Ontology for Biomarkers of Clinical Interest
type: Ontology
description: The Ontology for Biomarkers of Clinical Interest (OBCI) formally defines biomarkers for diseases, phenotypes, and effects.
license: http://creativecommons.org/licenses/by/4.0/
default-namespace: biomarker
saved-by: https://github.com/nataled
comment: The Ontology for Biomarkers of Clinical Interest is licensed under CC BY 4.0. Please see http://obofoundry.org/ontology/obci for details.
comment: Use the Hermit reasoner in Protege to see the correct hierarchy.
version info: 2025-11-24

editor preferred term
type: AnnotationProperty
editor preferred term: editor preferred term
has curation status: IAO_0000122
definition: The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has curation status
type: AnnotationProperty
editor preferred term: has curation status
term editor: PERSON:Alan Ruttenberg
term editor: PERSON:Bill Bug
term editor: PERSON:Melanie Courtot

definition
type: AnnotationProperty

editor note
type: AnnotationProperty
editor preferred term: editor note
has curation status: IAO_0000122
definition: 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: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>

term editor
type: AnnotationProperty
editor preferred term: term editor
has curation status: IAO_0000122
definition: 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
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
term editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

definition source
type: AnnotationProperty
editor preferred term: definition source
has curation status: IAO_0000122
definition: 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
term editor: PERSON:Daniel Schober
definition source: Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

has_alternative_id
type: AnnotationProperty

has_broad_synonym
type: AnnotationProperty

database_cross_reference
type: AnnotationProperty

has_exact_synonym
type: AnnotationProperty

has_narrow_synonym
type: AnnotationProperty

has_obo_namespace
type: AnnotationProperty

has_related_synonym
type: AnnotationProperty

has_synonym_type
type: AnnotationProperty

in_subset
type: AnnotationProperty

shorthand
type: AnnotationProperty

has part
type: ObjectProperty
editor preferred term: has part
IAO_0000112: my body has part my brain (continuant parthood, two material entities)
IAO_0000112: my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
IAO_0000112: this year has part this day (occurrent parthood)
definition: a core relation that holds between a whole and its part
editor note: 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.
editor note: 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/
editor note: 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'.
IAO_0000118: has_part
RO_0001900: RO_0001901
in_subset: valid for go annotation extension
in_subset: valid for go ontology
in_subset: valid for gocam

indicated by above normal level of
type: ObjectProperty
sub property of: indicated by difference in level of
definition: 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).
editor note: 'Level' here can refer to raw counts, percentages, ratios, concentrations, activities, etc., that can be measured along a continuum scale.
editor note: '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.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000009
has_obo_namespace: biomarker
id: indicated_by_above_normal_level_of
shorthand: indicated_by_above_normal_level_of

Axiom
annotated source: indicated by above normal level of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

has BEST classification
type: ObjectProperty
definition: A relationship between a biomarker 'b' and its purpose as defined by the BEST classification system.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000011
has_obo_namespace: biomarker
id: has_BEST_classification
shorthand: has_BEST_classification

Axiom
annotated source: has BEST classification
annotated property: definition
annotated target: A relationship between a biomarker 'b' and its purpose as defined by the BEST classification system.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

has CIViC classification
type: ObjectProperty
definition: A relationship between a biomarker 'b' and its evidence type as defined by the CIViC classification system.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000012
has_obo_namespace: biomarker
id: has_CIViC_classification
shorthand: has_CIViC_classification

Axiom
annotated source: has CIViC classification
annotated property: definition
annotated target: A relationship between a biomarker 'b' and its evidence type as defined by the CIViC classification system.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in level of
type: ObjectProperty
sub property of: indicated by difference in quantity of
definition: 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).
editor note: 'Level' here can refer to raw counts, percentages, ratios, concentrations, activities, etc., that can be measured along a continuum scale.
editor note: '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.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000014
has_obo_namespace: biomarker
id: indicated_by_difference_in_level_of
shorthand: indicated_by_difference_in_level_of

Axiom
annotated source: indicated by difference in level of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by below normal level of
type: ObjectProperty
sub property of: indicated by difference in level of
definition: 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).
editor note: 'Level' here can refer to raw counts, percentages, ratios, concentrations, activities, etc., that can be measured along a continuum scale.
editor note: '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.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000015
has_obo_namespace: biomarker
id: indicated_by_below_normal_level_of
shorthand: indicated_by_below_normal_level_of

Axiom
annotated source: indicated by below normal level of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by presence of
type: ObjectProperty
sub property of: indicated by difference in presence of
definition: 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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000016
has_obo_namespace: biomarker
id: indicated_by_presence_of
shorthand: indicated_by_presence_of

Axiom
annotated source: indicated by presence of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by absence of
type: ObjectProperty
sub property of: indicated by difference in presence of
definition: 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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000017
has_obo_namespace: biomarker
id: indicated_by_absence_of
shorthand: indicated_by_absence_of

Axiom
annotated source: indicated by absence of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

determined using sample from
type: ObjectProperty
definition: 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'.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000018
has_obo_namespace: biomarker
id: determined_using_sample_from
shorthand: determined_using_sample_from

Axiom
annotated source: determined using sample from
annotated property: definition
annotated target: 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'.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in presence of
type: ObjectProperty
sub property of: indicated by difference in quantity of
definition: 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).
editor note: 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.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000019
has_obo_namespace: biomarker
id: indicated_by_difference_in_presence_of
shorthand: indicated_by_difference_in_presence_of

Axiom
annotated source: indicated by difference in presence of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in quantity of
type: ObjectProperty
sub property of: indicated by difference in some aspect of
definition: 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).
editor note: '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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000020
has_obo_namespace: biomarker
id: indicated_by_difference_in_quantity_of
shorthand: indicated_by_difference_in_quantity_of

Axiom
annotated source: indicated by difference in quantity of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in some aspect of
type: ObjectProperty
definition: 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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000021
has_obo_namespace: biomarker
id: indicated_by_difference_in_some_aspect_of
shorthand: indicated_by_difference_in_some_aspect_of

Axiom
annotated source: indicated by difference in some aspect of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in morphology of
type: ObjectProperty
sub property of: indicated by difference in quality of
definition: 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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000022
has_obo_namespace: biomarker
id: indicated_by_difference_in_morphology_of
shorthand: indicated_by_difference_in_morphology_of

Axiom
annotated source: indicated by difference in morphology of
annotated property: definition
annotated target: 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).
database_cross_reference: https://orcid.org/0000-0001-5809-9523

indicated by difference in quality of
type: ObjectProperty
sub property of: indicated by difference in some aspect of
definition: 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).
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000020
has_obo_namespace: biomarker
id: indicated_by_difference_in_quality_of
shorthand: indicated_by_difference_in_quality_of

determined using image of
type: ObjectProperty
definition: 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'.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: OBCI:100000024
has_obo_namespace: biomarker
id: determined_using_image_of
shorthand: determined_using_image_of

Axiom
annotated source: determined using image of
annotated property: definition
annotated target: 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'.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

in taxon
type: ObjectProperty
sub property of: evolutionarily related to
has curation status: IAO_0000125
definition: 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.
term editor: 0000-0001-9227-417X
term editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/17921072
definition source: http://www.ncbi.nlm.nih.gov/pubmed/20973947
in_subset: ro-eco
comment: Connects a biological entity to its taxon of origin.

evolutionarily related to
type: ObjectProperty
sub property of: topObjectProperty
definition: A relationship that holds via some environmental process
term editor: https://orcid.org/0000-0002-6601-2165
IAO_0000232: Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution.

is marker for
type: ObjectProperty
definition: 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.
editor note: May be ceded to OBI

has numerator
type: ObjectProperty
sub property of: has part
definition: A relationship between a ratio or proportion and its dividend.
contributor: https://orcid.org/0000-0001-8314-2140
has_exact_synonym: has dividend

has denominator
type: ObjectProperty
sub property of: has part
definition: A relationship between a ratio or proportion and its divisor.
contributor: https://orcid.org/0000-0001-8314-2140
has_exact_synonym: has divisor

material entity
type: Class
editor note: Elucidation: An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.

molecular entity
type: Class
subclass of: chemical entity
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
has_exact_synonym: molecular entity
has_obo_namespace: chebi_ontology
has_related_synonym: entidad molecular
has_related_synonym: entidades moleculares
has_related_synonym: entite moleculaire
has_related_synonym: molecular entities
has_related_synonym: molekulare Entitaet
id: CHEBI:23367
in_subset: 3 STAR

Axiom
annotated source: molecular entity
annotated property: has_exact_synonym
annotated target: molecular entity
database_cross_reference: IUPAC
has_synonym_type: IUPAC NAME

Axiom
annotated source: molecular entity
annotated property: has_related_synonym
annotated target: entidad molecular
database_cross_reference: IUPAC

Axiom
annotated source: molecular entity
annotated property: has_related_synonym
annotated target: entidades moleculares
database_cross_reference: IUPAC

Axiom
annotated source: molecular entity
annotated property: has_related_synonym
annotated target: entite moleculaire
database_cross_reference: IUPAC

Axiom
annotated source: molecular entity
annotated property: has_related_synonym
annotated target: molecular entities
database_cross_reference: IUPAC

Axiom
annotated source: molecular entity
annotated property: has_related_synonym
annotated target: molekulare Entitaet
database_cross_reference: ChEBI

chemical entity
type: Class
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
has_exact_synonym: chemical entity
has_obo_namespace: chebi_ontology
id: CHEBI:24431
in_subset: 3 STAR

Axiom
annotated source: chemical entity
annotated property: has_exact_synonym
annotated target: chemical entity
database_cross_reference: UniProt

cell
type: Class
definition: 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.
database_cross_reference: CALOHA:TS-2035
database_cross_reference: FBbt:00007002
database_cross_reference: FMA:68646
database_cross_reference: GO:0005623
database_cross_reference: KUPO:0000002
database_cross_reference: MESH:D002477
database_cross_reference: VHOG:0001533
database_cross_reference: WBbt:0004017
database_cross_reference: XAO:0003012
database_cross_reference: ZFA:0009000
in_subset: cellxgene subset
in_subset: upper level
comment: 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).

Axiom
annotated source: cell
annotated property: definition
annotated target: 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.
database_cross_reference: CARO:mah

atom
type: Class
subclass of: material entity
disjoint with: molecule
definition: A material entity consisting of exactly one atomic nucleus and the electron(s) orbiting it.
editor note: This atom is closely related to ChEBI's atom, but not exactly equivalent to.

molecule
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: atom
definition: 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.
editor note: This molecular entity is different than ChEBI's 'molecular entity'.
editor note: We would like to have cardinality restrictions on the logic, but there are some technical limitations.

complex of molecules
type: Class
subclass of: material entity
subclass of: Restriction
  on property: has part
  some values from: molecule
definition: A complex of two or more molecules that are not covalently bound.

disease of metabolism
type: Class
subclass of: disease
definition: A disease that involving errors in metabolic processes of building or degradation of molecules.
database_cross_reference: ICD10CM:E88.9
database_cross_reference: ICD9CM:277.9
database_cross_reference: MESH:D008659
database_cross_reference: NCI:C3235
database_cross_reference: SNOMEDCT_US_2023_03_01:75934005
database_cross_reference: UMLS_CUI:C0025517
has_exact_synonym: metabolic disease
has_obo_namespace: disease_ontology
id: DOID:0014667
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: NCIthesaurus

Axiom
annotated source: disease of metabolism
annotated property: definition
annotated target: A disease that involving errors in metabolic processes of building or degradation of molecules.
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/books/NBK22259/

disease by infectious agent
type: Class
subclass of: disease
definition: 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.
OBI_9991118: infectious disease
has_alternative_id: DOID:10115
has_alternative_id: DOID:11078
has_alternative_id: DOID:1304
has_alternative_id: DOID:1321
has_alternative_id: DOID:2040
has_alternative_id: DOID:2288
has_alternative_id: DOID:3099
has_alternative_id: DOID:4120
has_alternative_id: DOID:4620
has_alternative_id: DOID:5256
has_alternative_id: DOID:945
has_alternative_id: DOID:95
has_alternative_id: DOID:9532
has_alternative_id: DOID:9696
database_cross_reference: ICD9CM:079.0
database_cross_reference: UMLS_CUI:C0001485
has_exact_synonym: infectious disease
has_obo_namespace: disease_ontology
id: DOID:0050117
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: DO infectious disease slim
comment: DO:wk

