosuccinic acidemia
arginosuccinase deficiency
deficiency of argininosuccinate lyase
argininosuccinic aciduria
A disease of anatomical entity that is located_in reproductive system organs.
genital system disease
reproductive system disease
A disease of mental health that affects cognitive functions including memory processing, perception and problem solving.
cognitive disease
Organic Mental disorder
cognitive disorder
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
respiratory system disease
A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
integumentary system disease
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
malignant neoplasm
malignant tumor
primary cancer
Updating out dated UMLS CUI.
cancer
A disease of anatomical entity that occurs in the muscular and/or skeletal system.
musculoskeletal system disease
A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
Non-neoplastic urinary tract disease
urinary tract disease
urinary system disease
A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
female reproductive system disease
A female reproductive organ cancer that is located_in the ovary.
malignant Ovarian tumor
malignant tumour of ovary
ovarian neoplasm
ovary neoplasm
primary ovarian cancer
tumor of the Ovary
ovarian cancer
A disease of anatomical entity that is located_in endocrine glands which secretes a type of hormone directly into the bloodstream to regulate the body.
endocrine system disease
A disease of anatomical entity that is located_in the immune system.
immune system disease
A tuberculosis that is a contagious disease located_in lungs. The infection has_symptom fever, has_symptom cough, has_symptom difficulty in breathing, has_symptom inflammatory infiltrations, has_symptom formation of tubercles, has_symptom caseation, has_symptom pleural effusion, and has_symptom fibrosis.
pulmonary tuberculosis
An inherited metabolic disorder that involves the creation and degradation of lipids.
dyslipidemia
fatty acid metabolism disorder
lipid metabolism disorder
A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
disease
A viral infectious disease that results in destruction of immune system, leading to life-threatening opportunistic infections and cancers, has_material_basis_in Human immunodeficiency virus 1 or has_material_basis_in Human immunodeficiency virus 2, which are transmitted by sexual contact, transmitted by transfer of blood, semen, vaginal fluid, pre-ejaculate, or breast milk, transmitted by congenital method, and transmitted by contaminated needles. The virus infects helper T cells (CD4+ T cells) which are directly or indirectly destroyed, macrophages, and dendritic cells. The infection has symptom diarrhea, has symptom fatigue, has symptom fever, has symptom vaginal yeast infection, has symptom headache, has symptom mouth sores, has symptom muscle aches, has symptom sore throat, and has symptom swollen lymph glands.
HIV infection
human immunodeficiency virus infectious disease
A disease that has_material_basis_in genetic variations in the human genome.
genetic disease
A disease of metabolism that is characterized by enzyme deficiency or accumulation of enzymes or toxins which interfere with normal function due to inherited enzyme abnormality.
Inborn Errors of Metabolism
Metabolic hereditary disorder
inborn metabolism disorder
inherited metabolic disorder
A disease that manifests in a defined anatomical structure.
disease of anatomical entity
An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
Arthritis or polyarthritis, rheumatic
atrophic Arthritis
rheumatoid arthritis
A disease of anatomical entity that has_material_basis_in hematopoietic cells.
Blood disease
Blood dyscrasia
DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
Hematological disease
blood disorder
disease of haematopoietic system
disease of hematopoietic system
haematopoietic system disease
hematopoietic system disease
A disease of anatomical entity that is located_in the gastrointestinal tract.
GIT disease
Gastroenteropathy
alimentary system disease
digestive system disorder
gastrointestinal disease
gastrointestinal disorder
gastrointestinal system disease
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
Updating out dated CUI and removing lung abscess as a synonym.
lung disease
A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
nervous system disease
An inherited metabolic disorder that is characterized by impaired synthesis and degradation of amino acids.
inborn errors of amino acid metabolism
amino acid metabolic disorder
A large intestine cancer that is located_in the colon and/or located_in the rectum.
colorectal cancer
An amino acid metabolic disorder that involves an accumulation of homocysteine in the serum and an increased excretion of homocysteine in the urine.
CBS deficiency
cystathionine beta synthase deficiency
cystathionine synthase deficiency
homocystinuria
An organic acidemia that is caused by a deficiency of decarboxylase leading to high concentrations of valine, leucine, isoleucine, and alloisoleucine in the blood, urine, and cerebrospinal fluid and characterized by an odor of maple syrup to the urine, vomiting, hypertonicity, severe mental retardation, seizures, and eventually death unless the condition is treated with dietary measures.
