Biomarker Ontology (BMONT)
type: Ontology
version IRI: bmont.owl
contributor: Marc Jacobs
contributor: Martin Hofmann Aptius
creator: Astghik Sargsyan
description: The Biomarker Ontology (BMONT) is a comprehensive knowledge representation involving a variety of fields of medical and biological aspects. BMONT is built in line with Basic Formal Ontology (BFO) and Open Biological and Biomedical Ontology (OBO) principles. Entities and definitions are added by reviewing the old biomarker terminology that was created by Fraunhofer SCAI 10 years ago and was used for mining biomarker information in biomedical literature. In addition, related terms were collected from scientific publications and books capturing various disease fields. The ontology is proposed to be used for improving biomarker identification tasks, as well as a supportive integratable tool for abundant AI techniques, such as Machine Learning (ML) and Large Learning Model (LLM).
license: http://creativecommons.org/licenses/by/4.0/
comment: Biomarker Ontology (BMONT), created by Fraunhofer SCAI, is licensed under CC BY 4.0. You are free to share (copy and redistribute the material in any medium or format) and adapt (remix, transform, and build upon the material) for any purpose, even commercially. for any purpose, even commercially. The licensor cannot revoke these freedoms as long as you follow the license terms. You must give appropriate credit (by using the original ontology IRI for the whole ontology and original term IRIs for individual terms), provide a link to the license, and indicate if any changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
version info: 2025-06-20
version info: Version Release: 0.5.8

has close match
type: AnnotationProperty
definition: Has close match establishes a connection between two resources that have a high degree of agreement in meaning such that they can be used interchangeably. [Allotrope]
note: Property is related to core:closeMatch. core:closeMatch is an object property whereas this property is an annotation property to allow for weak semantic coupling. [Allotrope]
sub property of: note

imported from
type: AnnotationProperty
has close match: importedFrom
change note: 2020-12-15 Property has been added in order to replace pav:importedFrom. The difference between af-x:AFX_0002865 and pav:importedFrom is that the former is an annotation property whereas the latter is an object property. We added a new property in order to avoid issues of redeclaration of pav:importedFrom as annotation property. [Allotrope]
definition: The original source of imported information. [PAV]
sub property of: note

BFO OWL specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
curator note: Really of interest to developers only
sub property of: label

BFO CLIF specification label
type: AnnotationProperty
definition: Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
definition source: Person:Alan Ruttenberg
curator note: Really of interest to developers only
sub property of: label

fromOldVersion
type: AnnotationProperty

editor preferred label
type: AnnotationProperty
editor preferred label: editor preferred label
editor preferred label: editor preferred term
editor preferred label: editor preferred term~editor preferred label
editor preferred label: 编辑首选术语 @zh
editor preferred label: 编辑首选标签 @zh
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)
definition: 对于一类或属性的简洁的、有意义的、与人类友好的名称由本体开发商首选。 （美国英语） @zh
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: editor preferred term
label: editor preferred term~editor preferred label
label: 编辑首选术语
label: 编辑首选术语~编辑首选标签
label: 编辑首选标签

example of usage
type: AnnotationProperty
editor preferred label: example of usage
has curation status: IAO_0000122
definition: A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
database cross reference: IAO:0000112
has_obo_namespace: uberon
id: example_of_usage
is metadata tag: true
shorthand: example_of_usage

has curation status
type: AnnotationProperty
editor preferred label: has curation status
editor preferred label: 有管理状态 @zh
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bill Bug
definition editor: PERSON:Melanie Courtot
definition source: OBI_0000281
label: 有管理状态

definition
type: AnnotationProperty
editor preferred label: definition
editor preferred label: textual definition
editor preferred label: 定义 @zh
has curation status: IAO_0000122
definition: A property representing the English language definitions of what NCI means by the concept. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
definition: English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software.
definition: OBI的官方定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。 @zh
definition: The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition: The official definition.
definition: 官方的定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。 @zh
editor note: 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note: 2012-04-05: Barry Smith OBI的官方定义解释了一个类或属性的含义：'应该是亚里士多德式的，形式化和规范化的。可以用口语定义'是糟糕的。 您能解决这样的问题吗？ 解释关于类或属性的表达含义的必要和充分条件的陈述。 Alan Ruttenberg 您提出的定义是一个合理的备选，除非它很常见，没有给出必要和充分的条件。大多数情况下它们是必要的，偶尔是必要的，充分的或者仅仅仅充分的。它们通常使用不是自己定义的术语，因此它们实际上不能通过这些标准进行评估。 关于拟议定义的具体内容： 我们没有“含义”，或“表达”或“属性”的定义。对于在预期意义上的“参考”，我认为我们使用术语“指示”。对于'表达'，我认为我们和你的意思是符号，或标识符。对于“含义”，它不同于类和属性。对于类，我们希望文档能够让读者确定一个实体是否是该类的实例。对于属性，让我们的目标读者决定，给定一对潜在的关系，判断关系成立的断言正确与否。 “目标读者”部分表明我们也指定了我们期望的能够理解定义的人，并且概括了人类和计算机读者以包含文本和逻辑定义。 就我个人而言，我更愿意削弱对文档的定义，并指出什么是可取的。 我们还有一个悬而未决的问题，就是如何针对不同的受众定位不同的定义。临床读者阅读chebi需要来自受过化学训练的受众的不同类型的定义文档/定义，同样需要一个适合本体工作者的定义。
definition editor: PERSON:Daniel Schober
alternative term: DEFINITION
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
description adapted from source: no
has exact synonym: DEFINITION
label: textual definition
label: 定义
label: 文本定义

editor note
type: AnnotationProperty
editor preferred label: editor note
editor preferred label: 编者注 @zh
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.
definition: 管理者注释用于其编辑器。它可能不包含在本体的出版版本中，所以它应该不包含最终用户了解本体所需的信息。 @zh
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
definition source: GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
has db xref: IAO:0000116
has OBO namespace: uberon
id: editor_note
id: 编辑_注释 @zh
is metadata tag: true
shorthand: editor_note
shorthand: 编辑_注释 @zh
database cross reference: IAO:0000116
has_obo_namespace: uberon
is metadata tag: 1
label: 编者注

definition editor
type: AnnotationProperty
editor preferred label: definition editor
editor preferred label: term editor
editor preferred label: 术语编辑者 @zh
has curation status: IAO_0000122
definition: Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people
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
definition: 输入文件中术语编辑者的名称。术语编辑者是有关术语的信息交汇点。术语编辑者可以是，但并不总是，定义的作者，这可能是由几个人完成 @zh
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
editor note: 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
editor note: 20110707，MC：术语编辑和定义进行相应的修改。见http://code.google.com/p/information-artifact-ontology/issues/detail?id=115。 @zh
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
label: definition_editor
label: term editor
label: 术语编辑者

alternative term
type: AnnotationProperty
editor preferred label: alternative label
editor preferred label: alternative term
editor preferred label: 替代术语 @zh
has curation status: IAO_0000125
definition: A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.
definition: An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
definition: 一类或属性的替代名称，这意味着与所述首选名称同样的事物（语义上等价） @zh
definition editor: OBO Operations committee
definition editor: PERSON:Daniel Schober
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
comment: Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).
label: 替代术语

definition source
type: AnnotationProperty
editor preferred label: definition source
editor preferred label: 定义来源 @zh
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
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
definition: 正式引用，例如在外部数据库中的标识符，用于表示/定义的属性源（S）。自由文本表示/为定义属性源（S）。实例：在2007年1月31日的作者姓名，URI，MeSH术语C04，PUBMEDID，维基uri @zh
definition 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>
definition source: 论OBO-讨论邮件-列表，请参阅http://bit.ly/hgm99w @zh
label: definition_source
label: 定义来源

has obsolescence reason
type: AnnotationProperty
editor preferred label: has obsolescence reason
definition: Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification.
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot

curator note
type: AnnotationProperty
editor preferred label: curator note
has curation status: IAO_0000122
definition: An administrative note of use for a curator but of no use for a user
definition editor: PERSON:Alan Ruttenberg
database cross reference: IAO:0000232
has_obo_namespace: uberon
id: curator_notes
is metadata tag: true
is metadata tag: 1
shorthand: curator_notes
label: curator notes

term tracker item
type: AnnotationProperty
editor preferred label: term tracker item
example of usage: the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
has curation status: IAO_0000125
definition: An IRI or similar locator for a request or discussion of an ontology term.
definition editor: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
definition source: Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
database cross reference: IAO:0000233
has_obo_namespace: external
has_obo_namespace: uberon
id: term_tracker_item
is class level: true
is metadata tag: true
shorthand: term_tracker_item
comment: The 'tracker item' can associate a tracker with a specific ontology term.

imported from
type: AnnotationProperty
editor preferred label: imported from
has curation status: IAO_0000125
definition: For external terms/classes, the ontology from which the term was imported
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBI:<http://purl.obolibrary.org/obo/obi>

expand assertion to
type: AnnotationProperty

OBO foundry unique label
type: AnnotationProperty
editor preferred label: OBO foundry unique label
has curation status: IAO_0000125
definition: An alternative name for a class or property which is unique across the OBO Foundry.
editor note: The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools .
definition editor: PERSON:Alan Ruttenberg
definition editor: PERSON:Bjoern Peters
definition editor: PERSON:Chris Mungall
definition editor: PERSON:Melanie Courtot
definition source: GROUP:OBO Foundry <http://obofoundry.org/>

elucidation
type: AnnotationProperty

has associated axiom(nl)
type: AnnotationProperty

has associated axiom(fol)
type: AnnotationProperty

has axiom label
type: AnnotationProperty

term replaced by
type: AnnotationProperty
editor preferred label: term replaced by
has curation status: IAO_0000125
definition: Use on obsolete terms, relating the term to another term that can be used as a substitute
definition editor: Person:Alan Ruttenberg
definition source: Person:Alan Ruttenberg

RUBRIC
type: AnnotationProperty
definition editor: Cooper Stansbury
curator note: This annotation property specifies classes that were developed as part of an alignment effort between the Common Rule Ontology and the Informed Consent Ontology in the Summer of 2018. These classes represent entities that are necessary for understanding the regularatory frameworks that influence informed consent, often at a different level of granularity than individual consent processes. These classes were created to be compatible with regulatory frameworks outside the Unitied States, hence they are general.

Related_To_Genetic_Biomarker
type: AnnotationProperty
definition: An association that indicates that a finding or lab test is related to a gene, possibly through a variant or product.
code: A13
Semantic_Type: Conceptual Entity
Preferred_Name: Related_To_Genetic_Biomarker
has exact synonym: Related_To_Genetic_Biomarker

Has_PCDC_Data_Type
type: AnnotationProperty
definition: An association that specifies one of three data types for a particular variable, String, Code or Number.
code: A23
Semantic_Type: Conceptual Entity
Preferred_Name: Has_PCDC_Data_Type
has exact synonym: Has_PCDC_Data_Type

Is_PCDC_AML_Authorized_Value_For_Variable
type: AnnotationProperty
definition: An association that indicates a PCDC AML concept is a Authorized Value for a PCDC AML Variable concept.
code: A24
Semantic_Type: Conceptual Entity
Preferred_Name: Is_PCDC_AML_Authorized_Value_For_Variable
has exact synonym: Is_PCDC_AML_Authorized_Value_For_Variable

Is_PCDC_EWS_Authorized_Value_For_Variable
type: AnnotationProperty
definition: An association that indicates a PCDC EWS concept is a Authorized Value for a specific PCDC EWS Variable concept.
code: A28
Semantic_Type: Conceptual Entity
Preferred_Name: Is_PCDC_EWS_Authorized_Value_For_Variable
has exact synonym: Is_PCDC_EWS_Authorized_Value_For_Variable

Has_PCDC_EWS_Authorized_Value
type: AnnotationProperty
definition: An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept.
code: A29
Semantic_Type: Conceptual Entity
Preferred_Name: Has_PCDC_EWS_Authorized_Value
has exact synonym: Has_PCDC_EWS_Authorized_Value

Has_GDC_Value
type: AnnotationProperty
definition: An association that connects a concept representing a GDC property to its dedicated value concept(s).
code: A31
Semantic_Type: Conceptual Entity
Preferred_Name: Has_GDC_Value
has exact synonym: Has_GDC_Value

Is_Value_For_GDC_Property
type: AnnotationProperty
definition: An association that that connects a concept representing a GDC value to any associated GDC property concept(s).
code: A32
Semantic_Type: Conceptual Entity
Preferred_Name: Is_Value_For_GDC_Property
has exact synonym: Is_Value_For_GDC_Property

Is_PCDC_GCT_Authorized_Value_For_Variable
type: AnnotationProperty
definition: An association that indicates a concept is a dedicated Authorized Value concept for a specific PCDC GCT Variable.
definition: An association that indicates a concept is a dedicated Permissible Value concept for a specific PCDC GCT Variable.
code: A33
Semantic_Type: Conceptual Entity
Preferred_Name: Is_PCDC_GCT_Authorized_Value_For_Variable
Preferred_Name: Is_PCDC_GCT_Permissible_Value_For_Variable
has exact synonym: Is_PCDC_GCT_Authorized_Value_For_Variable
has exact synonym: Is_PCDC_GCT_Permissible_Value_For_Variable
label: Is_PCDC_GCT_Permissible_Value_For_Variable

Has_PCDC_GCT_Permissible_Value
type: AnnotationProperty
definition: An association that shows which Permissible Values are possible for a specific PCDC GCT Variable.
code: A34
Semantic_Type: Conceptual Entity
Preferred_Name: Has_PCDC_GCT_Permissible_Value
has exact synonym: Has_PCDC_GCT_Permissible_Value

Is_PCDC_ALL_Authorized_Value_For_Variable
type: AnnotationProperty
definition: An association that indicates a PCDC ALL concept is a Authorized Value for a PCDC ALL Variable concept.
code: A35
Semantic_Type: Conceptual Entity
Preferred_Name: Is_PCDC_ALL_Authorized_Value_For_Variable
has exact synonym: Is_PCDC_ALL_Authorized_Value_For_Variable

Has_SeroNet_Permissible_Value
type: AnnotationProperty
definition: An association that shows which Permissible Values are possible for a specific SeroNet Variable.
code: A37
Semantic_Type: Conceptual Entity
Preferred_Name: Has_SeroNet_Permissible_Value
has exact synonym: Has_SeroNet_Permissible_Value

Has_PCDC_OS_Authorized_Value
type: AnnotationProperty
definition: An association that shows which Authorized Values are possible for a specific PCDC OS Variable.
definition: An association that shows which Permissible Values are possible for a specific PCDC OS Variable.
code: A38
Semantic_Type: Conceptual Entity
Preferred_Name: Has_PCDC_OS_Authorized_Value
Preferred_Name: Has_PCDC_OS_Permissible_Value
has exact synonym: Has_PCDC_OS_Authorized_Value
has exact synonym: Has_PCDC_OS_Permissible_Value
label: Has_PCDC_OS_Permissible_Value

Has_PCDC_HL_Authorized_Value
type: AnnotationProperty
definition: An association that shows which Authorized Values are possible for a specific PCDC HL Variable.
code: A39
Semantic_Type: Conceptual Entity
Preferred_Name: Has_PCDC_HL_Authorized_Value
has exact synonym: Has_PCDC_HL_Authorized_Value

Has_DIPG_DMG_Authorized_Value
type: AnnotationProperty
definition: An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable.
code: A40
Semantic_Type: Conceptual Entity
Preferred_Name: Has_DIPG_DMG_Authorized_Value
has exact synonym: Has_DIPG_DMG_Authorized_Value

Has_OORO_PC_Value
type: AnnotationProperty
definition: An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute.
code: A42
Semantic_Type: Conceptual Entity
Preferred_Name: Has_OORO_PC_Value
has exact synonym: Has_OORO_PC_Value

code
type: AnnotationProperty
read only: true
definition: A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus.
code: NHC0
Semantic_Type: Conceptual Entity
Preferred_Name: code
has exact synonym: code

Semantic_Type
type: AnnotationProperty
definition: A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
definition: The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
code: P106
Semantic_Type: Conceptual Entity
Display_Name: Semantic Type
Preferred_Name: Semantic_Type
DesignNote: In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS.
has exact synonym: Semantic_Type

Display_Name
type: AnnotationProperty
definition: A property representing an alternative Preferred Name for use in some NCI systems.
definition: Provides an alternative Preferred Name for use in some NCI systems.
code: P107
Semantic_Type: Conceptual Entity
Display_Name: Display Name
Preferred_Name: Display_Name
has exact synonym: Display Name
has exact synonym: Display_Name

Preferred_Name
type: AnnotationProperty
definition: A property representing the word or phrase that NCI uses by preference to refer to the concept.
definition: The word or phrase that NCI uses by preference to refer to the concept.
code: P108
Semantic_Type: Conceptual Entity
Display_Name: Preferred Name
Preferred_Name: Preferred_Name
has exact synonym: Preferred Name
has exact synonym: Preferred Term
has exact synonym: Preferred_Name

UMLS_CUI
type: AnnotationProperty
definition: A property representing the concept unique identifier (CUI) assigned by the National Library of Medicine (NLM). If a concept in any NCI-maintained knowledgebase exists in the NLM Unified Medical Language System (UMLS), NCI includes the NLM CUI among the information we provide about the concept.
code: P207
Semantic_Type: Conceptual Entity
Display_Name: UMLS CUI
Preferred_Name: UMLS_CUI
has exact synonym: UMLS_CUI

NCI_META_CUI
type: AnnotationProperty
definition: A property representing the concept unique identifier (CUI) for those concepts that appear in NCI Metathesaurus but not in the National Library of Medicine Unified Medical Language System (NLM UMLS).
code: P208
Semantic_Type: Conceptual Entity
Display_Name: NCI Metathesaurus CUI
Preferred_Name: NCI_META_CUI
has exact synonym: NCI_META_CUI

FDA_Table
type: AnnotationProperty
definition: A property used to flag terms that are part of an FDA data standard manual, including Route of Administration, Dosage Form, Package Type and Potency.
code: P317
Semantic_Type: Conceptual Entity
Display_Name: FDA Table
Preferred_Name: FDA_Table
has exact synonym: FDA_Table

Contributing_Source
type: AnnotationProperty
definition: A property is used to indicate when a non-EVS entity has contributed to, and has a stake in, a concept. This is used where such entities, within or outside NCI, have indicated the need to be able to track their own concepts. A single concept can have multiple instances of this property if multiple entities have such a defined stake.
code: P322
Semantic_Type: Conceptual Entity
Display_Name: Contributing Source
Preferred_Name: Contributing_Source
has exact synonym: Contributing_Source

ALT_DEFINITION
type: AnnotationProperty
definition: A property representing the English language definition of a concept from a source other than NCI.
code: P325
Semantic_Type: Conceptual Entity
Display_Name: [source] Definition
Preferred_Name: ALT_DEFINITION
has exact synonym: ALT_DEFINITION

miRBase_ID
type: AnnotationProperty
definition: A property representing the accession number for an miRNA within the Sanger miRBase database.
code: P362
Semantic_Type: Conceptual Entity
Preferred_Name: miRBase_ID
has exact synonym: miRBase_ID

Legacy Concept Name
type: AnnotationProperty
read only: true
definition: A property representing a retired unique concept identifier created and stored as Concept Name by legacy EVS software. Use of these values was long discouraged, but continued as late as 2009 when creation of new values ceased and Concept Name was retired. Legacy values are intended solely to help resolve and update earlier coding.
code: P366
Semantic_Type: Conceptual Entity
Preferred_Name: Legacy Concept Name
has exact synonym: Legacy Concept Name
has exact synonym: Legacy_Concept_Name

Maps_To
type: AnnotationProperty
definition: A property representing that a term in another terminology has been mapped to a term in NCIt and describes the relationship between the mapped terms.
code: P375
Semantic_Type: Conceptual Entity
Preferred_Name: Maps_To
has exact synonym: Maps_To

DesignNote
type: AnnotationProperty
definition: A property representing notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
definition: Design notes are notations made by NCI vocabulary curators. They are intended to provide supplemental, unstructured information to the user or additional insight about the concept.
code: P98
Semantic_Type: Conceptual Entity
Display_Name: DesignNote
Preferred_Name: DesignNote
has exact synonym: DesignNote

ISA alternative term
type: AnnotationProperty
editor preferred label: ISA alternative term
has curation status: IAO_0000122
definition: An alternative term used by the ISA tools project (http://isa-tools.org).
editor note: Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
definition editor: Person: Alejandra Gonzalez-Beltran
definition editor: Person: Philippe Rocca-Serra
definition source: ISA tools project (http://isa-tools.org)
sub property of: alternative term

IEDB alternative term
type: AnnotationProperty
editor preferred label: IEDB alternative term
has curation status: IAO_0000122
definition: An alternative term used by the IEDB.
definition editor: PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
definition source: IEDB
sub property of: alternative term

symbol from nomenclature authority
type: AnnotationProperty
definition: the symbol assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

full name from nomenclature authority
type: AnnotationProperty
definition: the full name assigned by the nomenclature authority
definition editor: Oliver He, Yue Liu

NCBI GeneID
type: AnnotationProperty
definition: A GeneID in the NCBI Gene database
definition editor: Oliver He, Yue Liu

NCBI LocusTag
type: AnnotationProperty
definition: the NCBI LocusTag name of a gene
definition editor: Oliver He, Yue Liu

gene map location
type: AnnotationProperty
definition: the map location of a gene
definition editor: Oliver He, Yue Liu

modification date
type: AnnotationProperty
definition: a date of content modification
definition editor: Oliver He, Yue Liu

organism NCBITaxon ID
type: AnnotationProperty
definition: The NCBITaxon ontology ID of an organism.
definition editor: Oliver He, Yue Liu

chromosome ID of gene
type: AnnotationProperty
definition: A chromosome ID where a gene is located.
definition editor: Oliver He

type of gene
type: AnnotationProperty
definition: an annotation property that specifies the type of a gene
definition editor: Oliver He

nomenclature status
type: AnnotationProperty
definition: an annotation property that specifies a nomenclature status
definition editor: Oliver He

has GO association
type: AnnotationProperty
definition: an annotation property that shows the GO information associated with a specific gene.
definition editor: Yongqun He

has PubMed association
type: AnnotationProperty
definition: An annotation property that represents a gene's association with PubMed publication(s).
definition editor: Yongqun He

never in taxon
type: AnnotationProperty
example of usage: tooth SubClassOf 'never in taxon' value 'Aves'
definition: S never_in_taxon T iff: S SubClassOf in_taxon only not T.
definition: x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL.
definition 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
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
expand assertion to: Class: ?X DisjointWith: RO_0002162 some ?Y
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX never_in_taxon: <http://purl.obolibrary.org/obo/RO_0002161> CONSTRUCT { in_taxon: a owl:ObjectProperty . a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . ?x rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom [ a owl:Class ; owl:complementOf ?taxon ] ] . } WHERE { ?x never_in_taxon: ?taxon . }
database cross reference: RO:0002161
has_obo_namespace: uberon
id: never_in_taxon
is class level: true
is metadata tag: true
shorthand: never_in_taxon
label: never_in_taxon

mutually_spatially_disjoint_with
type: AnnotationProperty
definition: A is mutually_spatially_disjoint_with B if both A and B are classes, and there exists no p such that p is part_of some A and p is part_of some B.
alternative term: non-overlapping with
alternative term: shares no parts with
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
expand assertion to: Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
OMO_0002000: PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX part_of: <http://purl.obolibrary.org/obo/BFO_0000050> PREFIX mutually_spatially_disjoint_with: <http://purl.obolibrary.org/obo/RO_0002171> CONSTRUCT { part_of: a owl:ObjectProperty . [ a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?x ; a owl:Restriction ; owl:onProperty part_of: ; owl:someValuesFrom ?y ] ] } WHERE { ?x mutually_spatially_disjoint_with: ?y . }
database cross reference: RO:0002171
has_obo_namespace: uberon
id: mutually_spatially_disjoint_with
is class level: true
is metadata tag: true
shorthand: mutually_spatially_disjoint_with
label: mutually spatially disjoint with

present_in_taxon
type: AnnotationProperty
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
definition: S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.
definition editor: https://orcid.org/0000-0002-6601-2165
definition source: http://www.ncbi.nlm.nih.gov/pubmed/22293552
OMO_0002000: PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> PREFIX present_in_taxon: <http://purl.obolibrary.org/obo/RO_0002175> CONSTRUCT { in_taxon: a owl:ObjectProperty . ?witness rdfs:label ?label . ?witness rdfs:subClassOf ?x . ?witness rdfs:subClassOf [ a owl:Restriction ; owl:onProperty in_taxon: ; owl:someValuesFrom ?taxon ] . } WHERE { ?x present_in_taxon: ?taxon . BIND(IRI(CONCAT( "http://purl.obolibrary.org/obo/RO_0002175#", MD5(STR(?x)), "-", MD5(STR(?taxon)) )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) }
database cross reference: RO:0002175
has exact synonym: applicable for taxon
has_obo_namespace: uberon
id: present_in_taxon
is class level: true
is metadata tag: true
shorthand: present_in_taxon
comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology.
label: present in taxon

is opposite of
type: AnnotationProperty
example of usage: 'anterior end of organism' is-opposite-of 'posterior end of organism'
example of usage: 'increase in temperature' is-opposite-of 'decrease in temperature'
definition: x is the opposite of y if there exists some distance metric M, and there exists no z such as M(x,z) <= M(x,y) or M(y,z) <= M(y,x).
database cross reference: RO:0002604
has_obo_namespace: quality
id: is_opposite_of
is class level: true
is metadata tag: true
shorthand: is_opposite_of
label: is_opposite_of

curator note
type: AnnotationProperty
definition: An administrative note of use for a curator but of no use for a user.
definition source: curator note
description adapted from source: no
property has curation status: organizational term
database cross reference: IAO:0000232
has exact synonym: editor_notes

definition source
type: AnnotationProperty
definition: A source from where the formal description was derived. This can be in the form of a link to a relevant webpage, the IRI of a term in an existing ontology, a reference to specific literature, etc.
definition source: definition source
description adapted from source: yes
property has curation status: metadata complete - requires restrictions and relationships
database cross reference: IAO:0000119
preferred label: description source

description adapted from source
type: AnnotationProperty
definition: An assertion of whether or not the term/class description is an adaptation of the description in the description source.
curator note: Requested inclusion of this property into RO. Check details here again after inclusion.
property has curation status: metadata complete - requires restrictions and relationships
creator: SCDO

property has curation status
type: AnnotationProperty
definition: Description inherent in name (not provided by source)
description adapted from source: Only label adapted
property has curation status: organizational term

existence in other ontologies
type: AnnotationProperty
definition: An indication of whether a term/class already exists in other ontologies. Only used for term (descriptions) that were not taken directly from an existing ontology.
creator: SCDO (Jade Hotchkiss)

previous identifier
type: AnnotationProperty
definition: Used to record the identifier that had been used previously but is no longer in use.
creator: SCDO (Jade Hotchkiss)

STATO alternative term
type: AnnotationProperty
definition: an alternative term used for STATO statistical ontology and ISA team
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra

external_definition
type: AnnotationProperty
definition: An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
database cross reference: UBPROP:0000001
has_obo_namespace: uberon
id: external_definition
is metadata tag: true
shorthand: external_definition
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

axiom_lost_from_external_ontology
type: AnnotationProperty
definition: A textual description of an axiom loss in this ontology compared to an external ontology.
database cross reference: UBPROP:0000002
has_obo_namespace: uberon
id: axiom_lost_from_external_ontology
is metadata tag: true
shorthand: axiom_lost_from_external_ontology
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

homology_notes
type: AnnotationProperty
definition: Notes on the homology status of this class.
database cross reference: UBPROP:0000003
has_obo_namespace: uberon
id: homology_notes
is metadata tag: true
shorthand: homology_notes
comment: This annotation property may be replaced with an annotation property from an external ontology such as IAO

has_relational_adjective
type: AnnotationProperty
curator note: Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
database cross reference: UBPROP:0000007
has_obo_namespace: uberon
id: has_relational_adjective
is metadata tag: true
shorthand: has_relational_adjective

taxon_notes
type: AnnotationProperty
definition: Notes on the how instances of this class vary across species.
database cross reference: UBPROP:0000008
has_obo_namespace: uberon
id: taxon_notes
is metadata tag: true
shorthand: taxon_notes

function_notes
type: AnnotationProperty
definition: Notes on the evolved function of instances of this class.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database cross reference: UBPROP:0000009
has_obo_namespace: uberon
id: function_notes
is metadata tag: true
shorthand: function_notes

external_ontology_notes
type: AnnotationProperty
definition: Notes on how similar or equivalent classes are represented in other ontologies.
editor note: This annotation property may be replaced with an annotation property from an external ontology such as IAO
database cross reference: UBPROP:0000012
has_obo_namespace: uberon
id: external_ontology_notes
is metadata tag: true
shorthand: external_ontology_notes

fma_set_term
type: AnnotationProperty
external_ontology_notes: FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
database cross reference: UBPROP:0000202
has_obo_namespace: uberon
id: fma_set_term
is metadata tag: true
shorthand: fma_set_term

excluded subClassOf
type: AnnotationProperty
id: excluded_subClassOf
is metadata tag: true

creator
type: AnnotationProperty
definition: An entity primarily responsible for making the resource. (This property is used in the SCDO when a term was created by the SCDO Working Group or a curator.) The SCDO uses this especially to apply to term descriptions.
definition source: creator
description adapted from source: no
property has curation status: ready for release
description: Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity.
has_obo_namespace: uberon
id: dc-creator
is metadata tag: true
shorthand: dc-creator
comment: An entity primarily responsible for making the content of the resource.
label: Creator
label: dc:creator

Description
type: AnnotationProperty
description: Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content.
has_obo_namespace: uberon
id: dc-description
is metadata tag: true
shorthand: dc-description
comment: An account of the content of the resource.
label: description

identifier
type: AnnotationProperty
python name: identifier_dc

dc:source
type: AnnotationProperty
definition: A related resource from which the described class/term's annotations are derived.
definition source: source
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers

contributor
type: AnnotationProperty
has_obo_namespace: uberon
id: dc-contributor
is metadata tag: true
shorthand: dc-contributor

branch class
type: AnnotationProperty
comment: For use in the EMBL-EBI ArrayExpress interface.

definition_citation
type: AnnotationProperty
definition: A definition citation is a document, ontology class, person or organization from which the definition of the class is derived. It is used in the same sense as a citation in literature, in that the definition may have been derived from these sources or that this definition is related to these source.

consider
type: AnnotationProperty

created_by
type: AnnotationProperty
definition: Author of the class.
sub property of: creator

creation date
type: AnnotationProperty
definition: Date class was created.
label: creation_date

has_alternative_id
type: AnnotationProperty
definition: ID of merged class.

has_broad_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/18
label: has broad synonym

database cross reference
type: AnnotationProperty
definition: A database cross-reference. An annotation which directs one to information contained within a database.
definition: A property representing a reference to an identical or very similar object in another database.
definition: Reference database or publication source.
Semantic_Type: Conceptual Entity
Preferred_Name: xRef
definition source: SBO:0000554
property has curation status: metadata complete - requires restrictions and relationships
database cross reference: IAO:0100001
database cross reference: SBO:0000554
has exact synonym: DbXref
has exact synonym: Xref
has exact synonym: database cross-reference
has exact synonym: database_cross_reference
has exact synonym: db xref
has exact synonym: hasDbXref
label: database_cross_reference
label: has database cross reference
label: xRef
label: 数据库_交叉_引用

has exact synonym
type: AnnotationProperty
definition: A property representing a fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
definition: An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle.
definition: An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
definition: An alternative label for a given entity such as a commonly used abbreviation or synonym.
definition: Exact synonym.
definition: Fully qualified synonym, contains the string, term type, source, and an optional source code if appropriate. Each subfield is deliniated to facilitate interpretation by software.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/20
description adapted from source: no
property has curation status: pending vetting by the SCDO developers
database cross reference: IAO:0100001
has exact synonym: FULL_SYN
has exact synonym: Synonym with Source Data
label: hasExactSynonym
label: has_exact_synonym

has_narrow_synonym
type: AnnotationProperty
definition: An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/19
label: has narrow synonym

has_obo_namespace
type: AnnotationProperty
definition: Name space of the ontology.
database cross reference: IAO:0100001
comment: disease_ontology
label: 有_obo_命名空间

has_related_synonym
type: AnnotationProperty
definition: An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct.
definition: Has related synonym.
definition editor: http://orcid.org/0000-0001-5208-3432
term tracker item: https://github.com/information-artifact-ontology/ontology-metadata/issues/21
label: has related synonym

has synonym
type: AnnotationProperty

id
type: AnnotationProperty
definition: An identifier for an individual entity.
definition: An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.

in subset
type: AnnotationProperty
definition: An association that connects the concept defining a particular terminology subset with concepts that belong to this subset.
definition: In subset.
has exact synonym: Concept_In_Subset
label: in_subset

shorthand
type: AnnotationProperty
editor preferred label: shorthand
database cross reference: IAO:0100001

comment
type: AnnotationProperty
definition: Comment.

rdfs:isDefinedBy
type: AnnotationProperty
definition: Is defined by.
OBO foundry unique label: is defined by

label
type: AnnotationProperty
editor preferred label: label
definition: A human readable name for this class.
definition: A human-readable name for the class/term.
description adapted from source: yes
comment: A human-readable name for the subject.
label: rdfs:label
label: 标签

see also
type: AnnotationProperty
database cross reference: seeAlso
has_obo_namespace: spatial
has_obo_namespace: uberon
id: seeAlso
is class level: true
is metadata tag: true
shorthand: seeAlso
python name: see_also_rdf_schema
label: seeAlso

change note
type: AnnotationProperty
imported from: core
definition: A note about a modification to a concept.
sub property of: note

definition
type: AnnotationProperty
imported from: core
definition: A statement or formal explanation of the meaning of a concept.

has exact match
type: AnnotationProperty
definition: A skos concept mapping used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably.

note
type: AnnotationProperty
imported from: core
definition: A general note, for any purpose.
scope note: This property may be used directly, or as a super-property for more specific note types.

preferred label
type: AnnotationProperty
imported from: core
definition: A preferred label.
description adapted from source: yes
property has curation status: pending vetting by the SCDO developers
label: skos:prefLabel
definition: The preferred lexical label for a resource, in a given language.
sub property of: label

scope note
type: AnnotationProperty
imported from: core
definition: A note that helps to clarify the meaning and/or the use of a concept.
sub property of: note

depicted by
type: AnnotationProperty
has_obo_namespace: uberon
id: depicted_by
is metadata tag: true
shorthand: depicted_by

alternate name
type: AnnotationProperty

isCandidateBiomarkerFor
type: ObjectProperty

isPrognosticBiomarkerFor
type: ObjectProperty

isDiagnosticBiomarkerFor
type: ObjectProperty

isMonitoringBiomarkerFor
type: ObjectProperty

isPredictiveBiomarkerFor
type: ObjectProperty

isDigitalBiomarkerFor
type: ObjectProperty

isImagingBiomarkerFor
type: ObjectProperty

isBiomarkerOfAging
type: ObjectProperty

procedure
type: Class
subclass of: realizable entity
imported from: latest.xml
definition: A procedure is plan containing multiple activities that are intended to be executed in an order following a procedure specification. [Allotrope]

total tau
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein that is regarded as a general marker of neurodegeneration for evaluation in future population-based studies and represents the total tau concentration in a given sample.
imported from: ado.owl
has db xref: https://pubmed.ncbi.nlm.nih.gov/15178952/

phosphorylated tau
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein that is phosphorylated through post-translational modification. Its accumulation reflects the formation of neurofibrillary tangles, synaptic impairment, and neuronal dysfunction.
imported from: ado.owl
has db xref: https://pubmed.ncbi.nlm.nih.gov/32812023/

entity
type: Class
subclass of: Thing
BFO OWL specification label: entity
BFO CLIF specification label: Entity
example of usage: Julius Caesar
example of usage: Verdi’s Requiem
example of usage: the Second World War
example of usage: your body mass index
editor note: BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
editor note: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
elucidation: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])

Axiom
annotated source: entity
annotated property: editor note
annotated target: Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000004
comment: per discussion with Barry Smith

Axiom
annotated source: entity
annotated property: elucidation
annotated target: An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/001-001

continuant
type: Class
subclass of: entity
disjoint with: occurrent
BFO OWL specification label: continuant
BFO CLIF specification label: Continuant
editor note: BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
editor note: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
elucidation: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has associated axiom(nl): if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has associated axiom(nl): if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has associated axiom(nl): if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has associated axiom(fol): (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has associated axiom(fol): (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has associated axiom(fol): (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

Axiom
annotated source: continuant
annotated property: editor note
annotated target: Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000007

Axiom
annotated source: continuant
annotated property: elucidation
annotated target: A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/008-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/126-001

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/009-002

Axiom
annotated source: continuant
annotated property: has associated axiom(nl)
annotated target: if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/011-002

occurrent
type: Class
subclass of: entity
BFO OWL specification label: occurrent
BFO CLIF specification label: Occurrent
editor note: BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
editor note: BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
editor note: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
editor note: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
elucidation: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has associated axiom(nl): Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has associated axiom(nl): b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has associated axiom(fol): (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has associated axiom(fol): (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000006
comment: per discussion with Barry Smith

Axiom
annotated source: occurrent
annotated property: editor note
annotated target: Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000012

Axiom
annotated source: occurrent
annotated property: elucidation
annotated target: An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/077-002

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(nl)
annotated target: b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/108-001