Axiom
annotated source: disease by infectious agent
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=14.10d&code=C26726

congenital hypothyroidism
type: Class
subclass of: physical disorder
subclass of: endocrine system disease
subclass of: disease
definition: A hypothyroidism that is present at birth.
has_alternative_id: DOID:11631
has_alternative_id: DOID:11632
database_cross_reference: GARD:1487
database_cross_reference: ICD10CM:E00.1
database_cross_reference: ICD10CM:E03.1
database_cross_reference: ICD9CM:243
database_cross_reference: MESH:D003409
database_cross_reference: MIM:PS275200
database_cross_reference: NCI:C26734
database_cross_reference: NCI:C98921
database_cross_reference: SNOMEDCT_US_2023_03_01:217710005
database_cross_reference: SNOMEDCT_US_2023_03_01:75065003
database_cross_reference: UMLS_CUI:C0010308
database_cross_reference: UMLS_CUI:C0342200
has_obo_namespace: disease_ontology
id: DOID:0050328
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: congenital hypothyroidism
annotated property: definition
annotated target: A hypothyroidism that is present at birth.
database_cross_reference: url:http://en.wikipedia.org/wiki/Congenital_hypothyroidism
database_cross_reference: url:http://ghr.nlm.nih.gov/condition/congenital-hypothyroidism

organ system cancer
type: Class
subclass of: cancer
definition: A cancer that is classified based on the organ it starts in.
created by: snadendla
creation date: 2011-06-13T03:28:33Z
database_cross_reference: MESH:D009371
has_obo_namespace: disease_ontology
id: DOID:0050686

Axiom
annotated source: organ system cancer
annotated property: definition
annotated target: A cancer that is classified based on the organ it starts in.
database_cross_reference: url:https://www.cancer.gov/types/by-body-location

3-methylcrotonyl-CoA carboxylase deficiency
type: Class
subclass of: autosomal recessive disease
subclass of: musculoskeletal system disease
subclass of: disease
subclass of: amino acid metabolic disorder
definition: 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.
created by: lschriml
creation date: 2012-05-22T10:32:44Z
database_cross_reference: GARD:10954
database_cross_reference: MIM:PS210200
database_cross_reference: ORDO:6
has_exact_synonym: 3-Methylcrotonylglycinuria
has_exact_synonym: 3MCC deficiency
has_exact_synonym: BMCC deficiency
has_obo_namespace: disease_ontology
id: DOID:0050710
in_subset: DO rare slim

Axiom
annotated source: 3-methylcrotonyl-CoA carboxylase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/3-Methylcrotonyl-CoA_carboxylase_deficiency
database_cross_reference: url:http://omim.org/entry/210200

tyrosinemia type I
type: Class
subclass of: amino acid metabolic disorder
definition: 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.
created by: lschriml
creation date: 2012-07-06T02:55:45Z
database_cross_reference: MIM:276700
has_exact_synonym: hepatorenal tyrosinemia
has_obo_namespace: disease_ontology
id: DOID:0050726

Axiom
annotated source: tyrosinemia type I
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/Type_I_tyrosinemia

autosomal recessive disease
type: Class
subclass of: disease
subclass of: genetic disease
definition: 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.
created by: lschriml
creation date: 2012-07-24T12:51:47Z
has_obo_namespace: disease_ontology
id: DOID:0050737

Axiom
annotated source: autosomal recessive disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://ghr.nlm.nih.gov/handbook/inheritance/inheritancepatterns
database_cross_reference: url:http://www.nlm.nih.gov/medlineplus/ency/article/002052.htm

guanidinoacetate methyltransferase deficiency
type: Class
subclass of: amino acid metabolic disorder
definition: 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.
created by: lschriml
creation date: 2013-11-21T12:10:58Z
database_cross_reference: GARD:2578
database_cross_reference: MESH:C537622
database_cross_reference: MIM:612736
has_exact_synonym: Cerebral creatine deficiency syndrome 2
has_exact_synonym: GAMT deficiency
has_obo_namespace: disease_ontology
id: DOID:0050799
in_subset: DO rare slim

Axiom
annotated source: guanidinoacetate methyltransferase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://rarediseases.info.nih.gov/diseases/2578/guanidinoacetate-methyltransferase-deficiency

congenital adrenal hyperplasia
type: Class
subclass of: physical disorder
subclass of: lipid metabolism disorder
definition: 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.
created by: lschriml
creation date: 2013-12-04T12:52:02Z
database_cross_reference: GARD:1465
database_cross_reference: GARD:1467
database_cross_reference: ICD10CM:E25
database_cross_reference: ICD9CM:255.2
database_cross_reference: MIM:201710
database_cross_reference: MIM:201810
database_cross_reference: MIM:201910
database_cross_reference: MIM:202010
database_cross_reference: MIM:202110
database_cross_reference: ORDO:418
database_cross_reference: SNOMEDCT_US_2023_03_01:154706003
database_cross_reference: UMLS_CUI:C0701163
has_exact_synonym: adrenal hyperplasia 1
has_exact_synonym: congenital lipoid adrenal hyperplasia
has_exact_synonym: lipoid CAH
has_obo_namespace: disease_ontology
id: DOID:0050811
in_subset: DO rare slim
comment: Xref MGI.

Axiom
annotated source: congenital adrenal hyperplasia
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://omim.org/entry/201710
database_cross_reference: url:http://www.genome.jp/dbget-bin/www_bget?ds:H00216
database_cross_reference: url:http://www.orpha.net/consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=418.0

thoracic disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the thoracic cavity.
created by: lschriml
creation date: 2011-07-25T02:23:47Z
has_obo_namespace: disease_ontology
id: DOID:0060118
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim

Axiom
annotated source: thoracic disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the thoracic cavity.
database_cross_reference: url:http://en.wikipedia.org/wiki/Thoracic_cavity

organic acidemia
type: Class
subclass of: amino acid metabolic disorder
definition: An amino acid metabolic disorder that disrupts normal amino acid metabolism causing a building up of branched-chain amino acids.
created by: lschriml
creation date: 2011-08-26T11:17:14Z
database_cross_reference: GARD:9433
has_exact_synonym: organic acid metabolism disorder
has_exact_synonym: organic aciduria
has_obo_namespace: disease_ontology
id: DOID:0060159
in_subset: DO rare slim

Axiom
annotated source: organic acidemia
annotated property: definition
annotated target: An amino acid metabolic disorder that disrupts normal amino acid metabolism causing a building up of branched-chain amino acids.
database_cross_reference: url:http://en.wikipedia.org/wiki/Aciduria

methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency
type: Class
subclass of: methylmalonic acidemia
definition: 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.
database_cross_reference: ICD10CM:E71.1
database_cross_reference: MESH:C565390
database_cross_reference: MIM:251000
database_cross_reference: ORDO:27
has_exact_synonym: methylmalonic acidemia due to methylmalonyl-CoA mutase deficiency
has_exact_synonym: methylmalonic aciduria mut type
has_exact_synonym: vitamin B12-unresponsive methylmalonic aciduria
has_obo_namespace: disease_ontology
id: DOID:0060740
in_subset: DO rare slim

Axiom
annotated source: methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/1975493
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/1977311

methylmalonic acidemia cblB type
type: Class
subclass of: methylmalonic acidemia
definition: 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.
database_cross_reference: ICD10CM:E71.1
database_cross_reference: MIM:251110
database_cross_reference: ORDO:79311
has_exact_synonym: methylmalonic aciduria cblB type
has_exact_synonym: methylmalonic aciduria, vitamin B12-responsive, due to defect in synthesis of adenosylcobalamin, cblB complementation type
has_obo_namespace: disease_ontology
id: DOID:0060743
in_subset: DO rare slim

Axiom
annotated source: methylmalonic acidemia cblB type
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/12471062
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/7213387

3-hydroxy-3-methylglutaryl-CoA lyase deficiency
type: Class
subclass of: autosomal recessive disease
subclass of: amino acid metabolic disorder
definition: 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.
database_cross_reference: GARD:8387
database_cross_reference: MESH:C538324
database_cross_reference: MIM:246450
database_cross_reference: NCI:C84523
database_cross_reference: ORDO:20
database_cross_reference: UMLS_CUI:C0268601
has_exact_synonym: 3-hydroxy-3-methylglutaryl-coenzyme A lyase deficiency
has_exact_synonym: HMG-CoA lyase deficiency
has_exact_synonym: HMGCL deficiency
has_exact_synonym: HMGCLD
has_exact_synonym: hydroxymethylglutaric aciduria
has_obo_namespace: disease_ontology
has_related_synonym: HL deficiency
id: DOID:0070541

Axiom
annotated source: 3-hydroxy-3-methylglutaryl-CoA lyase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://pubmed.ncbi.nlm.nih.gov/3128690/

Axiom
annotated source: 3-hydroxy-3-methylglutaryl-CoA lyase deficiency
annotated property: has_exact_synonym
annotated target: HMGCLD
has_synonym_type: OMO_0003012

physical disorder
type: Class
subclass of: disease
definition: A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
has_exact_synonym: congenital disorder
has_obo_namespace: disease_ontology
id: DOID:0080015
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim

Axiom
annotated source: physical disorder
annotated property: definition
annotated target: A disease that has_material_basis_in a genetic abnormality, error with embryonic development, infection or compromised intrauterine environment.
database_cross_reference: url:http://en.wikipedia.org/wiki/Congenital_disorder

very long chain acyl-CoA dehydrogenase deficiency
type: Class
subclass of: lipid metabolism disorder
definition: 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.
database_cross_reference: GARD:5508
database_cross_reference: MIM:201475
database_cross_reference: ORDO:26793
has_exact_synonym: VLCAD deficiency
has_obo_namespace: disease_ontology
id: DOID:0080155
in_subset: DO rare slim

Axiom
annotated source: very long chain acyl-CoA dehydrogenase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://rarediseases.org/rare-diseases/very-long-chain-acyl-coa-dehydrogenase-deficiency-lcad/
database_cross_reference: url:https://ghr.nlm.nih.gov/condition/very-long-chain-acyl-coa-dehydrogenase-deficiency

COVID-19
type: Class
subclass of: viral infectious disease
definition: A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.
database_cross_reference: ICD10CM:U07.1
database_cross_reference: MESH:D000086382
database_cross_reference: NCI:C171133
database_cross_reference: SNOMEDCT_US_2023_03_01:840539006
database_cross_reference: UMLS_CUI:C5203670
has_exact_synonym: 2019 Novel Coronavirus (2019-nCoV)
has_exact_synonym: 2019-nCoV infection
has_exact_synonym: COVID19
has_exact_synonym: SARS-CoV-2 infection
has_exact_synonym: Wuhan coronavirus infection
has_exact_synonym: Wuhan seafood market pneumonia virus infection
has_obo_namespace: disease_ontology
id: DOID:0080600
in_subset: DO infectious disease slim
in_subset: NCIthesaurus

Axiom
annotated source: COVID-19
annotated property: definition
annotated target: A Coronavirus infectious disease that is characterized by fever, cough and shortness of breath and that has_material_basis_in SARS-CoV-2.
database_cross_reference: url:https://www.cdc.gov/coronavirus/2019-ncov/about/index.html
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2697049
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/?term=32007143
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/?term=32007145
database_cross_reference: url:https://www.who.int/emergencies/diseases/novel-coronavirus-2019

Axiom
annotated source: COVID-19
annotated property: has_exact_synonym
annotated target: COVID19
has_synonym_type: OMO_0003012

glutaric acidemia I
type: Class
subclass of: autosomal recessive disease
subclass of: organic acidemia
definition: 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.
database_cross_reference: GARD:6522
database_cross_reference: MESH:C536833
database_cross_reference: MIM:231670
database_cross_reference: ORDO:25
has_exact_synonym: GA1
has_exact_synonym: glutaric academia type 1
has_exact_synonym: glutaric aciduria 1
has_exact_synonym: glutaric aciduria type I
has_exact_synonym: glutaryl-coA dehydrogenase deficiency
has_exact_synonym: glutaryl-coenzyme A dehydrogenase deficiency
has_obo_namespace: disease_ontology
id: DOID:0111254
in_subset: DO rare slim

Axiom
annotated source: glutaric acidemia I
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pubmed/16602100

Axiom
annotated source: glutaric acidemia I
annotated property: has_exact_synonym
annotated target: GA1
has_synonym_type: OMO_0003012

malaria
type: Class
subclass of: disease by infectious agent
definition: 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.
has_alternative_id: DOID:12552
database_cross_reference: EFO:0001068
database_cross_reference: GARD:6961
database_cross_reference: ICD10CM:B54
database_cross_reference: ICD9CM:084
database_cross_reference: MESH:D008288
database_cross_reference: NCI:C34797
database_cross_reference: ORDO:673
database_cross_reference: SNOMEDCT_US_2023_03_01:154374002
database_cross_reference: UMLS_CUI:C0024530
has_exact_synonym: induced malaria
has_obo_namespace: disease_ontology
id: DOID:12365
in_subset: DO infectious disease slim
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI.