Ketoacidaemia
branched chain ketoaciduria
dihydrolipoamide dehydrogenase deficiency
maple syrup urine disease
An amino acid metabolic disorder that is characterized by a mutation in the gene for the hepatic enzyme phenylalanine hydroxylase (PAH), rendering it nonfunctional.
Folling's disease
PKU
maternal phenylketonuria
phenylalaninemia
phenylketonuria
A disease by infectious agent that results in infection, has_material_basis_in Viruses.
Viral Infection
Viral disease
virus infection
viral infectious disease
An interaction between an exposure stressor and an exposure_receptor.
A compound consisting of monosaccharides linked by glycosidic bonds.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
Any kind of illness or circumstance which requires medical monitoring.
The air that moves out of the chest during expiration. It contains a higher percentage of carbon dioxide and a lower percentage of oxygen compared to the inhaled air.
The air that moves out of the chest during expiration. It contains a higher percentage of carbon dioxide and a lower percentage of oxygen compared to the inhaled air. (NCI)
A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or biological responses to an exposure or intervention, including therapeutic interventions.
Biomarkers require comparison between characteristics of interest obtained in test cases vs those in normal cases. What is considered 'normal' will depend on the biomarker; in some cases the comparison will be to a population average, in others it will be to an individual's known healthy state.
We make a distinction between 'biomarker' and 'biomarker assessed entity'. The former derives from result of measurement or observation of the latter. For example, in and of itself, 'blood sugar' is not considered a biomarker in our treatment, but 'elevated blood sugar' is. Another example is BRCA1; despite appearing on lists of cancer-implicated genes, BRCA1 is _not_ a biomarker of cancer in our treatment. However, the presence of a particular allele of BRCA1 can be a biomarker, or BRCA1 over-expression can be a biomarker.
Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. A biomarker is not an assessment of how an individual feels, functions, or survives.
A biomarker that is used to detect or confirm the presence of a disease or condition of interest or to identify individuals with a subtype of the disease.
For a perfect diagnostic biomarker test, all patients with the disease or disease subset would be detected (100% sensitivity, i.e., the fraction of people with disease who test positive) and no patients without the disease would be diagnosed with the disease (100% specificity, i.e., the fraction of people without the disease who test negative). In practice no biomarker test has perfect clinical and analytical sensitivity and specificity. [NCBI:books/NBK402285]
Per CIVic, such biomarkers can help a clinician diagnose or exclude a particular disease.
A biomarker that is measured serially to assess the status of a disease or medical condition, or for evidence of exposure to (or effect of) a medical product or an environmental agent.
A biomarker that is used to show that a biological response has occurred in an individual who has been exposed to a medical product or an environmental agent.
A biomarker that is used to identify individuals who are more likely than similar individuals without the biomarker to experience a favorable or unfavorable effect from exposure to a medical product or an environmental agent.
Per CIVic, such biomarkers help predict drug sensitivity or therapeutic response and are valuable in deciding further treatments. Predictive evidence items often explain mechanisms of drug resistance.
A biomarker that is used to identify the likelihood of a clinical event, disease recurrence or progression in patients who have the disease or medical condition of interest.
Per CIVic, such biomarkers are those that predict survival outcome.
A biomarker that is used to indicate the likelihood, presence, or extent of toxicity as an adverse effect. Such biomarkers are measured before and after exposure to a medical product or an environmental agent.
A biomarker that is used to indicate the potential for developing a disease or medical condition in an individual who does not currently have clinically apparent disease or the medical condition.
Per CIVic, such biomarkers are those that indicate an increased likelihood of developing a particular disease.
A biomarker that provides clinical information about a disease.
A biomarker that provides clinical information about COVID-19.
A biomarker that provides clinical information about cancer.
A biomarker that indicates the clinical effect of or response to exposure to a substance.
A biomarker that is assessed using urine as the anatomical source.
A biomarker that is assessed using blood plasma as the anatomical source.
A biomarker that provides clinical information about some current or potential medical condition.
A biomarker that has an indicated BEST category.
A biomarker that has an indicated assessed entity.
biomarker with specified assessed entity
A biomarker that has an indicated clinical focus.
A biomarker that has an indicated anatomical source.
biomarker with specified anatomical source
A biomarker in which the assessed entity is a physiological characteristic.