Axiom
annotated source: occurrent
annotated property: has associated axiom(fol)
annotated target: (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/079-001

independent continuant
type: Class
subclass of: continuant
disjoint with: specifically dependent continuant
disjoint with: generically dependent continuant
BFO OWL specification label: ic
BFO CLIF specification label: IndependentContinuant
example of usage: a chair
example of usage: a heart
example of usage: a leg
example of usage: a molecule
example of usage: a spatial region
example of usage: an atom
example of usage: an orchestra.
example of usage: an organism
example of usage: the bottom right portion of a human torso
example of usage: the interior of your mouth
definition: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has associated axiom(nl): For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has associated axiom(nl): For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has associated axiom(fol): (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has associated axiom(fol): (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has associated axiom(fol): (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]

Axiom
annotated source: independent continuant
annotated property: definition
annotated target: b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(nl)
annotated target: For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/134-001

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/018-002

Axiom
annotated source: independent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/017-002

spatial region
type: Class
subclass of: immaterial entity
disjoint with: site
disjoint with: continuant fiat boundary
BFO OWL specification label: s-region
BFO CLIF specification label: SpatialRegion
editor note: BFO 2 Reference: Spatial regions do not participate in processes.
editor note: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
elucidation: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has associated axiom(nl): All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has associated axiom(fol): (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has associated axiom(fol): (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]

Axiom
annotated source: spatial region
annotated property: editor note
annotated target: Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000002
comment: per discussion with Barry Smith

Axiom
annotated source: spatial region
annotated property: elucidation
annotated target: A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(nl)
annotated target: All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/036-001

Axiom
annotated source: spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/035-001

temporal region
type: Class
subclass of: occurrent
disjoint with: spatiotemporal region
disjoint with: process
disjoint with: process boundary
BFO OWL specification label: t-region
BFO CLIF specification label: TemporalRegion
editor note: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
elucidation: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has associated axiom(nl): All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has associated axiom(nl): Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has associated axiom(fol): (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has associated axiom(fol): (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has associated axiom(fol): (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]

Axiom
annotated source: temporal region
annotated property: editor note
annotated target: Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000003
comment: per discussion with Barry Smith

Axiom
annotated source: temporal region
annotated property: elucidation
annotated target: A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(nl)
annotated target: Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/119-002

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/101-001

Axiom
annotated source: temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/100-001

two-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 2d-s-region
BFO CLIF specification label: TwoDimensionalSpatialRegion
example of usage: an infinitely thin plane in space.
example of usage: the surface of a sphere-shaped part of space
elucidation: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has associated axiom(fol): (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]

Axiom
annotated source: two-dimensional spatial region
annotated property: elucidation
annotated target: A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

Axiom
annotated source: two-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/039-001

spatiotemporal region
type: Class
subclass of: occurrent
BFO OWL specification label: st-region
BFO CLIF specification label: SpatiotemporalRegion
example of usage: the spatiotemporal region occupied by a human life
example of usage: the spatiotemporal region occupied by a process of cellular meiosis.
example of usage: the spatiotemporal region occupied by the development of a cancer tumor
elucidation: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has associated axiom(nl): All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has associated axiom(nl): Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has associated axiom(nl): Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has associated axiom(nl): Every spatiotemporal region occupies_spatiotemporal_region itself.
has associated axiom(nl): Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has associated axiom(fol): (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has associated axiom(fol): (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has associated axiom(fol): (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has associated axiom(fol): (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]

Axiom
annotated source: spatiotemporal region
annotated property: elucidation
annotated target: A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(nl)
annotated target: Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/107-002

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/099-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/096-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/095-001

Axiom
annotated source: spatiotemporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/098-001

process
type: Class
subclass of: occurrent
BFO OWL specification label: process
BFO CLIF specification label: Process
example of usage: a process of cell-division, \ a beating of the heart
example of usage: a process of meiosis
example of usage: a process of sleeping
example of usage: the course of a disease
example of usage: the flight of a bird
example of usage: the life of an organism
example of usage: your process of aging.
definition: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
editor note: BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
has associated axiom(fol): (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]

Axiom
annotated source: process
annotated property: definition
annotated target: p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

Axiom
annotated source: process
annotated property: has associated axiom(fol)
annotated target: (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/083-003

disposition
type: Class
subclass of: realizable entity
disjoint with: role
BFO OWL specification label: disposition
BFO CLIF specification label: Disposition
example of usage: an atom of element X has the disposition to decay to an atom of element Y
example of usage: certain people have a predisposition to colon cancer
example of usage: children are innately disposed to categorize objects in certain ways.
example of usage: the cell wall is disposed to filter chemicals in endocytosis and exocytosis
editor note: BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
elucidation: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has associated axiom(nl): If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has associated axiom(fol): (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has associated axiom(fol): (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]

Axiom
annotated source: disposition
annotated property: elucidation
annotated target: b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

Axiom
annotated source: disposition
annotated property: has associated axiom(nl)
annotated target: If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/063-002

Axiom
annotated source: disposition
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/062-002

realizable entity
type: Class
subclass of: specifically dependent continuant
disjoint with: quality
BFO OWL specification label: realizable
BFO CLIF specification label: RealizableEntity
example of usage: the disposition of this piece of metal to conduct electricity.
example of usage: the disposition of your blood to coagulate
example of usage: the function of your reproductive organs
example of usage: the role of being a doctor
example of usage: the role of this boundary to delineate where Utah and Colorado meet
elucidation: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has associated axiom(nl): All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has associated axiom(fol): (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has associated axiom(fol): (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]

Axiom
annotated source: realizable entity
annotated property: elucidation
annotated target: To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(nl)
annotated target: All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/060-002

Axiom
annotated source: realizable entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/058-002

zero-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 0d-s-region
BFO CLIF specification label: ZeroDimensionalSpatialRegion
elucidation: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]

Axiom
annotated source: zero-dimensional spatial region
annotated property: elucidation
annotated target: A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

Axiom
annotated source: zero-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/037-001

quality
type: Class
subclass of: specifically dependent continuant
BFO OWL specification label: quality
BFO CLIF specification label: Quality
example of usage: the ambient temperature of this portion of air
example of usage: the color of a tomato
example of usage: the length of the circumference of your waist
example of usage: the mass of this piece of gold.
example of usage: the shape of your nose
example of usage: the shape of your nostril
elucidation: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has associated axiom(nl): If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has associated axiom(fol): (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has associated axiom(fol): (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]

Axiom
annotated source: quality
annotated property: elucidation
annotated target: a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(nl)
annotated target: If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/055-001

Axiom
annotated source: quality
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/105-001

specifically dependent continuant
type: Class
subclass of: continuant
disjoint with: generically dependent continuant
BFO OWL specification label: sdc
BFO CLIF specification label: SpecificallyDependentContinuant
example of usage: Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
example of usage: of one-sided specifically dependent continuants: the mass of this tomato
example of usage: of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
example of usage: the disposition of this fish to decay
example of usage: the function of this heart: to pump blood
example of usage: the mutual dependence of proton donors and acceptors in chemical reactions [79
example of usage: the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
example of usage: the pink color of a medium rare piece of grilled filet mignon at its center
example of usage: the role of being a doctor
example of usage: the shape of this hole.
example of usage: the smell of this portion of mozzarella
definition: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
editor note: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has associated axiom(fol): (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]

Axiom
annotated source: specifically dependent continuant
annotated property: definition
annotated target: b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

Axiom
annotated source: specifically dependent continuant
annotated property: editor note
annotated target: Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000005
comment: per discussion with Barry Smith

Axiom
annotated source: specifically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/050-003

role
type: Class
subclass of: realizable entity
BFO OWL specification label: role
BFO CLIF specification label: Role
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: the priest role
example of usage: the role of a boundary to demarcate two neighboring administrative territories
example of usage: the role of a building in serving as a military target
example of usage: the role of a stone in marking a property boundary
example of usage: the role of subject in a clinical trial
example of usage: the student role
editor note: BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
elucidation: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has associated axiom(fol): (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]

Axiom
annotated source: role
annotated property: elucidation
annotated target: b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

Axiom
annotated source: role
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/061-001

fiat object part
type: Class
subclass of: material entity
BFO OWL specification label: fiat-object-part
BFO CLIF specification label: FiatObjectPart
example of usage: or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
example of usage: the FMA:regional parts of an intact human body.
example of usage: the Western hemisphere of the Earth
example of usage: the division of the brain into regions
example of usage: the division of the planet into hemispheres
example of usage: the dorsal and ventral surfaces of the body
example of usage: the upper and lower lobes of the left lung
editor note: BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
elucidation: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has associated axiom(fol): (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]

Axiom
annotated source: fiat object part
annotated property: elucidation
annotated target: b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

Axiom
annotated source: fiat object part
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/027-004

one-dimensional spatial region
type: Class
subclass of: spatial region
disjoint with: three-dimensional spatial region
BFO OWL specification label: 1d-s-region
BFO CLIF specification label: OneDimensionalSpatialRegion
example of usage: an edge of a cube-shaped portion of space.
elucidation: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]

Axiom
annotated source: one-dimensional spatial region
annotated property: elucidation
annotated target: A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

Axiom
annotated source: one-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/038-001

object aggregate
type: Class
subclass of: material entity
BFO OWL specification label: object-aggregate
BFO CLIF specification label: ObjectAggregate
example of usage: a collection of cells in a blood biobank.
example of usage: a swarm of bees is an aggregate of members who are linked together through natural bonds
example of usage: a symphony orchestra
example of usage: an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)
example of usage: defined by fiat: the aggregate of members of an organization
example of usage: defined through physical attachment: the aggregate of atoms in a lump of granite
example of usage: defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
example of usage: defined via attributive delimitations such as: the patients in this hospital
example of usage: the aggregate of bearings in a constant velocity axle joint
example of usage: the aggregate of blood cells in your body
example of usage: the nitrogen atoms in the atmosphere
example of usage: the restaurants in Palo Alto
example of usage: your collection of Meissen ceramic plates.
editor note: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
editor note: BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee).
definition source: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
elucidation: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has associated axiom(fol): (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000011

Axiom
annotated source: object aggregate
annotated property: editor note
annotated target: An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000301

Axiom
annotated source: object aggregate
annotated property: definition source
annotated target: ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000300

Axiom
annotated source: object aggregate
annotated property: elucidation
annotated target: b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

Axiom
annotated source: object aggregate
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/025-004

three-dimensional spatial region
type: Class
subclass of: spatial region
BFO OWL specification label: 3d-s-region
BFO CLIF specification label: ThreeDimensionalSpatialRegion
example of usage: a cube-shaped region of space
example of usage: a sphere-shaped region of space,
elucidation: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has associated axiom(fol): (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]

Axiom
annotated source: three-dimensional spatial region
annotated property: elucidation
annotated target: A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

Axiom
annotated source: three-dimensional spatial region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/040-001

site
type: Class
subclass of: immaterial entity
BFO OWL specification label: site
BFO CLIF specification label: Site
example of usage: Manhattan Canyon)
example of usage: a hole in the interior of a portion of cheese
example of usage: a rabbit hole
example of usage: an air traffic control region defined in the airspace above an airport
example of usage: the Grand Canyon
example of usage: the Piazza San Marco
example of usage: the cockpit of an aircraft
example of usage: the hold of a ship
example of usage: the interior of a kangaroo pouch
example of usage: the interior of the trunk of your car
example of usage: the interior of your bedroom
example of usage: the interior of your office
example of usage: the interior of your refrigerator
example of usage: the lumen of your gut
example of usage: your left nostril (a fiat part – the opening – of your left nasal cavity)
elucidation: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has associated axiom(fol): (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]

Axiom
annotated source: site
annotated property: elucidation
annotated target: b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

Axiom
annotated source: site
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/034-002

object
type: Class
subclass of: material entity
BFO OWL specification label: object
BFO CLIF specification label: Object
example of usage: atom
example of usage: cell
example of usage: cells and organisms
example of usage: engineered artifacts
example of usage: grain of sand
example of usage: molecule
example of usage: organelle
example of usage: organism
example of usage: planet
example of usage: solid portions of matter
example of usage: star
editor note: BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting.
editor note: BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below).
editor note: BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47
editor note: BFO 2 Reference: an object is a maximal causally unified material entity
editor note: BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
elucidation: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])

Axiom
annotated source: object
annotated property: elucidation
annotated target: b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/024-001

generically dependent continuant
type: Class
subclass of: continuant
BFO OWL specification label: gdc
BFO CLIF specification label: GenericallyDependentContinuant
example of usage: The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
example of usage: the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
example of usage: the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
definition: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has associated axiom(fol): (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]

Axiom
annotated source: generically dependent continuant
annotated property: definition
annotated target: b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

Axiom
annotated source: generically dependent continuant
annotated property: has associated axiom(fol)
annotated target: (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/074-001

function
type: Class
subclass of: disposition
BFO OWL specification label: function
BFO CLIF specification label: Function
example of usage: the function of a hammer to drive in nails
example of usage: the function of a heart pacemaker to regulate the beating of a heart through electricity
example of usage: the function of amylase in saliva to break down starch into sugar
editor note: BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
elucidation: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has associated axiom(fol): (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]

Axiom
annotated source: function
annotated property: elucidation
annotated target: A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

Axiom
annotated source: function
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/064-001

process boundary
type: Class
subclass of: occurrent
BFO OWL specification label: p-boundary
BFO CLIF specification label: ProcessBoundary
example of usage: the boundary between the 2nd and 3rd year of your life.
definition: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has associated axiom(nl): Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has associated axiom(fol): (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has associated axiom(fol): (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]

Axiom
annotated source: process boundary
annotated property: definition
annotated target: p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

Axiom
annotated source: process boundary
annotated property: has associated axiom(nl)
annotated target: Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/085-002

Axiom
annotated source: process boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/084-001

one-dimensional temporal region
type: Class
subclass of: temporal region
disjoint with: zero-dimensional temporal region
BFO OWL specification label: 1d-t-region
BFO CLIF specification label: OneDimensionalTemporalRegion
example of usage: the temporal region during which a process occurs.
editor note: BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
elucidation: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has associated axiom(fol): (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]

Axiom
annotated source: one-dimensional temporal region
annotated property: elucidation
annotated target: A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

Axiom
annotated source: one-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/103-001

material entity
type: Class
subclass of: independent continuant
disjoint with: immaterial entity
BFO OWL specification label: material
BFO CLIF specification label: MaterialEntity
example of usage: a flame
example of usage: a forest fire
example of usage: a human being
example of usage: a hurricane
example of usage: a photon
example of usage: a puff of smoke
example of usage: a sea wave
example of usage: a tornado
example of usage: an aggregate of human beings.
example of usage: an energy wave
example of usage: an epidemic
example of usage: the undetached arm of a human being
editor note: BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
editor note: BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
editor note: BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
elucidation: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has associated axiom(nl): Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has associated axiom(nl): every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has associated axiom(fol): (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has associated axiom(fol): (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: elucidation
annotated target: A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/020-002

Axiom
annotated source: material entity
annotated property: has associated axiom(nl)
annotated target: every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/021-002

Axiom
annotated source: material entity
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/019-002

continuant fiat boundary
type: Class
subclass of: immaterial entity
BFO OWL specification label: cf-boundary
BFO CLIF specification label: ContinuantFiatBoundary
definition: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
editor note: BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
editor note: BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
editor note: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has associated axiom(nl): Every continuant fiat boundary is located at some spatial region at every time at which it exists
has associated axiom(fol): (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]

Axiom
annotated source: continuant fiat boundary
annotated property: definition
annotated target: b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

Axiom
annotated source: continuant fiat boundary
annotated property: editor note
annotated target: Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000008

Axiom
annotated source: continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/029-001

immaterial entity
type: Class
subclass of: independent continuant
BFO OWL specification label: immaterial
BFO CLIF specification label: ImmaterialEntity
editor note: BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10

one-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
disjoint with: two-dimensional continuant fiat boundary
disjoint with: zero-dimensional continuant fiat boundary
BFO OWL specification label: 1d-cf-boundary
BFO CLIF specification label: OneDimensionalContinuantFiatBoundary
example of usage: The Equator
example of usage: all geopolitical boundaries
example of usage: all lines of latitude and longitude
example of usage: the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
example of usage: the median sulcus of your tongue
elucidation: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has associated axiom(fol): (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

Axiom
annotated source: one-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/032-001

process profile
type: Class
subclass of: process
disjoint with: history
BFO OWL specification label: process-profile
BFO CLIF specification label: ProcessProfile
example of usage: On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
example of usage: One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
example of usage: The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
definition: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
elucidation: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has associated axiom(fol): (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has associated axiom(fol): (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]

Axiom
annotated source: process profile
annotated property: definition
annotated target: b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

Axiom
annotated source: process profile
annotated property: elucidation
annotated target: b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/094-005

Axiom
annotated source: process profile
annotated property: has associated axiom(fol)
annotated target: (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/093-002

relational quality
type: Class
subclass of: quality
BFO OWL specification label: r-quality
BFO CLIF specification label: RelationalQuality
example of usage: John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
example of usage: a marriage bond, an instance of requited love, an obligation between one person and another.
definition: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has associated axiom(fol): (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]

Axiom
annotated source: relational quality
annotated property: definition
annotated target: b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

Axiom
annotated source: relational quality
annotated property: has associated axiom(fol)
annotated target: (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/057-001

two-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 2d-cf-boundary
BFO CLIF specification label: TwoDimensionalContinuantFiatBoundary
elucidation: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has associated axiom(fol): (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

Axiom
annotated source: two-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/033-001

zero-dimensional continuant fiat boundary
type: Class
subclass of: continuant fiat boundary
BFO OWL specification label: 0d-cf-boundary
BFO CLIF specification label: ZeroDimensionalContinuantFiatBoundary
example of usage: the geographic North Pole
example of usage: the point of origin of some spatial coordinate system.
example of usage: the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
editor note: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
elucidation: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has associated axiom(fol): (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: editor note
annotated target: zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/0000001
comment: requested by Melanie Courtot

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: elucidation
annotated target: a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

Axiom
annotated source: zero-dimensional continuant fiat boundary
annotated property: has associated axiom(fol)
annotated target: (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/031-001

zero-dimensional temporal region
type: Class
subclass of: temporal region
BFO OWL specification label: 0d-t-region
BFO CLIF specification label: ZeroDimensionalTemporalRegion
example of usage: a temporal region that is occupied by a process boundary
example of usage: right now
example of usage: the moment at which a child is born
example of usage: the moment at which a finger is detached in an industrial accident
example of usage: the moment of death.
alternative term: temporal instant.
elucidation: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has associated axiom(fol): (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]

Axiom
annotated source: zero-dimensional temporal region
annotated property: elucidation
annotated target: A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

Axiom
annotated source: zero-dimensional temporal region
annotated property: has associated axiom(fol)
annotated target: (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/102-001

history
type: Class
subclass of: process
BFO OWL specification label: history
BFO CLIF specification label: History
elucidation: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])

Axiom
annotated source: history
annotated property: elucidation
annotated target: A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
has axiom label: http://purl.obolibrary.org/obo/bfo/axiom/138-001

copy number variant biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker of genomic variation in which blocks of DNA are missing or for which multiple copies exist.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/
has exact synonym: CNV biomarker

screening biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker to discriminate between healthy individuals and those in an early stage of the disease.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/
has exact synonym: screening marker

companion endpoint
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that is essential to the efficacy and safety of a corresponding therapeutic product.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/

target biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that reports interaction of the drug with its target
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/

staging biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that distinguishes between different stages of chronic disease.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/
has exact synonym: disease stage biomarker

efficacy biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that predicts a beneficial effect of a given treatment.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/

toxicity biomarker
type: Class
subclass of: Safety Biomarker
fromOldVersion: yes
definition: A biomarker that reports to the toxic effect of a drug on an in vitro or in vivo system.
definition source: https://pubmed.ncbi.nlm.nih.gov/22752797/

COX proportional hazards regression model
type: Class
subclass of: Model
fromOldVersion: yes
definition: The Cox proportional hazards regression model, often referred to as Cox regression or just proportional hazards model, is a statistical technique used to analyze the relationship between the survival time of subjects and predictor variables. It's commonly employed in survival analysis, a branch of statistics that deals with time-to-event data, such as time until death or time until recurrence of a disease.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

context of use
type: Class
subclass of: information content entity
definition: The context of use is a concise description of a biomarker's specified use in drug developement.
definition source: https://www.fda.gov/media/122319/download
has exact synonym: COU

biomarker validation
type: Class
subclass of: validation
definition: Validation is a process to establish that the performance of a test, tool, or instrument is acceptable for its intended purpose.
definition source: https://pubmed.ncbi.nlm.nih.gov/33545385/

analitical validation
type: Class
subclass of: biomarker validation
definition: Analytical validation aims to establish the performance characteristics of a biomarker including sensitivity, specificity, accuracy, precision, inter-laboratory reproducibility and other relevant performance characteristics following a pre-specified protocol.
definition source: https://pubmed.ncbi.nlm.nih.gov/33545385/

clinical validation
type: Class
subclass of: biomarker validation
definition: Clinical validation aims to establish an association between the biomarker and the endpoint of interest and to demonstrate the usefulness of the biomarker. Clinical validation relies on external validation and can be done by retrospective use of clinical trial data or by prospective clinical trials. Retrospective use of clinical trial data is a form of external clinical validation where the biomarker evaluation is not part of the original study design.
definition source: https://pubmed.ncbi.nlm.nih.gov/33545385/

clinical specificity
type: Class
subclass of: parameter
definition: Specificity of the biomarker, referred to as the ability of a biomarker or a change in biomarker to distinguish patients who are responders to an intervention from those who are non-responders in terms of changes in clinical endpoints.
definition source: https://pubmed.ncbi.nlm.nih.gov/27891226/

companion diagnostics
type: Class
subclass of: assay
definition: When a biomarker test is designed to be used in conjunction with specific treatment, the test is known as a CDx. Safety and efficacy of the new drug and of the CDx are typically demonstrated in the same clinical trial for both the drug and the test.
definition source: https://pubmed.ncbi.nlm.nih.gov/27891226/
has exact synonym: CDx

complementary diagnostics
type: Class
subclass of: assay
definition: Complementary diagnostics are tests that, although not needed for the prescription of the corresponding therapeutic product, provide useful information on the drug risk/benefit in specific patient subsets
definition source: https://pubmed.ncbi.nlm.nih.gov/27891226/

biomarker regulatory entity
type: Class
subclass of: independent continuant
definition: A biomarker regulatory entity refers to a regulatory organization responsible for qualification and acceptance of biomarkers for futrher use in pharmaceutical research and development.

Japan’s Pharmaceuticals and Medical Devices Agency
type: Class
subclass of: biomarker regulatory entity
definition: Pharmaceuticals and Medical Devices Agency (PMDA) is Japanese regulatory agency, working together with Ministry of Health, Labour and Welfare. Its obligation is to protect the public health by assuring safety, efficacy and quality of pharmaceuticals and medical devices. Conduct scientific reviews of marketing authorization application of pharmaceuticals and medical devices, monitoring of their post-marketing safety. PMDA is also responsible for providing relief compensation for sufferers from adverse drug reaction and infections by pharmaceuticals or biological products.
definition source: https://www.pmda.go.jp/english/about-pmda/outline/0005.html
has exact synonym: PMDA
has exact synonym: The Japanese Pharmaceuticals and Medical Device Agency

chronic pain biomarker
type: Class
subclass of: biomarker
definition: Biomarkers that represent acute and chronic pain, predisposition to develop chronic pain and , and pain chronification, recovery and treatment outcomes.
definition source: https://pubmed.ncbi.nlm.nih.gov/32541893/

drug development tool
type: Class
subclass of: material entity
definition: A biomarker, clinical outcome assesment, or any other method, material, or measure determined to aid drug development and regulatory review (FD&C Act, section 507(e)(5)).
definition source: https://www.fda.gov/media/133511/download

Qualification of Medical Device Development Tools Guidance for Industry, Tool Developers, and Food and Drug Administration Staff
type: Class
subclass of: regulatory document
definition: A guidance that describes a voluntary program for the qualification of medical device development tools (MDDTs) for use in the evaluation of devices regulated by CDRH. Specifically, this guidance describes the framework for voluntary proposal and qualification of an MDDT, including definitions of applicable terms, criteria for evaluating an MDDT for a specific context of use, considerations for qualification, and the contents of a qualification package. CDRH believes that MDDTs will facilitate the development and timely evaluation of medical devices by providing a more efficient and predictable means for collecting information to support regulatory submissions and associated decision-making.
definition source: https://www.fda.gov/regulatory-information/search-fda-guidance-documents/qualification-medical-device-development-tools

Qualification Process for Drug Development Tools Guidance for Industry and FDA Staff
type: Class
subclass of: regulatory document
definition: The guidance representing the Center for Drug Evaluation and Research’s (CDER’s) and the Center for Biologics Evaluation and Research’s (CBER’s) current thinking on implementation of section 507 of the FD&C Act with respect to describing the process for requestors5 interested in qualifying DDTs and on taxonomy for biomarkers and other DDTs.
definition source: https://www.fda.gov/media/133511/download

21st Century Cures Act
type: Class
subclass of: regulatory document
definition: The 21st Century Cures Act (Cures Act), signed into law on December 13, 2016, is designed to help accelerate medical product development and bring new innovations and advances to patients who need them faster and more efficiently.
definition source: https://www.fda.gov/regulatory-information/selected-amendments-fdc-act/21st-century-cures-act

Pharmacogenetic Tests and Genetic Tests for Heritable Markers Guidance for Industry and FDA Staff
type: Class
subclass of: regulatory document
definition: The guidance document is intended to facilitate progress in the field of pharmacogenomics and genetics by helping to shorten development and review timelines, facilitate rapid transfer of new technology from the research bench to the clinical diagnostic laboratory, and encourage informed use of pharmacogenomic and genetic diagnostic devices. It provides recommendations to sponsors and FDA reviewers in preparing and reviewing premarket approval applications (PMA) and premarket notification (510(k)) submissions for pharmacogenetic and other human genetic tests, whether testing is for single markers or for multiple markers simultaneously (multiplex tests). Array-based tests (commonly referred to as microarrays) are a subset of multiplex tests and are included in the scope of this document. The recommendations within this guidance for elements of a genetic test submission apply to pharmacogenetic (e.g., drug-metabolizing enzyme allele tests, single nucleotide polymorphism (SNP) analysis) and other types of genetic tests. Tests of gene expression and tests for non-heritable (somatic) mutations are not specifically addressed, although many of the same principles may apply. In addition, this guidance considers nucleic acid-based analysis only, but the principles may be applied to other matrices (e.g., protein) when the purpose is to provide genetic information.

qualified biomarker
type: Class
subclass of: biomarker
definition: Qualified biomarkers have the potential to provide valuable information that may reduce uncertainty in regulatory decisions during drug development. When a biomarker is qualified, it means that it has undergone a formal regulatory process to ensure that we can rely on it to have a specific interpretation and application in medical product development and regulatory review, within the stated context of use (COU) . It is important to note that a biomarker is qualified, and not the biomarker measurement method.
definition source: https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification

total kidney volume
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: Total Kidney Volume (TKV) is the primary measure of kidney growth and can provide information on disease status and its progression. MRI or CT scan are the best methods to obtain TKV measurements.
definition source: https://resources.pkdcure.org/resources/what-is-total-kidney-volume-tkv-and-why-is-it-important-to-me/
has exact synonym: TKV
has exact synonym: total renal volume

urine total potein
type: Class
subclass of: protein
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: Urinary total protein (UTP) includes all proteins in urine samples. The presence of some quantities of proteins (<150 mg/day) is considered normal.
definition source: https://www.human.de/lab-professionals/trends-topics/urinary-total-protein-more-than-just-protein
has exact synonym: total protein

cross-validation testing
type: Class
subclass of: planned process
definition: Cross-validation or out-of-sample testing is a technique that is used to ensure that a model is robust if separate training and test data sets are not available.
definition source: https://pubmed.ncbi.nlm.nih.gov/32541893/
has exact synonym: out-of-sample testing

composite biomarkers
type: Class
subclass of: biomarker
definition: Composite biomarkers, also known as multimarker panels or signatures, are combinations of multiple individual biomarkers that are used collectively to assess biological processes, disease states, or responses to treatments. These biomarkers can be diverse, including genetic, molecular, cellular, or clinical markers.
definition source: generated with ChatGPT version 3,5 on 02.04.2024
has exact synonym: multimarker panel
has exact synonym: multimarker signature

regulatory standard
type: Class
subclass of: Document
definition: A regulatory standard refers to a set of rules, guidelines, specifications, or requirements established by regulatory authorities to ensure the safety, efficacy, quality, and compliance of products, services, processes, or systems within a particular industry or jurisdiction. Regulatory standards play a critical role in protecting public health, safety, and welfare, promoting fair trade practices, and maintaining consumer confidence in regulated sectors.
definition source: generated with ChatGPT version 4,0 on 22․05․24

regulatory guideline
type: Class
subclass of: Document
definition: Regulatory guidelines are documents issued by regulatory authorities or standardization organizations to provide recommendations, interpretations, instructions, or best practices for complying with regulatory requirements, industry standards, or established norms within a specific jurisdiction or field of activity. These guidelines offer guidance to regulated entities, stakeholders, and practitioners on how to interpret, implement, and adhere to applicable regulations, standards, or policies effectively.
definition source: generated with ChatGPT version 4,0 on 22․05․24

biomarker qualification
type: Class
subclass of: planned process
definition: Qualification is the evidentiary process of linking a biomarker with biological processes and clinical end points.
definition source: https://pubmed.ncbi.nlm.nih.gov/20199395/

cardiac function
type: Class
subclass of: biological_process
fromOldVersion: yes
definition: Cardiac function refers to the hearts capability to fulfill its task as the motor or pump of the blood circuit satisfying the bodies demands of oxygen and nutritive substances as well as the removal of waste products.
definition source: https://doi.org/10.53347/rID-85803

systolic function
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: Systolic function refers to the heart's ability to throw out a specific amount of blood in a certain amount of time.
definition source: https://doi.org/10.53347/rID-85803
has exact synonym: cardiac systolic function
has exact synonym: ventricular systolic function

epigenetic biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that measures epigenetic alterations, such as DNA methylation, histone methylation, histone acetylation, microRNAs, or other non-coding RNA.
definition source: https://pubmed.ncbi.nlm.nih.gov/22122639/

stratification biomarker
type: Class
subclass of: biomarker
definition: A stratification biomarker is a biological characteristic or measurement used to categorize individuals into different subgroups based on their likelihood of responding to a particular treatment or exhibiting certain disease characteristics. These biomarkers are especially valuable in the context of personalized or precision medicine, where treatments can be tailored to individual patients based on their unique characteristics.
definition source: generated with ChatGPT version 3,5 on 02.04.2024

prediction model
type: Class
subclass of: Model
fromOldVersion: yes
definition: A prediction model, also known as a predictive model or forecasting model, is a statistical or computational tool used to make predictions or forecasts about future events or outcomes based on historical data and patterns. Prediction models are widely used across various fields, including finance, healthcare, marketing, weather forecasting, and sports analytics, among others. These models leverage patterns and relationships within the data to make predictions about future behavior or events.
definition source: generated with ChatGPT version 3,5 on 02.04.2024

lipoprotein a
type: Class
subclass of: protein
definition: A lipoprotein that resembles the LOW-DENSITY LIPOPROTEINS but with an extra protein moiety, APOPROTEIN (A) also known as APOLIPOPROTEIN (A), linked to APOLIPOPROTEIN B-100 on the LDL by one or two disulfide bonds. High plasma level of lipoprotein (a) is associated with increased risk of atherosclerotic cardiovascular disease.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68017270

biomarker repurposing
type: Class
subclass of: planned process
definition: Biomarker repurposing, the novel application of existing biomarkers for other purposes.
definition source: https://pubmed.ncbi.nlm.nih.gov/30044870/

candidate biomarker
type: Class
subclass of: biomarker
definition: Properly performed, biomarker discovery can lead to effective candidates that can ultimately serve as predictors of disease, medical condition, define therapeutic parameters, and many other applications in medicine.
definition source: https://pubmed.ncbi.nlm.nih.gov/27975230/

diagnostic biomarker text mining bin
type: Class
equivalent class: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'diagnostic biomarker TM_BIN' allows for the compilation of diverse concepts related to diagnostic biomarkers in a specific disease via the axiom 'isDiagnosticBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to diagnostic biomarkers within a specific disease.
definition: A placeholder for diagnostic biomarkers, organized based on the reasoning application 'isDiagnosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

monitoring biomarker text mining bin
type: Class
equivalent class: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'monitoring biomarker TM_BIN' allows for the compilation of diverse concepts related to monitoring biomarkers in a specific disease via the axiom 'isMonitoringBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to monitoring biomarkers within a specific disease.
definition: A placeholder for monitoring biomarkers, organized based on the reasoning application 'isMonitoringBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

prognostic biomarker text minig bin
type: Class
equivalent class: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'prognostic biomarker TM_BIN' allows for the compilation of diverse concepts related to prognostic biomarkers in a specific disease via the axiom 'isPrognosticBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to prognostic biomarkers within a specific disease.
definition: A placeholder for prognostic biomarkers, organized based on the reasoning application 'isPrognosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

predictive biomarker text minig bin
type: Class
equivalent class: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'predictive biomarker TM_BIN' allows for the compilation of diverse concepts related to predictive biomarkers in a specific disease via the axiom 'isPredictiveBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to predictive biomarkers within a specific disease.
definition: A placeholder for predictive biomarkers, organized based on the reasoning application 'isPredictiveBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

therapeutic biomarker
type: Class
subclass of: biomarker
definition: A therapeutic biomarker is a measurable biological characteristic or indicator that is used to assess the response to a therapeutic intervention, such as a medication, treatment, or therapy. These biomarkers provide valuable information about the effectiveness, safety, and potential side effects of the intervention, helping healthcare professionals tailor treatment plans to individual patients and optimize therapeutic outcomes.
definition source: generated with ChatGPT version 4,0 on 22․05․24

digital biomarker
type: Class
subclass of: biomarker
definition: Digital biomarkers are objective, quantifiable, physiological, and behavioral measures that are collected by means of digital devices that are portable, wearable, implantable, or digestible.
definition source: https://pubmed.ncbi.nlm.nih.gov/32095769/

digital device
type: Class
subclass of: device
definition: A digital device refers to any electronic tool, gadget, or hardware that utilizes digital technology to perform specific functions or tasks. These devices are prevalent in various aspects of modern life, including communication, entertainment, productivity, health, and education. Digital devices encompass a wide range of technologies, from computers and smartphones to wearables and smart home appliances.
definition source: generated with ChatGPT version 4,0 on 22․05․24

wearable
type: Class
subclass of: digital device
definition: Wearables are electronic devices that can be worn on the body, typically as accessories or clothing items, to provide functionality, collect data, and offer convenience and connectivity. These devices have gained popularity in recent years for their ability to track health metrics, provide notifications, and integrate with smartphones and other digital platforms, enhancing users' lifestyles and well-being.
definition source: generated with ChatGPT version 4,0 on 22․05․24
has exact synonym: wearable device

smartwatch
type: Class
subclass of: wearable
definition: A smartwatch is a wearable device that combines the functionality of a traditional wristwatch with features typically associated with smartphones and other electronic devices. Smartwatches offer a wide range of capabilities, including timekeeping, notifications, health and fitness tracking, communication, and app integration, all accessible from the user's wrist.
definition source: generated with ChatGPT version 4,0 on 22․05․24

metric
type: Class
subclass of: measurement
definition: A metric is a quantifiable measure or indicator used to assess, analyze, and evaluate performance, progress, or quality in various contexts. Metrics provide objective data that can be compared, tracked over time, and used to make informed decisions, set goals, and drive improvement. In different fields and industries, metrics serve specific purposes and may encompass a wide range of parameters, variables, and key performance indicators (KPIs).
definition source: generated with ChatGPT version 4,0 on 22․05․24

augmentation index
type: Class
subclass of: arterial stiffness measurement
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Augmentation index is a measure of systemic arterial stiffness derived from the ascending aortic pressure waveform.
definition source: https://pubmed.ncbi.nlm.nih.gov/10811742/
has exact synonym: AIx

arterial compliance
type: Class
subclass of: arterial stiffness measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Arterial compliance is a change in dimension in response to a given change in stress.
definition source: https://pubmed.ncbi.nlm.nih.gov/9549658/

stiffness index
type: Class
subclass of: arterial stiffness measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The stiffness index (SI) derived from the analysis of digital volume pulse (DVP) is a noninvasive indirect technique of measuring arterial stiffness peripherally.
definition source: https://pubmed.ncbi.nlm.nih.gov/18551104/
has exact synonym: arterial stiffness index

activity level
type: Class
subclass of: metric
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Activity level refers to the amount and intensity of physical activity an individual engages in over a specific period. It is an important factor in maintaining overall health, fitness, and well-being. Understanding and monitoring activity levels can help individuals achieve their health and fitness goals, manage weight, and reduce the risk of chronic diseases.
definition source: generated with ChatGPT version 4,0 on 22.05.2024

step count
type: Class
subclass of: activity level
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Step count is a widely used metric for tracking physical activity, particularly walking. It measures the total number of steps an individual takes over a specified period, typically daily. Step count is a simple yet effective way to monitor activity levels and promote a healthy lifestyle.
definition source: generated with ChatGPT version 4,0 on 22․05․24

distance walked
type: Class
subclass of: activity level
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Distance walked is a straightforward and important metric that reflects the total length covered by an individual during a specified period, typically measured in meters or miles. This metric is widely used in various fields, including healthcare, fitness, sports, and rehabilitation, to assess physical activity levels, mobility, and overall health.
definition source: generated with ChatGPT version 4,0 on 22․05․24

distance run
type: Class
subclass of: activity level
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: Distance run refers to the total length covered by an individual while running, typically measured in miles or kilometers. It is a fundamental metric used to assess a runner's performance, track progress, and set goals for training and competition. Distance running is a popular form of aerobic exercise that provides numerous health benefits and is enjoyed by people of all ages and fitness levels.
definition source: generated with ChatGPT version 4,0 on 22․05․24

active minute
type: Class
subclass of: activity level
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Active minutes refer to the total duration of physical activity during which an individual engages in moderate to vigorous intensity exercise. This metric is commonly used to track and quantify the amount of time spent being physically active, providing insight into one's overall activity level and adherence to recommended exercise guidelines.
definition source: generated with ChatGPT version 4,0 on 22․05․24

gait analysis
type: Class
subclass of: process
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Determination of the level of functional limitation that may be due to pathology, and evaluating rehabilitative intervention of the way in which the body moves from one point to another. Most often, this is done by walking.
definition source: https://www.ncbi.nlm.nih.gov/mesh/2027898

blood volume pulse
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Photoplethysmographic blood volume pulse (BVP) is a noninvasive sensor and is used to measure blood volume changes and vasodilator function in the microvessels of the finger. BVP is widely used to detect the peripheral pulse waveform that is converted to blood volume amplitude (BVA). Blood volume amplitude reflects arterial dilation and contraction that are controlled by the autonomic nervous system (ANS).
definition source: https://pubmed.ncbi.nlm.nih.gov/24842231/

digital biomarker text mining bin
type: Class
equivalent class: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'digital biomarker TM_BIN' allows for the compilation of diverse concepts related to digital biomarkers in a specific disease via the axiom 'isDigitalBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to digital biomarkers within a specific disease.
definition: A placeholder for digital biomarkers, organized based on the reasoning application 'isDigitalBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

imaging biomarker text mining bin
type: Class
equivalent class: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'imaging biomarker TM_BIN' allows for the compilation of diverse concepts related to imaging biomarkers in a specific disease via the axiom 'isImagingBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to imaging biomarkers within a specific disease.
definition: A placeholder for imaging biomarkers, organized based on the reasoning application 'isImagingBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.