Axiom
annotated source: malaria
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/Malaria
database_cross_reference: url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=malaria

cardiovascular system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: 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.
has_alternative_id: DOID:73
database_cross_reference: ICD9CM:429.2
database_cross_reference: MESH:D002318
database_cross_reference: NCI:C2931
database_cross_reference: SNOMEDCT_US_2023_03_01:266275004
database_cross_reference: UMLS_CUI:C0007222
has_exact_synonym: disease of subdivision of hemolymphoid system
has_obo_namespace: disease_ontology
id: DOID:1287
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: DO RAD slim
in_subset: NCIthesaurus

Axiom
annotated source: cardiovascular system disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/Circulatory_system

lung cancer
type: Class
subclass of: organ system cancer
subclass of: respiratory system disease
subclass of: cancer
subclass of: lung disease
definition: A respiratory system cancer that is located_in the lung.
has_alternative_id: DOID:13075
has_alternative_id: DOID:1322
has_alternative_id: DOID:9881
database_cross_reference: ICD10CM:C34.1
database_cross_reference: ICD10CM:C34.2
database_cross_reference: ICD10CM:C34.3
database_cross_reference: ICD9CM:162.3
database_cross_reference: ICD9CM:162.4
database_cross_reference: ICD9CM:162.5
database_cross_reference: ICD9CM:162.8
database_cross_reference: MIM:211980
database_cross_reference: MIM:608935
database_cross_reference: MIM:612571
database_cross_reference: MIM:612593
database_cross_reference: MIM:614210
database_cross_reference: SNOMEDCT_US_2023_03_01:187860004
database_cross_reference: SNOMEDCT_US_2023_03_01:187864008
database_cross_reference: SNOMEDCT_US_2023_03_01:187868006
database_cross_reference: SNOMEDCT_US_2023_03_01:187874006
database_cross_reference: UMLS_CUI:C0024624
database_cross_reference: UMLS_CUI:C0153491
database_cross_reference: UMLS_CUI:C0153492
database_cross_reference: UMLS_CUI:C0153493
has_obo_namespace: disease_ontology
has_related_synonym: lung neoplasm
id: DOID:1324
in_subset: DO CFDE slim
in_subset: DO cancer slim
in_subset: TopNodes DOcancerslim

Axiom
annotated source: lung cancer
annotated property: definition
annotated target: A respiratory system cancer that is located_in the lung.
database_cross_reference: url:http://en.wikipedia.org/wiki/Lung_cancer

disease of cellular proliferation
type: Class
subclass of: disease
definition: A disease that is characterized by abnormally rapid cell division.
OBI_9991118: neoplasm
has_alternative_id: DOID:0000818
has_exact_synonym: cell process disease
has_exact_synonym: neoplasm
has_obo_namespace: disease_ontology
id: DOID:14566
in_subset: DO FlyBase slim
in_subset: DO RAD slim

Axiom
annotated source: disease of cellular proliferation
annotated property: definition
annotated target: A disease that is characterized by abnormally rapid cell division.
database_cross_reference: url:http://en.wikipedia.org/w/index.php?title=Cell_proliferation

propionic acidemia
type: Class
subclass of: organic acidemia
definition: An organic acidemia that involes a nonfunctional propionyl CoA carboxylase affecting conversion of amino acids and fats into sugar for energy.
has_alternative_id: DOID:14706
database_cross_reference: GARD:467
database_cross_reference: ICD10CM:E71.121
database_cross_reference: MESH:D056693
database_cross_reference: MIM:606054
database_cross_reference: NCI:C85030
database_cross_reference: SNOMEDCT_US_2023_03_01:69080001
database_cross_reference: UMLS_CUI:C0268579
database_cross_reference: UMLS_CUI:C2717876
has_exact_synonym: GLYCINEMIA, KETOTIC
has_exact_synonym: KETOTIC HYPERGLYCINEMIA
has_exact_synonym: ketotic II glycinemia
has_exact_synonym: ketotic glycinemia
has_exact_synonym: propionic aciduria
has_exact_synonym: propionyl-CoA carboxylase deficiency
has_obo_namespace: disease_ontology
id: DOID:14701
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: propionic acidemia
annotated property: definition
annotated target: An organic acidemia that involes a nonfunctional propionyl CoA carboxylase affecting conversion of amino acids and fats into sugar for energy.
database_cross_reference: url:http://en.wikipedia.org/wiki/Propionic_acidemia

beta-ketothiolase deficiency
type: Class
subclass of: autosomal recessive disease
subclass of: amino acid metabolic disorder
definition: 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.
database_cross_reference: GARD:872
database_cross_reference: MESH:C535818
database_cross_reference: MIM:203750
database_cross_reference: ORDO:134
database_cross_reference: SNOMEDCT_US_2023_03_01:238067002
database_cross_reference: UMLS_CUI:C1533628
has_exact_synonym: 2-methyl-3-hydroxybutyricacidemia
has_exact_synonym: 3-ketothiolase deficiency
has_exact_synonym: 3-oxothiolase deficiency
has_exact_synonym: Mitochondrial acetoacetyl-CoA Thiolase deficiency
has_exact_synonym: alpha-methylacetoaceticaciduria
has_exact_synonym: peroxisomal thiolase deficiency
has_obo_namespace: disease_ontology
id: DOID:14723
in_subset: DO rare slim
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: beta-ketothiolase deficiency
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://ghr.nlm.nih.gov/condition/beta-ketothiolase-deficiency#statistics

methylmalonic acidemia
type: Class
subclass of: organic acidemia
definition: An organic acidemia that involves an accumulation of methylmalonic acid in the blood.
has_alternative_id: DOID:14782
has_alternative_id: DOID:14802
database_cross_reference: GARD:7033
database_cross_reference: MESH:C537358
has_exact_synonym: methylmalonic aciduria
has_obo_namespace: disease_ontology
id: DOID:14749
in_subset: DO rare slim
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: methylmalonic acidemia
annotated property: definition
annotated target: An organic acidemia that involves an accumulation of methylmalonic acid in the blood.
database_cross_reference: url:http://ghr.nlm.nih.gov/condition/methylmalonic-acidemia

isovaleric acidemia
type: Class
subclass of: organic acidemia
definition: An organic acidemia that disrupts or prevents normal metabolism of the branched-chain amino acid leucine.
database_cross_reference: GARD:465
database_cross_reference: ICD10CM:E71.110
database_cross_reference: MESH:C538167
database_cross_reference: MIM:243500
database_cross_reference: NCI:C98964
database_cross_reference: SNOMEDCT_US_2023_03_01:87827003
database_cross_reference: UMLS_CUI:C0268575
has_exact_synonym: Isovaleryl-CoA dehydrogenase deficiency
has_exact_synonym: isovaleric acid CoA dehydrogenase deficiency
has_exact_synonym: isovaleric aciduria
has_obo_namespace: disease_ontology
id: DOID:14753
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: isovaleric acidemia
annotated property: definition
annotated target: An organic acidemia that disrupts or prevents normal metabolism of the branched-chain amino acid leucine.
database_cross_reference: url:http://en.wikipedia.org/wiki/Isovaleric_acidemia

argininosuccinic aciduria
type: Class
subclass of: amino acid metabolic disorder
definition: An amino acid metabolic disorder that involves the accumulation of argininosuccinic acid (ASA) in the blood and urine.
database_cross_reference: GARD:5843
database_cross_reference: MESH:D056807
database_cross_reference: MIM:207900
database_cross_reference: NCI:C84569
database_cross_reference: SNOMEDCT_US_2023_03_01:41013004
database_cross_reference: UMLS_CUI:C0268547
has_exact_synonym: Argininosuccinate lyase deficiency
has_exact_synonym: argininosuccinic acidemia
has_exact_synonym: arginosuccinase deficiency
has_exact_synonym: deficiency of argininosuccinate lyase
has_obo_namespace: disease_ontology
id: DOID:14755
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: argininosuccinic aciduria
annotated property: definition
annotated target: An amino acid metabolic disorder that involves the accumulation of argininosuccinic acid (ASA) in the blood and urine.
database_cross_reference: url:http://en.wikipedia.org/wiki/Argininosuccinic_aciduria

reproductive system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in reproductive system organs.
has_alternative_id: DOID:6309
database_cross_reference: NCI:C27613
database_cross_reference: UMLS_CUI:C1335037
has_exact_synonym: genital system disease
has_obo_namespace: disease_ontology
id: DOID:15
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: reproductive system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in reproductive system organs.
database_cross_reference: url:http://en.wikipedia.org/wiki/Reproductive_system

cognitive disorder
type: Class
subclass of: disease
definition: A disease of mental health that affects cognitive functions including memory processing, perception and problem solving.
database_cross_reference: ICD10CM:F09
database_cross_reference: MESH:D019965
database_cross_reference: NCI:C34870
database_cross_reference: SNOMEDCT_US_2023_03_01:111479008
database_cross_reference: UMLS_CUI:C0029227
has_exact_synonym: cognitive disease
has_obo_namespace: disease_ontology
has_related_synonym: Organic Mental disorder
id: DOID:1561
in_subset: DO RAD slim
in_subset: NCIthesaurus

Axiom
annotated source: cognitive disorder
annotated property: definition
annotated target: A disease of mental health that affects cognitive functions including memory processing, perception and problem solving.
database_cross_reference: url:http://en.wikipedia.org/wiki/Cognitive_disorder

respiratory system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
has_alternative_id: DOID:3226
database_cross_reference: ICD10CM:J98
database_cross_reference: ICD9CM:519
database_cross_reference: SNOMEDCT_US_2023_03_01:155603009
database_cross_reference: UMLS_CUI:C0029582
has_obo_namespace: disease_ontology
id: DOID:1579
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: DO RAD slim

Axiom
annotated source: respiratory system disease
annotated property: definition
annotated target: A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
database_cross_reference: url:http://en.wikipedia.org/wiki/File:Respiratory_system_complete_en.svg

integumentary system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
has_obo_namespace: disease_ontology
id: DOID:16
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim

Axiom
annotated source: integumentary system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the integumentary system comprising the skin and its appendages.
database_cross_reference: url:http://en.wikipedia.org/wiki/Integumentary_system

cancer
type: Class
subclass of: disease of cellular proliferation
definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
database_cross_reference: ICD10CM:C80.1
database_cross_reference: ICD9CM:199
database_cross_reference: ICDO:8000/3
database_cross_reference: MESH:D009369
database_cross_reference: NCI:C9305
database_cross_reference: SNOMEDCT_US_2023_03_01:269513004
database_cross_reference: UMLS_CUI:C0006826
has_exact_synonym: malignant neoplasm
has_exact_synonym: malignant tumor
has_exact_synonym: primary cancer
has_obo_namespace: disease_ontology
id: DOID:162
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO FlyBase slim
in_subset: DO GXD slim
in_subset: DO RAD slim
in_subset: DO cancer slim
in_subset: NCIthesaurus
comment: Updating out dated UMLS CUI.