This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
A biomarker in which the assessed entity is a cell.
A biomarker in which the assessed entity is a sequence variation.
Sequence variations of genetic material can be assessed via direct sequencing or can be inferred from protein (for example, by using sequence-specific antibodies).
A biomarker in which the assessed entity is a glycan variation.
A biomarker in which the assessed entity is a glycan.
A biomarker in which the assessed entity is a small molecule.
A biomarker in which the assessed entity is an RNA.
This class is specifically for cases where the assessed entity pertains to RNA as a biochemical; that is, without regard to sequence. Sequence-based biomarkers are classed under sequence variation biomarker (OBCI:000000022).
A biomarker that is assessed using exhaled breath as the anatomical source.
A biomarker that is assessed using blood as the anatomical source.
A biomarker in which the assessed entity is a protein-containing molecular entity.
A biomarker in which the assessed entity is a molecular entity.
A biomarker that is measured serially to assess the status of a disease or medical condition.
monitoring biomarker - clinical condition
A biomarker that is measured serially to assess exposure to (or effect of) a medical product or an environmental agent.
monitoring biomarker - exposure
A biomarker that is assessed using cerebrospinal fluid as the anatomical source.
A biomarker that provides clinical information about some respiratory system disease.
A biomarker that provides clinical information about some cognitive disorder.
A biomarker that provides clinical information about some disease by infectious agent.
biomarker of disease by infectious agent
A biomarker that provides clinical information about some disease of anatomical entity.
biomarker of disease of anatomical entity
A biomarker that provides clinical information about some cardiovascular system disease.
biomarker of cardiovascular system disease
A biomarker that provides clinical information about some endocrine system disease.
A biomarker that provides clinical information about some gastrointestinal system disease.
biomarker of gastrointestinal system disease
A biomarker that provides clinical information about some hematopoietic system disease.
biomarker of hematopoietic system disease
A biomarker that provides clinical information about some immune system disease.
A biomarker that provides clinical information about some integumentary system disease.
biomarker of integumentary system disease
A biomarker that provides clinical information about some musculoskeletal system disease.
biomarker of musculoskeletal system disease
A biomarker that provides clinical information about some nervous system disease.
A biomarker that provides clinical information about some reproductive system disease.
biomarker of reproductive system disease
A biomarker that provides clinical information about some thoracic disease.
A biomarker that provides clinical information about some urinary system disease.
A biomarker that provides clinical information about some disease of cellular proliferation.
biomarker of disease of cellular proliferation
A biomarker that provides clinical information about some disease of metabolism.
A biomarker that provides clinical information about some genetic disease.
A biomarker that is assessed using saliva as the anatomical source.
A biomarker in which the assessed entity is some DNA.
This class is specifically for cases where the assessed entity pertains to DNA as a biochemical; that is, without regard to sequence. Sequence-based biomarkers are classed under sequence variation biomarker (OBCI:000000022).
A defined characteristic or set of characteristics derived from two or more data sources evaluated through an algorithm as an indicator of normal biological processes, pathogenic processes or responses to an exposure or intervention, including therapeutic interventions and environmental exposures.
A biomarker that is assessed using blood serum as the anatomical source.
A biomarker in which the assessed entity is a vocal characteristic.
A biomarker in which the assessed entity is blood pressure.
A biomarker in which the assessed entity is some bodily movement.
A biomarker in which the assessed entity is some manner of walking.
A biomarker in which the assessed entity is an ocular characteristic.
A biomarker in which the assessed entity is cellular morphology.
A biomarker in which the assessed entity is an image.
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
The number of entities of this type that are part of the whole organism.
This term was originally named "presence". It has been renamed to reduce ambiguity. Consider annotating with the reciprocal relation,PATO:0001555, has_number_of. For example, rather than E=fin ray Q=count in organism C=10, say E=organism Q=has number of E2= fin ray C=10.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB).
A sequence variant that is segregating in one or more natural populations of a species.
Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006)
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
Excretion that is the output of a kidney.
kidney excreta from some taxa (e.g. in aves) may not be liquid
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
EHDAA2 models this as developing from CP, which is wrong
the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
The liquid component of blood, in which erythrocytes are suspended.
The portion of blood plasma that excludes clotting factors.
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
An object property that represents a relation between a molecular variant and a gene or protein where the variant derives from the gene or protein
variant of
A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity.
Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
has component
causally related to
relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause.
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.