heart rate recovery
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The rate at which the heart rate returns to baseline after physical activity, indicative of cardiovascular fitness and recovery capacity.
definition source: generated with ChatGPT version 3,5 on 03.05.2024

blood lipid level
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Blood lipid levels refer to the concentration of various lipid molecules in the blood. These lipids include cholesterol (including LDL cholesterol, HDL cholesterol, and total cholesterol) and triglycerides.
definition source: generated with ChatGPT version 3,5 on 03.05.2024

myelin water fraction
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The myelin water fraction (MWF) is defined as the ratio of the myelin water signal (15 ms < T2 < 40 ms) to the total water signal and correlates strongly with histological staining for myelin.
definition source: https://pubmed.ncbi.nlm.nih.gov/27923744/

dynamic susceptibility contrast
type: Class
subclass of: Magnetic Resonance Imaging
definition: Dynamic susceptibility contrast magnetic resonance imaging (DSC MRI) provides a noninvasive means to create high resolution maps of the regional distribution of cerebral blood volume (CBV). Most DSC MRI studies conducted to date have focused on the evaluation of patients with cerebral neoplasms, ischemia or infarction, and epilepsy.
definition source: https://pubmed.ncbi.nlm.nih.gov/9370546/

cerebral blood volume
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Cerebral blood volume (CBV) is one of the parameters generated by perfusion techniques (CT perfusion and MR perfusion). CBV is defined as the volume of blood in a given amount of brain tissue, most commonly milliliters of blood per 100 g of brain tissue.
definition source: Gaillard F, Sharma R, Foster T, et al. Cerebral blood volume (CBV). Reference article, Radiopaedia.org (Accessed on 07 May 2024) https://doi.org/10.53347/rID-43778

tumor metabolism
type: Class
subclass of: biological_process
definition: Tumor metabolism refers to the biochemical processes occurring within cancer cells to meet their energy demands, support growth, and sustain proliferation. Cancer cells exhibit distinct metabolic characteristics compared to normal cells, which enable them to adapt to the unique microenvironment of tumors and support their uncontrolled growth.
definition source: generated with ChatGPT version 3,5 on 07.05.2024
has exact synonym: cancer metabolism

lesion load
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Lesion load codes the amount of damage to a given brain region of interest. Lesion load aims to reduce the complex 3D lesion information into a feature that can reflect both site of damage, defined by the location of the region of interest, and size of damage within that region of interest.
definition source: https://pubmed.ncbi.nlm.nih.gov/36947181/
has exact synonym: lesion burden
has exact synonym: overall lesion burden

gray matter volume
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Gray matter volume refers to the amount or volume of gray matter present in the brain. Gray matter consists of neuronal cell bodies, dendrites, and synapses, and it plays a crucial role in processing information and coordinating various functions within the brain. Measurements of gray matter volume are typically obtained using structural magnetic resonance imaging (MRI) techniques. MRI allows researchers and clinicians to visualize and quantify the volume of gray matter in specific brain regions or across the entire brain.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

tissue attenuation coefficient
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: The attenuation coefficient is a measure of how much the incident energy beam (e.g. ultrasound or x-rays) is weakened by the material it is passing through.
definition source: Nadrljanski M, McKay L, Worsley C, et al. Attenuation coefficient. Reference article, Radiopaedia.org (Accessed on 07 May 2024) https://doi.org/10.53347/rID-9035
has exact synonym: tissue attenuation value

functional connectivity density
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Functional connectivity density (FCD) is a measure used in neuroimaging, particularly in functional magnetic resonance imaging (fMRI) studies, to quantify the strength and distribution of functional connections between different brain regions.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

blood oxygen level-dependent signal
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The blood-oxygen-level-dependent (BOLD) signal, detected in fMRI, reflects changes in deoxyhemoglobin driven by localized changes in brain blood flow and blood oxygenation, which are coupled to underlying neuronal activity by a process termed neurovascular coupling.
definition source: https://pubmed.ncbi.nlm.nih.gov/25032494/
has exact synonym: BOLD signal

axonal water fraction
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Axonal water fraction (AWF) is a metric used in diffusion MRI (dMRI) to characterize the microstructural properties of white matter in the brain. It quantifies the proportion of water molecules associated specifically with the axonal compartments within white matter tissue.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

apparent fiber density
type: Class
subclass of: metric
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Apparent Fiber Density (AFD) is a metric derived from diffusion MRI (dMRI) data, particularly from high-angular resolution diffusion imaging (HARDI) or diffusion spectrum imaging (DSI). It quantifies the density of axons within a specific region of interest or white matter pathway in the brain. AFD is calculated based on the orientation distribution functions (ODFs) obtained from dMRI data. It reflects the density of axons within the imaging voxel and provides information about the microstructural integrity of white matter tracts.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

fractional anisotropy
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Fractional Anisotropy (FA) is a metric derived from diffusion tensor imaging (DTI), a magnetic resonance imaging (MRI) technique used to study the microstructural organization of tissues, particularly white matter in the brain. FA quantifies the degree of anisotropy of water diffusion within tissue. In white matter, water molecules tend to diffuse more easily along the direction of the fiber tracts (axonal bundles) than perpendicular to them. FA values range from 0 to 1, where higher values indicate greater directionality or organization of the tissue microstructure, typically reflecting intact white matter tracts.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

tau deposition
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Tau deposition refers to the accumulation of abnormal tau protein aggregates in the brain, which is a characteristic feature of several neurodegenerative disorders, including Alzheimer's disease (AD), frontotemporal dementia (FTD), and certain forms of Parkinson's disease (PD), among others. In neuroimaging, techniques such as positron emission tomography (PET) using radioligands targeting tau can visualize and quantify tau deposition in the brain. These imaging methods enable researchers and clinicians to detect the presence of abnormal tau aggregates and assess their distribution and severity.
definition source: generated with ChatGPT version 3,5 on 07.05.2024
has exact synonym: tau accumulation
has exact synonym: tau aggregation
has exact synonym: tau burden

mean diffusivity
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Mean diffusivity (MD) is a metric derived from diffusion-weighted magnetic resonance imaging (DW-MRI) data. It quantifies the average magnitude of water molecule diffusion within a particular tissue or region of interest. MD is calculated based on the diffusion tensor, which characterizes the rate and directionality of water diffusion in tissue. Unlike fractional anisotropy (FA), which measures the degree of diffusion directionality, MD represents the overall magnitude of diffusion regardless of direction.
definition source: generated with ChatGPT version 3,5 on 07.05.2024

gait speed
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Gait speed, also known as walking speed, is a crucial parameter in the study of human locomotion and biomechanics. It is defined as the distance covered per unit of time while walking. Gait speed is often measured in meters per second (m/s) or feet per second (ft/s) and is an important indicator of overall health, functional status, and mobility.
definition source: generated with ChatGPT version 4,0 on 22․05․24
has exact synonym: walking speed

stride length
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Stride length is a key parameter in the study of human gait and biomechanics. It refers to the distance covered between two successive placements of the same foot. Essentially, it is the distance traveled during one complete gait cycle, involving both the left and right foot.
definition source: generated with ChatGPT version 4,0 on 22․05․24
has exact synonym: gait stride length

gait cycle time
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Gait cycle time is an important parameter in the study of human locomotion and biomechanics. It refers to the duration of a complete gait cycle, which encompasses all the phases of walking from one foot making contact with the ground to the same foot making contact again.
definition source: generated with ChatGPT version 4,0 on 22․05․24

leukocyte telomere length
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Leukocyte telomere length (LTL) is a complex genetic trait. It shortens with age and is associated with a host of aging-related disorders.
definition source: https://pubmed.ncbi.nlm.nih.gov/18282113/
has exact synonym: LTL
has exact synonym: WBC telomere length
has exact synonym: White blood cell telomere length

mitochondrial function
type: Class
subclass of: metabolic process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Mitochondrial function refers to the various vital processes performed by mitochondria, which are the energy-producing organelles in cells.
definition source: generated with ChatGPT version 4,0 on 19․08․24
has exact synonym: mitochondrial behaviour
has exact synonym: mitochondrial performance

tissue
type: Class
subclass of: material anatomical entity
definition: Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
editor note: relabel 'tissue'?
alternative term: portion of tissue
imported from: caro.owl
id: CARO:0000043

cholesterol
type: Class
subclass of: lipid
fromOldVersion: yes
definition: A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.
imported from: chebi.owl
charge: 0
formula: C27H46O
inchi: InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1
inchikey: HVYWMOMLDIMFJA-DPAQBDIFSA-N
mass: 386.655
monoisotopicmass: 386.35487
has_alternative_id: CHEBI:13982
has_alternative_id: CHEBI:23204
has_alternative_id: CHEBI:3659
has_alternative_id: CHEBI:41564
database cross reference: Beilstein:2060565
database cross reference: CAS:57-88-5
database cross reference: DrugBank:DB04540
database cross reference: Gmelin:550297
database cross reference: HMDB:HMDB0000067
database cross reference: KEGG:C00187
database cross reference: KEGG:D00040
database cross reference: KNApSAcK:C00003648
database cross reference: LIPID_MAPS_instance:LMST01010001
database cross reference: MetaCyc:CHOLESTEROL
database cross reference: PDBeChem:CLR
database cross reference: PMID:10901445
database cross reference: PMID:11412894
database cross reference: PMID:16341241
database cross reference: PMID:24287311
database cross reference: PMID:25308664
database cross reference: PMID:25451949
database cross reference: PMID:25522988
database cross reference: PMID:25658343
database cross reference: PMID:25977713
database cross reference: PMID:4696527
database cross reference: PMID:8838010
database cross reference: Reaxys:2060565
database cross reference: Wikipedia:Cholesterol
has exact synonym: CHOLESTEROL
has exact synonym: Cholesterol
has exact synonym: cholest-5-en-3beta-ol
has exact synonym: cholesterol
has_obo_namespace: chebi_ontology
has_related_synonym: (3beta,14beta,17alpha)-cholest-5-en-3-ol
has_related_synonym: Cholest-5-en-3beta-ol
has_related_synonym: Cholesterin
has_related_synonym: total cholesterol
id: CHEBI:16113
in subset: 3 STAR

peptide
type: Class
subclass of: molecular entity
definition: Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. X = OH, OR, NH2, NHR, etc.
imported from: chebi.owl
charge: 0
formula: (C2H2NOR)nC2H3NOR
has_alternative_id: CHEBI:14753
has_alternative_id: CHEBI:25906
has_alternative_id: CHEBI:7990
database cross reference: KEGG:C00012
has exact synonym: Peptide
has exact synonym: peptides
has_obo_namespace: chebi_ontology
has_related_synonym: Peptid
has_related_synonym: peptido
has_related_synonym: peptidos
id: CHEBI:16670
in subset: 3 STAR

creatinine
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: kidney disease
fromOldVersion: yes
definition: A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
imported from: chebi.owl
charge: 0
formula: C4H7N3O
inchi: InChI=1S/C4H7N3O/c1-7-2-3(8)6-4(7)5/h2H2,1H3,(H2,5,6,8)
inchikey: DDRJAANPRJIHGJ-UHFFFAOYSA-N
mass: 113.11800
monoisotopicmass: 113.05891
smiles: CN1CC(=O)NC1=N
has_alternative_id: CHEBI:14029
has_alternative_id: CHEBI:23406
has_alternative_id: CHEBI:3910
database cross reference: CAS:60-27-5
database cross reference: HMDB:HMDB0000562
database cross reference: KEGG:C00791
database cross reference: KEGG:D03600
database cross reference: MetaCyc:CREATININE
database cross reference: PMID:11256540
database cross reference: PMID:11981083
database cross reference: PMID:17190852
database cross reference: PMID:17422601
database cross reference: PMID:18182718
database cross reference: PMID:19236048
database cross reference: PMID:19715855
database cross reference: PMID:19968328
database cross reference: PMID:21775764
database cross reference: PMID:22047975
database cross reference: PMID:22121923
database cross reference: PMID:22166252
database cross reference: PMID:22207347
database cross reference: PMID:22212624
database cross reference: PMID:22223530
database cross reference: PMID:22331238
database cross reference: PMID:22338083
database cross reference: PMID:22349552
database cross reference: PMID:22390548
database cross reference: PMID:22432114
database cross reference: PMID:22441184
database cross reference: PMID:22459582
database cross reference: PMID:22498455
database cross reference: Reaxys:112064
database cross reference: Wikipedia:Creatinine
has exact synonym: 2-imino-1-methylimidazolidin-4-one
has exact synonym: Creatinine
has exact synonym: creatinine
has_obo_namespace: chebi_ontology
has_related_synonym: 1-Methylglycocyamidine
has_related_synonym: 1-Methylhydantoin-2-imide
has_related_synonym: 1-methylglycocyamidine
has_related_synonym: 2-Amino-1-methylimidazolin-4-one
has_related_synonym: 2-amino-1,5-dihydro-1-methyl-4H-Imidazol-4-one
has_related_synonym: Creatine anhydride
has_related_synonym: Kreatinin
has_related_synonym: creatinina
id: CHEBI:16737
in subset: 3 STAR

glucose
type: Class
subclass of: molecular entity
fromOldVersion: yes
definition: An aldohexose used as a source of energy and metabolic intermediate.
imported from: chebi.owl
charge: 0
formula: C6H12O6
mass: 180.15588
monoisotopicmass: 180.06339
has_alternative_id: CHEBI:14313
has_alternative_id: CHEBI:24277
has_alternative_id: CHEBI:33929
has_alternative_id: CHEBI:5418
database cross reference: CAS:50-99-7
database cross reference: KEGG:C00293
database cross reference: Wikipedia:Glucose
has exact synonym: Glucose
has exact synonym: gluco-hexose
has exact synonym: glucose
has_obo_namespace: chebi_ontology
has_related_synonym: DL-glucose
has_related_synonym: Glc
has_related_synonym: Glukose
id: CHEBI:17234
in subset: 3 STAR

testosterone
type: Class
subclass of: steroid
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5..
imported from: chebi.owl
charge: 0
formula: C19H28O2
inchi: InChI=1S/C19H28O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h11,14-17,21H,3-10H2,1-2H3/t14-,15-,16-,17-,18-,19-/m0/s1
inchikey: MUMGGOZAMZWBJJ-DYKIIFRCSA-N
mass: 288.42440
monoisotopicmass: 288.20893
has_alternative_id: CHEBI:15214
has_alternative_id: CHEBI:26883
has_alternative_id: CHEBI:45798
has_alternative_id: CHEBI:9461
database cross reference: Beilstein:1915399
database cross reference: Beilstein:3653705
database cross reference: CAS:58-22-0
database cross reference: DrugBank:DB00624
database cross reference: Drug_Central:2607
database cross reference: Gmelin:538843
database cross reference: HMDB:HMDB0000234
database cross reference: KEGG:C00535
database cross reference: KEGG:D00075
database cross reference: KNApSAcK:C00003675
database cross reference: LIPID_MAPS_instance:LMST02020002
database cross reference: PDBeChem:TES
database cross reference: PMID:10438974
database cross reference: PMID:11786693
database cross reference: PMID:18900503
database cross reference: PMID:24498482
database cross reference: Reaxys:1915399
database cross reference: Wikipedia:Testosterone
has exact synonym: 17beta-hydroxyandrost-4-en-3-one
has exact synonym: TESTOSTERONE
has exact synonym: Testosterone
has exact synonym: testosterone
has_obo_namespace: chebi_ontology
has_related_synonym: 17beta-Hydroxy-4-androsten-3-one
has_related_synonym: 17beta-hydroxy-4-androsten-3-one
has_related_synonym: 4-androsten-17beta-ol-3-one
has_related_synonym: Androderm
has_related_synonym: Testosteron
has_related_synonym: testosterona
has_related_synonym: testosterone
has_related_synonym: testosteronum
id: CHEBI:17347
in subset: 3 STAR

triglyceride
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids.
imported from: chebi.owl
charge: 0
formula: C6H5O6R3
mass: 173.10030
monoisotopicmass: 173.00861
smiles: [*]C(=O)OCC(COC([*])=O)OC([*])=O
has_alternative_id: CHEBI:15255
has_alternative_id: CHEBI:27085
has_alternative_id: CHEBI:9664
database cross reference: KEGG:C00422
database cross reference: LIPID_MAPS_class:LMGL0301
database cross reference: PMID:2474544
has exact synonym: Triglyceride
has exact synonym: triglycerides
has_obo_namespace: chebi_ontology
has_related_synonym: Triacylglycerol
has_related_synonym: Triglycerid
has_related_synonym: Triglyzerid
has_related_synonym: a triacylglycerol
has_related_synonym: triacylglycerols
has_related_synonym: triglycerides
id: CHEBI:17855
in subset: 3 STAR

N(omega),N(omega)-dimethyl-L-arginine
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: A L-arginine derivative having two methyl groups both attached to the primary amino moiety of the guanidino group.
imported from: chebi.owl
charge: 0
formula: C8H18N4O2
inchi: InChI=1S/C8H18N4O2/c1-12(2)8(10)11-5-3-4-6(9)7(13)14/h6H,3-5,9H2,1-2H3,(H2,10,11)(H,13,14)/t6-/m0/s1
inchikey: YDGMGEXADBMOMJ-LURJTMIESA-N
mass: 202.25428
monoisotopicmass: 202.14298
smiles: CN(C)C(=N)NCCC[C@H](N)C(O)=O
has_alternative_id: CHEBI:12680
has_alternative_id: CHEBI:21908
has_alternative_id: CHEBI:25683
has_alternative_id: CHEBI:41833
has_alternative_id: CHEBI:7432
database cross reference: Beilstein:2261521
database cross reference: CAS:30315-93-6
database cross reference: DrugBank:DB01686
database cross reference: KEGG:C03626
database cross reference: PDBeChem:DA2
has exact synonym: (2S)-2-amino-5-(N',N'-dimethylcarbamimidamido)pentanoic acid
has exact synonym: (2S)-2-amino-5-{[(dimethylamino)(imino)methyl]amino}pentanoic acid
has exact synonym: N(5)-(N,N-dimethylcarbamimidoyl)-L-ornithine
has exact synonym: N(5)-[(dimethylamino)(imino)methyl]-L-ornithine
has_obo_namespace: chebi_ontology
has_related_synonym: ADMA
has_related_synonym: N(5)-((dimethylamino)iminomethyl)-L-ornithine
has_related_synonym: N(G),N(G)-dimethylarginine
has_related_synonym: N(G)-dimethylarginine
has_related_synonym: N(G1),N(G1)-dimethylarginine
has_related_synonym: N,N-dimethylarginine
has_related_synonym: NG,NG-DIMETHYL-L-ARGININE
has_related_synonym: NG,NG-Dimethyl-L-arginine
has_related_synonym: asymmetric dimethylarginine
has_related_synonym: guanidino-N,N-dimethylarginine
id: CHEBI:17929
in subset: 3 STAR

lipid
type: Class
subclass of: molecular entity
fromOldVersion: yes
definition: 'Lipids' is a loosely defined term for substances of biological origin that are soluble in nonpolar solvents. They consist of saponifiable lipids, such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable lipids, principally steroids.
imported from: chebi.owl
has_alternative_id: CHEBI:14517
has_alternative_id: CHEBI:25054
has_alternative_id: CHEBI:6486
database cross reference: KEGG:C01356
has exact synonym: Lipid
has exact synonym: lipids
has_obo_namespace: chebi_ontology
id: CHEBI:18059
in subset: 3 STAR

molecular entity
type: Class
subclass of: chemical entity
fromOldVersion: yes
definition: Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
imported from: chebi.owl
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

estradiol
type: Class
subclass of: steroid
definition: A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17.
imported from: chebi.owl
charge: 0
formula: C18H24O2
inchi: InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17?,18+/m1/s1
inchikey: VOXZDWNPVJITMN-WKUFJEKOSA-N
mass: 272.38196
monoisotopicmass: 272.17763
has_alternative_id: CHEBI:42364
database cross reference: PMID:10696569
database cross reference: PMID:24084694
database cross reference: Wikipedia:Estradiol
has exact synonym: estra-1,3,5(10)-triene-3,17-diol
has_obo_namespace: chebi_ontology
has_related_synonym: oestradiol
id: CHEBI:23965
in subset: 3 STAR

chemical entity
type: Class
subclass of: object
fromOldVersion: yes
definition: A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
imported from: chebi.owl
has exact synonym: chemical entity
has_obo_namespace: chebi_ontology
id: CHEBI:24431
in subset: 3 STAR

biological role
type: Class
subclass of: role
definition: A role played by the molecular entity or part thereof within a biological context.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: biological function
id: CHEBI:24432
in subset: 3 STAR

hormone
type: Class
subclass of: biological role
definition: Originally referring to an endogenous compound that is formed in specialized organ or group of cells and carried to another organ or group of cells, in the same organism, upon which it has a specific regulatory function, the term is now commonly used to include non-endogenous, semi-synthetic and fully synthetic analogues of such compounds.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: endocrine
has_related_synonym: hormones
id: CHEBI:24621
in subset: 3 STAR

uric acid
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: An oxopurine that is the final oxidation product of purine metabolism.
imported from: chebi.owl
charge: 0
formula: C5H4N4O3
mass: 168.11042
monoisotopicmass: 168.02834
database cross reference: HMDB:HMDB0000289
database cross reference: Wikipedia:Uric_acid
has_obo_namespace: chebi_ontology
has_related_synonym: uric acids
id: CHEBI:27226
in subset: 3 STAR

galactomannan
type: Class
subclass of: molecular entity
definition: A heteroglycan consisting of a mannan backbone with galactose side groups.
imported from: chebi.owl
has_alternative_id: CHEBI:24146
has_alternative_id: CHEBI:5255
database cross reference: PMID:1375195
database cross reference: PMID:2426444
has_obo_namespace: chebi_ontology
id: CHEBI:27680
in subset: 3 STAR

cisplatin
type: Class
subclass of: molecular entity
fromOldVersion: yes
definition: A diamminedichloroplatinum compound in which the two ammine ligands and two chloro ligands are oriented in a cis planar configuration around the central platinum ion. An anticancer drug that interacts with, and forms cross-links between, DNA and proteins, it is used as a neoplasm inhibitor to treat solid tumours, primarily of the testis and ovary. Commonly but incorrectly described as an alkylating agent due to its mechanism of action (but it lacks alkyl groups).
imported from: chebi.owl
charge: 0
formula: Cl2H6N2Pt
formula: H6Cl2N2Pt
inchi: InChI=1S/2ClH.2H3N.Pt/h2*1H;2*1H3;/q;;;;+2/p-2
inchikey: LXZZYRPGZAFOLE-UHFFFAOYSA-L
mass: 300.04452
monoisotopicmass: 298.95560
has_alternative_id: CHEBI:23314
has_alternative_id: CHEBI:3722
database cross reference: CAS:15663-27-1
database cross reference: DrugBank:DB00515
database cross reference: Gmelin:2519
database cross reference: HMDB:HMDB0014656
database cross reference: KEGG:C06911
database cross reference: KEGG:D00275
database cross reference: MetaCyc:CPD0-1392
database cross reference: MolBase:25
database cross reference: PMID:10883661
database cross reference: PMID:12537968
database cross reference: PMID:12831510
database cross reference: PMID:12935404
database cross reference: PMID:16327988
database cross reference: PMID:18472761
database cross reference: PMID:1855275
database cross reference: PMID:23554447
database cross reference: PMID:23604226
database cross reference: PMID:23651576
database cross reference: PMID:28494534
database cross reference: Patent:DE2318020
database cross reference: Patent:DE2329485
database cross reference: Reaxys:11324567
database cross reference: Wikipedia:Cisplatin
has exact synonym: (SP-4-2)-diamminedichloridoplatinum
has exact synonym: (SP-4-2)-diamminedichloroplatinum
has exact synonym: Cisplatin
has exact synonym: cis-diamminedichloridoplatinum(II)
has exact synonym: cis-diamminedichloroplatinum(II)
has_obo_namespace: chebi_ontology
has_related_synonym: Briplatin
has_related_synonym: CDDP
has_related_synonym: Cismaplat
has_related_synonym: Lederplatin
has_related_synonym: Neoplatin
has_related_synonym: Peyrone's chloride
has_related_synonym: Peyrone's salt
has_related_synonym: Platamine
has_related_synonym: Platinex
has_related_synonym: Platinol
has_related_synonym: Randa
has_related_synonym: [PtCl2(NH3)2]
has_related_synonym: cis-DDP
has_related_synonym: cis-Diamminedichloroplatinum(II)
has_related_synonym: cis-[PtCl2(NH3)2]
has_related_synonym: cis-diamminedichloroplatinum
has_related_synonym: cis-diammineplatinum(II) dichloride
has_related_synonym: cis-dichlorodiammineplatinum(II)
has_related_synonym: cis-platin
has_related_synonym: cisplatin
has_related_synonym: cisplatine
has_related_synonym: cisplatino
has_related_synonym: cisplatinum
id: CHEBI:27899
in subset: 3 STAR

hemoglobin
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
fromOldVersion: yes
imported from: chebi.owl
database cross reference: COMe:PRX000321
has exact synonym: hemoglobin
has_obo_namespace: chebi_ontology
has_related_synonym: haemoglobin
has_related_synonym: vertebrate haemoglobin
id: CHEBI:35143
in subset: 3 STAR

steroid
type: Class
subclass of: lipid
definition: Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from squalene which is a triterpene.
imported from: chebi.owl
charge: 0
formula: C19H31R
mass: 259.450
monoisotopicmass: 259.24258
smiles: C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C
has_alternative_id: CHEBI:13687
has_alternative_id: CHEBI:26768
has_alternative_id: CHEBI:9263
database cross reference: KEGG:C00377
database cross reference: MetaCyc:Steroids
has exact synonym: Steroid
has exact synonym: steroids
has_obo_namespace: chebi_ontology
has_related_synonym: a steroid
id: CHEBI:35341
in subset: 3 STAR

EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor
type: Class
subclass of: role
fromOldVersion: yes
definition: Any EC 1.1.1.* (oxidoreductase acting on donor CH-OH group, NAD(+) or NADP(+) acceptor) inhibitor that inhibits HMG-CoA reductases. Hydroxymethylglutaryl-CoA reductase inhibitors have been shown to lower directly cholesterol synthesis. The Enzyme Commission designation is EC 1.1.1.34 for the NADPH-dependent enzyme and EC 1.1.1.88 for an NADH-dependent enzyme.
imported from: chebi.owl
database cross reference: PMID:1464741
database cross reference: PMID:15531285
database cross reference: PMID:20467214
database cross reference: Wikipedia:HMG-CoA_reductase
has_obo_namespace: chebi_ontology
has_related_synonym: HMG-CoA reductase inhibitor
has_related_synonym: HMG-CoA reductase inhibitors
has_related_synonym: hydroxymethylglutaryl-CoA reductase inhibitor
has_related_synonym: hydroxymethylglutaryl-CoA reductase inhibitors
id: CHEBI:35664
in subset: 3 STAR

low-density lipoprotein cholesterol
type: Class
subclass of: molecular entity
definition: Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: LDL cholesterol
has_related_synonym: LDL-C
has_related_synonym: beta-lipoprotein cholesterol
id: CHEBI:47774
in subset: 3 STAR

high-density lipoprotein cholesterol
type: Class
subclass of: molecular entity
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
definition: Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: HDL cholesterol
has_related_synonym: HDL-C
has_related_synonym: alpha-lipoprotein cholesterol
id: CHEBI:47775
in subset: 3 STAR

indicator
type: Class
subclass of: role
fromOldVersion: yes
definition: Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
imported from: chebi.owl
has_obo_namespace: chebi_ontology
has_related_synonym: Indikator
has_related_synonym: prognostic indicator
id: CHEBI:47867
in subset: 3 STAR

insulin (human)
type: Class
subclass of: molecular entity
definition: An insulin that is produced in the pancreas and involved in regulating the metabolism of carbohydrates (particularly glucose) and fats. Commonly thought of as a protein, it consists of two peptide chains, one containing 21 amino acid residues and the other containing 30; the chains are joined together by 2 disulfide bonds. Recombinant insulin is identical to human insulin, but is synthesised by inserting the human insulin gene into E. coli, which then produces insulin for human use. It is used in the treatment of type I and type II diabetes.
imported from: chebi.owl
charge: 0
formula: C257H383N65O77S6
inchikey: PBGKTOXHQIOBKM-FHFVDXKLSA-N
mass: 5807.630
monoisotopicmass: 5803.63765
database cross reference: CAS:11061-68-0
database cross reference: DrugBank:DB00030
database cross reference: KEGG:C00723
database cross reference: KEGG:D00085
database cross reference: PMID:22249812
database cross reference: PMID:22617471
database cross reference: PMID:22715632
database cross reference: PMID:22843207
database cross reference: PMID:31301295
database cross reference: PMID:31821343
database cross reference: PMID:31876563
database cross reference: PMID:32208558
database cross reference: PMID:32398693
database cross reference: PMID:32629793
database cross reference: PMID:32797824
database cross reference: PMID:8019699
has_obo_namespace: chebi_ontology
has_related_synonym: Exubera
has_related_synonym: Insulin
has_related_synonym: Insulin recombinant
has_related_synonym: human insulin
has_related_synonym: insulin (recombinant)
has_related_synonym: insulin human
has_related_synonym: insulina humana
has_related_synonym: insuline humaine
has_related_synonym: insulinum humanum
id: CHEBI:5931
in subset: 3 STAR

amyloid-beta
type: Class
subclass of: peptide
definition: A peptide of 36-43 amino acids that is processed from the amyloid precursor protein. Appears to be the main constituent of amyloid plaques (deposits found in the brains of Alzheimer's disease patients).
imported from: chebi.owl
has_alternative_id: CHEBI:53002
database cross reference: KEGG:C16514
database cross reference: KEGG:C16515
database cross reference: PMID:21892760
database cross reference: PMID:22226401
database cross reference: PMID:22457725
database cross reference: PMID:22459190
database cross reference: PMID:22561032
database cross reference: PMID:22569063
database cross reference: Wikipedia:Beta_amyloid
has_obo_namespace: chebi_ontology
has_related_synonym: amyloid beta
has_related_synonym: beta amyloid
has_related_synonym: beta-amyloid
has_related_synonym: beta-amyloids
id: CHEBI:64645
in subset: 3 STAR

amyloid-beta polypeptide 40
type: Class
subclass of: amyloid-beta
definition: A beta-amyloid that is a 40 amino acid polypeptide of sequence Asp Ala Glu Phe Arg His Asp Ser Gly Tyr Glu Val His His Gln Lys Leu Val Phe Phe Ala Glu Asp Val Gly Ser Asn Lys Gly Ala Ile Ile Gly Leu Met Val Gly Gly Val Val.
imported from: chebi.owl
charge: 0
formula: C194H295N53O58S
inchikey: FEWOUVRMGWFWIH-ILZZQXMPSA-N
mass: 4329.80300
monoisotopicmass: 4327.14843
database cross reference: KEGG:C16514
database cross reference: PMID:11444969
database cross reference: PMID:15541300
database cross reference: PMID:16137568
database cross reference: PMID:17446087
database cross reference: PMID:18571334
database cross reference: Reaxys:21949886
has exact synonym: L-alpha-aspartyl-L-alanyl-L-alpha-glutamyl-L-phenylalanyl-L-arginyl-L-histidyl-L-alpha-aspartyl-L-serylglycyl-L-tyrosyl-L-alpha-glutamyl-L-valyl-L-histidyl-L-histidyl-L-glutaminyl-L-lysyl-L-leucyl-L-valyl-L-phenylalanyl-L-phenylalanyl-L-alanyl-L-alpha-glutamyl-L-alpha-aspartyl-L-valylglycyl-L-seryl-L-asparaginyl-L-lysylglycyl-L-alanyl-L-isoleucyl-L-isoleucylglycyl-L-leucyl-L-methionyl-L-valylglycylglycyl-L-valyl-L-valine
has_obo_namespace: chebi_ontology
has_related_synonym: Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val
has_related_synonym: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
has_related_synonym: beta-amyloid 40
has_related_synonym: beta-amyloid polypeptide 40
has_related_synonym: beta-amyloid protein 40
id: CHEBI:64646
in subset: 3 STAR

amyloid-beta polypeptide 42
type: Class
subclass of: amyloid-beta
definition: A beta-amyloid that ia a 42 amino acid polypeptide of sequence Asp Ala Glu Phe Arg His Asp Ser Gly Tyr Glu Val His His Gln Lys Leu Val Phe Phe Ala Glu Asp Val Gly Ser Asn Lys Gly Ala Ile Ile Gly Leu Met Val Gly Gly Val Val Ile Ala.
imported from: chebi.owl
charge: 0
formula: C203H311N55O60S
inchikey: DZHSAHHDTRWUTF-SIQRNXPUSA-N
mass: 4514.03900
monoisotopicmass: 4511.26960
database cross reference: KEGG:C16515
has exact synonym: L-alpha-aspartyl-L-alanyl-L-alpha-glutamyl-L-phenylalanyl-L-arginyl-L-histidyl-L-alpha-aspartyl-L-serylglycyl-L-tyrosyl-L-alpha-glutamyl-L-valyl-L-histidyl-L-histidyl-L-glutaminyl-L-lysyl-L-leucyl-L-valyl-L-phenylalanyl-L-phenylalanyl-L-alanyl-L-alpha-glutamyl-L-alpha-aspartyl-L-valylglycyl-L-seryl-L-asparaginyl-L-lysylglycyl-L-alanyl-L-isoleucyl-L-isoleucylglycyl-L-leucyl-L-methionyl-L-valylglycylglycyl-L-valyl-L-valyl-L-isoleucyl-L-alanine
has_obo_namespace: chebi_ontology
has_related_synonym: Asp-Ala-Glu-Phe-Arg-His-Asp-Ser-Gly-Tyr-Glu-Val-His-His-Gln-Lys-Leu-Val-Phe-Phe-Ala-Glu-Asp-Val-Gly-Ser-Asn-Lys-Gly-Ala-Ile-Ile-Gly-Leu-Met-Val-Gly-Gly-Val-Val-Ile-Ala
has_related_synonym: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA
has_related_synonym: beta-amyloid 42
has_related_synonym: beta-amyloid polypeptide 42
has_related_synonym: beta-amyloid protein 42
id: CHEBI:64647
in subset: 3 STAR

spectroscopy
type: Class
subclass of: assay
definition: The study of the interaction of a sample with radiation or particles for measurement or detection.
imported from: chmo.owl
has exact synonym: spectrometry
id: CHMO:0000228

mass spectrometry
type: Class
subclass of: spectroscopy
definition: Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
imported from: chmo.owl
has exact synonym: MS
has exact synonym: mass spectroscopy
id: CHMO:0000470

cell
type: Class
subclass of: material anatomical entity
fromOldVersion: yes
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.
imported from: cl.owl
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
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).