Axiom
annotated source: cancer
annotated property: definition
annotated target: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
database_cross_reference: url:http://en.wikipedia.org/wiki/cancer
database_cross_reference: url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=cancer

musculoskeletal system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that occurs in the muscular and/or skeletal system.
database_cross_reference: MESH:D009140
database_cross_reference: NCI:C107377
database_cross_reference: SNOMEDCT_US_2023_03_01:268047003
database_cross_reference: UMLS_CUI:C0026857
has_obo_namespace: disease_ontology
id: DOID:17
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: musculoskeletal system disease
annotated property: definition
annotated target: A disease of anatomical entity that occurs in the muscular and/or skeletal system.
database_cross_reference: url:http://en.wikipedia.org/wiki/Human_musculoskeletal_system#Diseases_and_disorders

urinary system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
has_alternative_id: DOID:579
database_cross_reference: NCI:C27599
database_cross_reference: UMLS_CUI:C1335051
has_exact_synonym: Non-neoplastic urinary tract disease
has_exact_synonym: urinary tract disease
has_obo_namespace: disease_ontology
id: DOID:18
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: urinary system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in kidney, ureter, bladder and urethra.
database_cross_reference: url:http://en.wikipedia.org/wiki/Urinary_system

female reproductive system disease
type: Class
subclass of: reproductive system disease
subclass of: disease
definition: A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
database_cross_reference: ICD9CM:629.9
database_cross_reference: MESH:D005831
database_cross_reference: SNOMEDCT_US_2023_03_01:38233001
database_cross_reference: UMLS_CUI:C0017411
has_obo_namespace: disease_ontology
id: DOID:229

Axiom
annotated source: female reproductive system disease
annotated property: definition
annotated target: A reproductive system disease that impairs the ability to reproduce and is located in the uterus, vagina, cervix, ovaries or fallopian tubes.
database_cross_reference: url:http://en.wikipedia.org/wiki/Female_reproductive_system
database_cross_reference: url:http://en.wikipedia.org/wiki/Reproductive_system_disease

ovarian cancer
type: Class
subclass of: organ system cancer
subclass of: reproductive system disease
subclass of: cancer
subclass of: female reproductive system disease
subclass of: endocrine system disease
subclass of: disease
definition: A female reproductive organ cancer that is located_in the ovary.
has_alternative_id: DOID:0060070
has_alternative_id: DOID:2144
has_alternative_id: DOID:9595
database_cross_reference: GARD:7295
database_cross_reference: ICD10CM:C56
database_cross_reference: ICD9CM:183.0
database_cross_reference: MESH:D010051
database_cross_reference: MIM:167000
database_cross_reference: MIM:607893
database_cross_reference: NCI:C4984
database_cross_reference: NCI:C7431
database_cross_reference: ORDO:213500
database_cross_reference: ORDO:213517
database_cross_reference: SNOMEDCT_US_2023_03_01:123843001
database_cross_reference: SNOMEDCT_US_2023_03_01:372117006
database_cross_reference: SNOMEDCT_US_2023_03_01:93934004
database_cross_reference: UMLS_CUI:C0919267
database_cross_reference: UMLS_CUI:C1140680
database_cross_reference: UMLS_CUI:C1299247
has_exact_synonym: malignant Ovarian tumor
has_exact_synonym: malignant tumour of ovary
has_exact_synonym: ovarian neoplasm
has_exact_synonym: ovary neoplasm
has_exact_synonym: primary ovarian cancer
has_exact_synonym: tumor of the Ovary
has_obo_namespace: disease_ontology
id: DOID:2394
in_subset: DO CFDE slim
in_subset: DO FlyBase slim
in_subset: DO RAD slim
in_subset: DO cancer slim
in_subset: DO rare slim
in_subset: NCIthesaurus
in_subset: TopNodes DOcancerslim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: ovarian cancer
annotated property: definition
annotated target: A female reproductive organ cancer that is located_in the ovary.
database_cross_reference: url:http://www.cancer.gov/dictionary?CdrID=445074

endocrine system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: 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.
database_cross_reference: ICD10CM:E34.9
database_cross_reference: ICD9CM:259.9
database_cross_reference: MESH:D004700
database_cross_reference: NCI:C3009
database_cross_reference: SNOMEDCT_US_2023_03_01:67432001
database_cross_reference: UMLS_CUI:C0014130
has_obo_namespace: disease_ontology
id: DOID:28
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: DO RAD slim
in_subset: NCIthesaurus

Axiom
annotated source: endocrine system disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/Endocrine_system

immune system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the immune system.
database_cross_reference: EFO:0000540
database_cross_reference: ICD10CM:D89.9
database_cross_reference: ICD9CM:279.9
database_cross_reference: SNOMEDCT_US_2023_03_01:154782004
database_cross_reference: UMLS_CUI:C0041806
has_obo_namespace: disease_ontology
id: DOID:2914
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO FlyBase slim
in_subset: DO GXD slim
in_subset: DO MGI slim

Axiom
annotated source: immune system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the immune system.
database_cross_reference: url:http://en.wikipedia.org/wiki/Immune_system

pulmonary tuberculosis
type: Class
subclass of: disease by infectious agent
subclass of: disease
subclass of: lung disease
definition: 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.
database_cross_reference: ICD10CM:A15
database_cross_reference: ICD9CM:011
database_cross_reference: MESH:D014397
database_cross_reference: NCI:C26899
database_cross_reference: SNOMEDCT_US_2023_03_01:81483001
database_cross_reference: UMLS_CUI:C0041327
has_obo_namespace: disease_ontology
id: DOID:2957
in_subset: DO infectious disease slim
in_subset: NCIthesaurus
in_subset: gram-positive bacterial infectious disease

Axiom
annotated source: pulmonary tuberculosis
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.cdc.gov/tb/publications/factsheets/general/tb.htm
database_cross_reference: url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=tuberculosis

lipid metabolism disorder
type: Class
subclass of: inherited metabolic disorder
definition: An inherited metabolic disorder that involves the creation and degradation of lipids.
database_cross_reference: MESH:D008052
database_cross_reference: UMLS_CUI:C0023772
has_exact_synonym: dyslipidemia
has_exact_synonym: fatty acid metabolism disorder
has_obo_namespace: disease_ontology
id: DOID:3146
in_subset: DO FlyBase slim

Axiom
annotated source: lipid metabolism disorder
annotated property: definition
annotated target: An inherited metabolic disorder that involves the creation and degradation of lipids.
database_cross_reference: url:http://en.wikipedia.org/wiki/Lipid_metabolism

disease
type: Class
definition: 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.
database_cross_reference: MESH:D004194
database_cross_reference: NCI:C2991
database_cross_reference: SNOMEDCT_US_2023_03_01:64572001
database_cross_reference: UMLS_CUI:C0012634
has_obo_namespace: disease_ontology
id: DOID:4
in_subset: DO RAD slim
in_subset: NCIthesaurus

Axiom
annotated source: disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/

human immunodeficiency virus infectious disease
type: Class
subclass of: viral infectious disease
definition: 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.
database_cross_reference: ICD10CM:B20
database_cross_reference: ICD9CM:042-042.99
database_cross_reference: MESH:D015658
database_cross_reference: NCI:C3108
database_cross_reference: SNOMEDCT_US_2023_03_01:86406008
database_cross_reference: UMLS_CUI:C0019693
has_exact_synonym: HIV infection
has_obo_namespace: disease_ontology
id: DOID:526
in_subset: DO infectious disease slim
in_subset: NCIthesaurus
in_subset: zoonotic infectious disease

Axiom
annotated source: human immunodeficiency virus infectious disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/HIV
database_cross_reference: url:http://www.nlm.nih.gov/medlineplus/ency/article/000602.htm

genetic disease
type: Class
subclass of: disease
definition: A disease that has_material_basis_in genetic variations in the human genome.
database_cross_reference: MESH:D030342
database_cross_reference: NCI:C3101
database_cross_reference: SNOMEDCT_US_2023_03_01:32895009
database_cross_reference: UMLS_CUI:C0019247
has_obo_namespace: disease_ontology
id: DOID:630
in_subset: DO CFDE slim
in_subset: DO RAD slim
in_subset: NCIthesaurus

Axiom
annotated source: genetic disease
annotated property: definition
annotated target: A disease that has_material_basis_in genetic variations in the human genome.
database_cross_reference: url:http://ghr.nlm.nih.gov/

inherited metabolic disorder
type: Class
subclass of: disease of metabolism
subclass of: genetic disease
definition: 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.
database_cross_reference: MESH:D008661
database_cross_reference: NCI:C34816
database_cross_reference: SNOMEDCT_US_2023_03_01:86095007
database_cross_reference: UMLS_CUI:C0025521
has_exact_synonym: Inborn Errors of Metabolism
has_exact_synonym: Metabolic hereditary disorder
has_exact_synonym: inborn metabolism disorder
has_obo_namespace: disease_ontology
id: DOID:655
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: inherited metabolic disorder
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://en.wikipedia.org/wiki/Inborn_errors_of_metabolism
database_cross_reference: url:http://www.ncbi.nlm.nih.gov/mesh/68008659

disease of anatomical entity
type: Class
subclass of: disease
definition: A disease that manifests in a defined anatomical structure.
has_alternative_id: DOID:1
has_alternative_id: DOID:2
has_alternative_id: DOID:5
has_alternative_id: DOID:71
has_alternative_id: DOID:72
has_alternative_id: DOID:8
has_obo_namespace: disease_ontology
id: DOID:7
in_subset: DO RAD slim

Axiom
annotated source: disease of anatomical entity
annotated property: definition
annotated target: A disease that manifests in a defined anatomical structure.
database_cross_reference: url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic

rheumatoid arthritis
type: Class
subclass of: musculoskeletal system disease
subclass of: immune system disease
subclass of: disease
definition: An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
database_cross_reference: EFO:0000685
database_cross_reference: ICD10CM:M06.9
database_cross_reference: ICD9CM:714.0
database_cross_reference: KEGG:05323
database_cross_reference: MESH:D001172
database_cross_reference: MIM:180300
database_cross_reference: NCI:C2884
database_cross_reference: SNOMEDCT_US_2023_03_01:156471009
database_cross_reference: UMLS_CUI:C0003873
has_exact_synonym: Arthritis or polyarthritis, rheumatic
has_exact_synonym: atrophic Arthritis
has_obo_namespace: disease_ontology
id: DOID:7148
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: rheumatoid arthritis
annotated property: definition
annotated target: An arthritis that is an autoimmune disease which attacks healthy cells and tissue located_in joint.
database_cross_reference: url:http://en.wikipedia.org/wiki/Rheumatoid_arthritis
database_cross_reference: url:http://www.mayoclinic.org/diseases-conditions/rheumatoid-arthritis/home/ovc-20197388
database_cross_reference: url:http://www.nlm.nih.gov/medlineplus/ency/article/000431.htm

hematopoietic system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that has_material_basis_in hematopoietic cells.
database_cross_reference: ICD10CM:D75.9
database_cross_reference: ICD9CM:289.9
database_cross_reference: MESH:D006402
database_cross_reference: NCI:C26323
database_cross_reference: SNOMEDCT_US_2023_03_01:154785002
database_cross_reference: UMLS_CUI:C0018939
has_exact_synonym: Blood disease
has_exact_synonym: Blood dyscrasia
has_exact_synonym: DISEASE OF THE BLOOD AND BLOOD-FORMING ORGANS
has_exact_synonym: Hematological disease
has_exact_synonym: blood disorder
has_exact_synonym: disease of haematopoietic system
has_exact_synonym: disease of hematopoietic system
has_exact_synonym: haematopoietic system disease
has_obo_namespace: disease_ontology
id: DOID:74
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: hematopoietic system disease
annotated property: definition
annotated target: A disease of anatomical entity that has_material_basis_in hematopoietic cells.
database_cross_reference: url:http://en.wikipedia.org/wiki/Hematopathology
database_cross_reference: url:https://www.ncbi.nlm.nih.gov/books/NBK1741/

gastrointestinal system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the gastrointestinal tract.
has_alternative_id: DOID:27
has_alternative_id: DOID:944
database_cross_reference: ICD10CM:K92.9
database_cross_reference: ICD9CM:520-579.99
database_cross_reference: MESH:D004066
database_cross_reference: SNOMEDCT_US_2023_03_01:53619000
database_cross_reference: UMLS_CUI:C0012242
has_exact_synonym: GIT disease
has_exact_synonym: Gastroenteropathy
has_exact_synonym: alimentary system disease
has_exact_synonym: digestive system disorder
has_exact_synonym: gastrointestinal disease
has_exact_synonym: gastrointestinal disorder
has_obo_namespace: disease_ontology
id: DOID:77
in_subset: DO AGR slim
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim

Axiom
annotated source: gastrointestinal system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the gastrointestinal tract.
database_cross_reference: url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract

lung disease
type: Class
subclass of: respiratory system disease
subclass of: disease
definition: 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.
has_alternative_id: DOID:11894
has_alternative_id: DOID:11895
has_alternative_id: DOID:29
has_alternative_id: DOID:766
database_cross_reference: ICD10CM:J98.4
database_cross_reference: MESH:D008171
database_cross_reference: NCI:C3198
database_cross_reference: SNOMEDCT_US_2023_03_01:266374002
database_cross_reference: UMLS_CUI:C0024115
has_obo_namespace: disease_ontology
id: DOID:850
in_subset: DO RAD slim
in_subset: NCIthesaurus
comment: Updating out dated CUI and removing lung abscess as a synonym.