T cell
type: Class
subclass of: lymphocyte
fromOldVersion: yes
definition: A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
database cross reference: BTO:0000782
database cross reference: CALOHA:TS-1001
database cross reference: FMA:62870
database cross reference: MESH:D013601
database cross reference: VHOG:0001479
has exact synonym: T lymphocyte
has exact synonym: T-cell
has exact synonym: T-lymphocyte
has_related_synonym: immature T cell
has_related_synonym: mature T cell
in subset: human reference atlas

granulocyte
type: Class
subclass of: leukocyte
definition: A leukocyte with abundant granules in the cytoplasm.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
database cross reference: BTO:0000539
database cross reference: BTO:0001026
database cross reference: CALOHA:TS-0422
database cross reference: FMA:62854
has exact synonym: granular leucocyte
has exact synonym: granular leukocyte
has exact synonym: polymorphonuclear leukocyte
in subset: human reference atlas

lymphocyte
type: Class
subclass of: leukocyte
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
database cross reference: BTO:0000775
database cross reference: CALOHA:TS-0583
database cross reference: FMA:62863
database cross reference: MESH:D008214
database cross reference: VHOG:0001535
in subset: human reference atlas
comment: Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)

monocyte
type: Class
subclass of: leukocyte
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
database cross reference: BTO:0000876
database cross reference: CALOHA:TS-0638
database cross reference: FMA:62864
in subset: blood and immune upper slim
in subset: human reference atlas
comment: Morphology: Mononuclear cell, diameter, 14 to 20 _M, N/C ratio 2:1-1:1. Nucleus may appear in variety of shapes: round, kidney, lobulated, or convoluted. Fine azurophilic granules present; markers: CD11b (shared with other myeloid cells), human: CD14, mouse: F4/80-mid,GR1-low; location: Blood, but can be recruited into tissues; role or process: immune & tissue remodelling; lineage: hematopoietic, myeloid.

leukocyte
type: Class
subclass of: cell
definition: An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
database cross reference: BTO:0000751
database cross reference: CALOHA:TS-0549
database cross reference: FMA:62852
database cross reference: MESH:D007962
has exact synonym: leucocyte
has exact synonym: white blood cell
has_related_synonym: immune cell
in subset: human reference atlas

neutrophil
type: Class
subclass of: granulocyte
fromOldVersion: yes
definition: Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes.
imported from: cl.owl
present_in_taxon: NCBITaxon 9606
has_broad_synonym: PMN
has_broad_synonym: poly
has_broad_synonym: polymorphonuclear leucocyte
has_broad_synonym: polymorphonuclear leukocyte
has_broad_synonym: polymorphonuclear neutrophil
has_broad_synonym: polynuclear neutrophilic leucocyte
has_broad_synonym: polynuclear neutrophilic leukocyte
database cross reference: BTO:0000130
database cross reference: CALOHA:TS-0688
database cross reference: FMA:62860
database cross reference: MESH:D009504
has exact synonym: neutrocyte
has exact synonym: neutrophil leucocyte
has exact synonym: neutrophil leukocyte
has exact synonym: neutrophilic leucocyte
has exact synonym: neutrophilic leukocyte
in subset: blood and immune upper slim
in subset: human reference atlas

clinical measurement
type: Class
subclass of: measurement
definition: A quantitative or qualitative value which is the result of an act of assessing a morphological or physiological state or property in a single individual or sample or a group of individuals or samples, based on direct observation or experimental manipulation.
imported from: cmo.owl
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000000

blood glucose level
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Measurement of the amount of glucose, the monosaccharide sugar, C6H12O6, occurring widely in plant and animal tissues which is one of the three dietary monosaccharides that are absorbed directly into the bloodstream during digestion, is the end product of carbohydrate metabolism, and is the chief source of energy for living organisms, in a specified volume of blood, the fluid that circulates through the heart, arteries, capillaries and veins carrying nutrients and oxygen to the body tissues and metabolites away from them.
imported from: cmo.owl
created_by: mshimoyama
creation date: 2009-12-17T10:41:54Z
has_broad_synonym: glucose measurement
database cross reference: EFO:0004465
database cross reference: EFO:0004468
has_narrow_synonym: fasting blood glucose measurement
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000046

creatinine clearance
type: Class
subclass of: clinical measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The clearance rate of creatinine, that is, the volume of plasma that is cleared of creatinine by the kidneys per unit time. Creatinine clearance is calculated using the level of creatinine in a sample of urine, usually one collected over a period of 24 hours, the corresponding plasma creatinine level, and the volume of urine excreted. It is used as an approximation of the glomerular filtration rate (GFR).
imported from: cmo.owl
created_by: JSmith
creation date: 2012-03-28T10:49:24Z
database cross reference: CHEBI:16737
database cross reference: EFO:0007934
has exact synonym: CrCl
has exact synonym: creatinine clearance measurement
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000765

renal blood flow rate
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time.
imported from: cmo.owl
created_by: JSmith
creation date: 2012-07-11T10:38:08Z
has_obo_namespace: clinical_measurement_ontology
id: CMO:0000907

oxygen saturation
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity.
imported from: cmo.owl
created_by: JSmith
creation date: 2013-01-09T16:37:31Z
has_broad_synonym: oxygen saturation measurement
database cross reference: EFO:0005682
has exact synonym: blood oxygen saturation
has exact synonym: percent oxygen saturation
has_obo_namespace: clinical_measurement_ontology
id: CMO:0001324

heart rate variability
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Heart rate variability (HRV) is the physiological phenomenon of variation in the time interval between heartbeats. It is measured by the variation in the beat-to-beat interval.
imported from: cmo.owl
created_by: sjwang
creation date: 2018-11-13T15:12:25Z
database cross reference: EFO:0008003
database cross reference: PMID:26063669
has exact synonym: HRV
has exact synonym: RR variability
has exact synonym: cycle length variability
has exact synonym: heart rate variability measurement
has_obo_namespace: clinical_measurement_ontology
id: CMO:0002812

pulse wave velocity
type: Class
subclass of: arterial stiffness measurement
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Pulse wave velocity (PWV) is a measurement of arterial stiffness that is an independent predictor of cardiovascular risk. It can be measured simply and noninvasively by measuring the carotid and femoral pulse pressures and the time delay between the two or by other methods relying on pulse-wave analysis.
imported from: cmo.owl
created_by: slaulede
creation date: 2021-05-20T15:30:59Z
database cross reference: EFO:0004517
database cross reference: EFO:0004724
database cross reference: PMID:32088716
has exact synonym: Carotidfemoral PWV
has exact synonym: PWV
has exact synonym: arterial stiffness measurement
has exact synonym: carotid-femoral pulse wave velocity
has_obo_namespace: clinical_measurement_ontology
id: CMO:0003717

cerebral blood flow rate
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Cerebral blood flow (CBF) rate is the volume of blood delivered to or exiting the brain, through a network of cerebral arteries and veins, per unit time
imported from: cmo.owl
created_by: slaulede
creation date: 2021-07-29T16:36:46Z
database cross reference: EFO:0007980
database cross reference: PMID:27403447
database cross reference: PMID:29498562
has exact synonym: CBF rate
has exact synonym: cerebral blood flow measurement
has_obo_namespace: clinical_measurement_ontology
id: CMO:0003815

clinical trial
type: Class
subclass of: planned process
definition: a clinical trial is a medical interventional study where participants are assigned prospectively to an intervention or interventions according to a protocol to evaluate the safety and efficacy of the intervention(s) on biomedical or other health related outcomes. The Interventions include but are not restricted to drugs, cells and other biological products, surgical procedures, radiologic procedures, devices, behavioral treatments, process-of-care changes, preventive care, etc.
definition editor: Oliver He, Asiyah Yu Lin, Qingliang Li
alternative term: interventional trial
definition source: https://clinicaltrials.gov/ct2/search/map
definition source: https://en.wikipedia.org/wiki/Clinical_trial
definition source: https://prsinfo.clinicaltrials.gov/definitions.html
definition source: https://www.who.int/ictrp/en/
imported from: cto.owl

disease of metabolism
type: Class
subclass of: disease
definition: A disease that involving errors in metabolic processes of building or degradation of molecules.
imported from: doid.owl
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_2022_09_01:75934005
database cross reference: UMLS_CUI:C0025517
has exact synonym: metabolic disease
has exact synonym: metabolic disorder
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

inflammatory bowel disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: An intestinal disease characterized by inflammation located in all parts of digestive tract.
imported from: doid.owl
database cross reference: EFO:0003767
database cross reference: KEGG:05321
database cross reference: MESH:D015212
database cross reference: NCI:C3138
database cross reference: OMIM:PS266600
database cross reference: SNOMEDCT_US_2022_09_01:155759008
database cross reference: UMLS_CUI:C0021390
has_obo_namespace: disease_ontology
id: DOID:0050589
in subset: DO FlyBase slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

peripheral artery disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: An artery disease that is characterized by build up of plaque in the arteries that carry blood to your head, organs, and limbs.
imported from: doid.owl
created_by: lschriml
creation date: 2014-02-18T12:41:09Z
database cross reference: MESH:D058729
has exact synonym: peripheral arterial disease
has_obo_namespace: disease_ontology
id: DOID:0050830

thrombosis
type: Class
subclass of: vascular disease
definition: A vascular disease caused by the formation of a blood clot inside a blood vessel, obstructing the flow of blood through the circulatory system.
imported from: doid.owl
database cross reference: MESH:D013927
has_obo_namespace: disease_ontology
id: DOID:0060903

prostate cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A male reproductive organ cancer that is located_in the prostate.
imported from: doid.owl
has_alternative_id: DOID:514
database cross reference: ICD10CM:C61
database cross reference: ICD9CM:185
database cross reference: KEGG:05215
database cross reference: MESH:D011471
database cross reference: NCI:C3343
database cross reference: NCI:C7378
database cross reference: OMIM:176807
database cross reference: OMIM:300147
database cross reference: OMIM:300704
database cross reference: OMIM:601518
database cross reference: OMIM:602759
database cross reference: OMIM:608656
database cross reference: OMIM:608658
database cross reference: OMIM:609299
database cross reference: OMIM:609558
database cross reference: OMIM:610321
database cross reference: OMIM:610997
database cross reference: OMIM:611100
database cross reference: OMIM:611868
database cross reference: OMIM:611928
database cross reference: OMIM:611955
database cross reference: OMIM:611958
database cross reference: OMIM:611959
database cross reference: ORDO:1331
database cross reference: SNOMEDCT_US_2022_09_01:126906006
database cross reference: SNOMEDCT_US_2022_09_01:93974005
database cross reference: UMLS_CUI:C0033578
database cross reference: UMLS_CUI:C0376358
has exact synonym: NGP - new growth of prostate
has exact synonym: hereditary prostate cancer
has exact synonym: malignant tumor of the prostate
has exact synonym: prostate cancer, familial
has exact synonym: prostate neoplasm
has exact synonym: prostatic cancer
has exact synonym: prostatic neoplasm
has exact synonym: tumor of the prostate
has_obo_namespace: disease_ontology
id: DOID:10283
in subset: DO CFDE slim
in subset: DO FlyBase 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].

gastric fundus cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A stomach cancer that is located_in the gastric fundus.
imported from: doid.owl
database cross reference: ICD10CM:C16.1
database cross reference: ICD9CM:151.3
database cross reference: SNOMEDCT_US_2022_09_01:93809003
database cross reference: UMLS_CUI:C0153420
has exact synonym: Ca fundus - stomach
has exact synonym: malignant neoplasm of fundus of stomach
has exact synonym: malignant tumor of fundus of stomach
has_obo_namespace: disease_ontology
id: DOID:10538

pre-eclampsia
type: Class
subclass of: hypertension
fromOldVersion: yes
definition: A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy.
imported from: doid.owl
has_alternative_id: DOID:12684
database cross reference: ICD10CM:O14
database cross reference: MESH:D011225
database cross reference: NCI:C85021
database cross reference: OMIM:189800
database cross reference: OMIM:609402
database cross reference: OMIM:609403
database cross reference: OMIM:609404
database cross reference: OMIM:614592
database cross reference: ORDO:275555
database cross reference: SNOMEDCT_US_2022_09_01:6758009
database cross reference: UMLS_CUI:C0032914
has exact synonym: gestational hypertension
has exact synonym: hypertension induced by pregnancy
has exact synonym: pre-eclamptic toxaemia
has exact synonym: preeclampsia
has exact synonym: preeclampsia/eclampsia
has exact synonym: pregnancy associated hypertension
has exact synonym: pregnancy toxemia
has exact synonym: proteinuric hypertension of pregnancy
has exact synonym: toxaemia of pregnancy
has_obo_namespace: disease_ontology
id: DOID:10591
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

celiac disease
type: Class
subclass of: autoimmune disease
fromOldVersion: yes
definition: An autoimmune disease of gastrointestinal tract that is caused by a reaction located_in small intestine to gliadin, a prolamin (gluten protein) found in wheat, and similar proteins found in the crops of the tribe Triticeae. The disease is associated with HLA-DQ gene. It has_symptom abdominal pain, has_symptom constipation, has_symptom diarrhea, has_symptom nausea and vomiting, and has_symptom loss of appetite.
imported from: doid.owl
database cross reference: EFO:0001060
database cross reference: GARD:11998
database cross reference: ICD10CM:K90.0
database cross reference: ICD9CM:579.0
database cross reference: MESH:D002446
database cross reference: NCI:C26714
database cross reference: OMIM:607202
database cross reference: OMIM:609754
database cross reference: OMIM:611598
database cross reference: OMIM:612005
database cross reference: OMIM:612006
database cross reference: OMIM:612007
database cross reference: OMIM:612008
database cross reference: OMIM:612009
database cross reference: OMIM:612011
database cross reference: ORDO:555
database cross reference: SNOMEDCT_US_2022_09_01:197477005
database cross reference: UMLS_CUI:C0007570
has exact synonym: celiac sprue
has exact synonym: coeliac disease
has exact synonym: idiopathic steatorrhea
has_obo_namespace: disease_ontology
id: DOID:10608
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

hypertension
type: Class
subclass of: disease
fromOldVersion: yes
definition: An artery disease characterized by chronic elevated blood pressure in the arteries.
imported from: doid.owl
database cross reference: EFO:0000537
database cross reference: ICD10CM:I10
database cross reference: ICD9CM:401-405.99
database cross reference: MESH:D006973
database cross reference: NCI:C3117
database cross reference: SNOMEDCT_US_2022_09_01:38341003
database cross reference: UMLS_CUI:C0020538
has exact synonym: HTN
has exact synonym: hyperpiesia
has exact synonym: vascular hypertensive disorder
has_obo_namespace: disease_ontology
has_related_synonym: hypertensive disease
id: DOID:10763
in subset: NCIthesaurus

heart disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: A cardiovascular system disease that involves the heart.
imported from: doid.owl
database cross reference: ICD10CM:I51.9
database cross reference: ICD9CM:429.9
database cross reference: MESH:D006331
database cross reference: NCI:C3079
database cross reference: SNOMEDCT_US_2022_09_01:194707003
database cross reference: UMLS_CUI:C0018799
has_obo_namespace: disease_ontology
id: DOID:114
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: NCIthesaurus

polycystic ovary syndrome
type: Class
subclass of: disease
fromOldVersion: yes
definition: An ovarian dysfunction that is characterized by hyperandrogenism, polycystic ovaries, hirsutism, oligomenorrhea or amenorrhea, anovulation and excessive body weight.
imported from: doid.owl
database cross reference: EFO:0000660
database cross reference: ICD10CM:E28.2
database cross reference: ICD9CM:256.4
database cross reference: MESH:D011085
database cross reference: NCI:C26862
database cross reference: OMIM:184700
database cross reference: SNOMEDCT_US_2022_09_01:69878008
database cross reference: UMLS_CUI:C0032460
has exact synonym: Multicystic ovaries
has exact synonym: PCOS
has exact synonym: Polycystic Ovarian disease
has exact synonym: Polycystic ovaries
has exact synonym: Stein-Leventhal synd.
has exact synonym: Stein-Leventhal syndrome
has exact synonym: polycystic ovary
has_obo_namespace: disease_ontology
id: DOID:11612
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

Huntington's disease
type: Class
subclass of: neurodegenerative disease
fromOldVersion: yes
definition: A neurodegenerative disease that has_material_basis_in autosomal dominant inheritance and is characterized by unwanted choreatic movements, behavioral and psychiatric disturbances and dementia and has_material_basis_in expansion of CAG triplet repeats (glutamine) resulting in neuron degeneration affecting muscle coordination, cognitive abilities.
imported from: doid.owl
database cross reference: GARD:6677
database cross reference: ICD10CM:G10
database cross reference: ICD9CM:333.4
database cross reference: KEGG:05016
database cross reference: MESH:D006816
database cross reference: NCI:C82342
database cross reference: OMIM:143100
database cross reference: SNOMEDCT_US_2022_09_01:58756001
database cross reference: UMLS_CUI:C0020179
has exact synonym: HD
has exact synonym: Huntington disease
has exact synonym: Huntington's chorea
has_obo_namespace: disease_ontology
id: DOID:12858
in subset: DO FlyBase slim
in subset: DO rare slim
in subset: NCIthesaurus

cardiovascular system disease
type: Class
subclass of: disease
fromOldVersion: yes
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.
imported from: doid.owl
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_2022_09_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

lung cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A respiratory system cancer that is located_in the lung.
imported from: doid.owl
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: OMIM:211980
database cross reference: OMIM:608935
database cross reference: OMIM:612571
database cross reference: OMIM:612593
database cross reference: OMIM:614210
database cross reference: SNOMEDCT_US_2022_09_01:187860004
database cross reference: SNOMEDCT_US_2022_09_01:187864008
database cross reference: SNOMEDCT_US_2022_09_01:187868006
database cross reference: SNOMEDCT_US_2022_09_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

Fabry disease
type: Class
subclass of: metabolic syndrome
fromOldVersion: yes
definition: A sphingolipidosis that is characterized by the buildup of globotriaosylceramide in the body's cells and has_material_basis_in X-linked inherited mutations in the GLA gene, encoding alpha-galactosidase A, on chromosome Xq22.
imported from: doid.owl
database cross reference: GARD:6400
database cross reference: ICD10CM:E75.21
database cross reference: MESH:D000795
database cross reference: NCI:C84701
database cross reference: OMIM:301500
database cross reference: SNOMEDCT_US_2022_09_01:16652001
database cross reference: UMLS_CUI:C0002986
has exact synonym: Alpha-galactosidase A deficiency
has exact synonym: Angiokeratoma Corporis Diffusum
has exact synonym: Fabry Disease, Cardiac Variant
has exact synonym: Fabry's disease
has exact synonym: alpha galactosidase deficiency
has exact synonym: deficiency of melibiase
has_obo_namespace: disease_ontology
id: DOID:14499
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

rheumatic disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: A musculoskeletal system disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
imported from: doid.owl
has_obo_namespace: disease_ontology
id: DOID:1575

respiratory system disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
imported from: doid.owl
has_alternative_id: DOID:3226
database cross reference: ICD10CM:J98
database cross reference: ICD9CM:519
database cross reference: SNOMEDCT_US_2022_09_01:155603009
database cross reference: UMLS_CUI:C0029582
has exact synonym: respiratory disease
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

breast cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A thoracic cancer that originates in the mammary gland.
imported from: doid.owl
has_alternative_id: DOID:1648
has_alternative_id: DOID:4241
database cross reference: ICD10CM:C50
database cross reference: MESH:D001943
database cross reference: NCI:C9335
database cross reference: OMIM:114480
database cross reference: SNOMEDCT_US_2022_09_01:254837009
database cross reference: UMLS_CUI:C0006142
has exact synonym: breast tumor
has exact synonym: malignant neoplasm of breast
has exact synonym: malignant tumor of the breast
has exact synonym: mammary cancer
has exact synonym: mammary tumor
has exact synonym: primary breast cancer
has_obo_namespace: disease_ontology
has_related_synonym: mammary neoplasm
id: DOID:1612
in subset: DO CFDE slim
in subset: DO RAD slim
in subset: DO cancer slim
in subset: NCIthesaurus
in subset: TopNodes DOcancerslim
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

cancer
type: Class
subclass of: disease
fromOldVersion: yes
definition: A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
imported from: doid.owl
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_2022_09_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.

vascular disease
type: Class
subclass of: cardiovascular system disease
fromOldVersion: yes
definition: A cardiovascular system disease that primarily affects the blood vessels which includes the arteries, veins and capillaries that carry blood to and from the heart.
imported from: doid.owl
has_alternative_id: DOID:0000405
has_alternative_id: DOID:2403
has_alternative_id: DOID:2869
has_alternative_id: DOID:324
has_alternative_id: DOID:325
has_alternative_id: DOID:45
database cross reference: ICD10CM:I72.9
database cross reference: ICD9CM:442.9
database cross reference: MESH:D000783
database cross reference: MESH:D014652
database cross reference: MESH:D020758
database cross reference: MESH:D020760
database cross reference: NCI:C26693
database cross reference: NCI:C35117
database cross reference: SNOMEDCT_US_2022_09_01:27550009
database cross reference: SNOMEDCT_US_2022_09_01:371029002
database cross reference: SNOMEDCT_US_2022_09_01:432119003
database cross reference: UMLS_CUI:C0002940
database cross reference: UMLS_CUI:C0042373
database cross reference: UMLS_CUI:C0752127
database cross reference: UMLS_CUI:C0752130
has exact synonym: vascular tissue disease
has_obo_namespace: disease_ontology
id: DOID:178
in subset: DO RAD slim
in subset: NCIthesaurus

iron metabolism disease
type: Class
subclass of: disease of metabolism
imported from: doid.owl
database cross reference: ICD10CM:E83.1
database cross reference: ICD9CM:275.0
database cross reference: MESH:D019189
database cross reference: SNOMEDCT_US_2023_03_01:30913008
database cross reference: UMLS_CUI:C0012715
has exact synonym: disorder of iron metabolism
has exact synonym: iron disorder
has_obo_namespace: disease_ontology
id: DOID:2351

anemia
type: Class
subclass of: disease
fromOldVersion: yes
definition: A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
imported from: doid.owl
database cross reference: EFO:0004272
database cross reference: ICD10CM:D64.9
database cross reference: ICD9CM:285.9
database cross reference: MESH:D000740
database cross reference: NCI:C2869
database cross reference: SNOMEDCT_US_2022_09_01:64593003
database cross reference: UMLS_CUI:C0002871
has exact synonym: anaemia
has_obo_namespace: disease_ontology
id: DOID:2355
in subset: NCIthesaurus
comment: PRISM.

ovarian cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A female reproductive organ cancer that is located_in the ovary.
imported from: doid.owl
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: NCI:C4984
database cross reference: NCI:C7431
database cross reference: OMIM:167000
database cross reference: OMIM:607893
database cross reference: ORDO:213500
database cross reference: ORDO:213517
database cross reference: SNOMEDCT_US_2022_09_01:123843001
database cross reference: SNOMEDCT_US_2022_09_01:372117006
database cross reference: SNOMEDCT_US_2022_09_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].

asthma
type: Class
subclass of: lung disease
fromOldVersion: yes
definition: A bronchial disease that is characterized by chronic inflammation and narrowing of the airways, which is caused by a combination of environmental and genetic factors. The disease has_symptom recurring periods of wheezing (a whistling sound while breathing), has_symptom chest tightness, has_symptom shortness of breath, has_symptom mucus production and has_symptom coughing.
imported from: doid.owl
has_alternative_id: DOID:12703
has_alternative_id: DOID:13829
has_alternative_id: DOID:13830
has_alternative_id: DOID:2840
has_alternative_id: DOID:5783
database cross reference: EFO:0000270
database cross reference: GARD:10246
database cross reference: ICD10CM:J45
database cross reference: ICD9CM:493
database cross reference: KEGG:05310
database cross reference: MESH:D001249
database cross reference: NCI:C28397
database cross reference: OMIM:600807
database cross reference: SNOMEDCT_US_2022_09_01:187687003
database cross reference: UMLS_CUI:C0004096
has exact synonym: Exercise induced asthma
has exact synonym: bronchial hyperreactivity
has exact synonym: chronic obstructive asthma
has exact synonym: chronic obstructive asthma with acute exacerbation
has exact synonym: chronic obstructive asthma with status asthmaticus
has exact synonym: exercise-induced asthma
has_obo_namespace: disease_ontology
id: DOID:2841
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI.

interstitial lung disease
type: Class
subclass of: lung disease
fromOldVersion: yes
definition: A lung disease that is characterized by inflammation and altered lung interstitium compromising pulmonary function and often has_symptom shortness of breath, dyspnea, and/or cough.
imported from: doid.owl
database cross reference: GARD:13336
database cross reference: ICD10CM:J84.9
database cross reference: MESH:D017563
database cross reference: NCI:C164315
database cross reference: SNOMEDCT_US_2022_09_01:64667001
database cross reference: UMLS_CUI:C0206062
has exact synonym: ILD
has_obo_namespace: disease_ontology
id: DOID:3082
in subset: DO rare slim

bipolar disorder
type: Class
subclass of: disease
fromOldVersion: yes
definition: A mood disorder that involves alternating periods of mania and depression.
imported from: doid.owl
has_alternative_id: DOID:3311
has_alternative_id: DOID:9554
has_alternative_id: DOID:9555
database cross reference: EFO:0000289
database cross reference: GARD:10249
database cross reference: ICD10CM:F31
database cross reference: ICD9CM:296.40
database cross reference: ICD9CM:296.60
database cross reference: ICD9CM:296.80
database cross reference: MESH:D001714
database cross reference: NCI:C34423
database cross reference: NCI:C34424
database cross reference: NCI:C34805
database cross reference: SNOMEDCT_US_2022_09_01:16506000
database cross reference: SNOMEDCT_US_2022_09_01:191627008
database cross reference: SNOMEDCT_US_2022_09_01:192355004
database cross reference: SNOMEDCT_US_2022_09_01:68569003
database cross reference: UMLS_CUI:C0005586
database cross reference: UMLS_CUI:C0005587
database cross reference: UMLS_CUI:C0024713
database cross reference: UMLS_CUI:C0236780
has exact synonym: Manic Bipolar Affective disorder
has exact synonym: Manic Depressive disorder
has exact synonym: Manic bipolar I disorder
has exact synonym: bipolar depression
has exact synonym: bipolar disorder manic phase
has exact synonym: manic depression
has exact synonym: manic disorder
has exact synonym: mixed bipolar disorder
has_obo_namespace: disease_ontology
has_related_synonym: Depressive-manic psych.
id: DOID:3312
in subset: DO rare slim
in subset: NCIthesaurus

periodontal disease
type: Class
subclass of: nervous system disorder
fromOldVersion: yes
definition: A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth.
imported from: doid.owl
database cross reference: ICD10CM:K05.6
database cross reference: MESH:D010510
database cross reference: NCI:C63743
database cross reference: SNOMEDCT_US_2022_09_01:196354003
database cross reference: UMLS_CUI:C0031090
has exact synonym: disease of supporting structures of teeth
has exact synonym: periodontium disorder
has_obo_namespace: disease_ontology
id: DOID:3388
in subset: NCIthesaurus

skin disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: An integumentary system disease that is located_in skin.
imported from: doid.owl
has_alternative_id: DOID:1576
has_alternative_id: DOID:1698
has_alternative_id: DOID:187
has_alternative_id: DOID:6486
has_alternative_id: DOID:8948
database cross reference: ICD9CM:702
database cross reference: MESH:D012871
database cross reference: MESH:D012873
database cross reference: NCI:C156032
database cross reference: NCI:C3371
database cross reference: SNOMEDCT_US_2022_09_01:201095006
database cross reference: SNOMEDCT_US_2022_09_01:5613003
database cross reference: SNOMEDCT_US_2022_09_01:95320005
database cross reference: UMLS_CUI:C0029574
database cross reference: UMLS_CUI:C0037274
database cross reference: UMLS_CUI:C0037277
has exact synonym: Genodermatosis
has exact synonym: skin and subcutaneous tissue disease
has_obo_namespace: disease_ontology
id: DOID:37
in subset: DO RAD slim
in subset: NCIthesaurus

lung non-small cell carcinoma
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
imported from: doid.owl
database cross reference: EFO:0003060
database cross reference: KEGG:05223
database cross reference: MESH:D002289
database cross reference: NCI:C2926
database cross reference: SNOMEDCT_US_2022_09_01:254637007
database cross reference: UMLS_CUI:C0007131
has exact synonym: NSCLC
has exact synonym: Non-small cell lung cancer
has exact synonym: non-small cell lung carcinoma
has_obo_namespace: disease_ontology
id: DOID:3908
in subset: DO cancer slim
in subset: NCIthesaurus

disease
type: Class
subclass of: disposition
fromOldVersion: yes
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.
imported from: doid.owl
database cross reference: MESH:D004194
database cross reference: NCI:C2991
database cross reference: SNOMEDCT_US_2022_09_01:64572001
database cross reference: UMLS_CUI:C0012634
has_obo_namespace: disease_ontology
id: DOID:4
in subset: DO RAD slim
in subset: NCIthesaurus

liver disease
type: Class
subclass of: disease
fromOldVersion: yes
imported from: doid.owl
has_alternative_id: DOID:2164
has_alternative_id: DOID:2165
has_alternative_id: DOID:46
database cross reference: ICD10CM:K76.9
database cross reference: ICD9CM:573.9
database cross reference: MESH:D008107
database cross reference: NCI:C3196
database cross reference: SNOMEDCT_US_2022_09_01:62857009
database cross reference: UMLS_CUI:C0023895
has exact synonym: disorder of liver
has exact synonym: hepatic disorder
has_obo_namespace: disease_ontology
has_related_synonym: fatty liver disease
id: DOID:409
in subset: DO RAD slim
in subset: NCIthesaurus

autoimmune disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: An immune system disease that is an overactive immune response of the body against substances and tissues normally present in the body resulting from an abnormal functioning of the immune system that results in the production of antibodies or T cell directed against the host tissues.
imported from: doid.owl
IEDB alternative term: autoimmune disease
database cross reference: ICD9CM:720
database cross reference: OMIM:109100
database cross reference: UMLS_CUI:C0003089
has exact synonym: autoimmune hypersensitivity disease
has exact synonym: hypersensitivity reaction type II disease
has_obo_namespace: disease_ontology
id: DOID:417
comment: Xref MGI.

pancreatitis
type: Class
subclass of: disease
definition: A pancreas disease that is characterized by inflammation of the pancreas.
imported from: doid.owl
database cross reference: EFO:0000278
database cross reference: ICD10CM:K85.9
database cross reference: MESH:D010195
database cross reference: NCI:C3306
database cross reference: OMIM:167800
database cross reference: SNOMEDCT_US_2023_03_01:393591004
database cross reference: UMLS_CUI:C0030305
has_obo_namespace: disease_ontology
id: DOID:4989
in subset: NCIthesaurus

liver cirrhosis
type: Class
subclass of: liver disease
fromOldVersion: yes
imported from: doid.owl
database cross reference: EFO:0001422
database cross reference: ICD10CM:K74.60
database cross reference: MESH:D008103
database cross reference: NCI:C2951
database cross reference: SNOMEDCT_US_2022_09_01:19943007
database cross reference: UMLS_CUI:C0023890
has exact synonym: Cirrhosis
has exact synonym: cirrhosis of liver
has_obo_namespace: disease_ontology
has_related_synonym: liver fibrosis
id: DOID:5082
in subset: NCIthesaurus

kidney disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: A urinary system disease that is located_in the kidney.
imported from: doid.owl
has_alternative_id: DOID:11705
database cross reference: EFO:0003086
database cross reference: ICD10CM:N08
database cross reference: MESH:D007674
database cross reference: NCI:C3149
database cross reference: SNOMEDCT_US_2022_09_01:266612003
database cross reference: UMLS_CUI:C0022658
has exact synonym: impaired renal function disease
has exact synonym: nephropathy
has exact synonym: renal disease
has_obo_namespace: disease_ontology
id: DOID:557
in subset: DO FlyBase slim
in subset: DO RAD slim
in subset: NCIthesaurus

proteinuria
type: Class
subclass of: kidney disease
fromOldVersion: yes
definition: A kidney disease that is characterized by the presence of excess proteins in the urine.
imported from: doid.owl
database cross reference: ICD10CM:R80
database cross reference: ICD9CM:791.0
database cross reference: MESH:D011507
database cross reference: NCI:C38012
database cross reference: SNOMEDCT_US_2022_09_01:144515004
database cross reference: UMLS_CUI:C0033687
has_obo_namespace: disease_ontology
id: DOID:576
in subset: NCIthesaurus

myocardial infarction
type: Class
subclass of: heart disease
fromOldVersion: yes
definition: A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia.
imported from: doid.owl
database cross reference: EFO:0000612
database cross reference: ICD10CM:I21
database cross reference: MESH:D009203
database cross reference: NCI:C27996
database cross reference: OMIM:608557
database cross reference: SNOMEDCT_US_2022_09_01:66514008
database cross reference: UMLS_CUI:C0027051
has exact synonym: Myocardial infarct
has exact synonym: acute myocardial infarction
has exact synonym: heart attack
has_obo_namespace: disease_ontology
id: DOID:5844
in subset: NCIthesaurus
comment: Xref MGI.

congestive heart failure
type: Class
subclass of: heart disease
fromOldVersion: yes
definition: A heart disease that is characterized by any structural or functional cardiac disorder that impairs the ability of the heart to fill with or pump a sufficient amount of blood throughout the body.
imported from: doid.owl
has_alternative_id: DOID:395
database cross reference: ICD10CM:I50
database cross reference: ICD10CM:I50.9
database cross reference: ICD9CM:428
database cross reference: ICD9CM:428.0
database cross reference: MESH:D006333
database cross reference: NCI:C3080
database cross reference: NCI:C50577
database cross reference: SNOMEDCT_US_2022_09_01:155374007
database cross reference: SNOMEDCT_US_2022_09_01:195108009
database cross reference: UMLS_CUI:C0018801
database cross reference: UMLS_CUI:C0018802
has exact synonym: CHF
has exact synonym: Cardiac Failure Congestive
has exact synonym: Congestive heart disease
has exact synonym: Weak heart
has_obo_namespace: disease_ontology
id: DOID:6000
in subset: NCIthesaurus

cerebrovascular disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain.
imported from: doid.owl
has_alternative_id: DOID:12214
has_alternative_id: DOID:3455
has_alternative_id: DOID:8231
database cross reference: EFO:0000712
database cross reference: ICD10CM:I67.9
database cross reference: ICD9CM:437.9
database cross reference: MESH:D002561
database cross reference: NCI:C2938
database cross reference: SNOMEDCT_US_2022_09_01:266312006
database cross reference: UMLS_CUI:C0007820
has exact synonym: CVA
has exact synonym: cerebrovascular disorder
has exact synonym: stroke
has_obo_namespace: disease_ontology
id: DOID:6713
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

hepatocellular carcinoma
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A liver carcinoma that has_material_basis_in undifferentiated hepatocytes and located_in the liver.
imported from: doid.owl
has_alternative_id: DOID:5005
database cross reference: EFO:0000182
database cross reference: ICD10CM:C22.0
database cross reference: ICDO:8170/3
database cross reference: MESH:D006528
database cross reference: NCI:C3099
database cross reference: OMIM:114550
database cross reference: ORDO:88673
database cross reference: SNOMEDCT_US_2022_09_01:154469006
database cross reference: UMLS_CUI:C2239176
has exact synonym: Hepatoma
has_obo_namespace: disease_ontology
id: DOID:684
in subset: DO cancer slim
in subset: DO rare slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

chronic kidney disease
type: Class
subclass of: kidney disease
fromOldVersion: yes
definition: A kidney failure that is characterized by the gradual loss of kidney function.
imported from: doid.owl
database cross reference: ICD10CM:N18.9
database cross reference: ICD9CM:585.6
database cross reference: MESH:D007676
database cross reference: NCI:C9438
database cross reference: SNOMEDCT_US_2022_09_01:155856009
database cross reference: UMLS_CUI:C0022661
has exact synonym: CKD
has exact synonym: CRF
has exact synonym: chronic kidney failure
has exact synonym: chronic renal disease
has exact synonym: chronic renal failure syndrome
has exact synonym: renal failure - chronic
has_obo_namespace: disease_ontology
id: DOID:784
in subset: NCIthesaurus

lung disease
type: Class
subclass of: disease
fromOldVersion: yes
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.
imported from: doid.owl
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_2022_09_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.

psoriasis
type: Class
subclass of: skin disease
fromOldVersion: yes
definition: A skin disease that is characterized by patches of thick red skin and silvery scales.
imported from: doid.owl
database cross reference: EFO:0000676
database cross reference: GARD:10262
database cross reference: ICD10CM:L40
database cross reference: MESH:D011565
database cross reference: NCI:C3346
database cross reference: OMIM:PS177900
database cross reference: SNOMEDCT_US_2022_09_01:156369008
database cross reference: UMLS_CUI:C0033860
has_obo_namespace: disease_ontology
id: DOID:8893
in subset: DO rare slim
in subset: NCIthesaurus
comment: Xref MGI. Update outdated UMLS CUI from C00295134 to C0033860.

colorectal cancer
type: Class
subclass of: cancer
fromOldVersion: yes
definition: A large intestine cancer that is located_in the colon and/or located_in the rectum.
imported from: doid.owl
database cross reference: ICD10CM:C18.9
database cross reference: KEGG:05210
database cross reference: MESH:D015179
database cross reference: NCI:C2956
database cross reference: NCI:C4978
database cross reference: OMIM:114500
database cross reference: SNOMEDCT_US_2022_09_01:126837005
database cross reference: SNOMEDCT_US_2022_09_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
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

diabetes mellitus
type: Class
subclass of: disease
fromOldVersion: yes
definition: A glucose metabolism disease that is characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion, insulin action, or both.
imported from: doid.owl
has_alternative_id: DOID:0081062
database cross reference: ICD10CM:E08-E13
database cross reference: ICD9CM:250
database cross reference: MESH:D003920
database cross reference: NCI:C2985
database cross reference: SNOMEDCT_US_2022_09_01:267467004
database cross reference: UMLS_CUI:C0011849
has exact synonym: diabetes
has_obo_namespace: disease_ontology
id: DOID:9351
in subset: NCIthesaurus

type 2 diabetes mellitus
type: Class
subclass of: diabetes mellitus
fromOldVersion: yes
definition: A diabetes mellitus that is characterized by high blood sugar, insulin resistance, and relative lack of insulin.
imported from: doid.owl
database cross reference: EFO:0001360
database cross reference: ICD10CM:E11
database cross reference: KEGG:04930
database cross reference: MESH:D003924
database cross reference: NCI:C26747
database cross reference: OMIM:125853
database cross reference: OMIM:601283
database cross reference: OMIM:601407
database cross reference: OMIM:603694
database cross reference: OMIM:608036
database cross reference: SNOMEDCT_US_2022_09_01:44054006
database cross reference: UMLS_CUI:C0011860
has exact synonym: NIDDM
has exact synonym: T2DM
has exact synonym: insulin resistance
has exact synonym: non-insulin-dependent diabetes mellitus
has exact synonym: type 2 diabetes
has exact synonym: type II diabetes mellitus
has_obo_namespace: disease_ontology
id: DOID:9352
in subset: DO FlyBase slim
in subset: NCIthesaurus
comment: Xref MGI. OMIM mapping confirmed by DO. [SN].

obesity
type: Class
subclass of: disease
fromOldVersion: yes
definition: An overnutrition that is characterized by excess body fat, traditionally defined as an elevated ratio of weight to height (specifically 30 kilograms per meter squared), has_material_basis_in a multifactorial etiology related to excess nutrition intake, decreased caloric utilization, and genetic susceptibility, and possibly medications and certain disorders of metabolism, endocrine function, and mental illness.
imported from: doid.owl
database cross reference: EFO:0001073
database cross reference: ICD10CM:E66.9
database cross reference: ICD9CM:278.00
database cross reference: MESH:D009765
database cross reference: NCI:C159658
database cross reference: OMIM:601665
database cross reference: SNOMEDCT_US_2022_09_01:5476005
database cross reference: UMLS_CUI:C0028754
has_obo_namespace: disease_ontology
id: DOID:9970
in subset: DO FlyBase slim
in subset: NCIthesaurus
comment: OMIM mapping confirmed by DO. [SN].

angiogenesis
type: Class
subclass of: biological_process
definition: Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
imported from: go.owl
database cross reference: Wikipedia:Angiogenesis
has exact synonym: blood vessel formation from pre-existing blood vessels
has_obo_namespace: biological_process
id: GO:0001525

fibrinogen complex
type: Class
subclass of: anatomical entity
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds.
imported from: go.owl
has exact synonym: fibrinogen
has_narrow_synonym: fibrinogen alpha chain
has_narrow_synonym: fibrinogen beta chain
has_narrow_synonym: fibrinogen gamma chain
has_obo_namespace: cellular_component
id: GO:0005577

inflammatory response
type: Class
subclass of: biological_process
definition: The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
imported from: go.owl
has_broad_synonym: inflammation
database cross reference: Wikipedia:Inflammation
has_obo_namespace: biological_process
id: GO:0006954
in subset: goslim generic

immune response
type: Class
subclass of: biological_process
definition: Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
imported from: go.owl
has_obo_namespace: biological_process
id: GO:0006955
in subset: goslim drosophila

biological_process
type: Class
subclass of: process
definition: A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
term tracker item: https://github.com/geneontology/go-ontology/issues/24968
imported from: go.owl
created_by: jl
creation date: 2012-09-19T15:05:24Z
has_alternative_id: GO:0000004
has_alternative_id: GO:0007582
has_alternative_id: GO:0044699
database cross reference: Wikipedia:Biological_process
has exact synonym: biological process
has exact synonym: physiological process
has_obo_namespace: biological_process
has_related_synonym: single organism process
has_related_synonym: single-organism process
id: GO:0008150
in subset: goslim candida
in subset: goslim chembl
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim pombe
in subset: goslim yeast
comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this.

metabolic process
type: Class
subclass of: biological_process
definition: The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
term tracker item: https://github.com/geneontology/go-ontology/issues/26424
imported from: go.owl
created_by: jl
creation date: 2012-10-17T15:46:40Z
has_alternative_id: GO:0044236
has_alternative_id: GO:0044710
database cross reference: Wikipedia:Metabolism
has exact synonym: metabolism
has_narrow_synonym: metabolic process resulting in cell growth
has_narrow_synonym: metabolism resulting in cell growth
has_narrow_synonym: multicellular organism metabolic process
has_obo_namespace: biological_process
has_related_synonym: single-organism metabolic process
id: GO:0008152
in subset: gocheck do not annotate
in subset: goslim chembl
in subset: goslim euk cellular processes ribbon
in subset: goslim metagenomics
in subset: goslim pir
in subset: goslim plant
in subset: goslim prokaryote ribbon
comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.

cellular process
type: Class
subclass of: biological_process
definition: Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
imported from: go.owl
created_by: jl
creation date: 2012-12-11T16:56:55Z
has_alternative_id: GO:0008151
has_alternative_id: GO:0044763
has_alternative_id: GO:0050875
has exact synonym: cell physiology
has exact synonym: cellular physiological process
has_narrow_synonym: cell growth and/or maintenance
has_obo_namespace: biological_process
has_related_synonym: single-organism cellular process
id: GO:0009987
in subset: gocheck do not annotate
in subset: goslim plant
comment: This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.

gene expression
type: Class
subclass of: biological_process
definition: The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes.
term tracker item: https://github.com/geneontology/go-ontology/issues/22557
imported from: go.owl
database cross reference: Wikipedia:Gene_expression
has_obo_namespace: biological_process
id: GO:0010467
in subset: goslim flybase ribbon

protein-containing complex
type: Class
subclass of: material entity
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.
imported from: go.owl
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 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.

menopause
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Cessation of menstruation, occurring in (e.g.) the human female usually around the age of 50.
imported from: go.owl
database cross reference: Wikipedia:Menopause
has_obo_namespace: biological_process
id: GO:0042697
in subset: gocheck do not annotate
comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase. To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during).

cellular senescence
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
term tracker item: https://github.com/geneontology/go-ontology/issues/22788
imported from: go.owl
never in taxon: NCBITaxon 4751
created_by: tb
creation date: 2011-01-05T02:27:08Z
has_obo_namespace: biological_process
id: GO:0090398

replicative senescence
type: Class
subclass of: cellular process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging.
term tracker item: https://github.com/geneontology/go-ontology/issues/22788
imported from: go.owl
created_by: tb
creation date: 2011-01-05T02:32:29Z
has_obo_namespace: biological_process
id: GO:0090399

donor
type: Class
subclass of: independent continuant
definition: A person who makes a donation.
imported from: gsso.owl
alternate name: donors

statistical analysis
type: Class
subclass of: planned process
definition: Analyses regarding statistical data.
imported from: gsso.owl
database cross reference: https://en.wikipedia.org/wiki/Category:Statistical_analysis
database cross reference: https://www.wikidata.org/wiki/Q12718609
alternate name: statistical analyses

Phenotypic abnormality
type: Class
subclass of: phenotype
definition: A phenotypic abnormality.
imported from: hp.owl
database cross reference: UMLS:C4021819
has exact synonym: Organ abnormality
id: HP:0000118
comment: This is the root of the phenotypic abnormality subontology of the HPO.

Acute kidney injury
type: Class
subclass of: kidney disease
fromOldVersion: yes
definition: Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
imported from: hp.owl
database cross reference: MSH:D058186
database cross reference: SNOMEDCT_US:14350001000004108
database cross reference: SNOMEDCT_US:14669001
database cross reference: UMLS:C0022660
database cross reference: UMLS:C2609414
has exact synonym: Acute kidney failure
has exact synonym: Acute renal failure
id: HP:0001919
comment: Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies.

Unsteady gait
type: Class
subclass of: Abnormality of movement
imported from: hp.owl
database cross reference: SNOMEDCT_US:22631008
database cross reference: SNOMEDCT_US:394616008
database cross reference: UMLS:C0231686
has exact synonym: Gait instability
has exact synonym: Unsteady walk
id: HP:0002317

Vascular calcification
type: Class
subclass of: biological_process
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
definition: Abnormal calcification of the vasculature.
imported from: hp.owl
database cross reference: MSH:D061205
database cross reference: SNOMEDCT_US:237897009
database cross reference: UMLS:C0342649
id: HP:0004934

Brain atrophy
type: Class
subclass of: Phenotypic abnormality
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Partial or complete wasting (loss) of brain tissue that was once present.
imported from: hp.owl
creator: https://orcid.org/0000-0002-0736-9199
creation date: 2013-11-23T02:46:15Z
database cross reference: SNOMEDCT_US:278849000
database cross reference: SNOMEDCT_US:418143002
database cross reference: SNOMEDCT_US:52522001
database cross reference: UMLS:C0154671
database cross reference: UMLS:C0235946
has exact synonym: Brain degeneration
has exact synonym: Brain wasting
has exact synonym: whole brain volume loss
id: HP:0012444

Clinical modifier
type: Class
subclass of: quality
definition: This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects.
imported from: hp.owl
creator: https://orcid.org/0000-0002-0736-9199
creation date: 2014-06-06T06:34:24Z
has_alternative_id: HP:0000004
database cross reference: UMLS:C4021064
has exact synonym: Phenotypic modifier
id: HP:0012823
comment: Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term.

Recurrent
type: Class
subclass of: Clinical modifier
definition: Applies to a sign, symptom or manifestation that occurs multiple times separated by intervals in which the sign, symptom, or manifestation is not present.
imported from: hp.owl
date: 2018-02-25T14:40:47Z
creator: https://orcid.org/0000-0002-0736-9199
has exact synonym: Intermittent

Abnormality of movement
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements.
imported from: hp.owl
creator: https://orcid.org/0009-0006-4530-3154
creation date: 2010-05-28T11:48:50Z
has_alternative_id: HP:0001294
database cross reference: SNOMEDCT_US:60342002
database cross reference: UMLS:C0026650
has exact synonym: Abnormality of movement
has exact synonym: Movement disorder
has exact synonym: Unusual movement
id: HP:0100022
comment: Movement disorders are characterized by the phenotypic abnormalities including abnormal involuntary movements, akathisia, akinesia, athetosis, ataxia, ballismus, bradykinesia, chorea, dyskinesia, dystonia, and myoclonus tics, tremor, spasms, and stereotypy.

data item
type: Class
subclass of: information content entity
fromOldVersion: yes
editor preferred label: data item
example of usage: Data items include counts of things, analyte concentrations, and statistical summaries.
has curation status: IAO_0000125
definition: An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
editor note: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
editor note: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
editor note: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
editor note: 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
editor note: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
definition editor: PERSON: Alan Ruttenberg
definition editor: PERSON: Chris Stoeckert
definition editor: PERSON: Jonathan Rees
alternative term: data
imported from: iao.owl

information content entity
type: Class
subclass of: generically dependent continuant
fromOldVersion: yes
editor preferred label: information content entity
example of usage: Examples of information content entites include journal articles, data, graphical layouts, and graphs.
has curation status: IAO_0000122
definition: A generically dependent continuant that is about some thing.
editor note: 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ).
editor note: information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
definition editor: PERSON: Chris Stoeckert
definition source: OBI_0000142
imported from: iao.owl

measurement datum
type: Class
subclass of: data item
fromOldVersion: yes
editor preferred label: measurement datum
example of usage: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
has curation status: IAO_0000125
definition: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
editor note: 2/2/2009 is_specified_output of some assay?
definition editor: person:Chris Stoeckert
definition source: OBI_0000305
definition source: group:OBI
imported from: iao.owl

textual entity
type: Class
subclass of: information content entity
fromOldVersion: yes
editor preferred label: textual entity
example of usage: Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
has curation status: IAO_0000123
definition: A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.
editor note: AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc.
editor note: MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities.
definition editor: PERSON: Lawrence Hunter
alternative term: text
imported from: iao.owl

hypothesis textual entity
type: Class
subclass of: textual entity
fromOldVersion: yes
editor preferred label: hypothesis textual entity
example of usage: that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660
has curation status: IAO_0000120
definition: A textual entity that expresses an assertion that is intended to be tested.
editor note: 2009/09/28 Alan Ruttenberg. Fucoidan-use-case
definition editor: Person:Alan Ruttenberg
imported from: iao.owl

regulatory document
type: Class
subclass of: Document
definition: A document that either prescribes actions or prescribes the permissions, obligations, restrictions, or protections relating to public or legal policy.
definition editor: Cooper Stansbury
curator note: Rules, legal specifications, guidelines (both categorical and hypothetical), that exist together in one regulatory document. Regulations may contain a single, or multiple rules.
curator note: The clause ‘permissions, obligations, restrictions, or protections’ will be replaced with more general superclass, likely from d-acts, when that infrastructure becomes available. IOU Code.
imported from: ico.owl

sepsis
type: Class
subclass of: process
definition: A process that is a systemic inflammatory response to infection.
definition editor: Albert Goldfain
definition editor: Alexander Diehl
definition editor: Lindsay Cowell
imported from: ido.owl

medical action
type: Class
subclass of: planned process
definition: A clinically prescribed procedure, therapy, intervention, or recommendation.
imported from: maxo.owl
date: 2018-11-16T20:07:28Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: OGMS:0000096
has_narrow_synonym: health care process

therapeutic procedure
type: Class
subclass of: medical action
definition: All manners of treatment, be they pharmaceuticals, invasive procedures, etc. to relieve illness and injury in attempts to bring the body back to its normal state.
imported from: maxo.owl
date: 2018-11-16T20:08:29Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C25218
database cross reference: NCIT:C49236
database cross reference: OAE:0000094
database cross reference: OGMS:0000112
comment: An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.

diagnostic procedure
type: Class
subclass of: medical action
definition: Any procedure or test to diagnose a disease or disorder.
imported from: maxo.owl
date: 2018-11-16T20:10:20Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C18020
database cross reference: OGMS:0000104
has exact synonym: diagnostic technique procedure
has exact synonym: diagnostic testing

surgical procedure
type: Class
subclass of: medical action
definition: A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery.
imported from: maxo.owl
date: 2018-11-16T20:10:35Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: ERO:0000378
database cross reference: NCIT:C15329
database cross reference: NCIT:C17173
database cross reference: NCRO:0000228
database cross reference: OAE:0000067
database cross reference: SCDO:1000017
has exact synonym: operation
has exact synonym: surgery
has exact synonym: surgical intervention
has exact synonym: surgical operation

biomarker analysis
type: Class
subclass of: diagnostic procedure
definition: A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly.
imported from: maxo.owl
date: 2018-11-16T20:22:04Z
creator: http://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C63333
has exact synonym: biomarker assessment
has exact synonym: biomarker measurement
has exact synonym: biomarker test

genetic testing
type: Class
subclass of: therapeutic procedure
definition: The process of isolating and testing the DNA of an embryo or a person to detect the presence of genetic alterations or defects that may predispose to the future development of a disease or disorder.
imported from: maxo.owl
date: 2019-01-20T00:46:22Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C15709
has exact synonym: genetic analysis

chemotherapy
type: Class
subclass of: therapeutic procedure
definition: The use of synthetic or naturally-occurring chemicals for the treatment of diseases.
imported from: maxo.owl
date: 2020-06-02T13:10:41Z
created_by: http://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C15632
database cross reference: OGMS:0000113
has exact synonym: chemotherapeutic agent treatment
has exact synonym: chemotherapeutic drug treatment
has exact synonym: treatment with a chemotherapeutic agent
has exact synonym: treatment with a chemotherapeutic drug
has exact synonym: treatment with a chemotherapeutic medication
comment: Although this term is used to describe any therapy involving the use of chemical-based agents, it is particularly used to refer to the use of chemical-based agents to treat cancer. Antineoplastic chemotherapy works by arresting or killing the growth and spread of cancer cells. Chemotherapy may also include agents that enhance immune function or alter hormonal activity.

eye movement measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Assessment of the parameters of eye movement, including horizontal and vertical rotations of the eye, opening or closing of the eyes in response to stimuli, pupil response to light, and blink reflex.
imported from: maxo.owl
date: 2023-02-24T19:31:14Z
creator: https://orcid.org/0000-0001-7941-2961
database cross reference: NCIT:C162707
has exact synonym: eye movement assessment

echocardiography
type: Class
subclass of: diagnostic procedure
definition: The use of ultrasound to produce images of structures in the heart.
imported from: maxo.owl
date: 2020-01-24T20:39:14Z
created_by: http://orcid.org/0000-0001-7941-2961
has exact synonym: cardiac echo procedure
has exact synonym: echo procedure
has exact synonym: echocardiogram procedure
has exact synonym: heart diagnostic sonography
has exact synonym: heart medical ultrasound
has exact synonym: heart sonography
has exact synonym: heart ultrasound examination
has exact synonym: heart ultrasound imaging procedure
has exact synonym: heart ultrasound procedure
has exact synonym: sonography of heart
has exact synonym: ultrasonography of heart

biological feature
type: Class
subclass of: quality
definition: Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
imported from: mi.owl
has_obo_namespace: PSI-MI
id: MI:0252
in subset: PSI-MI slim

oral glucose tolerance test
type: Class
subclass of: assay
definition: A test in which glucose is given orally, often in solution, and blood samples taken afterward at specific time interval(s) to determine how quickly it is cleared from the blood.
imported from: mmo.owl
created_by: mshimoyama
creation date: 2010-08-05T01:56:02Z
has exact synonym: OGTT
has_obo_namespace: measurement_method_ontology
id: MMO:0000113

arterial disorder
type: Class
subclass of: cardiovascular system disease
fromOldVersion: yes
definition: An impairment of the structure or function of the blood vessels which carry blood away from the heart.
imported from: mondo.owl
conforms to: location.yaml
conforms to: location top.yaml
database cross reference: DOID:0050828
database cross reference: ICD9:447.8
database cross reference: ICD9:447.9
database cross reference: NCIT:C35317
database cross reference: SCTID:359557001
database cross reference: UMLS:C0852949
has exact synonym: arterial disease
has exact synonym: arterial disorder
has exact synonym: arteriopathy
has exact synonym: artery disease
has exact synonym: artery disease or disorder
has exact synonym: disease of artery
has exact synonym: disease or disorder of artery
has exact synonym: disorder of artery
id: MONDO:0000473

gastric cancer
type: Class
subclass of: cancer
definition: A primary or metastatic malignant neoplasm involving the stomach.
term tracker item: https://github.com/monarch-initiative/mondo/issues/4521
imported from: mondo.owl
conforms to: cancer.yaml
has_broad_synonym: gastric neoplasm
database cross reference: DOID:10534
database cross reference: ICD10CM:C16
database cross reference: ICD9:151
database cross reference: ICD9:151.4
database cross reference: ICD9:151.5
database cross reference: ICD9:151.6
database cross reference: ICD9:151.9
database cross reference: NCIT:C9331
database cross reference: OMIM:613659
database cross reference: Orphanet:63443
has exact synonym: Ca lesser curvature - stomach
has exact synonym: cancer of stomach
has exact synonym: gastric cancer
has exact synonym: gastric cancer risk after h. pylori infection
has exact synonym: gastric cancer, somatic
has exact synonym: malignant gastric neoplasm
has exact synonym: malignant gastric tumor
has exact synonym: malignant gastric tumour
has exact synonym: malignant neoplasm of lesser curve of stomach
has exact synonym: malignant neoplasm of stomach
has exact synonym: malignant neoplasm of the stomach
has exact synonym: malignant stomach neoplasm
has exact synonym: malignant tumor of body of stomach
has exact synonym: malignant tumor of greater curve of stomach
has exact synonym: malignant tumor of lesser curve of stomach
has exact synonym: malignant tumor of stomach
has exact synonym: malignant tumor of the stomach
has exact synonym: malignant tumour of body of stomach
has exact synonym: malignant tumour of greater curve of stomach
has exact synonym: malignant tumour of lesser curve of stomach
has exact synonym: malignant tumour of stomach
has exact synonym: malignant tumour of the stomach
has exact synonym: stomach cancer
has_narrow_synonym: Ca body - stomach
has_narrow_synonym: ca greater curvature of stomach
has_narrow_synonym: malignant neoplasm of body of stomach
has_related_synonym: gastric cancer, intestinal
id: MONDO:0001056

impaired renal function disease
type: Class
subclass of: kidney disease
definition: Any disease in which the causes of the disease is a perturbation of the kidney leading to its dysfunction.
imported from: mondo.owl
conforms to: disease by dysfunctional structure.yaml
conforms to: specific disease by dysfunctional structure.yaml
has_broad_synonym: disease of kidney
has_broad_synonym: kidney disease
database cross reference: DOID:11705
database cross reference: ICD10CM:N25
database cross reference: ICD9:588.8
database cross reference: ICD9:588.89
database cross reference: ICD9:588.9
database cross reference: SCTID:197663003
id: MONDO:0001343

digestive system disorder
type: Class
subclass of: disorder
fromOldVersion: yes
definition: A disease or disorder that involves the digestive system.
imported from: mondo.owl
conforms to: location.yaml
database cross reference: DOID:77
database cross reference: EFO:0000405
database cross reference: ICD10CM:K00-K95
database cross reference: ICD9:520-579.99
database cross reference: ICD9:V47.3
database cross reference: MESH:D005767
database cross reference: NCIT:C2990
database cross reference: SCTID:53619000
has exact synonym: alimentary system disease
has exact synonym: digestive disease
has exact synonym: digestive system disease
has exact synonym: digestive system disease or disorder
has exact synonym: digestive system disorder
has exact synonym: disease of digestive system
has exact synonym: disease or disorder of digestive system
has exact synonym: disorder of digestive system
has exact synonym: gastroenterological system disease
has exact synonym: gastroenterological system disorder
has exact synonym: gastroenteropathy
has exact synonym: gastrointestinal disease
has exact synonym: gastrointestinal disorder
has exact synonym: gastrointestinal system disease
has exact synonym: gastrointestinal system disorder
has exact synonym: git disease
has exact synonym: stomach or intestinal disorder
id: MONDO:0004335
in subset: rare grouping

Alzheimer disease
type: Class
subclass of: neurodegenerative disease
fromOldVersion: yes
definition: A progressive, neurodegenerative disease characterized by loss of function and death of nerve cells in several areas of the brain leading to loss of cognitive function such as memory and language.
term tracker item: https://github.com/monarch-initiative/mondo/issues/4013
imported from: mondo.owl
excluded from qc check: qc-single-child.sparql
database cross reference: DOID:10652
database cross reference: EFO:0000249
database cross reference: GARD:0000632
database cross reference: HP:0002511
database cross reference: ICD10CM:G30
database cross reference: ICD9:290.1
database cross reference: ICD9:331.0
database cross reference: MESH:D000544
database cross reference: NCIT:C2866
database cross reference: NIFSTD:birnlex_2092
database cross reference: Orphanet:238616
database cross reference: SCTID:142811000119104
database cross reference: UMLS:C0002395
has exact synonym: AD
has exact synonym: Alzheimer dementia
has exact synonym: Alzheimer disease
has exact synonym: Alzheimer's dementia
has exact synonym: Alzheimer's disease
has exact synonym: Alzheimers dementia
has exact synonym: Alzheimers disease
has exact synonym: presenile and senile dementia
has_narrow_synonym: Alzheimer disease, familial
id: MONDO:0004975
in subset: orphanet rare
in subset: rare

chronic obstructive pulmonary disease
type: Class
subclass of: lung disease
fromOldVersion: yes
definition: A chronic and progressive lung disorder characterized by the loss of elasticity of the bronchial tree and the air sacs, destruction of the air sacs wall, thickening of the bronchial wall, and mucous accumulation in the bronchial tree. The pathologic changes result in the disruption of the air flow in the bronchial airways. Signs and symptoms include shortness of breath, wheezing, productive cough, and chest tightness. The two main types of chronic obstructive pulmonary disease are chronic obstructive bronchitis and emphysema.
imported from: mondo.owl
excluded from qc check: qc-single-child.sparql
database cross reference: DOID:3083
database cross reference: EFO:0000341
database cross reference: ICD9:490-496.99
database cross reference: ICD9:496
database cross reference: MESH:D029424
database cross reference: NCIT:C3199
database cross reference: OMIM:606963
database cross reference: SCTID:13645005
has exact synonym: COPD
has exact synonym: COPD, chronic obstructive pulmonary disease
has exact synonym: chronic obstructive airway disease
has exact synonym: chronic obstructive airways disease
has exact synonym: chronic obstructive lung disease
has exact synonym: chronic obstructive pulmonary disease (COPD)
has exact synonym: chronic obstructive pulmonary disease, (COPD)
has exact synonym: cold
has exact synonym: cold (chronic obstructive lung disease)
has exact synonym: disease (COPD), chronic obstructive
has exact synonym: obstructive lung disease, chronic
has exact synonym: obstructive pulmonary disease (COPD), chronic
has exact synonym: pulmonary disease (COPD), chronic obstructive
id: MONDO:0005002

neoplasm
type: Class
subclass of: cancer
definition: A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias.
imported from: mondo.owl
OBO foundry unique label: neoplasm (disease)
has_broad_synonym: cell process disease
database cross reference: DOID:14566
database cross reference: EFO:0000616
database cross reference: HP:0002664
database cross reference: ICD10CM:C00-D49
database cross reference: ICD10CM:C7A-C7A
database cross reference: ICD10CM:C7B-C7B
database cross reference: ICD9:140-239.99
database cross reference: ICD9:239.8
database cross reference: ICD9:239.9
database cross reference: MESH:D009369
database cross reference: NCIT:C3262
database cross reference: ONCOTREE:OTHER
database cross reference: SCTID:55342001
database cross reference: UMLS:CN236628
has exact synonym: disease of cellular proliferation
has exact synonym: neoplasia
has exact synonym: neoplasm
has exact synonym: neoplasm (disease)
has exact synonym: neoplastic disease
has exact synonym: neoplastic growth
has exact synonym: tumor
has exact synonym: tumor disease
has_narrow_synonym: other neoplasm
id: MONDO:0005070
narrow match: C7A-C7A
narrow match: C7B-C7B

nervous system disorder
type: Class
subclass of: disease
definition: A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
imported from: mondo.owl
conforms to: location.yaml
database cross reference: DOID:863
database cross reference: EFO:0000618
database cross reference: ICD10CM:G00-G99
database cross reference: ICD9:349.89
database cross reference: ICD9:349.9
database cross reference: MESH:D009422
database cross reference: NCIT:C26835
database cross reference: SCTID:118940003
database cross reference: UMLS:C0027765
database cross reference: Wikipedia:Nervous_system_disease
has exact synonym: disease of nervous system
has exact synonym: disease or disorder of nervous system
has exact synonym: disorder of nervous system
has exact synonym: nervous system disease
has exact synonym: nervous system disease or disorder
has exact synonym: nervous system disorder
has exact synonym: neurologic disease
has exact synonym: neurologic disorder
has exact synonym: neurological disease
has exact synonym: neurological disorder
id: MONDO:0005071
in subset: rare grouping
comment: 'psychiatric disorder' is not classified as a 'nervous system disorder' in Mondo (though it is often as such): the hallmarks of psychiatric disorders are based in behavior and emotional state, and the relation with nervous system malfunction or damage is not always clearly determined.

bacterial infectious disease
type: Class
subclass of: disease
definition: An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections.
imported from: mondo.owl
conforms to: infectious disease by agent.yaml
database cross reference: DOID:104
database cross reference: EFO:0000771
database cross reference: ICD9:040.89
database cross reference: ICD9:041.89
database cross reference: ICD9:041.9
database cross reference: MESH:D001424
database cross reference: NCIT:C2890
database cross reference: SCTID:87628006
database cross reference: UMLS:C0004623
has exact synonym: Bacteria caused disease or disorder
has exact synonym: Bacteria disease or disorder
has exact synonym: Bacteria infectious disease
has exact synonym: bacterial disease
has exact synonym: bacterial disorder
has exact synonym: bacterial infection
has exact synonym: bacterial infectious disease
has exact synonym: infection, bacterial
has_related_synonym: infections, bacterial
id: MONDO:0005113

atherosclerosis
type: Class
subclass of: cardiovascular system disease
fromOldVersion: yes
definition: Build-up of fatty material and calcium deposition in the arterial wall resulting in partial or complete occlusion of the arterial lumen.
imported from: mondo.owl
database cross reference: DOID:1936
database cross reference: EFO:0003914
database cross reference: ICD10CM:I70
database cross reference: ICD9:440
database cross reference: ICD9:440.8
database cross reference: MESH:D050197
database cross reference: NCIT:C35768
database cross reference: NCIT:C35771
database cross reference: SCTID:441574008
has exact synonym: atherosclerosis of artery
has exact synonym: atherosclerotic cardiovascular disease
has_related_synonym: atherosclerosis artery
id: MONDO:0005311
comment: Note that NCIT distinguishes between atherosclerotic cardiovascular disease and atherosclerosis - we merge these here

bone disorder
type: Class
subclass of: disorder
definition: Diseases of bones.
imported from: mondo.owl
excluded subClassOf: MONDO_0003900
conforms to: location.yaml
conforms to: location top.yaml
database cross reference: DOID:0080001
database cross reference: EFO:0004260
database cross reference: ICD10CM:M80-M85
database cross reference: ICD9:731.8
database cross reference: ICD9:733.99
database cross reference: MESH:D001847
database cross reference: Orphanet:364803
database cross reference: SCTID:76069003
database cross reference: UMLS:C0005940
database cross reference: UMLS:CN204768
has exact synonym: bone element disease
has exact synonym: bone element disease or disorder
has exact synonym: disease of bone element
has exact synonym: disease or disorder of bone element
has exact synonym: disorder of bone element
has_related_synonym: rare bone disease related to a common gene or pathway defect
has_related_synonym: skeletal disease
id: MONDO:0005381
in subset: disease grouping
in subset: ordo group of disorders

metastatic malignant neoplasm in the lymph nodes
type: Class
subclass of: metastatic neoplasm
fromOldVersion: yes
definition: The spread of a malignant neoplasm to the lymph nodes.
imported from: mondo.owl
excluded subClassOf: MONDO_0004993
database cross reference: EFO:0004906
database cross reference: NCIT:C4904
database cross reference: UMLS:C0686619
has exact synonym: Metastases to lymph nodes
has exact synonym: lymph node metastasis
has exact synonym: metastasis to lymph node
has exact synonym: metastatic malignant neoplasm to the lymph nodes
has exact synonym: metastatic neoplasm to the lymph node
has exact synonym: metastatic tumor to lymph node
id: MONDO:0005438
in subset: mondo rare
in subset: rare

acute coronary syndrome
type: Class
subclass of: cardiovascular system disease
fromOldVersion: yes
definition: Signs and symptoms related to acute ischemia of the myocardium secondary to coronary artery disease. The clinical presentation covers a spectrum of heart diseases from unstable angina to myocardial infarction.
imported from: mondo.owl
excluded from qc check: qc-single-child.sparql
database cross reference: EFO:0005672
database cross reference: MESH:D054058
database cross reference: NCIT:C53652
database cross reference: SCTID:394659003
database cross reference: UMLS:C0948089
has exact synonym: acute coronary syndrome
has_related_synonym: acute coronary syndromes
has_related_synonym: coronary syndrome, acute
has_related_synonym: coronary syndromes, acute
has_related_synonym: syndrome, acute coronary
has_related_synonym: syndromes, acute coronary
id: MONDO:0005542

neurodegenerative disease
type: Class
subclass of: disease
fromOldVersion: yes
definition: A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function.
imported from: mondo.owl
has_broad_synonym: degenerative disease
database cross reference: DOID:1289
database cross reference: EFO:0005772
database cross reference: ICD9:349.89
database cross reference: MESH:D019636
database cross reference: NCIT:C4802
database cross reference: SCTID:80690008
has exact synonym: brain degeneration
has exact synonym: central nervous system degenerative disorder
has exact synonym: central nervous system neurodegenerative disorder
has exact synonym: degenerative disorder of central nervous system
has exact synonym: neurodegenerative disease
has_narrow_synonym: cerebral degeneration disease
id: MONDO:0005559
in subset: merged class
comment: Editor notes: DO treats this as two diseases

systemic lupus erythematosus
type: Class
subclass of: autoimmune disease
fromOldVersion: yes
definition: An autoimmune multi-organ disease typically associated with vasculopathy and autoantibody production. Most patients have antinuclear antibodies (ANA). The presence of anti-dsDNA or anti-Smith antibodies are highly-specific.
term tracker item: https://github.com/monarch-initiative/mondo/issues/4521
imported from: mondo.owl
OBO foundry unique label: systemic lupus erythematosus (disease)
excluded subClassOf: MONDO_0019724
excluded subClassOf: MONDO_0019737
database cross reference: DOID:9074
database cross reference: EFO:0002690
database cross reference: HP:0002725
database cross reference: ICD9:710.0
database cross reference: MESH:D008180
database cross reference: NCIT:C3201
database cross reference: OMIM:152700
database cross reference: Orphanet:536
database cross reference: SCTID:55464009
has exact synonym: SLE
has exact synonym: SLE - lupus erythematosus, systemic
has exact synonym: disseminated lupus erythematosus
has exact synonym: lupus erythematosus, systemic
has exact synonym: systemic lupus erythematosus
has exact synonym: systemic lupus erythematosus (disease)
has exact synonym: systemic lupus erythematosus susceptibility to
has exact synonym: systemic lupus erythematosus, susceptibility to
has_related_synonym: excess LMW-DNA
has_related_synonym: excess lymphocyte low molecular weight DNA
has_related_synonym: lupus nephritis, susceptibility to
id: MONDO:0007915
in subset: ordo disease
in subset: orphanet rare
in subset: rare

rheumatoid arthritis
type: Class
subclass of: autoimmune disease
fromOldVersion: yes
definition: A chronic, systemic autoimmune disorder characterized by inflammation in the synovial membranes and articular surfaces. It manifests primarily as a symmetric, erosive polyarthritis that spares the axial skeleton and is typically associated with the presence in the serum of rheumatoid factor.
term tracker item: https://github.com/monarch-initiative/mondo/issues/4521
term tracker item: https://github.com/monarch-initiative/mondo/issues/6094
imported from: mondo.owl
excluded from qc check: qc-omim-subsumption.sparql
has_broad_synonym: atrophic arthritis
database cross reference: DOID:7148
database cross reference: EFO:0000685
database cross reference: HP:0001370
database cross reference: ICD9:714.0
database cross reference: MESH:D001172
database cross reference: NCIT:C2884
database cross reference: OMIM:180300
database cross reference: Orphanet:284130
database cross reference: SCTID:69896004
database cross reference: UMLS:C0003873
has exact synonym: RA
has exact synonym: arthritis or polyarthritis, rheumatic
has exact synonym: arthritis, rheumatoid
has exact synonym: autoimmune arthritis
has exact synonym: rheumatoid arthritis
has exact synonym: rheumatoid arthritis, progression of
has_related_synonym: rheumatoid arthritis, susceptibility to
id: MONDO:0008383
in subset: orphanet rare
in subset: rare

myocardial ischemia
type: Class
subclass of: vascular disease
definition: A disorder of cardiac function caused by insufficient blood flow to the muscle tissue of the heart. The decreased blood flow may be due to narrowing of the coronary arteries (coronary artery disease), to obstruction by a thrombus (coronary thrombosis), or less commonly, to diffuse narrowing of arterioles and other small vessels within the heart. Severe interruption of the blood supply to the myocardial tissue may result in necrosis of cardiac muscle (myocardial infarction).
imported from: mondo.owl
database cross reference: EFO:1001375
database cross reference: ICD10CM:I20-I25
database cross reference: MESH:D017202
database cross reference: NCIT:C50625
database cross reference: SCTID:414545008
database cross reference: UMLS:C0151744
has exact synonym: IHD
has exact synonym: ischemic disease of myocardium
has exact synonym: ischemic heart disease
has exact synonym: myocardium ischemic disease
has_related_synonym: disease, ischemic heart
has_related_synonym: diseases, ischemic heart
has_related_synonym: heart disease, ischemic
has_related_synonym: heart diseases, ischemic
has_related_synonym: ischemia, myocardial
has_related_synonym: ischemias, myocardial
has_related_synonym: ischemic heart diseases
has_related_synonym: myocardial Ischemias
id: MONDO:0024644

brain injury
type: Class
subclass of: disease
definition: Acute and chronic (see also brain INJURIES, CHRONIC) injuries to the brain, including the cerebral hemispheres, CEREBELLUM, and brain STEM. Clinical manifestations depend on the nature of injury. Diffuse trauma to the brain is frequently associated with DIFFUSE AXONAL INJURY or COMA, POST-TRAUMATIC. Localized injuries may be associated with NEUROBEHAVIORAL MANIFESTATIONS; HEMIPARESIS, or other focal neurologic deficits.
imported from: mondo.owl
conforms to: location.yaml
database cross reference: MESH:D001930
database cross reference: Orphanet:90056
has exact synonym: brain injury
has exact synonym: injury of brain
has_related_synonym: brain Traumas
has_related_synonym: brain trauma
id: MONDO:0043510
narrow match: Orphanet_90056

traumatic brain injury
type: Class
subclass of: brain injury
definition: A brain disease that is characterized by brain dysfunction caused by an outside force, usually a violent blow to the head.
imported from: mondo.owl
database cross reference: DOID:0081292
id: MONDO:0858950

pathological entity
type: Class
subclass of: independent continuant
definition: Pathological structure or process
imported from: mpath.owl
has_obo_namespace: mouse_pathology.ontology
id: MPATH:0

apoptosis
type: Class
subclass of: pathologic process
definition: Energy dependent cell death induced by intrinsic genetic or developmental programme, or external stimuli such as addition or withdrawal of cytokines or trophic factors, radiation, chemotherapeutic agents etc. Characterised by cell shrinkage, increases in membrane permeability, endonucleolyis and nuclear fragmentation resulting in the formation of rapidly endocytosed apoptotic bodies.
imported from: mpath.owl
has_obo_namespace: mouse_pathology.ontology
has_related_synonym: programmed cell death
id: MPATH:3

amyloid deposition
type: Class
subclass of: pathological entity
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Extracellular deposition of amyloid protein.
imported from: mpath.owl
has_obo_namespace: mouse_pathology.ontology
has_related_synonym: Amyloidosis
id: MPATH:34
comment: Any group of chemically diverse proteins that appears microscopically homogeneous, but is composed of linear non-branching aggregated fibrils aranged in sheets when see under the electron microscope.