Axiom
annotated source: lung disease
annotated property: definition
annotated target: 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.
database_cross_reference: url:http://www.niehs.nih.gov/health/topics/conditions/lung-disease/index.cfm
database_cross_reference: url:http://www.nlm.nih.gov/medlineplus/ency/article/000066.htm

nervous system disease
type: Class
subclass of: disease
subclass of: disease of anatomical entity
definition: A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
database_cross_reference: ICD10CM:G98
database_cross_reference: ICD9CM:349.9
database_cross_reference: MESH:D009422
database_cross_reference: NCI:C26835
database_cross_reference: SNOMEDCT_US_2023_03_01:155262005
database_cross_reference: UMLS_CUI:C0027765
has_obo_namespace: disease_ontology
id: DOID:863
in_subset: DO CFDE slim
in_subset: DO GXD slim
in_subset: DO MGI slim
in_subset: NCIthesaurus

Axiom
annotated source: nervous system disease
annotated property: definition
annotated target: A disease of anatomical entity that is located_in the central nervous system or located_in the peripheral nervous system.
database_cross_reference: url:http://en.wikipedia.org/wiki/Nervous_system

amino acid metabolic disorder
type: Class
subclass of: inherited metabolic disorder
definition: An inherited metabolic disorder that is characterized by impaired synthesis and degradation of amino acids.
database_cross_reference: GARD:5793
database_cross_reference: ICD10CM:E72.9
database_cross_reference: ICD9CM:270
database_cross_reference: MESH:D000592
database_cross_reference: NCI:C97090
database_cross_reference: SNOMEDCT_US_2023_03_01:42930003
database_cross_reference: UMLS_CUI:C0002514
has_exact_synonym: inborn errors of amino acid metabolism
has_obo_namespace: disease_ontology
id: DOID:9252
in_subset: DO rare slim
in_subset: NCIthesaurus

Axiom
annotated source: amino acid metabolic disorder
annotated property: definition
annotated target: An inherited metabolic disorder that is characterized by impaired synthesis and degradation of amino acids.
database_cross_reference: url:http://en.wikipedia.org/wiki/Inborn_errors_of_amino_acid_metabolism

colorectal cancer
type: Class
subclass of: organ system cancer
subclass of: cancer
subclass of: disease
subclass of: gastrointestinal system disease
definition: A large intestine cancer that is located_in the colon and/or located_in the rectum.
database_cross_reference: ICD10CM:C18.9
database_cross_reference: KEGG:05210
database_cross_reference: MESH:D015179
database_cross_reference: MIM:114500
database_cross_reference: NCI:C2956
database_cross_reference: NCI:C4978
database_cross_reference: SNOMEDCT_US_2023_03_01:126837005
database_cross_reference: SNOMEDCT_US_2023_03_01:93854002
database_cross_reference: UMLS_CUI:C0009404
database_cross_reference: UMLS_CUI:C0346629
has_obo_namespace: disease_ontology
id: DOID:9256
in_subset: DO CFDE slim
in_subset: DO FlyBase slim
in_subset: DO RAD slim
in_subset: DO cancer slim
in_subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: colorectal cancer
annotated property: definition
annotated target: A large intestine cancer that is located_in the colon and/or located_in the rectum.
database_cross_reference: url:http://www.cancer.gov/dictionary?CdrID=444983

homocystinuria
type: Class
subclass of: amino acid metabolic disorder
definition: An amino acid metabolic disorder that involves an accumulation of homocysteine in the serum and an increased excretion of homocysteine in the urine.
database_cross_reference: GARD:10770
database_cross_reference: ICD10CM:E72.11
database_cross_reference: MESH:D006712
database_cross_reference: MIM:236200
database_cross_reference: MIM:236250
database_cross_reference: NCI:C84765
database_cross_reference: ORDO:394
database_cross_reference: SNOMEDCT_US_2023_03_01:190709008
database_cross_reference: UMLS_CUI:C0019880
has_exact_synonym: CBS deficiency
has_exact_synonym: cystathionine beta synthase deficiency
has_exact_synonym: cystathionine synthase deficiency
has_obo_namespace: disease_ontology
id: DOID:9263
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI.

Axiom
annotated source: homocystinuria
annotated property: definition
annotated target: An amino acid metabolic disorder that involves an accumulation of homocysteine in the serum and an increased excretion of homocysteine in the urine.
database_cross_reference: url:http://en.wikipedia.org/wiki/Homocystinuria

maple syrup urine disease
type: Class
subclass of: organic acidemia
definition: 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.
database_cross_reference: GARD:3228
database_cross_reference: ICD10CM:E71.0
database_cross_reference: MESH:D008375
database_cross_reference: MIM:246900
database_cross_reference: MIM:248600
database_cross_reference: MIM:615135
database_cross_reference: NCI:C34806
database_cross_reference: ORDO:511
database_cross_reference: SNOMEDCT_US_2023_03_01:27718001
database_cross_reference: UMLS_CUI:C0024776
has_exact_synonym: Ketoacidaemia
has_exact_synonym: branched chain ketoaciduria
has_obo_namespace: disease_ontology
has_related_synonym: dihydrolipoamide dehydrogenase deficiency
id: DOID:9269
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: maple syrup urine disease
annotated property: definition
annotated target: 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.

Axiom
annotated source: maple syrup urine disease
annotated property: has_related_synonym
annotated target: dihydrolipoamide dehydrogenase deficiency
database_cross_reference: MIM:246900

phenylketonuria
type: Class
subclass of: amino acid metabolic disorder
definition: An amino acid metabolic disorder that is characterized by a mutation in the gene for the hepatic enzyme phenylalanine hydroxylase (PAH), rendering it nonfunctional.
has_alternative_id: DOID:14455
database_cross_reference: GARD:7383
database_cross_reference: ICD9CM:270.1
database_cross_reference: MESH:D010661
database_cross_reference: MESH:D017042
database_cross_reference: MIM:261600
database_cross_reference: NCI:C81315
database_cross_reference: ORDO:716
database_cross_reference: SNOMEDCT_US_2023_03_01:154735006
database_cross_reference: SNOMEDCT_US_2023_03_01:297225000
database_cross_reference: UMLS_CUI:C0031485
database_cross_reference: UMLS_CUI:C0085547
has_exact_synonym: Folling's disease
has_exact_synonym: PKU
has_exact_synonym: maternal phenylketonuria
has_exact_synonym: phenylalaninemia
has_obo_namespace: disease_ontology
id: DOID:9281
in_subset: DO rare slim
in_subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Axiom
annotated source: phenylketonuria
annotated property: definition
annotated target: An amino acid metabolic disorder that is characterized by a mutation in the gene for the hepatic enzyme phenylalanine hydroxylase (PAH), rendering it nonfunctional.
database_cross_reference: url:http://en.wikipedia.org/wiki/Phenylketonuria
database_cross_reference: url:https://www.genome.gov/Genetic-Disorders/Phenylketonuria

Axiom
annotated source: phenylketonuria
annotated property: has_exact_synonym
annotated target: PKU
has_synonym_type: OMO_0003012

viral infectious disease
type: Class
subclass of: disease by infectious agent
subclass of: disease
definition: A disease by infectious agent that results in infection, has_material_basis_in Viruses.
has_alternative_id: DOID:1329
database_cross_reference: ICD10CM:A94
database_cross_reference: ICD10CM:B34.9
database_cross_reference: ICD9CM:060-066.99
database_cross_reference: MESH:D001102
database_cross_reference: MESH:D014777
database_cross_reference: NCI:C3439
database_cross_reference: NCI:C34396
database_cross_reference: SNOMEDCT_US_2023_03_01:34014006
database_cross_reference: SNOMEDCT_US_2023_03_01:40610006
database_cross_reference: UMLS_CUI:C0003723
database_cross_reference: UMLS_CUI:C0042769
has_exact_synonym: Viral Infection
has_exact_synonym: Viral disease
has_exact_synonym: virus infection
has_obo_namespace: disease_ontology
id: DOID:934
in_subset: DO AGR slim
in_subset: DO FlyBase slim
in_subset: DO infectious disease slim
in_subset: NCIthesaurus

Axiom
annotated source: viral infectious disease
annotated property: definition
annotated target: A disease by infectious agent that results in infection, has_material_basis_in Viruses.
database_cross_reference: url:http://www.merck.com/mmhe/sec17/ch198/ch198a.html

exposure event
type: Class
definition: An interaction between an exposure stressor and an exposure_receptor.
created by: cmattin
creation date: 2010-09-21T02:47:00Z
has_obo_namespace: exposure_event
id: ExO:0000002

Axiom
annotated source: exposure event
annotated property: definition
annotated target: An interaction between an exposure stressor and an exposure_receptor.
database_cross_reference: CTD:curators

glycan
type: Class
definition: A compound consisting of monosaccharides linked by glycosidic bonds.

protein-containing complex
type: Class
definition: 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.
has_alternative_id: GO:0043234
has_exact_synonym: macromolecular complex
has_exact_synonym: macromolecule complex
has_exact_synonym: protein containing complex
has_narrow_synonym: protein complex
has_narrow_synonym: protein-protein complex
has_obo_namespace: cellular_component
id: GO:0032991
in_subset: goslim agr
in_subset: goslim chembl
in_subset: goslim euk cellular processes ribbon
in_subset: goslim flybase ribbon
in_subset: goslim mouse
in_subset: goslim pir
comment: 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.

Axiom
annotated source: protein-containing complex
annotated property: definition
annotated target: 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.
database_cross_reference: GOC:dos
database_cross_reference: GOC:mah

Medical Condition
type: Class
definition: Any kind of illness or circumstance which requires medical monitoring.
NCIT NHC0: C156809
NCIT P106: Conceptual Entity
NCIT P108: Medical Condition
NCIT P208: CL935837
NCIT P322: CPTAC
has_exact_synonym: Medical Condition
in_subset: NCIT C156952
in_subset: NCIT C156953
in_subset: NCIT C156954

Expired Air
type: Class
subclass of: organism substance
definition: 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.
NCIT NHC0: C78741
NCIT P106: Body Substance
NCIT P108: Expired Air
NCIT P207: C0225387
NCIT P322: CDISC
NCIT P325: 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)
NCIT P366: Expired_Air
has_exact_synonym: EXPIRED AIR
has_exact_synonym: Exhaled Air
has_exact_synonym: Exhaled Breath
has_exact_synonym: Expired Air
has_exact_synonym: Expired Breath
id: NCIT:C78741
in_subset: NCIT C61410
in_subset: NCIT C66830
in_subset: NCIT C78734

biomarker
type: Class
equivalent class: Restriction
  on property: is marker for
  some values from: Class
    union of: disease
    union of: exposure event
    union of: Medical Condition
definition: 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.
editor note: 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.
editor note: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000001
comment: Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. A biomarker is not an assessment of how an individual feels, functions, or survives.