oxidative stress
type: Class
subclass of: metabolic process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: condition characterized by an accumulation of free radical groups in the body, which creates a potentially unstable and damaging cellular environment linked to tissue damage, accelerated aging, and degenerative disease; can result from many factors, including exposure to alcohol, medications, poor nutrition, trauma, cold or toxins; may be indicated by low antioxidant levels measured in blood plasma
imported from: mp.owl
has_obo_namespace: MPheno.ontology
has_related_synonym: increased ROS production
has_related_synonym: increased reactive oxygen species production
id: MP:0003674

insulin resistance
type: Class
subclass of: symptom
fromOldVersion: yes
definition: diminished effectiveness of insulin in lowering plasma glucose levels
imported from: mp.owl
has_obo_namespace: MPheno.ontology
id: MP:0005331

Kidney Injury Molecule-1 Measurement
type: Class
subclass of: measurement
definition: The determination of the amount of kidney injury molecule-1 present in a sample.
imported from: ncit.owl
Related_To_Genetic_Biomarker: NCIT C116606
code: C100433
Semantic_Type: Laboratory Procedure
Display_Name: Kidney Injury Molecule-1 Measurement
Preferred_Name: Kidney Injury Molecule-1 Measurement
UMLS_CUI: C2681921
Contributing_Source: CDISC
Contributing_Source: CTRP
ALT_DEFINITION: A measurement of the kidney injury molecule-1 (Kim-1) in a biological specimen.
has exact synonym: HAVCR1 Measurement
has exact synonym: HAVcr-1 Measurement
has exact synonym: Hepatitis A Virus Cellular Receptor 1
has exact synonym: Hepatitis A Virus Cellular Receptor 1 Measurement
has exact synonym: KIM-1
has exact synonym: KIM-1 Measurement
has exact synonym: KIM1
has exact synonym: KIM1 Measurement
has exact synonym: Kidney Injury Molecule 1 Measurement
has exact synonym: Kidney Injury Molecule-1
has exact synonym: Kidney Injury Molecule-1 Measurement
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800
in subset: NCIT C61410
in subset: NCIT C65047
in subset: NCIT C66830
in subset: NCIT C67154
in subset: NCIT C77526

MicroRNA 124
type: Class
subclass of: miRNA
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A 20 ribonucleotide sequence that is a final product of the processing of either MIR124-1 pre-miRNA, MIR124-2 pre-miRNA or MIR124-3 pre-miRNA. This oligonucleotide may be involved in the negative regulation of gene expression.
imported from: ncit.owl
code: C106407
Semantic_Type: Nucleic Acid, Nucleoside, or Nucleotide
Display_Name: MicroRNA 124
Preferred_Name: MicroRNA 124
UMLS_CUI: C2743231
Contributing_Source: CTRP
miRBase_ID: MIMAT0000422
has exact synonym: MIR124
has exact synonym: MIRN124
has exact synonym: MicroRNA 124
has exact synonym: hsa-miR-124
has exact synonym: hsa-miR-124-3p
has exact synonym: hsa-miR-124a
has exact synonym: miR-124
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800

Human Epidermal Growth Factor Receptor 2 Measurement
type: Class
subclass of: measurement
definition: The determination of the amount of human epidermal growth factor receptor 2 present in a sample.
imported from: ncit.owl
Related_To_Genetic_Biomarker: NCIT C17756
code: C112312
Semantic_Type: Laboratory Procedure
Preferred_Name: Human Epidermal Growth Factor Receptor 2 Measurement
UMLS_CUI: C3810543
Contributing_Source: CDISC
ALT_DEFINITION: A measurement of HER2 protein in a biological specimen.
has exact synonym: ERBB2
has exact synonym: HER2
has exact synonym: HER2/NEU
has exact synonym: Human Epidermal Growth Factor Receptor 2
has exact synonym: Human Epidermal Growth Factor Receptor 2 Measurement
has exact synonym: Receptor Tyrosine-Protein Kinase erbB-2 Measurement
in subset: NCIT C132262
in subset: NCIT C132263
in subset: NCIT C61410
in subset: NCIT C65047
in subset: NCIT C66830
in subset: NCIT C67154
in subset: NCIT C77526

Chronic Liver Disease
type: Class
subclass of: liver disease
fromOldVersion: yes
definition: Hepatic necrosis, inflammation, or scarring due to any cause that persists for more than 6 months. Manifestations may include signs and symptoms of cholestasis, portal hypertension, and/or abnormal liver function tests.
imported from: ncit.owl
Has_SeroNet_Permissible_Value: NCIT C17998
Has_SeroNet_Permissible_Value: NCIT C48660
Has_SeroNet_Permissible_Value: NCIT C49487
Has_SeroNet_Permissible_Value: NCIT C49488
code: C113609
Semantic_Type: Disease or Syndrome
Preferred_Name: Chronic Liver Disease
UMLS_CUI: C0341439
Contributing_Source: CPTAC
Contributing_Source: MedDRA
Contributing_Source: NICHD
Contributing_Source: SeroNet
ALT_DEFINITION: Hepatic necrosis, inflammation, or scarring due to any cause that persists for more than 6 months. Manifestations may include signs and symptoms of cholestasis, portal hypertension, and/or abnormal liver function tests.
Maps_To: Chronic liver disease
has exact synonym: Chronic Liver Disease
has exact synonym: Chronic_Liver_Disease
in subset: NCIT C118464
in subset: NCIT C156952
in subset: NCIT C158034
in subset: NCIT C158520
in subset: NCIT C178718
in subset: NCIT C179026
in subset: NCIT C90259

MicroRNA 181
type: Class
subclass of: miRNA
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A microRNA that has six isoforms that may play a role in the activity of phosphatidylinositol-4,5-bisphosphate 3-kinase and natural killer cells. The MIR181 isoforms have been implicated in a variety of cancers, including chronic lymphocytic leukemia, glioblastoma, multiple myeloma and hepatocellular carcinoma.
imported from: ncit.owl
code: C116021
Semantic_Type: Nucleic Acid, Nucleoside, or Nucleotide
Display_Name: MicroRNA 181
Preferred_Name: MicroRNA 181
UMLS_CUI: C3898411
Contributing_Source: CTRP
DesignNote: MIR181 isoforms include hsa-mir-181a-1, hsa-mir-181a-2, hsa-mir-181b-1, hsa-mir-181b-2, hsa-mir-181c and hsa-mir-181d.
has exact synonym: MIR181
has exact synonym: MIRN181
has exact synonym: MicroRNA 181
has exact synonym: hsa-mir-181
has exact synonym: mir-181
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800

MicroRNA 9
type: Class
subclass of: miRNA
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A 23 ribonucleotide sequence that is a final product of the processing of MIR9-1 pre-miRNA, MIR9-2 pre-miRNA or MIR9-3 pre-miRNA. This oligonucleotide is involved in gene regulation and may play a role in nerve cell differentiation, insulin secretion and nervous system tumors which display neuronal differentiation.
imported from: ncit.owl
code: C116401
Semantic_Type: Nucleic Acid, Nucleoside, or Nucleotide
Display_Name: MicroRNA 9
Preferred_Name: MicroRNA 9
UMLS_CUI: C3884166
Contributing_Source: CTRP
miRBase_ID: MIPF0000014
has exact synonym: MIR9
has exact synonym: MIRN9
has exact synonym: MicroRNA 9
has exact synonym: hsa-miR-9-5p
has exact synonym: hsa-mir-9
has exact synonym: miR-9
has exact synonym: miRNA 9
has exact synonym: miRNA-9
has exact synonym: miRNA9
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800

Diffusion Kurtosis Imaging
type: Class
subclass of: Magnetic Resonance Imaging
definition: An extension of conventional diffusion tension imaging, which estimates the kurtosis of the water diffusion probability distribution function. This technique is most commonly used to study the brain.
imported from: ncit.owl
code: C116487
Semantic_Type: Diagnostic Procedure
Display_Name: Diffusion Kurtosis Imaging
Preferred_Name: Diffusion Kurtosis Imaging
NCI_META_CUI: CL433731
Contributing_Source: CTRP
has exact synonym: DKI
has exact synonym: Diffusion Kurtosis Imaging
in subset: NCIT C116977
in subset: NCIT C118169

Apparent Diffusion Coefficient
type: Class
subclass of: metric
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
definition: A measurement of the magnitude of diffusion of water molecules within tissue.
imported from: ncit.owl
code: C116753
Semantic_Type: Conceptual Entity
Preferred_Name: Apparent Diffusion Coefficient
UMLS_CUI: C3890194
has exact synonym: ADC
has exact synonym: Apparent Diffusion Coefficient
has exact synonym: Effective Diffusion Coefficient

Pupillometry
type: Class
subclass of: procedure
definition: A technique used to measure the diameter of the pupil in response to stimuli.
imported from: ncit.owl
code: C120540
Semantic_Type: Diagnostic Procedure
Preferred_Name: Pupillometry
UMLS_CUI: C0260180
has exact synonym: Pupillometry

Creatine Kinase MB
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
definition: An isoenzyme complex comprised of a heterodimer of creatine kinase M-type and B-type.
imported from: ncit.owl
code: C122778
Semantic_Type: Amino Acid, Peptide, or Protein
Display_Name: Creatine Kinase MB
Preferred_Name: Creatine Kinase MB
UMLS_CUI: C0010290
Contributing_Source: CTRP
has exact synonym: CK-MB
has exact synonym: CKMB
has exact synonym: CPK-MB
has exact synonym: Creatine Kinase MB
has exact synonym: Creatine Kinase-MB
has exact synonym: Creatine Phosphokinase-MB
has exact synonym: MM-CK
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800

Perfusion-Weighted Magnetic Resonance Imaging
type: Class
subclass of: Magnetic Resonance Imaging
definition: A magnetic resonance imaging modality used to quantify the blood supply to an organ or tissue using signal measurement as detected from a parenterally administered contrast agent.
imported from: ncit.owl
code: C128056
Semantic_Type: Diagnostic Procedure
Display_Name: Perfusion-Weighted Magnetic Resonance Imaging
Preferred_Name: Perfusion-Weighted Magnetic Resonance Imaging
UMLS_CUI: C0879554
Contributing_Source: CTRP
has exact synonym: PWI
has exact synonym: Perfusion-Weighted MR
has exact synonym: Perfusion-Weighted MRI
has exact synonym: Perfusion-Weighted Magnetic Resonance Imaging
in subset: NCIT C116977
in subset: NCIT C118169

MicroRNA 16
type: Class
subclass of: miRNA
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A 22 ribonucleotide sequence that is a final product of the processing of either MIR16-1 pre-miRNA or MIR16-2 pre-miRNA. This oligonucleotide may be involved in the negative regulation of gene expression.
imported from: ncit.owl
code: C129416
Semantic_Type: Nucleic Acid, Nucleoside, or Nucleotide
Preferred_Name: MicroRNA 16
NCI_META_CUI: CL512801
miRBase_ID: MIMAT0000069
has exact synonym: MIR16
has exact synonym: MIRN16
has exact synonym: MiR-16
has exact synonym: MiRNA16
has exact synonym: MicroRNA 16
has exact synonym: hsa-miR-16
has exact synonym: hsa-miR-16-5p

European Medicines Agency
type: Class
subclass of: biomarker regulatory entity
definition: A public health agency based in London that is responsible for the scientific evaluation, supervision, and safety monitoring of medicines in the European Union.
imported from: ncit.owl
code: C142543
Semantic_Type: Organization
Preferred_Name: European Medicines Agency
NCI_META_CUI: CL541263
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: The regulatory agency for the EU.
has exact synonym: EMA
has exact synonym: European Medicines Agency
has exact synonym: European Medicines Agency (EMA)
in subset: NCIT C61410
in subset: NCIT C67497

Surrogate Marker
type: Class
subclass of: biomarker
definition: In a clinical trial, an assessment of an intervention's effects that takes the place of a patient-based conclusion.
imported from: ncit.owl
code: C142724
Semantic_Type: Functional Concept
Preferred_Name: Surrogate Marker
UMLS_CUI: C0086589
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A measurement of a drug's biological activity that substitutes for a clinically meaningful endpoint. [After Russell Katz, Biomarkers and Surrogate Markers: An FDA Perspective, NeuroRx. 2004 Apr;1(2):189-95.]
has exact synonym: Surrogate Marker
has exact synonym: surrogate biomarker
has exact synonym: surrogate marker
in subset: NCIT C61410
in subset: NCIT C67497

Risk Assessment
type: Class
subclass of: planned process
definition: An estimated probability that one or more adverse event(s) will occur as a result of exposure to an actual or potential hazardous situation or chemical.
imported from: ncit.owl
code: C15367
Semantic_Type: Health Care Activity
Display_Name: Risk Assessment
Preferred_Name: Risk Assessment
UMLS_CUI: C0086930
Contributing_Source: CTRP
ALT_DEFINITION: A process used to estimate the risk that a certain event will happen. In medicine, this may include a person's risk of having a child with a certain condition or disease, such as cancer. It may also be used to estimate the risk of carrying a certain gene mutation (change), or of having an adverse event (unexpected medical problem) in response to certain types of drugs or other substances. A risk assessment may be done by collecting information about a person's age, sex, personal and family medical history, ethnic background, lifestyle, and other factors and using statistics tools to calculate risk.
Legacy Concept Name: Risk_Assessment
has exact synonym: Risk Assessment
has exact synonym: risk assessment
in subset: NCIT C116977
in subset: NCIT C118169

Cancer Research
type: Class
subclass of: planned process
definition: Systematic investigation into the causes of cancer and development of strategies for prevention, diagnosis, treatment, and cure.
imported from: ncit.owl
code: C16199
Semantic_Type: Research Activity
Preferred_Name: Cancer Research
UMLS_CUI: C1516225
Legacy Concept Name: Cancer_Research_Project
has exact synonym: Cancer Research
has exact synonym: Cancer Research Programs
has exact synonym: Cancer Research Project

Clinical Sensitivity
type: Class
subclass of: parameter
imported from: ncit.owl
code: C16234
Semantic_Type: Qualitative Concept
Preferred_Name: Clinical Sensitivity
UMLS_CUI: C1516631
Legacy Concept Name: Clinical_Sensitivity
has exact synonym: Clinical Sensitivity

Magnetic Resonance Imaging
type: Class
subclass of: Imaging Technique
definition: Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders.
imported from: ncit.owl
Is_PCDC_EWS_Authorized_Value_For_Variable: NCIT C117438
Is_Value_For_GDC_Property: Imaging Technique
Is_PCDC_ALL_Authorized_Value_For_Variable: NCIT C178084
code: C16809
Semantic_Type: Diagnostic Procedure
Display_Name: Magnetic Resonance Imaging
Preferred_Name: Magnetic Resonance Imaging
UMLS_CUI: C0024485
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: DIPG/DMG
Contributing_Source: FDA
Contributing_Source: GDC
Contributing_Source: OORO
Contributing_Source: PCDC
Contributing_Source: mCode
ALT_DEFINITION: A procedure in which radio waves and a powerful magnet linked to a computer are used to create detailed pictures of areas inside the body. These pictures can show the difference between normal and diseased tissue. NMRI makes better images of organs and soft tissue than other scanning techniques, such as computed tomography (CT) or x-ray. NMRI is especially useful for imaging the brain, the spine, the soft tissue of joints, and the inside of bones.
ALT_DEFINITION: Imaging that uses radiofrequency waves and a strong magnetic field rather than x-rays to provide amazingly clear and detailed pictures of internal organs and tissues. The technique is valuable for the diagnosis of many pathologic conditions, including cancer, heart and vascular disease, stroke, and joint and musculoskeletal disorders.
Legacy Concept Name: Magnetic_Resonance_Imaging
Maps_To: MRI
has exact synonym: MR
has exact synonym: MR Imaging
has exact synonym: MRI
has exact synonym: MRI Scan
has exact synonym: Magnetic Resonance
has exact synonym: Magnetic Resonance Imaging
has exact synonym: Magnetic Resonance Imaging Scan
has exact synonym: Magnetic resonance imaging (procedure)
has exact synonym: Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance
has exact synonym: NMR Imaging
has exact synonym: NMRI
has exact synonym: Nuclear Magnetic Resonance Imaging
has exact synonym: magnetic resonance imaging
has exact synonym: nuclear magnetic resonance imaging
in subset: NCIT C101858
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C157711
in subset: NCIT C174237
in subset: NCIT C174261
in subset: NCIT C177537
in subset: NCIT C178115
in subset: NCIT C178127
in subset: NCIT C179478
in subset: NCIT C179481
in subset: NCIT C183088
in subset: NCIT C183096
in subset: NCIT C183102
in subset: NCIT C186320
in subset: NCIT C186325
in subset: NCIT C186333
in subset: NCIT C186341
in subset: NCIT C192234
in subset: NCIT C193006
in subset: NCIT C193245
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Magnetic Resonance Spectroscopy
type: Class
subclass of: Magnetic Resonance Imaging
definition: Detection and measurement of the resonant spectra of molecular species in a tissue or sample.
imported from: ncit.owl
code: C16810
Semantic_Type: Diagnostic Procedure
Preferred_Name: Magnetic Resonance Spectroscopy
UMLS_CUI: C0024487
Contributing_Source: CDISC
ALT_DEFINITION: A type of spectroscopy that detects and measures the resonant spectra of molecular species in a tissue or sample.
Legacy Concept Name: Magnetic_Resonance_Spectroscopy
has exact synonym: Magnetic Resonance Spectroscopy
has exact synonym: NMR Spectroscopy
has exact synonym: NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY
has exact synonym: Spectroscopy, MR
has exact synonym: Spectroscopy, NMR
has exact synonym: Spectroscopy, Nuclear Magnetic Resonance
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Model
type: Class
subclass of: information content entity
fromOldVersion: yes
definition: A representation of something, often idealized or modified to make it conceptually easier to understand.
imported from: ncit.owl
code: C16866
Semantic_Type: Intellectual Product
Preferred_Name: Model
UMLS_CUI: C3161035
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: A formal structure for representing and analyzing a process such as a clinical trial or the information pertaining to a restricted context (e.g., clinical trial data). [CDISC]
Legacy Concept Name: Model_System
has exact synonym: Model
has exact synonym: Model System
has exact synonym: Modeling System
has exact synonym: Models
has exact synonym: model
in subset: NCIT C61410
in subset: NCIT C67497

Positron Emission Tomography
type: Class
subclass of: Imaging Technique
definition: A technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance (for example, 2-fluoro-2-deoxy-D-glucose (FDG), which is similar to a naturally occurring sugar, glucose, with the addition of a radioactive fluorine atom). When living tissue containing the positron emitter is bombarded by electrons, gamma radiation produced by collisions of electrons and positrons is detected by a scanner, revealing in fine detail the tissue location of the metabolically-active substance administered.
imported from: ncit.owl
Is_Value_For_GDC_Property: Imaging Technique
Is_PCDC_GCT_Authorized_Value_For_Variable: NCIT C117438
code: C17007
Semantic_Type: Diagnostic Procedure
Display_Name: Positron Emission Tomography
Preferred_Name: Positron Emission Tomography
UMLS_CUI: C0032743
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: GDC
Contributing_Source: OORO
Contributing_Source: PCDC
Contributing_Source: mCode
ALT_DEFINITION: A procedure in which a small amount of radioactive glucose (sugar) is injected into a vein, and a scanner is used to make detailed, computerized pictures of areas inside the body where the glucose is used. Because cancer cells often use more glucose than normal cells, the pictures can be used to find cancer cells in the body.
ALT_DEFINITION: An imaging technique for measuring the gamma radiation produced by collisions of electrons and positrons (anti-electrons) within living tissue. In positron emission tomography (PET), a subject is given a dose of a positron-emitting radionuclide attached to a metabolically active substance. A scanner reveals the tissue location of the metabolically-active substance administered.
Legacy Concept Name: Positron_Emission_Tomography
Maps_To: PET
has exact synonym: Medical Imaging, Positron Emission Tomography
has exact synonym: PET
has exact synonym: PET SCAN
has exact synonym: PET Scan
has exact synonym: PET scan
has exact synonym: PT
has exact synonym: Pet Scan
has exact synonym: Positron Emission Tomography
has exact synonym: Positron Emission Tomography Scan
has exact synonym: Positron emission tomography (procedure)
has exact synonym: Positron-Emission Tomography
has exact synonym: positron emission tomography scan
has exact synonym: proton magnetic resonance spectroscopic imaging
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C157711
in subset: NCIT C177383
in subset: NCIT C177394
in subset: NCIT C177537
in subset: NCIT C186320
in subset: NCIT C186325
in subset: NCIT C186333
in subset: NCIT C186341
in subset: NCIT C192234
in subset: NCIT C193006
in subset: NCIT C193245
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Computed Tomography
type: Class
subclass of: Imaging Technique
definition: A method of examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis.
imported from: ncit.owl
Is_PCDC_EWS_Authorized_Value_For_Variable: NCIT C117438
Is_Value_For_GDC_Property: Imaging Technique
Is_PCDC_ALL_Authorized_Value_For_Variable: NCIT C178084
code: C17204
Semantic_Type: Diagnostic Procedure
Display_Name: Computed Tomography
Preferred_Name: Computed Tomography
UMLS_CUI: C0040405
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: DIPG/DMG
Contributing_Source: FDA
Contributing_Source: GDC
Contributing_Source: OORO
Contributing_Source: PCDC
Contributing_Source: mCode
ALT_DEFINITION: A series of detailed pictures of areas inside the body; the pictures are created by a computer linked to an x-ray machine.
ALT_DEFINITION: An imaging technique for examining structures within the body by scanning them with X rays and using a computer to construct a series of cross-sectional scans along a single axis.
Legacy Concept Name: Computed_Tomography
Maps_To: CT Scan
has exact synonym: CAT
has exact synonym: CAT Scan
has exact synonym: CAT scan
has exact synonym: CT
has exact synonym: CT SCAN
has exact synonym: CT Scan
has exact synonym: CT scan
has exact synonym: Computed Axial Tomography
has exact synonym: Computed Tomography
has exact synonym: Computerized Axial Tomography
has exact synonym: Computerized Tomography
has exact synonym: Computerized axial tomography (procedure)
has exact synonym: computed tomography
has exact synonym: computerized axial tomography
has exact synonym: computerized tomography
has exact synonym: tomography
in subset: NCIT C101858
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C157711
in subset: NCIT C174237
in subset: NCIT C174261
in subset: NCIT C177537
in subset: NCIT C178115
in subset: NCIT C178127
in subset: NCIT C179478
in subset: NCIT C179481
in subset: NCIT C183088
in subset: NCIT C183096
in subset: NCIT C183102
in subset: NCIT C186320
in subset: NCIT C186325
in subset: NCIT C186333
in subset: NCIT C186341
in subset: NCIT C192234
in subset: NCIT C193006
in subset: NCIT C193245
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Ultrasound Imaging
type: Class
subclass of: Imaging Technique
definition: The use of high-frequency sound waves to generate images of the body.
imported from: ncit.owl
code: C17230
Semantic_Type: Health Care Activity
Display_Name: Ultrasonography
Preferred_Name: Ultrasound Imaging
UMLS_CUI: C0041618
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: NICHD
Contributing_Source: OORO
ALT_DEFINITION: A procedure in which high-energy sound waves are bounced off internal tissues or organs and make echoes. The echo patterns are shown on the screen of an ultrasound machine, forming a picture of body tissues called a sonogram.
ALT_DEFINITION: A technique in which high-frequency sound waves are bounced off internal organs and the echo pattern is converted into a 2 dimensional picture of the structures beneath the transducer.
Legacy Concept Name: Ultrasound_Imaging
has exact synonym: 2-Dimensional Grayscale Ultrasound Imaging
has exact synonym: 2-Dimensional Ultrasound Imaging
has exact synonym: 2D-US
has exact synonym: ULTRASOUND
has exact synonym: US
has exact synonym: Ultrasonography
has exact synonym: Ultrasound
has exact synonym: Ultrasound Imaging
has exact synonym: Ultrasound Test
has exact synonym: Ultrasound, Medical
has exact synonym: ultrasonography
has exact synonym: ultrasound
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C192234
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492
in subset: NCIT C89506
in subset: NCIT C90259

Food and Drug Administration
type: Class
subclass of: biomarker regulatory entity
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
definition: One of the agencies of the U.S. Department of Health and Human Services. It assures the safety of foods and cosmetics, and the safety and efficacy of pharmaceuticals, biological products, radiation emitting products, medical devices, and also, animal feed and drugs.
imported from: ncit.owl
code: C17237
Semantic_Type: Health Care Related Organization
Preferred_Name: Food and Drug Administration
UMLS_CUI: C0041714
Contributing_Source: CDISC-GLOSS
Contributing_Source: FDA
ALT_DEFINITION: An agency in the U.S. federal government whose mission is to protect public health by making sure that food, cosmetics,and nutritional supplements are safe to use and truthfully labeled. The FDA also makes sure that drugs, medical devices, and equipment are safe and effective, and that blood for transfusions and transplant tissue are safe.
ALT_DEFINITION: The United States regulatory authority charged with, among other responsibilities, granting IND and NDA approvals.
Legacy Concept Name: Food_and_Drug_Administration
has exact synonym: FDA
has exact synonym: Food and Drug Administration
has exact synonym: Food and Drug Administration (FDA)
in subset: NCIT C54447
in subset: NCIT C61410
in subset: NCIT C67497
in subset: NCIT C88088

Imaging Technique
type: Class
subclass of: procedure
definition: Any technology or method that aids in the visualization of any biological process, cell, tissue or organ for use in screening, diagnosis, surgical procedures or therapy.
imported from: ncit.owl
Has_PCDC_Data_Type: NCIT C25162
Is_PCDC_AML_Authorized_Value_For_Variable: NCIT C173262
Is_PCDC_EWS_Authorized_Value_For_Variable: NCIT C117438
Has_GDC_Value: NCIT C162575
Has_GDC_Value: Magnetic Resonance Imaging
Has_GDC_Value: Positron Emission Tomography
Has_GDC_Value: Computed Tomography
Is_Value_For_GDC_Property: NCIT C177576
Is_PCDC_GCT_Authorized_Value_For_Variable: NCIT C117438
Is_PCDC_GCT_Authorized_Value_For_Variable: NCIT C173262
Is_PCDC_GCT_Authorized_Value_For_Variable: NCIT C173306
Is_PCDC_GCT_Authorized_Value_For_Variable: NCIT C178148
Has_PCDC_HL_Authorized_Value: NCIT C103512
Has_PCDC_HL_Authorized_Value: NCIT C103514
Has_PCDC_HL_Authorized_Value: Magnetic Resonance Imaging
Has_PCDC_HL_Authorized_Value: Positron Emission Tomography
Has_PCDC_HL_Authorized_Value: Computed Tomography
Has_PCDC_HL_Authorized_Value: NCIT C17646
Has_PCDC_HL_Authorized_Value: NCIT C19337
Has_PCDC_HL_Authorized_Value: NCIT C38087
Has_PCDC_HL_Authorized_Value: X-Ray Imaging
Has_DIPG_DMG_Authorized_Value: NCIT C12439
Has_DIPG_DMG_Authorized_Value: NCIT C12998
Has_DIPG_DMG_Authorized_Value: NCIT C48660
Has_OORO_PC_Value: NCIT C16588
Has_OORO_PC_Value: Magnetic Resonance Imaging
Has_OORO_PC_Value: Positron Emission Tomography
Has_OORO_PC_Value: NCIT C17203
Has_OORO_PC_Value: Computed Tomography
Has_OORO_PC_Value: NCIT C192579
Has_OORO_PC_Value: NCIT C192627
Has_OORO_PC_Value: NCIT C19337
Has_OORO_PC_Value: NCIT C48789
Has_OORO_PC_Value: NCIT C71695
code: C17369
Semantic_Type: Diagnostic Procedure
Display_Name: Imaging Technique
Preferred_Name: Imaging Technique
UMLS_CUI: C0079595
Contributing_Source: CTRP
Contributing_Source: DIPG/DMG
Contributing_Source: GDC
Contributing_Source: OORO
Contributing_Source: PCDC
Contributing_Source: mCode
ALT_DEFINITION: A method of producing pictures of areas inside the body.
ALT_DEFINITION: Method of imaging used to visualize and aspect of the patient for use in diagnosis or treatment.
Legacy Concept Name: Imaging_Technique
Maps_To: Imaging
has exact synonym: Diagnostic Imaging Technique
has exact synonym: IMAGING_METHOD
has exact synonym: Image Type
has exact synonym: Imaging
has exact synonym: Imaging (procedure)
has exact synonym: Imaging Procedures
has exact synonym: Imaging Technique
has exact synonym: Medical Imaging
has exact synonym: Type of imaging
has exact synonym: imaging
has exact synonym: imaging modality
has exact synonym: imaging procedure
has exact synonym: imaging type
has exact synonym: imaging_type
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C157711
in subset: NCIT C173232
in subset: NCIT C174019
in subset: NCIT C174237
in subset: NCIT C174261
in subset: NCIT C177383
in subset: NCIT C177393
in subset: NCIT C177394
in subset: NCIT C177407
in subset: NCIT C177536
in subset: NCIT C177537

Body Temperature
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: A measurement of the temperature of the body.
imported from: ncit.owl
Has_OORO_PC_Value: NCIT C41132
code: C174446
Semantic_Type: Quantitative Concept
Preferred_Name: Body Temperature
UMLS_CUI: C0005903
Contributing_Source: CDISC
Contributing_Source: ICDC
Contributing_Source: OORO
ALT_DEFINITION: A measurement of the temperature of the body.
ALT_DEFINITION: Temperature measured in Celsius or Fahrenheit
has exact synonym: Body Temperature
has exact synonym: TEMP
has exact synonym: Temperature
has exact synonym: Temperature in Celsius or Fahrenheit
has exact synonym: body temperature
has exact synonym: body_temperature
in subset: NCIT C165451
in subset: NCIT C166373
in subset: NCIT C192234
in subset: NCIT C61410
in subset: NCIT C66741
in subset: NCIT C66830
in subset: NCIT C67153
in subset: NCIT C77526

Smartphone
type: Class
subclass of: digital device
definition: A mobile cellular telephone that has an integrated computer with an operating system capable of web browsing and running downloaded applications. Smartphones typically have touchscreen interfaces, video calling capabilities, and other advanced built-in features and applications.
imported from: ncit.owl
code: C175504
Semantic_Type: Manufactured Object
Display_Name: Smartphone
Preferred_Name: Smartphone
UMLS_CUI: C3204335
Contributing_Source: CTRP
has exact synonym: Smartphone
in subset: NCIT C116977
in subset: NCIT C118169

Histologic Grade
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
definition: The degree of abnormality of cancer cells, a measure of differentiation, the extent to which cancer cells are similar in appearance and function to healthy cells of the same tissue type. The degree of differentiation often relates to the clinical behavior of the particular tumor. Based on the microscopic findings, tumor grade is commonly described by one of four degrees of severity. Histopathologic grade of a tumor may be used to plan treatment and estimate the future course, outcome, and overall prognosis of disease. Certain types of cancers, such as soft tissue sarcoma, primary brain tumors, lymphomas, and breast have special grading systems.
imported from: ncit.owl
Has_PCDC_Data_Type: NCIT C25162
Has_PCDC_GCT_Permissible_Value: NCIT C17998
Has_PCDC_GCT_Permissible_Value: NCIT C28077
Has_PCDC_GCT_Permissible_Value: NCIT C28078
Has_PCDC_GCT_Permissible_Value: NCIT C28079
Has_PCDC_GCT_Permissible_Value: NCIT C43234
Has_PCDC_OS_Authorized_Value: NCIT C17998
Has_PCDC_OS_Authorized_Value: NCIT C28077
Has_PCDC_OS_Authorized_Value: NCIT C28078
Has_PCDC_OS_Authorized_Value: NCIT C28079
Has_PCDC_OS_Authorized_Value: NCIT C43234
code: C18000
Semantic_Type: Qualitative Concept
Preferred_Name: Histologic Grade
UMLS_CUI: C0919553
Contributing_Source: CDISC
Contributing_Source: CPTAC
Contributing_Source: ICDC
Contributing_Source: NAACCR
Contributing_Source: PCDC
ALT_DEFINITION: A description of a tumor based on how abnormal the cancer cells look under a microscope and how quickly the tumor is likely to grow and spread. Grading systems are different for each type of cancer.
ALT_DEFINITION: An assigned tumor grade based on a defined scoring system.
Legacy Concept Name: Histopathologic_Grade
has exact synonym: Grade
has exact synonym: Grade (high/low)
has exact synonym: Grading
has exact synonym: HISTOLOGY_GRADE
has exact synonym: Histologic Grade
has exact synonym: Histopathologic Grade
has exact synonym: Histopathology Grade
has exact synonym: OVLTGRD
has exact synonym: Overall Tumor Grade
has exact synonym: Tumor Grade
has exact synonym: Tumor_Grade
has exact synonym: grade
has exact synonym: grading
has exact synonym: histological grade
has exact synonym: histological_grade
in subset: NCIT C132262
in subset: NCIT C132263
in subset: NCIT C156952
in subset: NCIT C156953
in subset: NCIT C157531
in subset: NCIT C159416
in subset: NCIT C159417
in subset: NCIT C159419
in subset: NCIT C160911
in subset: NCIT C165451
in subset: NCIT C166372
in subset: NCIT C166373
in subset: NCIT C177384
in subset: NCIT C177396
in subset: NCIT C179490
in subset: NCIT C186764
in subset: NCIT C61410
in subset: NCIT C66830

Document
type: Class
subclass of: textual entity
definition: A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.
imported from: ncit.owl
code: C19498
Semantic_Type: Intellectual Product
Preferred_Name: Document
NCI_META_CUI: CL414404
Contributing_Source: BRIDG
Contributing_Source: CDISC-GLOSS
ALT_DEFINITION: All records, in any form (including but not limited to written, electronic, magnetic, and optical records, and scans, x-rays, and electrocardiograms) that describe or record the methods, conduct, and/or results of a trial, the factors affecting a trial, and the actions taken. [ICH E6 Glossary]
ALT_DEFINITION: An organized representation of information in publishable, human-readable form (that persists over time). EXAMPLE(S): Study Protocol, Adverse Event Report, Expedited Adverse Event Report, Institutional Review Board (IRB) Report, X-Ray Report, Lab Summary Report, Autopsy Report OTHER NAME(S): NOTE(S): A document groups the various document versions and has the following characteristics: 1) Stewardship, 2) Potential for authentication, 3) Wholeness, 4) Human readability, 5) Persistence, 6) Global vs local context (the person that signs it is the author of all sections unless otherwise noted). Regulatory processes require the submission of documents from the Applicant to the Regulatory Authority. These documents are varied in focus and are often defined by the field of study or by the regulatory application requirements of the region or Regulatory Authority (e.g., Integrated Summary of Safety, Pharmacokinetics Written Summary).
ALT_DEFINITION: An organized representation of information in publishable, human-readable form (that persists over time). EXAMPLE(S): Adverse Event Report, Expedited Adverse Event Report, Institutional Review Board (IRB) Report, X-Ray Report, Lab Summary Report, Autopsy Report. NOTE(S): A document groups the various document versions and has the following characteristics: 1) Stewardship, 2) Potential for authentication, 3) Wholeness, 4) Human readability, 5) Persistence, 6) Global vs local context (the person that signs it is the author of all sections unless otherwise noted). Regulatory processes require the submission of documents from the Applicant to the Regulatory Authority. These documents are varied in focus and are often defined by the field of study or by the regulatory application requirements of the region or Regulatory Authority (e.g., Integrated Summary of Safety, Pharmacokinetics Written Summary).
Legacy Concept Name: Document_Type
DesignNote: Used here to organize a wide variety of concepts that are characterized by writing or text
has exact synonym: DOC
has exact synonym: Document
has exact synonym: Document Type
has exact synonym: documentation
in subset: NCIT C159501
in subset: NCIT C159503
in subset: NCIT C61410
in subset: NCIT C67497

Response Biomarker
type: Class
subclass of: biomarker
definition: A biomarker used to show that a biological response, potentially beneficial or harmful, has occurred in an individual who has been exposed to a medical product or an environmental agent. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
imported from: ncit.owl
code: C201303
Semantic_Type: Functional Concept
Preferred_Name: Response Biomarker
Contributing_Source: CDISC
ALT_DEFINITION: A biomarker used to show that a biological response, potentially beneficial or harmful, has occurred in an individual who has been exposed to a medical product or an environmental agent. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
has exact synonym: Exposure Response Biomarker
has exact synonym: Response Biomarker
in subset: NCIT C132298
in subset: NCIT C201267
in subset: NCIT C61410

Monitoring Biomarker
type: Class
subclass of: biomarker
definition: A biomarker measured repeatedly for assessing status of a disease or medical condition or for evidence of exposure to (or effect of) a medical product or an environmental agent. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
imported from: ncit.owl
code: C201362
Semantic_Type: Functional Concept
Preferred_Name: Monitoring Biomarker
NCI_META_CUI: CL1920311
Contributing_Source: CDISC
ALT_DEFINITION: A biomarker measured repeatedly for assessing status of a disease or medical condition or for evidence of exposure to (or effect of) a medical product or an environmental agent. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
has exact synonym: Exposure Monitoring Biomarker
has exact synonym: Monitoring Biomarker
in subset: NCIT C132298
in subset: NCIT C201267
in subset: NCIT C61410

Pharmacodynamic Biomarker
type: Class
subclass of: Response Biomarker
definition: A response biomarker that indicates biologic activity of a medical product or environmental agent without necessarily drawing conclusions about efficacy or disease outcome or necessarily linking this activity to an established mechanism of action. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
imported from: ncit.owl
code: C201365
Semantic_Type: Functional Concept
Preferred_Name: Pharmacodynamic Biomarker
NCI_META_CUI: CL1920306
Contributing_Source: CDISC
ALT_DEFINITION: A response biomarker that indicates biologic activity of a medical product or environmental agent without necessarily drawing conclusions about efficacy or disease outcome or necessarily linking this activity to an established mechanism of action. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
has exact synonym: Pharmacodynamic Biomarker
in subset: NCIT C132298
in subset: NCIT C201267
in subset: NCIT C61410

Safety Biomarker
type: Class
subclass of: biomarker
definition: A biomarker measured before or after an exposure to a medical product or an environmental agent to indicate the likelihood, presence, or extent of toxicity as an adverse effect. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
imported from: ncit.owl
code: C201367
Semantic_Type: Functional Concept
Preferred_Name: Safety Biomarker
NCI_META_CUI: CL1920308
Contributing_Source: CDISC
ALT_DEFINITION: A biomarker measured before or after an exposure to a medical product or an environmental agent to indicate the likelihood, presence, or extent of toxicity as an adverse effect. (NIH-FDA BEST (Biomarkers, Endpoints, and other Tools) Resource)
has exact synonym: Exposure Safety Biomarker
has exact synonym: Safety Biomarker
in subset: NCIT C132298
in subset: NCIT C201267
in subset: NCIT C61410

Epigenetic Process
type: Class
subclass of: gene expression
definition: Changes in the regulation of the expression of gene activity without alteration of genetic structure.
imported from: ncit.owl
code: C21051
Semantic_Type: Genetic Function
Display_Name: Epigenetic Process
Preferred_Name: Epigenetic Process
UMLS_CUI: C1516924
Contributing_Source: CTRP
Legacy Concept Name: Epigenetic_Process
has exact synonym: Epigenetic Change
has exact synonym: Epigenetic Mechanism
has exact synonym: Epigenetic Process
has exact synonym: Epigenetics
in subset: NCIT C116977
in subset: NCIT C142799

Fibrinogen
type: Class
subclass of: protein-containing complex
definition: A fibrillar protein present in blood plasma; it converts to fibrin during the process of blood clot formation.
imported from: ncit.owl
code: C25736
Semantic_Type: Amino Acid, Peptide, or Protein
Display_Name: Fibrinogen
Preferred_Name: Fibrinogen
UMLS_CUI: C0016006
Contributing_Source: CTRP
Legacy Concept Name: Fibrinogen
has exact synonym: Fibrinogen
in subset: NCIT C116977
in subset: NCIT C142799
in subset: NCIT C142800

Progression-free Survival
type: Class
subclass of: measurement
fromOldVersion: yes
imported from: ncit.owl
code: C28234
Semantic_Type: Quantitative Concept
Preferred_Name: Progression-free Survival
UMLS_CUI: C0242792
ALT_DEFINITION: The length of time during and after treatment in which a patient is living with a disease that does not get worse. Progression-free survival may be used in a clinical study or trial to help find out how well a new treatment works.
Legacy Concept Name: Progression-free_Survival
has exact synonym: PFS
has exact synonym: Progression-free Survival
has exact synonym: progression-free survival

Proliferation
type: Class
subclass of: biological_process
definition: Multiplying or increasing in number.
imported from: ncit.owl
code: C28378
Semantic_Type: Conceptual Entity
Preferred_Name: Proliferation
UMLS_CUI: C1514485
Contributing_Source: CDISC
ALT_DEFINITION: Multiplying or increasing in number. In biology, cell proliferation occurs by a process known as cell division.
ALT_DEFINITION: Pertaining to the state of proliferation, in which the entity is actively multiplying or increasing in number.
Legacy Concept Name: Proliferating
Legacy Concept Name: Proliferation
has exact synonym: PROLIFERATING
has exact synonym: Proliferating
has exact synonym: Proliferation
has exact synonym: proliferating
in subset: NCIT C181172
in subset: NCIT C61410
in subset: NCIT C66830

Coagulation Disorder
type: Class
subclass of: disease
definition: A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood.
imported from: ncit.owl
code: C2902
Semantic_Type: Disease or Syndrome
Preferred_Name: Coagulation Disorder
UMLS_CUI: C4229995
FDA_Table: Patient Code (Appendix B)
Contributing_Source: CPTAC
Contributing_Source: FDA
Contributing_Source: MedDRA
Contributing_Source: NICHD
Contributing_Source: mCode
ALT_DEFINITION: A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood.
ALT_DEFINITION: A condition of abnormal blood clotting or bleeding.
Legacy Concept Name: Coagulation_Disorder
Maps_To: Coagulopathy
database cross reference: IMDRF:E0302
has exact synonym: Coagulation Defect
has exact synonym: Coagulation Disorder
has exact synonym: Coagulation defect, unspecified
has exact synonym: Coagulopathy
has exact synonym: Coagulopathy, specify
in subset: NCIT C118464
in subset: NCIT C132009
in subset: NCIT C156952
in subset: NCIT C156953
in subset: NCIT C159416
in subset: NCIT C189762
in subset: NCIT C193006
in subset: NCIT C193181
in subset: NCIT C54450
in subset: NCIT C62596
in subset: NCIT C90259
in subset: NCIT C99147

X-Ray Imaging
type: Class
subclass of: Imaging Technique
definition: A radiographic procedure using the emission of x-rays to form an image of the structure penetrated by the radiation.
imported from: ncit.owl
Is_PCDC_EWS_Authorized_Value_For_Variable: NCIT C117438
Is_PCDC_ALL_Authorized_Value_For_Variable: NCIT C178084
code: C38101
Semantic_Type: Diagnostic Procedure
Display_Name: Radiography
Preferred_Name: X-Ray Imaging
UMLS_CUI: C0043299
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: OORO
Contributing_Source: PCDC
Contributing_Source: mCode
ALT_DEFINITION: A radiographic procedure using the emission of x-rays, a type of penetrating energy wave.
Legacy Concept Name: Radiography
has exact synonym: Conventional X-Ray
has exact synonym: Diagnostic Radiology
has exact synonym: Medical Imaging, X-Ray
has exact synonym: Plain film radiographs
has exact synonym: RG
has exact synonym: Radiographic Imaging
has exact synonym: Radiographic imaging procedure (procedure)
has exact synonym: Radiography
has exact synonym: Static X-Ray
has exact synonym: X-RAY
has exact synonym: X-Ray
has exact synonym: X-Ray Imaging
in subset: NCIT C101858
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C174237
in subset: NCIT C174261
in subset: NCIT C178115
in subset: NCIT C178127
in subset: NCIT C186320
in subset: NCIT C186325
in subset: NCIT C186333
in subset: NCIT C186341
in subset: NCIT C192234
in subset: NCIT C193006
in subset: NCIT C193245
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Positive Predictive Value of Diagnostic Test
type: Class
subclass of: data item
definition: The probability that an individual is affected with the condition when a positive test result is observed. Predictive values should only be calculated from cohort studies or studies that legitimately reflect the number of people in the population who have the condition of interest at that time since predictive values are inherently dependent upon the prevalence. PPVDT can be determined by calculating: number of true positive results divided by the sum of true positive results plus number of false positive results.
imported from: ncit.owl
code: C41389
Semantic_Type: Quantitative Concept
Preferred_Name: Positive Predictive Value of Diagnostic Test
UMLS_CUI: C1514243
ALT_DEFINITION: The likelihood that an individual with a positive test result truly has the particular gene and/or disease in question.
Legacy Concept Name: Positive_Predictive_Value_of_Diagnostic_Test
has exact synonym: PPV
has exact synonym: Positive Predictive Value of Diagnostic Test
has exact synonym: positive predictive value

Negative Predictive Value of Diagnostic Test
type: Class
subclass of: data item
definition: The probability that an individual is not affected with the condition when a negative test result is observed. This measure of accuracy should only be used if the data on the prevalence of condition of interest in given population is available. NPVDT can be determined by calculating: number of true negative results divided by the sum of true negative results plus number of false negative results.
imported from: ncit.owl
code: C41390
Semantic_Type: Quantitative Concept
Preferred_Name: Negative Predictive Value of Diagnostic Test
UMLS_CUI: C1513918
ALT_DEFINITION: The likelihood that an individual with a negative test result is truly unaffected and/or does not have the particular gene mutation in question.
Legacy Concept Name: Negative_Predictive_Value_of_Diagnostic_Test
has exact synonym: NPV
has exact synonym: Negative Predictive Value of Diagnostic Test
has exact synonym: negative predictive value

Spearman Correlation Test
type: Class
subclass of: statistical analysis
imported from: ncit.owl
code: C53249
Semantic_Type: Quantitative Concept
Preferred_Name: Spearman Correlation Test
UMLS_CUI: C1710141
Legacy Concept Name: Spearman_Correlation
has exact synonym: Spearman Correlation
has exact synonym: Spearman Correlation Test

Monitoring
type: Class
subclass of: process
definition: The act of observing something (and sometimes keeping a record of it).
imported from: ncit.owl
code: C61256
Semantic_Type: Activity
Display_Name: Monitoring
Preferred_Name: Monitoring
UMLS_CUI: C1283169
Contributing_Source: CDISC-GLOSS
Contributing_Source: CTRP
ALT_DEFINITION: Act of overseeing, tracking, observing, evaluating or supervising over time by a person, device or system. See also subject monitoring, medical monitoring, study monitoring, trial monitoring, data monitoring, risk based monitoring.
ALT_DEFINITION: In medicine, to regularly watch and check a person or condition to see if there is any change. Also refers to a device that records and/or displays patient data, such as for an electrocardiogram (EKG).
Legacy Concept Name: Monitoring
has exact synonym: Monitoring
has exact synonym: monitor
has exact synonym: monitoring
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C61410
in subset: NCIT C67497

Diffusion Tensor Imaging
type: Class
subclass of: Magnetic Resonance Imaging
definition: A type of diffusion-weighted magnetic resonance imaging (DW-MRI) that maps the diffusion of water in three dimensions, the principal purpose of which is to image the white matter of the brain, specifically measuring the anisotropy, location, and orientation of the neural tracts, which can demonstrate microstructural changes or differences with neuropathology and treatment.
imported from: ncit.owl
code: C64862
Semantic_Type: Diagnostic Procedure
Display_Name: Diffusion Tensor Imaging
Preferred_Name: Diffusion Tensor Imaging
UMLS_CUI: C1537007
Contributing_Source: CDISC
Contributing_Source: CTRP
Contributing_Source: DIPG/DMG
ALT_DEFINITION: A type of MRI technique that maps the diffusion of water in three dimensions.
Legacy Concept Name: Diffusion_Tensor_Imaging
has exact synonym: DIFFUSION TENSOR MRI
has exact synonym: DT-MRI
has exact synonym: DTI
has exact synonym: Diffusion Tensor Imaging
in subset: NCIT C116977
in subset: NCIT C118169
in subset: NCIT C183095
in subset: NCIT C183101
in subset: NCIT C61410
in subset: NCIT C66830
in subset: NCIT C85492

Neuropeptide
type: Class
subclass of: protein
definition: Peptides with direct synaptic effects or indirect modulatory effects on the nervous system. A neuropeptide is a molecule released by neurons as an intercellular neurotransmitter. Alternatively, neuropeptides can be released by non-neuronal cells as hormones. They are endogenous peptides such as endorphins that influence neural activity or functioning.
imported from: ncit.owl
code: C686
Semantic_Type: Amino Acid, Peptide, or Protein
Preferred_Name: Neuropeptide
UMLS_CUI: C0027895
ALT_DEFINITION: A member of a class of protein-like molecules made in the brain. Neuropeptides consist of short chains of amino acids, with some functioning as neurotransmitters and some functioning as hormones.
Legacy Concept Name: Neuropeptide
has exact synonym: Neuropeptide
has exact synonym: neuropeptide

Valid Biomarker
type: Class
subclass of: biomarker
imported from: ncit.owl
code: C68763
Semantic_Type: Indicator, Reagent, or Diagnostic Aid
Preferred_Name: Valid Biomarker
UMLS_CUI: C2349100
ALT_DEFINITION: A biomarker that is measured in an analytical test system with well established performance characteristics and for which there is an established scientific framework or body of evidence that elucidates the physiologic, toxicologic, pharmacologic, or clinical significance of the test results. The classification of biomarkers is context specific. Likewise, validation of a biomarker is context-specific and the criteria for validation will vary with the intended use of the biomarker. The clinical utility (e.g., predict toxicity, effectiveness or dosing) and use of epidemiology/population data (e.g., strength of genotype-phenotype associations) are examples of approaches that can be used to determine the specific context and the necessary criteria for validation. (From: Pharmacogenomic Data Submissions, FDA Guidance for Industry.)
Legacy Concept Name: Valid_Biomarker
has exact synonym: Valid Biomarker

Clinical Endpoint
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A characteristic or variable that reflects how a patient feels, functions, or survives. Clinical endpoints are distinct measurements or analyses of disease characteristics observed in a study or a clinical trial that reflect the effect of a therapeutic intervention. Clinical endpoints are the most credible characteristics used in the assessment of the benefits and risks of a therapeutic intervention in randomized clinical trials.
imported from: ncit.owl
code: C68771
Semantic_Type: Clinical Attribute
Preferred_Name: Clinical Endpoint
UMLS_CUI: C2347784
Legacy Concept Name: Clinical_Endpoint
has exact synonym: Clinical Endpoint
has_related_synonym: primary endpoint

Predictor
type: Class
subclass of: Clinical modifier
definition: Information or variable that supports a probabilistic estimate of future events.
imported from: ncit.owl
code: C75944
Semantic_Type: Clinical Attribute
Preferred_Name: Predictor
UMLS_CUI: C2698872
Legacy Concept Name: Predictor
has exact synonym: Predictor

Center for Drug Evaluation and Research
type: Class
subclass of: Food and Drug Administration
definition: The center within the Food and Drug Administration that assures the safety and effectiveness of drugs that are made available to improve the health of people in the United States. It regulates over-the-counter and prescription drugs, including biological therapeutics and generic drugs.
imported from: ncit.owl
code: C82669
Semantic_Type: Professional or Occupational Group
Preferred_Name: Center for Drug Evaluation and Research
UMLS_CUI: C2826368
Legacy Concept Name: Center_for_Drug_Evaluation_and_Research
has exact synonym: CDER
has exact synonym: Center for Drug Evaluation and Research

Center for Devices and Radiological Health
type: Class
subclass of: Food and Drug Administration
definition: The Center within the Food and Drug Administration that is responsible for regulating firms who manufacture, repackage, relabel, and/or import medical devices sold in the United States. In addition, it regulates radiation-emitting electronic products (medical and non-medical) such as lasers, x-ray systems, ultrasound equipment, microwave ovens and color televisions.
imported from: ncit.owl
code: C82670
Semantic_Type: Professional or Occupational Group
Preferred_Name: Center for Devices and Radiological Health
UMLS_CUI: C2826369
Legacy Concept Name: Center_for_Devices_and_Radiological_Health
has exact synonym: CDRH
has exact synonym: Center for Devices and Radiological Health

Cardiorespiratory Fitness
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The ability of the heart and lungs to deliver blood and oxygen to the tissues during aerobic activity. It is a general measure of the relative conditioning of the heart and respiratory system.
imported from: ncit.owl
code: C88164
Semantic_Type: Classification
Preferred_Name: Cardiorespiratory Fitness
UMLS_CUI: C2981722
has exact synonym: Cardiorespiratory Fitness

Serum Creatinine Assay
type: Class
subclass of: assay
definition: A laboratory test used for the measurement of creatinine levels in the serum to determine the glomerular filtration rate.
imported from: ncit.owl
code: C88227
Semantic_Type: Laboratory Procedure
Preferred_Name: Serum Creatinine Assay
UMLS_CUI: C2981751
has exact synonym: Serum Creatinine Assay

Healthy Control
type: Class
subclass of: role
definition: A healthy subject that is matched with an affected individual in a trial.
imported from: ncit.owl
code: C94342
Semantic_Type: Qualitative Concept
Display_Name: Healthy Control
Preferred_Name: Healthy Control
UMLS_CUI: C2986479
Contributing_Source: CTRP
ALT_DEFINITION: In a clinical study, a person who does not have the disorder or disease being studied. Results from healthy controls are compared to results from the group being studied.
has exact synonym: Healthy Control
has exact synonym: healthy control
in subset: NCIT C116977

Sleep Stage
type: Class
subclass of: sleep measurement
imported from: ncit.owl
code: C94416
Semantic_Type: Temporal Concept
Preferred_Name: Sleep Stage
UMLS_CUI: C0037319
ALT_DEFINITION: One of 5 parts or stages of the sleep cycle based on the type of brain activity that occurs during the stage. During stages 1 to 4, a person will feel drowsy, fall asleep, and move into a deep, dreamless sleep. Stage 5 is called rapid eye movement (REM) sleep, and it is during this stage that dreams occur. During several hours of normal sleep, a person will go through several sleep cycles that include REM sleep and the 4 stages of non-REM sleep (light to deep sleep).
has exact synonym: Sleep Stage
has exact synonym: sleep stage

Tumor Volume
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
definition: The volume of tumor.
imported from: ncit.owl
Has_PCDC_Data_Type: NCIT C25162
Has_PCDC_EWS_Authorized_Value: NCIT C175000
Has_PCDC_EWS_Authorized_Value: NCIT C175001
Has_PCDC_EWS_Authorized_Value: NCIT C17998
Has_PCDC_EWS_Authorized_Value: NCIT C43234
Has_PCDC_OS_Authorized_Value: NCIT C175000
Has_PCDC_OS_Authorized_Value: NCIT C175001
Has_PCDC_OS_Authorized_Value: NCIT C17998
Has_PCDC_OS_Authorized_Value: NCIT C43234
code: C94515
Semantic_Type: Quantitative Concept
Preferred_Name: Tumor Volume
UMLS_CUI: C0475276
Contributing_Source: ICDC
Contributing_Source: PCDC
ALT_DEFINITION: The size of a cancer measured by the amount of space taken up by the tumor. For example, the tumor volume of prostate cancer is the percentage of the prostate taken up by the tumor.
has exact synonym: TUMOR_VOLUME
has exact synonym: Tumor Volume
has exact synonym: tumor volume
has exact synonym: volume of tumor
has exact synonym: volume_of_tumor
in subset: NCIT C166373
in subset: NCIT C174239
in subset: NCIT C174261
in subset: NCIT C179481
in subset: NCIT C186764

adverse event
type: Class
subclass of: process
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: risk factor
definition: a pathological bodily process that occurs after a medical intervention. An adverse event is likely caused by the medical intervention; however, such a causal association is not required to be an adverse event.
editor note: Melanie Courtot and YH: More work is needed on how to restrict the scope of a term to be an 'adverse event', notably regarding temporal association. When is an appropirate time interval between a medical intervention and an adverse event observed? One week, one month, one year, or a lifetime? For some well-studied medical interventions (e.g., administration of many vaccines or drugs), we probably have a general idea. For many new interventions, we don't know much. In OAE, this issue is associated with defining the 'adverse event incubation time'.
editor note: YH: An adverse event is a process that has specified output of some adverse medical outcome (e.g., symptom, sign or accident) after a medical intervention (or process) (e.g., administration of drug or vaccine). The medical intervention can be an administration of a drug, a vaccine (i.e., vaccination), or a special nutritional product (for example, dietary supplement, infant formula, medical food), surgery, or usage of a medical device.
editor note: YH: An adverse event is possibly induced by the medical intervention. It can be caused by the medical intervention, or may not be caused by the medical intervention. One ultimate goal (or the goal in clinics) of study adverse events is to assess if the adverse event outcome is due to the medical intervention.
editor note: YH: In development of OAE, we initially use vaccine adverse event as our use case. A vaccine adverse event is associated with a vaccination (i.e. a medical intervention), regardless of whether it is considered vaccine-related, and includes any side effect, injury, toxicity, or sensitivity reaction or significant failure of immunization (i.e., a pharmacologic action). Ref: Baylor NW and Midthum K. Regulation and testing of vaccines. In: Vaccines (Editors: Plotkin S, Orenstein W, and Offit P). 2008. p1623.
editor note: YH: The current term 'adverse event' is different from the term definition shown in our paper: He Y, Xiang Z, Sarntivijai S, Toldo L, Ceusters W. OAE: a realism-based biomedical ontology for the representation of adverse events. Adverse Event Representation Workshop, International Conference on Biomedical Ontologies (ICBO), University at Buffalo, NY, July 26-30, 2011. Full lenghth conference proceeding paper. We made the name changing in order to make OAE cover the broader sense of the 'adverse event' which does not assume definite causal effect between an adverse event and a medical intervention. In current definition, the adverse event emphasizes the time association and assumes a likelihood of such a causal association. This term 'adverse event' is stil under the OGMS:pathological bodily process. The 'adverse event' defined in the above paper has now been changed to a new term: 'causal adverse event'. See more information in the new publication: Yongqun He Y, Sirarat Sarntivijai, Yu Lin, Zuoshuang Xiang, Abra Guo, Shelley Zhang, Desikan Jagannathan, Luca Toldo, Cui Tao and Barry Smith. OAE: The Ontology of Adverse Events. Journal of Biomedical Semantics. 2014, 5:29 doi:10.1186/2041-1480-5-29. PMID: 25093068.PMCID: PMC4120740.
editor note: YH: The main scope of OAE includes: (1) represent terms and relations in the area of adverse events, (2) assess possible associations between an adverse event and a medical intervention, particularly, identify any causal effect of a medical intervention to an adverse event; and (2) understand the mechanism (including molecular mechanisms) of causal adverse events.
editor note: YH: There has been discussion regarding whether the term 'side effect' is an alternative term for 'adverse event'. In AERO, the term 'AERO:adverse event' represents a subset of those adverse events for which causality has been established. In OAE, an adverse event for which causality has been established is called 'causal adverse event'.
definition editor: Yongqun He
alternative term: AE
alternative term: adverse reaction
definition source: WEB: http://en.wikipedia.org/wiki/Adverse_event
definition source: WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
definition source: WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
imported from: oae.owl
comment: The OAE official website is: http://www.oae-ontology.org/.

multivariate analysis
type: Class
subclass of: statistical analysis
definition: An inferential statistical data analysis that is used to analyze data that arises from more than one variable
definition editor: Yongqun He, Jie Zheng
definition source: MVA
definition source: WEB: http://www.camo.com/multivariate_analysis.html
imported from: obcs.owl

univariate analysis
type: Class
subclass of: statistical analysis
definition: An inferential statistical data analysis that has only one independent variable
definition editor: Yongqun He
imported from: obcs.owl

odds ratio
type: Class
subclass of: data item
fromOldVersion: yes
definition: A data item that refers to the odds that an individual with a specific condition has been exposed to a risk factor divided by the odds that a control has been exposed. The odds ratio is used in case-control studies. The odds ratio provides a reasonable estimate of the relative risk for uncommon conditions.
definition editor: Yongqun He
definition source: WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
imported from: obcs.owl
database cross reference: STATO_0000182

planned process
type: Class
subclass of: process
editor preferred label: planned process
example of usage: Injecting mice with a vaccine in order to test its efficacy
has curation status: IAO_0000122
definition: A process that realizes a plan which is the concretization of a plan specification.
editor note: 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
editor note: We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.
definition editor: Bjoern Peters
definition source: branch derived
curator note: 6/11/9: Edited at workshop. Used to include: is initiated by an agent
curator note: This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)
imported from: obi.owl

investigation
type: Class
subclass of: planned process
editor preferred label: investigation
example of usage: Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
has curation status: IAO_0000122
definition: a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
definition editor: Bjoern Peters
definition source: OBI branch derived
curator note: Could add specific objective specification
curator note: Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl
ISA alternative term: study

assay
type: Class
subclass of: planned process
editor preferred label: assay
example of usage: Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
has curation status: IAO_0000122
definition: A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
editor note: 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation.
definition editor: PlanAndPlannedProcess Branch
alternative term: measuring
alternative term: scientific observation
definition source: OBI branch derived
imported from: obi.owl
ISA alternative term: study assay
IEDB alternative term: any method

diagnosis textual entity
type: Class
subclass of: textual entity
fromOldVersion: yes
editor preferred label: diagnosis textual entity
has curation status: IAO_0000123
definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
definition editor: Jennifer Fostel
imported from: obi.owl

patient role
type: Class
subclass of: role
fromOldVersion: yes
editor preferred label: patient role
example of usage: a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
has curation status: IAO_0000120
definition: a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
definition editor: GROUP:Role Branch
alternative term: patient
definition source: OBI, CDISC
curator note: CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
imported from: obi.owl

participant under investigation role
type: Class
subclass of: role
editor preferred label: study subject role
example of usage: Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. Parasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study. Lake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake.
has curation status: IAO_0000122
definition: A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected.
editor note: A participant can realize both "specimen role" and "participant under investigation role" at the same time. However "participant under investigation role" is distinct from "specimen role", since a specimen could somehow be involved in an investigation without being the thing that is under investigation.
definition editor: GROUP: Role Branch
definition source: OBI
curator note: Following OBI call November 2012,26th: 1. it was decided there was no need for moving the children class and making them siblings of study subject role. 2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study This note closes the issue and validates the class definition to be part of the OBI core editor = PRS
imported from: obi.owl

placebo role
type: Class
subclass of: role
editor preferred label: placebo role
example of usage: Pill consisting of inert materials
has curation status: IAO_0000120
definition: a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance
definition editor: Person:Jennifer Fostel
alternative term: placebo
curator note: CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product.
imported from: obi.owl

p-value
type: Class
subclass of: data item
fromOldVersion: yes
editor preferred label: p-value
example of usage: PMID:19696660 in contrast to the in-vivo data AT-III increased significantly from 113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
has curation status: IAO_0000121
definition: A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
editor note: May be outside the scope of OBI long term, is needed so is retained
definition editor: PERSON:Chris Stoeckert
definition source: WEB: http://en.wikipedia.org/wiki/P-value
imported from: obi.owl

imaging assay
type: Class
subclass of: assay
editor preferred label: imaging assay
has curation status: IAO_0000125
definition: An assay that produces a picture of an entity.
definition editor: PlanAndPlannedProcess Branch
definition source: OBI branch derived
imported from: obi.owl

disease stage
type: Class
subclass of: process
editor preferred label: disease stage
example of usage: Stage II breast cancer, The timepoint of recovery from a disease
has curation status: IAO_0000123
definition: a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
definition editor: PERSON: Bjoern peters
imported from: obi.owl

blood specimen
type: Class
subclass of: specimen
editor preferred label: blood specimen
example of usage: blood drawn from a human for glucose assay
has curation status: IAO_0000122
definition: a material entity derived from a portion of blood collected from an organism
definition editor: Bjoern Peters
definition source: Bjoern Peters
imported from: obi.owl

enzyme-linked immunosorbent assay
type: Class
subclass of: assay
editor preferred label: enzyme-linked immunosorbent assay
example of usage: 1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme-linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
has curation status: IAO_0000120
definition: An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte.
definition editor: IEDB
alternative term: ELISA
definition source: IEDB
imported from: obi.owl

statistical hypothesis test
type: Class
subclass of: statistical analysis
editor preferred label: statistical hypothesis test
has curation status: IAO_0000120
definition: A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
definition editor: James Malone
definition source: PERSON: James Malone
imported from: obi.owl

center value
type: Class
subclass of: data item
fromOldVersion: yes
editor preferred label: center value
has curation status: IAO_0000125
definition: A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
definition editor: PERSON: James Malone
definition editor: PERSON: Monnie McGee
alternative term: median
imported from: obi.owl

western blot assay
type: Class
subclass of: assay
editor preferred label: western blot assay
example of usage: Running a cell lysate on an acrylamide gel in a western blot aparatus to separate the constituent proteins, followed by transfer of the proteins from the gel to a nitrocellulose membrane. Staining this membrane with specific antibodies to detect the presence of specific proteins of interest.
has curation status: IAO_0000120
definition: An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules.
definition editor: IEDB
definition editor: Philippe Rocca-Serra
definition source: IEDB
definition source: Philippe Rocca-Serra
imported from: obi.owl

flow cytometry assay
type: Class
subclass of: assay
editor preferred label: flow cytometry assay
example of usage: Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
has curation status: IAO_0000120
definition: A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution.
definition editor: IEDB
alternative term: FACS
definition source: IEDB
imported from: obi.owl

device
type: Class
subclass of: material entity
fromOldVersion: yes
editor preferred label: device
example of usage: A voltmeter is a measurement device which is intended to perform some measure function.
example of usage: An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
has curation status: IAO_0000122
definition: A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
editor note: 2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of "device", and are enumerating the types of roles that a reagent can perform. 2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example: (1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part. (2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay. (3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel. In the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent…
definition editor: PERSON: Helen Parkinson
alternative term: instrument
definition source: OBI development call 2012-12-17.
imported from: obi.owl

genotype information
type: Class
subclass of: data item
fromOldVersion: yes
editor preferred label: genotype information
example of usage: Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
has curation status: IAO_0000120
definition: a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
editor note: discussed on San Diego OBI workshop, March 2011
definition editor: Group: OBI group
definition source: Group: OBI group
imported from: obi.owl

immunohistochemistry
type: Class
subclass of: process
editor preferred label: immunohistochemistry
example of usage: Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques.
has curation status: IAO_0000120
definition: An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
definition editor: IEDB
definition source: IEDB
imported from: obi.owl

biopsy
type: Class
subclass of: planned process
editor preferred label: biopsy
example of usage: Biopsy of a potentially cancerous mole.
has curation status: IAO_0000122
definition: A specimen collection that obtains a sample of tissue or cell from a living multicellular organism body for diagnostic purposes by means intended to be minimally invasive.
definition editor: Damion Dooley
definition editor: Nicole Vasilevsky
definition source: https://en.wikipedia.org/wiki/Biopsy
imported from: obi.owl

blood serum specimen
type: Class
subclass of: specimen
editor preferred label: blood serum specimen
example of usage: PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
has curation status: IAO_0000120
definition: A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
definition editor: PERSON: Maura Gasparetto
definition editor: PERSON: Melanie Courtot
definition editor: PERSON: Philippe Rocca-Serra
definition source: WEB: http://en.wikipedia.org/wiki/Blood_plasma
imported from: obi.owl

specimen
type: Class
subclass of: material entity
editor preferred label: specimen
example of usage: Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
has curation status: IAO_0000122
definition: A material entity that has the specimen role.
editor note: Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
definition editor: PERSON: James Malone
definition editor: PERSON: Philippe Rocca-Serra
definition source: GROUP: OBI Biomaterial Branch
term tracker item: https://github.com/obi-ontology/obi/issues/1013
imported from: obi.owl

multiple linear regression analysis
type: Class
subclass of: statistical analysis
editor preferred label: multiple linear regression analysis
has curation status: IAO_0000125
definition: multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
definition editor: Tina Hernandez-Boussard
definition source: WEB:http://en.wikipedia.org/wiki/Linear_regression
imported from: obi.owl

staining
type: Class
subclass of: planned process
editor preferred label: staining
example of usage: PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
has curation status: IAO_0000125
definition: Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
definition editor: Philippe Rocca-Serra
definition source: adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
imported from: obi.owl

validation
type: Class
subclass of: planned process
editor preferred label: validation
example of usage: PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
has curation status: IAO_0000120
definition: a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
definition editor: Philippe Rocca-Serra
definition source: adapted from wordnet (wkipedia)
imported from: obi.owl

microarray
type: Class
subclass of: device
fromOldVersion: yes
editor preferred label: microarray
example of usage: An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
has curation status: IAO_0000122
definition: A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
definition editor: Daniel Schober
definition source: PERSON: Chris Stoeckert
imported from: obi.owl

pathologic process
type: Class
subclass of: process
editor preferred label: pathologic process
has curation status: IAO_0000123
definition: abnormal, harmful processes caused by or associated with a disease
definition editor: IEDB
definition source: IEDB
imported from: obi.owl

gene
type: Class
subclass of: material entity
definition: A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
definition editor: Oliver He
definition source: WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
imported from: ogg.owl

SIRT1
type: Class
subclass of: gene
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: SIR2L1
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: SIRT1
full name from nomenclature authority: sirtuin 1
NCBI GeneID: 23411
NCBI LocusTag: RP11-57G10.3
gene map location: 10q21.3
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 10
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0000012 (EC: IMP); GO_0000122 (EC: IDA, PMID: 12535671); GO_0000122 (EC: IMP); GO_0000183 (EC: IDA, PMID: 18485871); GO_0000720 (EC: IMP); GO_0000731 (EC: ISS); GO_0000790 (EC: IDA, PMID: 17505061); GO_0001525 (EC: IDA); GO_0001542 (EC: IEA); GO_0001678 (EC: ISS); GO_0001934 (EC: ISS); GO_0002039 (EC: IPI, PMID: 11672523); GO_0002821 (EC: IDA); GO_0003714 (EC: IDA, PMID: 12535671); GO_0003714 (EC: ISS); GO_0003950 (EC: TAS, Qualifier: NOT, PMID: 17456799); GO_0004407 (EC: IDA); GO_0005515 (EC: IPI, PMID: 11672523); GO_0005634 (EC: IDA); GO_0005635 (EC: IDA, PMID: 15469825); GO_0005637 (EC: IDA, PMID: 15469825); GO_0005654 (EC: IDA, PMID: 16079181); GO_0005677 (EC: IDA, PMID: 18485871); GO_0005719 (EC: IDA, PMID: 15469825); GO_0005720 (EC: IDA, PMID: 15469825); GO_0005730 (EC: IDA, PMID: 15469825); GO_0005730 (EC: IDA, Qualifier: NOT); GO_0005737 (EC: IDA); GO_0005737 (EC: IDA, Qualifier: NOT, PMID: 15469825); GO_0005739 (EC: IDA); GO_0006260 (EC: TAS, PMID: 17317627); GO_0006281 (EC: TAS, PMID: 17317627); GO_0006342 (EC: TAS, PMID: 10381378); GO_0006343 (EC: IDA, PMID: 15469825); GO_0006344 (EC: IMP, PMID: 15469825); GO_0006346 (EC: TAS); GO_0006351 (EC: IEA); GO_0006364 (EC: IEA); GO_0006471 (EC: TAS, Qualifier: NOT, PMID: 17456799); GO_0006476 (EC: IDA, PMID: 18203716); GO_0006476 (EC: IMP, PMID: 11672523); GO_0006642 (EC: ISS); GO_0006974 (EC: IDA, PMID: 18203716); GO_0006979 (EC: IDA, PMID: 14976264); GO_0007283 (EC: IEA); GO_0007346 (EC: IDA, PMID: 15692560); GO_0007517 (EC: IEA); GO_0007569 (EC: TAS, PMID: 11672523); GO_0008022 (EC: IPI, PMID: 18203716); GO_0008284 (EC: IMP); GO_0009267 (EC: ISS); GO_0010875 (EC: ISS); GO_0010906 (EC: ISS); GO_0016032 (EC: IEA); GO_0016239 (EC: IDA, PMID: 18296641); GO_0016567 (EC: IDA); GO_0016575 (EC: IDA, PMID: 12006491); GO_0016605 (EC: IDA, PMID: 12006491); GO_0017136 (EC: IDA, PMID: 12006491); GO_0018394 (EC: IMP, PMID: 18004385); GO_0019213 (EC: IDA, PMID: 18203716); GO_0030308 (EC: IMP, PMID: 17505061); GO_0030512 (…
has PubMed association: PMID: 10381378; 10873683; 11230166; 11672522; 11672523; 12006491; 12297502; 12413881; 12477932; 12535671; 12930829; 12939617; 14702039; 14976264; 14980222; 15126506; 15152190; 15164054; 15175761; 15205477; 15302935; 15469825; 15489334; 15632193; 15639232; 15640142; 15684044; 15692560; 15719057; 15744310; 15749705; 15780941; 16079181; 16154098; 16166628; 16183991; 16207712; 16257164; 16269335; 16288004; 16328012; 16344560; 16354677; 16385451; 16628003; 16751189; 16892051; 16923962; 16959573; 16964243; 16998474; 16998810; 17041012; 17081983; 17098745; 17099246; 17112576; 17172643; 17180656; 17213307; 17283066; 17317627; 17334224; 17373700; 17456799; 17487425; 17505061; 17516504; 17581637; 17601350; 17612497; 17624472; 17638871; 17680780; 17785417; 17806102; 17895433; 17901049; 17916362; 17934453; 17936707; 17937892; 17964266; 17996922; 18004385; 18029348; 18174544; 18184747; 18193082; 18203716; 18230337; 18235501; 18235502; 18296641; 18329615; 18342601; 18344999; 18414679; 18438697; 18482975; 18485871; 18485895; 18556572; 18563176; 18573234; 18636124; 18660489; 18662546; 18662547; 18681908; 18687677; 18689793; 18704159; 18723829; 18724249; 18755897; 18774777; 18800364; 18820948; 18821472; 18823944; 18829436; 18829956; 18834855; 18835033; 18838864; 18850005; 18922603; 18957417; 18977241; 19008647; 19014491; 19017485; 19047049; 19060927; 19071085; 19075016; 19104446; 19132007; 19149601; 19166820; 19167483; 19188449; 19218236; 19220062; 19229036; 19236849; 19244234; 19267881; 19285077; 19286634; 19289152; 19322201; 19343720; 19364925; 19376817; 19377286; 19404850; 19430421; 19433578; 19478080; 19491102; 19498162; 19509139; 19553684; 19555662; 19568959; 19578370; 19581416; 19615732; 19643082; 19649206; 19664641; 19680556; 19690166; 19713122; 19714620; 19716821; 19720090; 19741164; 19786632; 19819989; 19883617; 19887452; 19895790; 19923004; 19934257; 19934264; 19995796; 19996091; 20027304; 20033348; 20041875; 20042607; 20060806; 20068143; 20071779; 20089851; 20100829; 2010…
description: sirtuin 1
database cross reference: Ensembl:ENSG00000096717
database cross reference: HGNC:14929
database cross reference: HPRD:08381
database cross reference: MIM:604479
database cross reference: Vega:OTTHUMG00000018340