Axiom
annotated source: biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group

Axiom
annotated source: biomarker
annotated property: comment
annotated target: Molecular, histologic, radiographic, or physiologic characteristics are types of biomarkers. A biomarker is not an assessment of how an individual feels, functions, or survives.
comment: FDA-NIH Biomarker Working Group

diagnostic biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020327
      some values from: Class
        union of: disease
        union of: Medical Condition
    union of: Restriction
      on property: has BEST classification
      has value: diagnostic (BEST)
    union of: Restriction
      on property: has CIViC classification
      has value: diagnostic (CIViC)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_exact_synonym: diagnostic evidence type
has_obo_namespace: biomarker
id: OBCI:000000002
comment: 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]
comment: Per CIVic, such biomarkers can help a clinician diagnose or exclude a particular disease.

Axiom
annotated source: diagnostic biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402285

Axiom
annotated source: diagnostic biomarker
annotated property: has_exact_synonym
annotated target: diagnostic evidence type
database_cross_reference: PMID:31796060

monitoring biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: has BEST classification
    has value: monitoring (BEST)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000003

Axiom
annotated source: monitoring biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402282

pharmacodynamic/response biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020329
      some values from: exposure event
    union of: Restriction
      on property: has BEST classification
      has value: pharmacodynamic/response (BEST)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000004

Axiom
annotated source: pharmacodynamic/response biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402286

predictive biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020330
      some values from: exposure event
    union of: Restriction
      on property: has BEST classification
      has value: predictive (BEST)
    union of: Restriction
      on property: has CIViC classification
      has value: predictive (CIViC)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_exact_synonym: predictive evidence type
has_obo_namespace: biomarker
id: OBCI:000000005
comment: 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.

Axiom
annotated source: predictive biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402283

Axiom
annotated source: predictive biomarker
annotated property: has_exact_synonym
annotated target: predictive evidence type
database_cross_reference: PMID:31796060

prognostic biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020331
      some values from: Class
        union of: disease
        union of: Medical Condition
    union of: Restriction
      on property: has BEST classification
      has value: prognostic (BEST)
    union of: Restriction
      on property: has CIViC classification
      has value: prognostic (CIViC)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_exact_synonym: prognostic evidence type
has_obo_namespace: biomarker
id: OBCI:000000006
comment: Per CIVic, such biomarkers are those that predict survival outcome.

Axiom
annotated source: prognostic biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402289

Axiom
annotated source: prognostic biomarker
annotated property: has_exact_synonym
annotated target: prognostic evidence type
database_cross_reference: PMID:31796060

safety biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020332
      some values from: exposure event
    union of: Restriction
      on property: has BEST classification
      has value: safety (BEST)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000007

Axiom
annotated source: safety biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402287

susceptibility/risk biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: RO_0020333
      some values from: Class
        union of: disease
        union of: Medical Condition
    union of: Restriction
      on property: has BEST classification
      has value: susceptibility/risk (BEST)
    union of: Restriction
      on property: has CIViC classification
      has value: predisposing (CIViC)
subclass of: biomarker with specified BEST category
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_exact_synonym: predisposing evidence type
has_obo_namespace: biomarker
id: OBCI:000000008
comment: Per CIVic, such biomarkers are those that indicate an increased likelihood of developing a particular disease.

Axiom
annotated source: susceptibility/risk biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group
database_cross_reference: NCBI:books/NBK402288

Axiom
annotated source: susceptibility/risk biomarker
annotated property: has_exact_synonym
annotated target: predisposing evidence type
database_cross_reference: PMID:31796060

biomarker of disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: disease
subclass of: biomarker of medical condition
definition: A biomarker that provides clinical information about a disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000009

Axiom
annotated source: biomarker of disease
annotated property: definition
annotated target: A biomarker that provides clinical information about a disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of COVID-19
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: COVID-19
subclass of: biomarker of disease by infectious agent
definition: A biomarker that provides clinical information about COVID-19.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000010

Axiom
annotated source: biomarker of COVID-19
annotated property: definition
annotated target: A biomarker that provides clinical information about COVID-19.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of cancer
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: cancer
subclass of: biomarker of disease of cellular proliferation
definition: A biomarker that provides clinical information about cancer.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000011

Axiom
annotated source: biomarker of cancer
annotated property: definition
annotated target: A biomarker that provides clinical information about cancer.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of exposure
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020334
    some values from: exposure event
subclass of: biomarker with specified clinical focus
definition: A biomarker that indicates the clinical effect of or response to exposure to a substance.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000012

Axiom
annotated source: biomarker of exposure
annotated property: definition
annotated target: A biomarker that indicates the clinical effect of or response to exposure to a substance.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

urine biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: urine
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using urine as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
database_cross_reference: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000013

blood plasma biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: blood plasma
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using blood plasma as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000014

biomarker of medical condition
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: Class
      union of: disease
      union of: Medical Condition
subclass of: biomarker with specified clinical focus
definition: A biomarker that provides clinical information about some current or potential medical condition.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000015

Axiom
annotated source: biomarker of medical condition
annotated property: definition
annotated target: A biomarker that provides clinical information about some current or potential medical condition.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker with specified BEST category
type: Class
equivalent class: Class
  union of: diagnostic biomarker
  union of: monitoring biomarker
  union of: pharmacodynamic/response biomarker
  union of: predictive biomarker
  union of: prognostic biomarker
  union of: safety biomarker
  union of: susceptibility/risk biomarker
subclass of: biomarker
definition: A biomarker that has an indicated BEST category.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000016
comment: This is a grouping term.

Axiom
annotated source: biomarker with specified BEST category
annotated property: definition
annotated target: A biomarker that has an indicated BEST category.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker with specified assessed entity
type: Class
subclass of: biomarker
definition: A biomarker that has an indicated assessed entity.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000017
comment: This is a grouping term.

Axiom
annotated source: biomarker with specified assessed entity
annotated property: definition
annotated target: A biomarker that has an indicated assessed entity.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker with specified clinical focus
type: Class
equivalent class: Class
  union of: biomarker of exposure
  union of: biomarker of medical condition
subclass of: biomarker
definition: A biomarker that has an indicated clinical focus.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000018
comment: This is a grouping term.

Axiom
annotated source: biomarker with specified clinical focus
annotated property: definition
annotated target: A biomarker that has an indicated clinical focus.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker with specified anatomical source
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Class
    union of: Restriction
      on property: determined using sample from
      some values from: anatomical entity
    union of: Restriction
      on property: determined using image of
      some values from: anatomical entity
subclass of: biomarker
definition: A biomarker that has an indicated anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000019
comment: This is a grouping term.

Axiom
annotated source: biomarker with specified anatomical source
annotated property: definition
annotated target: A biomarker that has an indicated anatomical source.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

physiological characteristic biomarker
type: Class
subclass of: biomarker with specified assessed entity
definition: A biomarker in which the assessed entity is a physiological characteristic.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000020

cellular biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in some aspect of
    some values from: cell
subclass of: biomarker with specified assessed entity
definition: A biomarker in which the assessed entity is a cell.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000021

Axiom
annotated source: cellular biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is a cell.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

sequence variation biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in presence of
    some values from: polymorphic_sequence_variant
subclass of: biomarker with specified assessed entity
definition: A biomarker in which the assessed entity is a sequence variation.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000022
comment: Sequence variations of genetic material can be assessed via direct sequencing or can be inferred from protein (for example, by using sequence-specific antibodies).

Axiom
annotated source: sequence variation biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is a sequence variation.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

glycan biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in some aspect of
    some values from: glycan
subclass of: molecular biomarker
definition: A biomarker in which the assessed entity is a glycan variation.
definition: A biomarker in which the assessed entity is a glycan.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000023

Axiom
annotated source: glycan biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is a glycan variation.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

small molecule biomarker
type: Class
subclass of: molecular biomarker
definition: A biomarker in which the assessed entity is a small molecule.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000024

Axiom
annotated source: small molecule biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is a small molecule.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

RNA biomarker
type: Class
subclass of: molecular biomarker
definition: A biomarker in which the assessed entity is an RNA.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
editor note: 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).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000025

Axiom
annotated source: RNA biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is an RNA.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

exhaled breath biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: Expired Air
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using exhaled breath as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000026

Axiom
annotated source: exhaled breath biomarker
annotated property: definition
annotated target: A biomarker that is assessed using exhaled breath as the anatomical source.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

blood biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: blood
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using blood as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000029

Axiom
annotated source: blood biomarker
annotated property: definition
annotated target: A biomarker that is assessed using blood as the anatomical source.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

protein biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in some aspect of
    some values from: Class
      union of: protein-containing complex
      union of: protein
subclass of: molecular biomarker
definition: A biomarker in which the assessed entity is a protein-containing molecular entity.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000032

molecular biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in some aspect of
    some values from: Class
      union of: molecular entity
      union of: molecule
      union of: complex of molecules
subclass of: biomarker with specified assessed entity
definition: A biomarker in which the assessed entity is a molecular entity.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000034

monitoring biomarker - clinical condition
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020328
    some values from: Class
      union of: disease
      union of: Medical Condition
subclass of: monitoring biomarker
definition: A biomarker that is measured serially to assess the status of a disease or medical condition.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000035

monitoring biomarker - exposure
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020335
    some values from: exposure event
subclass of: monitoring biomarker
definition: A biomarker that is measured serially to assess exposure to (or effect of) a medical product or an environmental agent.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000036

cerebrospinal fluid biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: cerebrospinal fluid
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using cerebrospinal fluid as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000039

biomarker of respiratory system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: respiratory system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some respiratory system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000041

Axiom
annotated source: biomarker of respiratory system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some respiratory system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of cognitive disorder
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: cognitive disorder
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some cognitive disorder.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000042

Axiom
annotated source: biomarker of cognitive disorder
annotated property: definition
annotated target: A biomarker that provides clinical information about some cognitive disorder.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of disease by infectious agent
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: disease by infectious agent
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some disease by infectious agent.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000043

Axiom
annotated source: biomarker of disease by infectious agent
annotated property: definition
annotated target: A biomarker that provides clinical information about some disease by infectious agent.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of disease of anatomical entity
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: disease of anatomical entity
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some disease of anatomical entity.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000044

Axiom
annotated source: biomarker of disease of anatomical entity
annotated property: definition
annotated target: A biomarker that provides clinical information about some disease of anatomical entity.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of cardiovascular system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: cardiovascular system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some cardiovascular system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000045

Axiom
annotated source: biomarker of cardiovascular system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some cardiovascular system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of endocrine system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: endocrine system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some endocrine system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000046

Axiom
annotated source: biomarker of endocrine system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some endocrine system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of gastrointestinal system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: gastrointestinal system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some gastrointestinal system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000047

Axiom
annotated source: biomarker of gastrointestinal system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some gastrointestinal system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of hematopoietic system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: hematopoietic system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some hematopoietic system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000048

Axiom
annotated source: biomarker of hematopoietic system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some hematopoietic system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of immune system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: immune system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some immune system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000049

Axiom
annotated source: biomarker of immune system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some immune system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of integumentary system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: integumentary system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some integumentary system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000050

Axiom
annotated source: biomarker of integumentary system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some integumentary system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of musculoskeletal system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: musculoskeletal system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some musculoskeletal system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000051

Axiom
annotated source: biomarker of musculoskeletal system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some musculoskeletal system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of nervous system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: nervous system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some nervous system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000052

Axiom
annotated source: biomarker of nervous system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some nervous system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of reproductive system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: reproductive system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some reproductive system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000053

Axiom
annotated source: biomarker of reproductive system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some reproductive system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of thoracic disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: thoracic disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some thoracic disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000054

Axiom
annotated source: biomarker of thoracic disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some thoracic disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of urinary system disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: urinary system disease
subclass of: biomarker of disease of anatomical entity
definition: A biomarker that provides clinical information about some urinary system disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000055

Axiom
annotated source: biomarker of urinary system disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some urinary system disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of disease of cellular proliferation
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: disease of cellular proliferation
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some disease of cellular proliferation.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000056

Axiom
annotated source: biomarker of disease of cellular proliferation
annotated property: definition
annotated target: A biomarker that provides clinical information about some disease of cellular proliferation.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of disease of metabolism
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: disease of metabolism
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some disease of metabolism.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000057

Axiom
annotated source: biomarker of disease of metabolism
annotated property: definition
annotated target: A biomarker that provides clinical information about some disease of metabolism.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

biomarker of genetic disease
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: RO_0020326
    some values from: genetic disease
subclass of: biomarker of disease
definition: A biomarker that provides clinical information about some genetic disease.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000058

Axiom
annotated source: biomarker of genetic disease
annotated property: definition
annotated target: A biomarker that provides clinical information about some genetic disease.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

saliva biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: saliva
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using saliva as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000059

DNA biomarker
type: Class
subclass of: molecular biomarker
definition: A biomarker in which the assessed entity is some DNA.
editor note: This class includes cases where the biomarker assesses multiple entities of the same type (for example, by using a panel).
editor note: 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).
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000063

multi-component biomarker
type: Class
subclass of: biomarker with specified assessed entity
definition: 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.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000067

Axiom
annotated source: multi-component biomarker
annotated property: definition
annotated target: 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.
database_cross_reference: FDA-NIH Biomarker Working Group

blood serum biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using sample from
    some values from: blood serum
subclass of: biomarker with specified anatomical source
definition: A biomarker that is assessed using blood serum as the anatomical source.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000014

voice biomarker
type: Class
subclass of: physiological characteristic biomarker
definition: A biomarker in which the assessed entity is a vocal characteristic.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000066

blood pressure biomarker
type: Class
subclass of: physiological characteristic biomarker
definition: A biomarker in which the assessed entity is blood pressure.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000067

bodily movement biomarker
type: Class
subclass of: physiological characteristic biomarker
definition: A biomarker in which the assessed entity is some bodily movement.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000070

gait biomarker
type: Class
subclass of: bodily movement biomarker
definition: A biomarker in which the assessed entity is some manner of walking.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000071

ocular biomarker
type: Class
subclass of: physiological characteristic biomarker
definition: A biomarker in which the assessed entity is an ocular characteristic.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000072

cellular morphology biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: indicated by difference in morphology of
    some values from: cell
subclass of: cellular biomarker
definition: A biomarker in which the assessed entity is cellular morphology.
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000076

image biomarker
type: Class
equivalent class: Class
  intersection of: biomarker
  intersection of: Restriction
    on property: determined using image of
    some values from: anatomical entity
subclass of: biomarker with specified assessed entity
subclass of: biomarker with specified anatomical source
definition: A biomarker in which the assessed entity is an image.
created by: https://orcid.org/0000-0001-5809-9523
has_exact_synonym: imaging biomarker
has_narrow_synonym: radiographic biomarker
has_obo_namespace: biomarker
id: OBCI:000000094

Axiom
annotated source: image biomarker
annotated property: definition
annotated target: A biomarker in which the assessed entity is an image.
database_cross_reference: https://orcid.org/0000-0001-5809-9523

concentration of
type: Class
subclass of: amount
definition: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
has_exact_synonym: concentration
has_obo_namespace: quality
id: PATO:0000033
in_subset: attribute slim
in_subset: relational slim
in_subset: scalar slim

Axiom
annotated source: concentration of
annotated property: definition
annotated target: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
database_cross_reference: Wikipedia:http://en.wikipedia.org/wiki/concentration

amount
type: Class
definition: The number of entities of this type that are part of the whole organism.
has_alternative_id: PATO:0000053
has_alternative_id: PATO:0000071
has_alternative_id: PATO:0001169
has_alternative_id: PATO:0001226
has_exact_synonym: presence or absence in organism
has_exact_synonym: quantitative
has_obo_namespace: quality
has_related_synonym: count in organism
has_related_synonym: number
has_related_synonym: presence
id: PATO:0000070
in_subset: attribute slim
comment: 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.

Axiom
annotated source: amount
annotated property: definition
annotated target: The number of entities of this type that are part of the whole organism.
database_cross_reference: PATOC:GVG

protein
type: Class
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
has_exact_synonym: natural protein
has_narrow_synonym: native protein
has_obo_namespace: protein
id: PR:000000001
comment: 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).

Axiom
annotated source: protein
annotated property: definition
annotated target: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
database_cross_reference: PRO:DAN
database_cross_reference: PRO:WCB

Axiom
annotated source: protein
annotated property: has_exact_synonym
annotated target: natural protein
database_cross_reference: PRO:DAN

Axiom
annotated source: protein
annotated property: has_narrow_synonym
annotated target: native protein
database_cross_reference: IEDB:BP

polymorphic_sequence_variant
type: Class
definition: A sequence variant that is segregating in one or more natural populations of a species.
has_exact_synonym: polymorphic sequence variant
has_obo_namespace: sequence
id: SO:0001025

Axiom
annotated source: polymorphic_sequence_variant
annotated property: definition
annotated target: A sequence variant that is segregating in one or more natural populations of a species.
database_cross_reference: SO:immuno_workshop

amniotic fluid
type: Class
subclass of: organism substance
definition: 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.
database_cross_reference: BTO:0000068
database_cross_reference: CALOHA:TS-0034
database_cross_reference: EMAPA:36771
database_cross_reference: ENVO:02000021
database_cross_reference: EV:0100123
database_cross_reference: FMA:305905
database_cross_reference: GAID:1155
database_cross_reference: MA:0002893
database_cross_reference: MESH:D000653
database_cross_reference: NCIT:C13188
database_cross_reference: UMLS:C0002638
database_cross_reference: VHOG:0001267
has_obo_namespace: uberon
has_related_synonym: acqua amnii
has_related_synonym: liquor amnii
id: UBERON:0000173
in_subset: pheno slim

Axiom
annotated source: amniotic fluid
annotated property: definition
annotated target: 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.
database_cross_reference: ENVO:02000021
database_cross_reference: MP:MP

Axiom
annotated source: amniotic fluid
annotated property: database_cross_reference
annotated target: UMLS:C0002638
source: ncithesaurus:Amniotic_Fluid

Axiom
annotated source: amniotic fluid
annotated property: has_related_synonym
annotated target: acqua amnii
database_cross_reference: BTO:0000068
has_synonym_type: OMO_0003011

Axiom
annotated source: amniotic fluid
annotated property: has_related_synonym
annotated target: liquor amnii
database_cross_reference: BTO:0000068
has_synonym_type: OMO_0003011

blood
type: Class
subclass of: haemolymphatic fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
IAO_0000232: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
RO_0002175: NCBITaxon 9606
UBPROP_0000001: 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]
UBPROP_0000001: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
UBPROP_0000002: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
UBPROP_0000003: 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]
database_cross_reference: AAO:0000046
database_cross_reference: BTO:0000089
database_cross_reference: CALOHA:TS-0079
database_cross_reference: EFO:0000296
database_cross_reference: EHDAA2:0000176
database_cross_reference: EHDAA:418
database_cross_reference: EMAPA:16332
database_cross_reference: ENVO:02000027
database_cross_reference: EV:0100047
database_cross_reference: FMA:9670
database_cross_reference: GAID:965
database_cross_reference: MA:0000059
database_cross_reference: MESH:D001769
database_cross_reference: MIAA:0000315
database_cross_reference: NCIT:C12434
database_cross_reference: TAO:0000007
database_cross_reference: UMLS:C0005767
database_cross_reference: VHOG:0000224
database_cross_reference: Wikipedia:Blood
database_cross_reference: XAO:0000124
database_cross_reference: ZFA:0000007
database_cross_reference: galen:Blood
has_exact_synonym: portion of blood
has_exact_synonym: vertebrate blood
has_obo_namespace: uberon
has_related_synonym: whole blood
id: UBERON:0000178
in_subset: efo slim
in_subset: human reference atlas
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: blood
annotated property: definition
annotated target: A fluid that is composed of blood plasma and erythrocytes.
database_cross_reference: FMA:9670
database_cross_reference: Wikipedia:Blood
database_cross_reference: http://orcid.org/0000-0002-6601-2165
database_cross_reference: https://github.com/obophenotype/uberon/issues/9

Axiom
annotated source: blood
annotated property: UBPROP_0000001
annotated target: 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]
source: ZFIN:curator

Axiom
annotated source: blood
annotated property: UBPROP_0000001
annotated target: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
source: AAO:LAP

Axiom
annotated source: blood
annotated property: UBPROP_0000003
annotated target: 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]
source: 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)
source: http://bgee.unil.ch/

Axiom
annotated source: blood
annotated property: database_cross_reference
annotated target: UMLS:C0005767
source: ncithesaurus:Blood

Axiom
annotated source: blood
annotated property: has_related_synonym
annotated target: whole blood
database_cross_reference: BTO:0000089

haemolymphatic fluid
type: Class
subclass of: organism substance
subclass of: bodily fluid
definition: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
contributor: https://orcid.org/0000-0002-6601-2165
creation date: 2009-04-08T04:38:19Z
database_cross_reference: CARO:0000081
has_obo_namespace: uberon
has_related_synonym: blood or blood analog
has_related_synonym: circulating fluid
id: UBERON:0000179

Axiom
annotated source: haemolymphatic fluid
annotated property: definition
annotated target: Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

organism substance
type: Class
subclass of: anatomical entity
definition: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
database_cross_reference: AAO:0010839
database_cross_reference: AEO:0000004
database_cross_reference: BILA:0000004
database_cross_reference: CALOHA:TS-2101
database_cross_reference: CARO:0000004
database_cross_reference: EHDAA2:0003004
database_cross_reference: EMAPA:35178
database_cross_reference: FBbt:00007019
database_cross_reference: FMA:9669
database_cross_reference: HAO:0000004
database_cross_reference: MA:0002450
database_cross_reference: NCIT:C13236
database_cross_reference: SPD:0000008
database_cross_reference: TAO:0001487
database_cross_reference: TGMA:0001824
database_cross_reference: VHOG:0001726
database_cross_reference: XAO:0004001
database_cross_reference: ZFA:0001487
database_cross_reference: galen:BodySubstance
has_exact_synonym: body fluid or substance
has_exact_synonym: body substance
has_exact_synonym: organism substance
has_exact_synonym: portion of body substance
has_exact_synonym: portion of organism substance
has_obo_namespace: uberon
id: UBERON:0000463
in_subset: common anatomy
in_subset: pheno slim
in_subset: upper level

Axiom
annotated source: organism substance
annotated property: definition
annotated target: 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.
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: organism substance
annotated property: has_exact_synonym
annotated target: body fluid or substance
database_cross_reference: MA:0002450

Axiom
annotated source: organism substance
annotated property: has_exact_synonym
annotated target: body substance
database_cross_reference: FMA:9669

Axiom
annotated source: organism substance
annotated property: has_exact_synonym
annotated target: organism substance
database_cross_reference: CARO:0000004

Axiom
annotated source: organism substance
annotated property: has_exact_synonym
annotated target: portion of body substance
database_cross_reference: FMA:9669

Axiom
annotated source: organism substance
annotated property: has_exact_synonym
annotated target: portion of organism substance
database_cross_reference: ZFA:0001487

anatomical entity
type: Class
definition: 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.
RO_0002175: NCBITaxon_33090
RO_0002175: NCBITaxon_33208
RO_0002175: NCBITaxon 4751
database_cross_reference: AAO:0010841
database_cross_reference: AEO:0000000
database_cross_reference: BFO:0000004
database_cross_reference: BILA:0000000
database_cross_reference: BIRNLEX:6
database_cross_reference: CARO:0000000
database_cross_reference: EHDAA2:0002229
database_cross_reference: FBbt:10000000
database_cross_reference: FMA:62955
database_cross_reference: HAO:0000000
database_cross_reference: MA:0000001
database_cross_reference: NCIT:C12219
database_cross_reference: TAO:0100000
database_cross_reference: TGMA:0001822
database_cross_reference: UMLS:C1515976
database_cross_reference: WBbt:0000100
database_cross_reference: XAO:0000000
database_cross_reference: ZFA:0100000
has_obo_namespace: uberon
id: UBERON:0001062
in_subset: common anatomy
in_subset: upper level

Axiom
annotated source: anatomical entity
annotated property: definition
annotated target: 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.
database_cross_reference: FMA:62955
database_cross_reference: http://orcid.org/0000-0001-9114-8737

Axiom
annotated source: anatomical entity
annotated property: database_cross_reference
annotated target: UMLS:C1515976
source: ncithesaurus:Anatomic_Structure_System_or_Substance

urine
type: Class
subclass of: organism substance
definition: Excretion that is the output of a kidney.
UBPROP_0000008: kidney excreta from some taxa (e.g. in aves) may not be liquid
database_cross_reference: BTO:0001419
database_cross_reference: CALOHA:TS-1092
database_cross_reference: EFO:0001939
database_cross_reference: EMAPA:36554
database_cross_reference: ENVO:00002047
database_cross_reference: FMA:12274
database_cross_reference: GAID:1189
database_cross_reference: MA:0002545
database_cross_reference: MAT:0000058
database_cross_reference: MESH:D014556
database_cross_reference: MIAA:0000058
database_cross_reference: NCIT:C13283
database_cross_reference: UMLS:C0042036
database_cross_reference: Wikipedia:Urine
database_cross_reference: galen:Urine
has_obo_namespace: uberon
id: UBERON:0001088
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim

Axiom
annotated source: urine
annotated property: definition
annotated target: Excretion that is the output of a kidney.
database_cross_reference: Wikipedia:Urine
database_cross_reference: https://github.com/geneontology/go-ontology/issues/11025

Axiom
annotated source: urine
annotated property: database_cross_reference
annotated target: UMLS:C0042036
source: ncithesaurus:Urine

cerebrospinal fluid
type: Class
subclass of: organism substance
subclass of: bodily fluid
definition: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
editor note: many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
UBPROP_0000001: Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
UBPROP_0000003: 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]
UBPROP_0000012: EHDAA2 models this as developing from CP, which is wrong
UBPROP_0000012: 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.
database_cross_reference: BIRNLEX:1798
database_cross_reference: BTO:0000237
database_cross_reference: CALOHA:TS-0130
database_cross_reference: EFO:0000329
database_cross_reference: EHDAA2:0004441
database_cross_reference: ENVO:02000029
database_cross_reference: EV:0100311
database_cross_reference: FMA:20935
database_cross_reference: GAID:1181
database_cross_reference: MA:0002503
database_cross_reference: MAT:0000499
database_cross_reference: MESH:D002555
database_cross_reference: NCIT:C12692
database_cross_reference: TAO:0002184
database_cross_reference: UMLS:C0007806
database_cross_reference: VHOG:0001278
database_cross_reference: Wikipedia:Cerebrospinal_fluid
database_cross_reference: ZFA:0001626
has_exact_synonym: CSF
has_exact_synonym: cerebral spinal fluid
has_obo_namespace: uberon
has_related_synonym: liquor cerebrospinalis
has_related_synonym: spinal fluid
id: UBERON:0001359
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim
in_subset: vertebrate core

Axiom
annotated source: cerebrospinal fluid
annotated property: definition
annotated target: A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
database_cross_reference: Wikipedia:Cerebrospinal_fluid

Axiom
annotated source: cerebrospinal fluid
annotated property: UBPROP_0000001
annotated target: Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
source: ZFIN:curator

Axiom
annotated source: cerebrospinal fluid
annotated property: UBPROP_0000003
annotated target: 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]
source: 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)
source: http://bgee.unil.ch/

Axiom
annotated source: cerebrospinal fluid
annotated property: database_cross_reference
annotated target: UMLS:C0007806
source: BIRNLEX:1798
source: ncithesaurus:Cerebrospinal_Fluid

Axiom
annotated source: cerebrospinal fluid
annotated property: has_exact_synonym
annotated target: cerebral spinal fluid
database_cross_reference: ZFA:0001626

Axiom
annotated source: cerebrospinal fluid
annotated property: has_related_synonym
annotated target: liquor cerebrospinalis
database_cross_reference: Wikipedia:Cerebrospinal_fluid

Axiom
annotated source: cerebrospinal fluid
annotated property: has_related_synonym
annotated target: spinal fluid
database_cross_reference: BTO:0000237

saliva
type: Class
subclass of: organism substance
definition: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
UBPROP_0000007: salivary
UBPROP_0000008: 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
database_cross_reference: BTO:0001202
database_cross_reference: CALOHA:TS-0891
database_cross_reference: EMAPA:36536
database_cross_reference: ENVO:02000036
database_cross_reference: FMA:59862
database_cross_reference: GAID:1167
database_cross_reference: MA:0002507
database_cross_reference: MAT:0000444
database_cross_reference: MESH:D012463
database_cross_reference: NCIT:C13275
database_cross_reference: UMLS:C0036087
database_cross_reference: Wikipedia:Saliva
database_cross_reference: galen:Saliva
has_exact_synonym: salivary gland secretion
has_obo_namespace: uberon
has_related_synonym: sailva normalis
has_related_synonym: saliva atomaris
has_related_synonym: saliva molecularis
id: UBERON:0001836
in_subset: uberon slim

Axiom
annotated source: saliva
annotated property: definition
annotated target: A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
database_cross_reference: GO:0046541
database_cross_reference: Wikipedia:Saliva

Axiom
annotated source: saliva
annotated property: UBPROP_0000008
annotated target: 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
source: GO

Axiom
annotated source: saliva
annotated property: database_cross_reference
annotated target: UMLS:C0036087
source: ncithesaurus:Saliva

Axiom
annotated source: saliva
annotated property: has_exact_synonym
annotated target: salivary gland secretion
database_cross_reference: FMA:59862

Axiom
annotated source: saliva
annotated property: has_related_synonym
annotated target: sailva normalis
database_cross_reference: Wikipedia:Saliva
has_synonym_type: OMO_0003011

Axiom
annotated source: saliva
annotated property: has_related_synonym
annotated target: saliva atomaris
database_cross_reference: Wikipedia:Saliva
has_synonym_type: OMO_0003011

Axiom
annotated source: saliva
annotated property: has_related_synonym
annotated target: saliva molecularis
database_cross_reference: Wikipedia:Saliva
has_synonym_type: OMO_0003011

blood plasma
type: Class
subclass of: haemolymphatic fluid
subclass of: organism substance
definition: The liquid component of blood, in which erythrocytes are suspended.
has_broad_synonym: plasma
has_broad_synonym: portion of plasma
database_cross_reference: BTO:0000131
database_cross_reference: CALOHA:TS-0800
database_cross_reference: EFO:0001905
database_cross_reference: EMAPA:35690
database_cross_reference: FMA:62970
database_cross_reference: GAID:1178
database_cross_reference: MA:0002501
database_cross_reference: MAT:0000052
database_cross_reference: MESH:D010949
database_cross_reference: MIAA:0000052
database_cross_reference: NCIT:C13356
database_cross_reference: UMLS:C0032105
database_cross_reference: Wikipedia:Blood_plasma
has_exact_synonym: blood plasm
has_exact_synonym: portion of blood plasma
has_obo_namespace: uberon
id: UBERON:0001969
in_subset: efo slim
in_subset: pheno slim
in_subset: uberon slim

Axiom
annotated source: blood plasma
annotated property: definition
annotated target: The liquid component of blood, in which erythrocytes are suspended.
database_cross_reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: blood plasma
annotated property: has_broad_synonym
annotated target: plasma
database_cross_reference: MA:0002501

Axiom
annotated source: blood plasma
annotated property: has_broad_synonym
annotated target: portion of plasma
database_cross_reference: FMA:62970

Axiom
annotated source: blood plasma
annotated property: database_cross_reference
annotated target: UMLS:C0032105
source: ncithesaurus:Plasma

blood serum
type: Class
subclass of: haemolymphatic fluid
definition: The portion of blood plasma that excludes clotting factors.
database_cross_reference: BTO:0000133
database_cross_reference: BTO:0001239
database_cross_reference: CALOHA:TS-0923
database_cross_reference: EHDAA2:0004728
database_cross_reference: EMAPA:35770
database_cross_reference: FMA:63083
database_cross_reference: MA:0002502
database_cross_reference: MESH:D044967
database_cross_reference: NCIT:C13325
database_cross_reference: UMLS:C0229671
database_cross_reference: Wikipedia:Serum_(blood)
has_exact_synonym: serum
has_obo_namespace: uberon
id: UBERON:0001977
in_subset: pheno slim
in_subset: uberon slim

Axiom
annotated source: blood serum
annotated property: definition
annotated target: The portion of blood plasma that excludes clotting factors.
database_cross_reference: Wikipedia:Serum_(blood)
database_cross_reference: http://orcid.org/0000-0002-6601-2165

Axiom
annotated source: blood serum
annotated property: database_cross_reference
annotated target: UMLS:C0229671
source: ncithesaurus:Serum

bodily fluid
type: Class
subclass of: organism substance
definition: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
has_broad_synonym: fluid
database_cross_reference: BIRNLEX:20
database_cross_reference: EMAPA:37441
database_cross_reference: FMA:280556
database_cross_reference: GAID:266
database_cross_reference: MESH:D001826
database_cross_reference: Wikipedia:Body_fluid
database_cross_reference: galen:BodyFluid
has_exact_synonym: body fluid
has_obo_namespace: uberon
id: UBERON:0006314
in_subset: pheno slim

Axiom
annotated source: bodily fluid
annotated property: definition
annotated target: Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
database_cross_reference: MESH:A12.207
database_cross_reference: Wikipedia:Body_fluid

Axiom
annotated source: bodily fluid
annotated property: database_cross_reference
annotated target: EMAPA:37441
source: MA:th

Axiom
annotated source: bodily fluid
annotated property: has_exact_synonym
annotated target: body fluid
database_cross_reference: GAID:266

susceptibility/risk (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000082

diagnostic (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000083

monitoring (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000084

prognostic (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000085

predictive (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000086

pharmacodynamic/response (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000087

safety (BEST)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000088

diagnostic (CIViC)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000089

predictive (CIViC)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000090

predisposing (CIViC)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000091

prognostic (CIViC)
type: NamedIndividual
created by: https://orcid.org/0000-0001-5809-9523
has_obo_namespace: biomarker
id: OBCI:000000092

variant of
term editor: Oliver He
definition: 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

functional (CIViC)
has_obo_namespace: biomarker
created by: https://orcid.org/0000-0001-5809-9523
id: OBCI:000000093

ratio
in_subset: relational slim
has_exact_synonym: proportionality to
has_obo_namespace: quality
definition: A quality inhering in a bearer by virtue of the bearer's magnitude in proportion to the magnitude of another entity.
has_exact_synonym: proportionality
in_subset: attribute slim
has_exact_synonym: proportion
has_exact_synonym: quotient
comment: Examples: height to weight; brain size to body size; root to shoot ratio; urinary sodium to potassium ratio. waist-hip ratio.
id: PATO:0001470
has_related_synonym: rate

has component
IAO_0000232: 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.
definition: 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.
editor note: The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
RO_0001900: RO_0001901
has curation status: IAO_0000125
in_subset: ro-eco

causally related to
definition: 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.
term editor: https://orcid.org/0000-0002-6601-2165
editor note: 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 yie…
IAO_0000232: Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.

Axiom
annotated source: causally related to
annotated property: definition
annotated target: 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.
database_cross_reference: https://en.wikipedia.org/wiki/Causality

gene
has_obo_namespace: sequence
id: SO:0000704
definition: 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.
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
database_cross_reference: http://en.wikipedia.org/wiki/Gene
in_subset: SOFA
has_exact_synonym: INSDC_feature:gene

Axiom
annotated source: gene
annotated property: definition
annotated target: 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.
database_cross_reference: SO:immuno_workshop

wiki
type: Axiom
annotated source: gene
annotated property: database_cross_reference
annotated target: http://en.wikipedia.org/wiki/Gene

has_obo_format_version