SIRT7
type: Class
subclass of: gene
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition editor: Bin Zhao, Yue Liu, Oliver He
alternative term: SIR2L7
definition source: WEB: http://www.ncbi.nlm.nih.gov/gene
imported from: ogg.owl
symbol from nomenclature authority: SIRT7
full name from nomenclature authority: sirtuin 7
NCBI GeneID: 51547
gene map location: 17q25
modification date: 20140408
organism NCBITaxon ID: 9606
chromosome ID of gene: 17
type of gene: protein-coding
nomenclature status: Official from a nomenclature committee
has GO association: GO_0000122 (EC: IDA); GO_0003682 (EC: IDA); GO_0005515 (EC: IPI, PMID: 19174463); GO_0005730 (EC: IDA, PMID: 16079181); GO_0005731 (EC: IDA, PMID: 19174463); GO_0005737 (EC: IEA); GO_0007072 (EC: IMP, PMID: 19174463); GO_0009303 (EC: IMP, PMID: 19174463); GO_0046872 (EC: IEA); GO_0070403 (EC: IEA); GO_0070932 (EC: IDA); GO_0070933 (EC: IDA); GO_0097372 (EC: IDA)
has PubMed association: PMID: 9776767; 10873683; 11953824; 12454780; 12477932; 14702039; 15489334; 16079181; 16169070; 16525639; 16618798; 17003781; 19174463; 20375098; 21832049; 22147730; 22586326; 22722849; 23079745; 23680022; 23750001; 24207024; 24250222
description: sirtuin 7
database cross reference: Ensembl:ENSG00000187531
database cross reference: HGNC:14935
database cross reference: HPRD:12094
database cross reference: MIM:606212
database cross reference: Vega:OTTHUMG00000177957

phenotype
type: Class
subclass of: quality
fromOldVersion: yes
definition: A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2010-07-19T11:13:49Z
imported from: ogms.owl

disorder
type: Class
subclass of: disease
fromOldVersion: yes
definition: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:39:44Z
imported from: ogms.owl

disease course
type: Class
subclass of: process
definition: The totality of all processes through which a given disease instance is realized.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T11:55:44Z
imported from: ogms.owl

diagnosis
type: Class
subclass of: data item
definition: The representation of a conclusion of a diagnostic process.
definition editor: Albert Goldfain
definition source: http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
curator note: creation date: 2009-06-23T12:42:23Z
imported from: ogms.owl

treatment
type: Class
subclass of: planned process
definition: A planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate a disorder, the signs and symptoms of a disorder, or a pathological process
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T04:51:11Z
imported from: ogms.owl

prognosis
type: Class
subclass of: data item
fromOldVersion: yes
definition: A hypothesis about some future part of a disease course.
definition editor: Albert Goldfain
definition source: http://code.google.com/p/ogms/issues/detail
curator note: creation date: 2010-03-31T12:42:23Z
imported from: ogms.owl

remission
type: Class
subclass of: disease stage
definition: A disease stage which is characterized by the lack of a manifestation of a disease
editor note: A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased.
definition editor: Albert Goldfain Richard Scheuermann Sagar Jain
definition source: http://code.google.com/p/ogms/issues/detail
imported from: ogms.owl
date: 10 NOV 2015

transplantation
type: Class
subclass of: therapeutic procedure
definition: A therapeutic procedure in which a body part is transferred into a organism
imported from: ogms.owl

Trastuzumab
type: Class
subclass of: antibody
fromOldVersion: yes
definition: A humanized monoclonal antibody against the ERBB-2 RECEPTOR (HER2). As an ANTINEOPLASTIC AGENT, it is used to treat BREAST CANCER where HER2 is overexpressed.
definition source: https://www.ncbi.nlm.nih.gov/mesh/2009893
imported from: omit.owl

Calcium Metabolism Disorders
type: Class
subclass of: disorder
definition: Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Diet Therapy
type: Class
subclass of: therapeutic procedure
definition: Adjusting the quantity and quality of food intake to improve health status of an individual. This term does not include the methods of food intake (NUTRITIONAL SUPPORT).
definition source: https://www.ncbi.nlm.nih.gov/mesh/68004035
imported from: omit.owl

Galvanic Skin Response
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
definition: A change in electrical resistance of the skin, occurring in emotion and in certain other conditions.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl
has exact synonym: skin conductance

Growth Disorders
type: Class
subclass of: disorder
definition: Deviations from the average values for a specific age and sex in any or all of the following: height, weight, skeletal proportions, osseous development, or maturation of features. Included here are both acceleration and retardation of growth.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl
has exact synonym: growth disorder

Intracranial Pressure
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: Pressure within the cranial cavity. It is influenced by brain mass, the circulatory system, CSF dynamics, and skull rigidity.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68007427
imported from: omit.owl

Liver Function Tests
type: Class
subclass of: assay
definition: Blood tests that are used to evaluate how well a patient's liver is working and also to help diagnose liver conditions.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Neoplastic Cells, Circulating
type: Class
subclass of: cell
fromOldVersion: yes
definition: Exfoliate neoplastic cells circulating in the blood and associated with metastasizing tumors.
imported from: omit.owl

Probability
type: Class
subclass of: mathematical entity
fromOldVersion: yes
definition: The study of chance processes or the relative frequency characterizing a chance process.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68011336
imported from: omit.owl

Prostatectomy
type: Class
subclass of: surgical procedure
definition: Complete or partial surgical removal of the prostate. Three primary approaches are commonly employed: suprapubic - removal through an incision above the pubis and through the urinary bladder; retropubic - as for suprapubic but without entering the urinary bladder; and transurethral (TRANSURETHRAL RESECTION OF PROSTATE).
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

ROC Curve
type: Class
subclass of: statistical analysis
fromOldVersion: yes
definition: A graphic means for assessing the ability of a screening test to discriminate between healthy and diseased persons; may also be used in other studies, e.g., distinguishing stimuli responses as to a faint stimuli or nonstimuli.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Lipid Peroxidation
type: Class
subclass of: Biochemical Processes
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Peroxidase catalyzed oxidation of lipids using hydrogen peroxide as an electron acceptor.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68015227
imported from: omit.owl

Ki-67 Antigen
type: Class
subclass of: protein
definition: definition A CELL CYCLE and tumor growth marker which can be readily detected using IMMUNOCYTOCHEMISTRY methods. Ki-67 is a nuclear antigen present only in the nuclei of cycling cells.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68019394
imported from: omit.owl

Natriuretic Peptide, Brain
type: Class
subclass of: peptide
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: A PEPTIDE that is secreted by the BRAIN and the HEART ATRIA, stored mainly in cardiac ventricular MYOCARDIUM. It can cause NATRIURESIS; DIURESIS; VASODILATION; and inhibits secretion of RENIN and ALDOSTERONE. It improves heart function. It contains 32 AMINO ACIDS.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Leukoaraiosis
type: Class
subclass of: pathologic process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl
has exact synonym: white matter hyperintensity
definition: Non-specific white matter changes in the BRAIN, often seen after age 65. Changes include loss of AXONS; MYELIN pallor, GLIOSIS, loss of ependymal cells, and enlarged perivascular spaces. Leukoaraiosis is a risk factor for DEMENTIA and CEREBROVASCULAR DISORDERS.

Dyslipidemias
type: Class
subclass of: disease of metabolism
fromOldVersion: yes
definition: Abnormalities in the serum levels of LIPIDS, including overproduction or deficiency. Abnormal serum lipid profiles may include high total CHOLESTEROL, high TRIGLYCERIDES, low HIGH DENSITY LIPOPROTEIN CHOLESTEROL, and elevated LOW DENSITY LIPOPROTEIN CHOLESTEROL.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Adipokines
type: Class
subclass of: peptide
fromOldVersion: yes
definition: Polypeptides produced by the ADIPOCYTES. They include LEPTIN; ADIPONECTIN; RESISTIN; and many cytokines of the immune system, such as TUMOR NECROSIS FACTOR-ALPHA; INTERLEUKIN-6; and COMPLEMENT FACTOR D (also known as ADIPSIN). They have potent autocrine, paracrine, and endocrine functions.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68054392
imported from: omit.owl
has exact synonym: adipokine

Elastic Modulus
type: Class
subclass of: arterial stiffness measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: Numerical expression indicating the measure of stiffness in a material. It is defined by the ratio of stress in a unit area of substance to the resulting deformation (strain). This allows the behavior of a material under load (such as bone) to be calculated.
definition source: https://www.ncbi.nlm.nih.gov/mesh/
imported from: omit.owl

Growth Differentiation Factor 15
type: Class
subclass of: cytokine
definition: A growth differentiation factor that is secreted in response to cell stress and in response to MACROPHAGE ACTIVATION. In addition growth differentiation factor 15 demonstrates a diverse array of biological properties including the induction of cartilage formation, the inhibition of hematopoietic progenitor proliferation, and the induction of neuronal migration.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68055436
imported from: omit.owl

Biochemical Processes
type: Class
subclass of: process
definition: Adjusting the quantity and quality of food intake to improve health status of an individual. This term does not include the methods of food intake (NUTRITIONAL SUPPORT).
definition source: https://www.ncbi.nlm.nih.gov/mesh/68004035
imported from: omit.owl

Carcinogenesis
type: Class
subclass of: neoplasm
definition: The origin, production or development of cancer through genotypic and phenotypic changes which upset the normal balance between cell proliferation and cell death. Carcinogenesis generally requires a constellation of steps, which may occur quickly or over a period of many years.
definition source: https://www.ncbi.nlm.nih.gov/mesh/68063646
imported from: omit.owl

ARG1
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:383
comment: arginase 1

KLRB1
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:3820
comment: killer cell lectin like receptor B1

MAF
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:4094
has exact synonym: musculoaponeurotic fibrosarcoma oncogene homolog
comment: v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog

MAFG
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:4097
comment: v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G

TPST1
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:8460
comment: tyrosylprotein sulfotransferase 1

AKR1C3
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:8644
comment: aldo-keto reductase family 1, member C3

WWC3
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
imported from: omit.owl
database cross reference: Entrez:55841
has exact synonym: KIBRA
comment: WWC family member 3

susceptibility biomarker
type: Class
subclass of: biomarker
definition: Measurable indicator including genetic or acquired host factors and intrinsic factors, influencing the response of an individual to a (dietary) exposure.
definition editor: ENPADASI_WP4
definition source: https://www.ncbi.nlm.nih.gov/pubmed/28974991
imported from: ons.owl

biomarker
type: Class
subclass of: drug development tool
fromOldVersion: yes
definition: A material entity that has a measurable quality or process profile(s), which can be used as an indicator of an underlying biological state or identity.
editor note: The NIH Biomarkers and Surrogate Endpoint Working Group defined a biomarker as “A characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention” (https://pubmed.ncbi.nlm.nih.gov/11240971/). However, the definition of 'characteriistc' is unclear, so we do not use the exact definintion in the ontology.
definition editor: Yingtong Liu, Anthony Huffman, Oliver He
definition source: https://en.wikipedia.org/wiki/Biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)
imported from: opmi.owl
has exact synonym: biological marker

immune biomarker
type: Class
subclass of: biomarker
definition editor: Anthony Huffman, Oliver He
definition source: A biomarker that is indicative of an immune response
definition source: https://pubmed.ncbi.nlm.nih.gov/22072636/
definition source: https://pubmed.ncbi.nlm.nih.gov/32286245/
imported from: opmi.owl

cytokine biomarker
type: Class
subclass of: immune biomarker
definition editor: Anthony Huffman, Oliver He
imported from: opmi.owl

inflammatory cytokine biomarker
type: Class
subclass of: cytokine biomarker
definition editor: Anthony Huffman, Oliver He
imported from: opmi.owl

disease biomarker
type: Class
subclass of: biomarker
definition: A biomarker that is indicative of a disease
definition editor: Yingtong Liu, Anthony Huffman, Oliver He
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)
imported from: opmi.owl
has exact synonym: disease marker
has exact synonym: marker of disease

cell lineage biomarker
type: Class
subclass of: biomarker
definition: A biomarker that is an indicator of a cell lineage or cell type
definition editor: Yingtong Liu, Anthony Huffman, Oliver He
alternative term: cell marker
alternative term: cell type marker
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)
imported from: opmi.owl

molecular biomarker
type: Class
subclass of: biomarker
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers
imported from: opmi.owl

cellular biomarker
type: Class
subclass of: biomarker
definition: Cellular biomarkers are marked cells that can be isolated, sorted, quantified and characterized by their morphology and physiology, and used in both clinical and laboratory settings for different biomarker applications. An example of a cellular biomarker sorting technique is Fluorescent-activated cell sorting.
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)#Cellular_Biomarkers
imported from: opmi.owl

imaging biomarker
type: Class
subclass of: biomarker
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)#Imaging_Biomarkers
imported from: opmi.owl

predictive biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that can predict clincal outcome.
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker
imported from: opmi.owl
has exact synonym: predictive marker

prognostic biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that provides information about the patient's overall outcome, regardless of therapy.
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker
imported from: opmi.owl

diagnostic biomarker
type: Class
subclass of: biomarker
fromOldVersion: yes
definition: A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients.
definition editor: Oliver He, Yingtong Liu
definition source: https://en.wikipedia.org/wiki/Biomarker
imported from: opmi.owl
has exact synonym: diagnostic marker

DNA biomarker
type: Class
subclass of: molecular biomarker
definition: A molecular biomarker at the DNA gene level
definition: Oliver He, Yingtong Liu
alternative term: genomic biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers
imported from: opmi.owl

RNA biomarker
type: Class
subclass of: molecular biomarker
definition: A molecular biomarker at the RNA level
definition: Oliver He, Yingtong Liu
alternative term: transcriptomic biomarker
definition source: https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers
imported from: opmi.owl

imaging disease biomarker
type: Class
subclass of: disease biomarker
subclass of: imaging biomarker
definition: A biomarker that is indicative of a disease and achieved through imaging.
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI)
imported from: opmi.owl

imaging disease biomarkers by MRI
type: Class
subclass of: imaging disease biomarker
definition editor: Oliver He
alternative term: imaging disease biomarkers by magnetic resonance imaging
definition source: https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI)
imported from: opmi.owl

cancer marker
type: Class
subclass of: disease biomarker
fromOldVersion: yes
definition editor: Oliver He
definition source: A biomarker that is indicative of the presence of cancer in the body
definition source: https://en.wikipedia.org/wiki/Cancer_biomarker
imported from: opmi.owl
has exact synonym: cancer biomarker
has exact synonym: tumor biomarker
has exact synonym: tumour marker

age
type: Class
subclass of: physical object quality
fromOldVersion: yes
definition: A time quality inhering in a bearer by virtue of how long the bearer has existed.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000011
in subset: attribute slim
in subset: scalar slim

concentration of
type: Class
subclass of: physical object quality
definition: A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
imported from: pato.owl
has exact synonym: concentration
has_obo_namespace: quality
id: PATO:0000033
in subset: attribute slim
in subset: relational slim
in subset: scalar slim

frequency
type: Class
subclass of: process quality
definition: A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0000044
in subset: attribute slim
in subset: scalar slim

sensitivity toward
type: Class
subclass of: physical object quality
fromOldVersion: yes
definition: A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
imported from: pato.owl
has exact synonym: sensitivity
has_obo_namespace: quality
id: PATO:0000085
in subset: attribute slim
in subset: disposition slim
in subset: relational slim

physical object quality
type: Class
subclass of: quality
fromOldVersion: yes
definition: A quality which inheres in a continuant.
imported from: pato.owl
has_alternative_id: PATO:0001237
has_alternative_id: PATO:0001238
database cross reference: snap:Quality
has exact synonym: monadic quality of a continuant
has exact synonym: multiply inhering quality of a physical entity
has exact synonym: quality of a continuant
has exact synonym: quality of a single physical entity
has exact synonym: quality of an object
has exact synonym: quality of continuant
has_narrow_synonym: monadic quality of an object
has_narrow_synonym: monadic quality of continuant
has_obo_namespace: quality
id: PATO:0001241
comment: Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.

chronological age
type: Class
subclass of: age
definition: An age quality that exists by virtue of the time (years and months) that the bearer has existed.
imported from: pato.owl
has_obo_namespace: quality
id: PATO:0001486
in subset: attribute slim

progressive
type: Class
subclass of: process quality
definition: A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time.
imported from: pato.owl
is opposite of: PATO_0002026
has_obo_namespace: quality
id: PATO:0001818
in subset: hpo slim
in subset: mpath slim
in subset: value slim

neoplastic, non-malignant
type: Class
subclass of: quality
fromOldVersion: yes
definition: A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize.
imported from: pato.owl
contributor: 0000-0002-2061-091X
creation date: 2009-10-05T12:47:14Z
has_obo_namespace: quality
has_related_synonym: benign
id: PATO:0002096
in subset: disposition slim
in subset: mpath slim
in subset: value slim

protein
type: Class
subclass of: molecular entity
fromOldVersion: yes
definition: An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
imported from: pr.owl
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].

interleukin-6
type: Class
subclass of: interleukin
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: PIRSF:PIRSF001935
has exact synonym: B-cell hybridoma growth factor
has exact synonym: B-cell stimulatory factor 2
has exact synonym: BSF-2
has exact synonym: CDF
has exact synonym: CTL differentiation factor
has exact synonym: IFN-beta-2
has exact synonym: IL-6
has exact synonym: IL6
has exact synonym: hybridoma growth factor
has exact synonym: interferon beta-2
has exact synonym: interleukin HP-1
has_obo_namespace: protein
has_related_synonym: IFNB2
id: PR:000001393
comment: Category=gene.

apoptosis regulator Bcl-2
type: Class
subclass of: protein
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: prostate cancer
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: lung cancer
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: breast cancer
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: colorectal cancer
fromOldVersion: yes
definition: A Bcl-2-like apoptosis inhibitor that is a translation product of the human BCL2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: IUPHARobj:2844
has exact synonym: BCL2
has_obo_namespace: protein
has_related_synonym: Bcl-2
id: PR:000002307
comment: Category=gene.

prostate-specific antigen
type: Class
subclass of: protein
fromOldVersion: yes
definition: A trypsin that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: IUPHARobj:2373
has exact synonym: KLK3
has exact synonym: P-30 antigen
has exact synonym: gamma-seminoprotein
has exact synonym: kallikrein-3
has exact synonym: semenogelase
has exact synonym: seminin
has_obo_namespace: protein
has_related_synonym: APS
has_related_synonym: PSA
id: PR:000003015
comment: Category=gene.

cellular tumor antigen p53
type: Class
subclass of: protein
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: cancer
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: cancer
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: cancer
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: A protein that is a translation product of the human TP53 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: PIRSF:PIRSF002089
has exact synonym: TP53
has exact synonym: antigen NY-CO-13
has exact synonym: antigen p53
has exact synonym: phosphoprotein p53
has exact synonym: tumor suppressor p53
has_obo_namespace: protein
has_related_synonym: P53
has_related_synonym: Trp53
id: PR:000003035
comment: Category=gene.

adiponectin
type: Class
subclass of: protein
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease of metabolism
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: cardiovascular disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease of metabolism
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: cardiovascular disease
fromOldVersion: yes
definition: A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: 30 kDa adipocyte complement-related protein
has exact synonym: ADIPOQ
has exact synonym: adipocyte complement-related 30 kDa protein
has exact synonym: adipocyte, C1q and collagen domain-containing protein
has exact synonym: adipocyte-specific protein AdipoQ
has exact synonym: adipose most abundant gene transcript 1 protein
has exact synonym: apM-1
has exact synonym: gelatin-binding protein
has_obo_namespace: protein
has_related_synonym: ACDC
has_related_synonym: ACRP30
has_related_synonym: APM1
has_related_synonym: GBP28
id: PR:000003777
comment: Category=gene.

albumin
type: Class
subclass of: protein
definition: A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: ALB
has exact synonym: serum albumin
has_obo_namespace: protein
has_related_synonym: Alb-1
has_related_synonym: Alb1
has_related_synonym: GIG20
has_related_synonym: GIG42
has_related_synonym: PRO0903
has_related_synonym: PRO1708
has_related_synonym: PRO2044
has_related_synonym: PRO2619
has_related_synonym: PRO2675
has_related_synonym: UNQ696/PRO1341
id: PR:000003918
comment: Category=gene.

brain-derived neurotrophic factor
type: Class
subclass of: gene
subclass of: Restriction
  on property: isCandidateBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A neurotrophin that is a translation product of the human BDNF gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: BDNF
has exact synonym: abrineurin
has_obo_namespace: protein
id: PR:000004716
comment: Category=gene.

chitinase-3-like protein 1
type: Class
subclass of: protein
definition: A protein that is a translation product of the human CHI3L1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: 39 kDa synovial protein
has exact synonym: BRP39 protein
has exact synonym: CGP-39
has exact synonym: CHI3L1
has exact synonym: GP-39
has exact synonym: YKL-40
has exact synonym: cartilage glycoprotein 39
has_obo_namespace: protein
has_related_synonym: Brp39
id: PR:000005423
comment: Category=gene.

clusterin
type: Class
subclass of: protein
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: chronic kidney disease
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: Acute kidney injury
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: Alzheimer disease
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: heart failure
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: cancer
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: kidney disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: Alzheimer disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: heart failure
definition: A protein that is a translation product of the human CLU gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: CLU
has exact synonym: Ku70-binding protein 1
has exact synonym: NA1/NA2
has exact synonym: SGP-2
has exact synonym: TRPM-2
has exact synonym: aging-associated gene 4 protein
has exact synonym: apo-J
has exact synonym: apolipoprotein J
has exact synonym: clustrin
has exact synonym: complement cytolysis inhibitor
has exact synonym: complement-associated protein SP-40,40
has exact synonym: sulfated glycoprotein 2
has exact synonym: testosterone-repressed prostate message 2
has_obo_namespace: protein
has_related_synonym: AAG4
has_related_synonym: APOJ
has_related_synonym: CLI
has_related_synonym: KUB1
has_related_synonym: Msgp-2
id: PR:000005615
comment: Category=gene.

C-reactive protein
type: Class
subclass of: protein
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: CRP
has_obo_namespace: protein
has_related_synonym: PTX1
id: PR:000005897
comment: Category=gene.

cystatin-C
type: Class
subclass of: protein
fromOldVersion: yes
definition: A protein that is a translation product of the human CST3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: CST3
has exact synonym: cystatin-3
has exact synonym: gamma-trace
has exact synonym: neuroendocrine basic polypeptide
has exact synonym: post-gamma-globulin
has_obo_namespace: protein
id: PR:000005965
comment: Category=gene.

epidermal growth factor receptor
type: Class
subclass of: protein
fromOldVersion: yes
definition: An EGF receptor type tyrosine-protein kinase that is a translation product of the human EGFR gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: IUPHARobj:1797
has exact synonym: EGFR
has exact synonym: proto-oncogene c-ErbB-1
has exact synonym: receptor tyrosine-protein kinase erbB-1
has_obo_namespace: protein
has_related_synonym: ERBB
has_related_synonym: ERBB1
has_related_synonym: HER1
id: PR:000006933
comment: Category=gene.

estrogen receptor
type: Class
subclass of: protein
fromOldVersion: yes
definition: A protein that is a translation product of the human ESR1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
database cross reference: IUPHARobj:620
has exact synonym: ER
has exact synonym: ER-alpha
has exact synonym: ESR1
has exact synonym: estradiol receptor
has exact synonym: nuclear receptor subfamily 3 group A member 1
has_obo_namespace: protein
has_related_synonym: ESR
has_related_synonym: Estr
has_related_synonym: Estra
has_related_synonym: NR3A1
id: PR:000007204
comment: Category=gene.

glial fibrillary acidic protein
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: GFAP
has_obo_namespace: protein
id: PR:000007939
comment: Category=gene. Requested by=CL.

neutrophil gelatinase-associated lipocalin
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has_broad_synonym: p25
has exact synonym: 25 kDa alpha-2-microglobulin-related subunit of MMP-9
has exact synonym: LCN2
has exact synonym: SV-40-induced 24P3 protein
has exact synonym: lipocalin-2
has exact synonym: oncogene 24p3
has_obo_namespace: protein
has_related_synonym: HNL
has_related_synonym: NGAL
id: PR:000009725
comment: Category=gene. Requested by=CL.

leptin
type: Class
subclass of: protein
fromOldVersion: yes
definition: A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: LEP
has exact synonym: obese protein
has exact synonym: obesity factor
has_obo_namespace: protein
has_related_synonym: OB
has_related_synonym: OBS
id: PR:000009758
comment: Category=gene.

neurogranin
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein that is a translation product of the human NRGN gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: NRGN
has exact synonym: Ng
has exact synonym: RC3
has_obo_namespace: protein
id: PR:000011426
comment: Category=gene.

osteopontin
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein that is a translation product of the human SPP1 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: 2AR
has exact synonym: SPP-1
has exact synonym: SPP1
has exact synonym: bone sialoprotein 1
has exact synonym: calcium oxalate crystal growth inhibitor protein
has exact synonym: early T-lymphocyte activation 1 protein
has exact synonym: minopontin
has exact synonym: nephropontin
has exact synonym: secreted phosphoprotein 1
has exact synonym: urinary stone protein
has exact synonym: uropontin
has_obo_namespace: protein
has_related_synonym: BNSP
has_related_synonym: Eta-1
has_related_synonym: OPN
has_related_synonym: Op
has_related_synonym: PSEC0156
id: PR:000015561
comment: Category=gene.

trefoil factor 3
type: Class
subclass of: protein
definition: A protein that is a translation product of the human TFF3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: P1.B
has exact synonym: TFF3
has exact synonym: intestinal trefoil factor
has exact synonym: polypeptide P1.B
has_obo_namespace: protein
has_related_synonym: ITF
has_related_synonym: TFI
id: PR:000016276
comment: Category=gene.

troponin I, cardiac muscle
type: Class
subclass of: protein
fromOldVersion: yes
definition: A protein that is a translation product of the human TNNI3 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: TNNI3
has exact synonym: cTnI
has exact synonym: cardiac troponin I
has exact synonym: troponin I
has_obo_namespace: protein
has_related_synonym: TNNC1
id: PR:000016506
comment: Category=gene.

troponin T, cardiac muscle
type: Class
subclass of: protein
definition: A protein that is a translation product of the human TNNT2 gene or a 1:1 ortholog thereof.
imported from: pr.owl
has exact synonym: TNNT2
has exact synonym: TnTc
has exact synonym: cTnT
has exact synonym: cardiac muscle troponin T
has_obo_namespace: protein
id: PR:000016509
comment: Category=gene.

D-dimer (human)
type: Class
subclass of: protein
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A protein-containing complex that is the remnant of fibrin mesh degradation (fibrinolysis) by plasmin in human.
imported from: pr.owl
has exact synonym: D-dimer
has exact synonym: hFDP/D-dimer
has_obo_namespace: protein
id: PR:000050369
comment: Category=organism-complex. Requested by=MAxO.

hemoglobin A1c
type: Class
subclass of: protein-containing complex
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits.
imported from: pr.owl
has_broad_synonym: glycated hemoglobin
has_broad_synonym: glycohemoglobin
has exact synonym: HbA1c
has exact synonym: HgbA1c
has_obo_namespace: protein
id: PR:000050469
comment: Category=complex. Note: The precise definition of hemoglobin A1c has evolved over time [https://medcraveonline.com/JNMR/laboratory-diagnosis-of-hba1c-a-review.html]. This PRO term is based on the most-precise definition currently in use.

Respiratory Rate
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute.
imported from: scdo.owl
definition source: D056152
existence in other ontologies: Sufficient
previous identifier: SCDO:0000993
database cross reference: MESH:D056152
has exact synonym: Breathing Frequency
has exact synonym: Pulmonary Ventilation Rate
has exact synonym: Respiration Rate

Intestinal Injury
type: Class
subclass of: disease
definition: Damage inflicted on the intestine.
imported from: scdo.owl
existence in other ontologies: Few but definitions not available
creator: SCDO (Jade Hotchkiss)
dc:source: https://www.ncbi.nlm.nih.gov/pubmed/31146745
has exact synonym: Intestinal Damage

miRNA
type: Class
subclass of: gene
fromOldVersion: yes
definition: Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors.
imported from: so.owl
has_alternative_id: SO:0000649
has_broad_synonym: INSDC_feature:ncRNA
database cross reference: http://en.wikipedia.org/wiki/MiRNA
database cross reference: http://en.wikipedia.org/wiki/StRNA
has exact synonym: INSDC_qualifier:miRNA
has exact synonym: micro RNA
has exact synonym: microRNA
has exact synonym: small temporal RNA
has exact synonym: stRNA
has_obo_namespace: sequence
id: SO:0000276
in subset: SOFA

false negative rate
type: Class
subclass of: data item
has curation status: IAO_0000122
definition: the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
definition editor: Alejandra Gonzalez-Beltran
definition editor: Orlaith Burke
definition editor: Philippe Rocca-Serra
definition source: STATO, adapted from
imported from: stato.owl
STATO alternative term: type II error rate
STATO alternative term: β
has exact synonym: probability of false negatives

prevalence
type: Class
subclass of: data item
fromOldVersion: yes
has curation status: IAO_0000122
definition: prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.
definition editor: Philippe Rocca-Serra
definition source: adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm
imported from: stato.owl

accuracy
type: Class
subclass of: data item
has curation status: IAO_0000122
definition: in the context of binary classification, accuracy is defined as the proportion of true results (both true positives and true negatives) to the total number of cases examined (the sum of true positive, true negative, false positive and false negative). It can be understood as a measure of the proximity of measurement results to the true value.
definition editor: Philippe Rocca-Serra
alternative term: Rand accuracy
alternative term: Rand index
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016
imported from: stato.owl

precision
type: Class
subclass of: data item
has curation status: IAO_0000122
definition: precision or positive predictive value is defined as the proportion of the true positives against all the positive results (both true positives and false positives)
definition editor: Philippe Rocca-Serra
alternative term: positive predictive value
definition source: adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016
imported from: stato.owl
ALT_DEFINITION: The probability that people with a positive screening test result do indeed have the condition of interest, taking into account the prevalence of the disease or condition.

Axiom
annotated source: precision
annotated property: ALT_DEFINITION
annotated target: The probability that people with a positive screening test result do indeed have the condition of interest, taking into account the prevalence of the disease or condition.

inflammation
type: Class
subclass of: symptom
definition: Inflammation is a general symptom where there is a local response to cellular injury that is marked by capillary dilatation, leukocytic infiltration, redness, heat, pain, swelling, and often loss of function and that serves as a mechanism initiating the elimination of noxious agents and of damaged tissue.
imported from: symp.owl
has_obo_namespace: symptoms
id: SYMP:0000061

weight loss
type: Class
subclass of: symptom
definition: A weight symptom that is characterized by a reduction of the total body mass, by a mean loss of fluid, body fat (adipose tissue), or lean mass (namely bone mineral deposits, muscle, tendon, and other connective tissue). Weight loss can either occur unintentionally because of malnourishment or an underlying disease.
imported from: symp.owl
has_alternative_id: SYMP:0000476
database cross reference: ICD9CM_2005:783.21
database cross reference: UMLS_CUI:C0043096
database cross reference: UMLS_ICD9CM_2005_AUI:A1605347
has exact synonym: loss of weight
has_obo_namespace: symptoms
id: SYMP:0000178

symptom
type: Class
subclass of: realizable entity
definition: A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease.
imported from: symp.owl
has_obo_namespace: symptoms
id: SYMP:0000462

chronic pain
type: Class
subclass of: symptom
definition: A pain that is characterized by ranging from mild to severe and which continues beyond the expected healing phase.
imported from: symp.owl
has_obo_namespace: symptoms
id: SYMP:0000837

anatomical structure
type: Class
subclass of: material anatomical entity
definition: Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
imported from: uberon.owl
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: NCBITaxon 4751
database cross reference: AAO:0010825
database cross reference: AEO:0000003
database cross reference: BILA:0000003
database cross reference: CARO:0000003
database cross reference: EHDAA2:0003003
database cross reference: EMAPA:0
database cross reference: FBbt:00007001
database cross reference: FMA:305751
database cross reference: FMA:67135
database cross reference: GAID:781
database cross reference: HAO:0000003
database cross reference: MA:0003000
database cross reference: MESH:D000825
database cross reference: SCTID:362889002
database cross reference: TAO:0000037
database cross reference: TGMA:0001823
database cross reference: VHOG:0001759
database cross reference: XAO:0003000
database cross reference: ZFA:0000037
database cross reference: http://dbpedia.org/ontology/AnatomicalStructure
has exact synonym: biological structure
has exact synonym: connected biological structure
has_obo_namespace: uberon
id: UBERON:0000061
in subset: common anatomy
in subset: upper level

organ
type: Class
subclass of: anatomical system
fromOldVersion: yes
definition: Anatomical structure that performs a specific function or group of functions [WP].
imported from: uberon.owl
never in taxon: NCBITaxon_110815
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: NCBITaxon 4751
external_definition: Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
external_ontology_notes: CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
database cross reference: BIRNLEX:4
database cross reference: CARO:0020004
database cross reference: EFO:0000634
database cross reference: EMAPA:35949
database cross reference: ENVO:01000162
database cross reference: FMA:67498
database cross reference: MA:0003001
database cross reference: NCIT:C13018
database cross reference: SCTID:272625005
database cross reference: UMLS:C0178784
database cross reference: WBbt:0003760
database cross reference: Wikipedia:Organ_(anatomy)
has_obo_namespace: uberon
has_related_synonym: anatomical unit
has_related_synonym: body organ
has_related_synonym: element
id: UBERON:0000062
in subset: common anatomy
in subset: upper level

excreta
type: Class
subclass of: organism substance
definition: A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity.
imported from: uberon.owl
has_alternative_id: UBERON:0000324
has_alternative_id: UBERON:0007550
database cross reference: AEO:0000184
database cross reference: BTO:0000491
database cross reference: EHDAA2_RETIRED:0003184
database cross reference: ENVO:02000022
database cross reference: FMA:9674
database cross reference: galen:Excretion
has exact synonym: excreted substance
has exact synonym: portion of excreted substance
has exact synonym: waste substance
has_obo_namespace: uberon
has_related_synonym: excretion
id: UBERON:0000174

blood
type: Class
subclass of: bodily fluid
definition: A fluid that is composed of blood plasma and erythrocytes.
curator note: This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
imported from: uberon.owl
present_in_taxon: NCBITaxon 9606
external_definition: 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]
external_definition: Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
axiom_lost_from_external_ontology: relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
homology_notes: 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]
contributor: cmungall
contributor: tmeehan
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

organism substance
type: Class
subclass of: anatomical structure
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.
imported from: uberon.owl
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: 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

material anatomical entity
type: Class
subclass of: anatomical entity
definition: Anatomical entity that has mass.
imported from: uberon.owl
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: NCBITaxon 4751
database cross reference: AAO:0010264
database cross reference: AEO:0000006
database cross reference: BILA:0000006
database cross reference: CARO:0000006
database cross reference: EHDAA2:0003006
database cross reference: FBbt:00007016
database cross reference: FMA:67165
database cross reference: HAO:0000006
database cross reference: TAO:0001836
database cross reference: TGMA:0001826
database cross reference: VHOG:0001721
has_obo_namespace: uberon
id: UBERON:0000465
in subset: common anatomy
in subset: upper level

anatomical system
type: Class
subclass of: anatomical structure
definition: Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
imported from: uberon.owl
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: NCBITaxon 4751
has_broad_synonym: system
database cross reference: AAO:0000007
database cross reference: AEO:0000011
database cross reference: BILA:0000011
database cross reference: BIRNLEX:14
database cross reference: BSA:0000049
database cross reference: CALOHA:TS-2088
database cross reference: CARO:0000011
database cross reference: EHDAA2:0003011
database cross reference: EHDAA:392
database cross reference: EMAPA:16103
database cross reference: EV:0100000
database cross reference: FBbt:00004856
database cross reference: FMA:7149
database cross reference: HAO:0000011
database cross reference: MA:0000003
database cross reference: NCIT:C12919
database cross reference: SCTID:278195005
database cross reference: TAO:0001439
database cross reference: TGMA:0001831
database cross reference: UMLS:C0460002
database cross reference: VHOG:0001725
database cross reference: WBbt:0005746
database cross reference: WBbt:0005763
database cross reference: Wikipedia:Organ_system
database cross reference: XAO:0003002
database cross reference: ZFA:0001439
database cross reference: galen:AnatomicalSystem
has exact synonym: body system
has exact synonym: connected anatomical system
has exact synonym: organ system
has_obo_namespace: uberon
has_related_synonym: anatomical systems
id: UBERON:0000467
in subset: common anatomy
in subset: pheno slim
in subset: uberon slim
in subset: upper level

anatomical entity
type: Class
subclass of: independent continuant
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.
imported from: uberon.owl
present_in_taxon: NCBITaxon_33090
present_in_taxon: NCBITaxon_33208
present_in_taxon: NCBITaxon 4751
database cross reference: AAO:0010841
database cross reference: AEO:0000000
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

urine
type: Class
subclass of: excreta
definition: Excretion that is the output of a kidney.
imported from: uberon.owl
taxon_notes: 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

cerebrospinal fluid
type: Class
subclass of: bodily fluid
fromOldVersion: yes
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]
imported from: uberon.owl
external_definition: Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
homology_notes: 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]
external_ontology_notes: EHDAA2 models this as developing from CP, which is wrong
external_ontology_notes: 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

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.
imported from: uberon.owl
has_relational_adjective: salivary
taxon_notes: 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

blood plasma
type: Class
subclass of: blood
definition: The liquid component of blood, in which erythrocytes are suspended.
imported from: uberon.owl
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

blood serum
type: Class
subclass of: blood
definition: The portion of blood plasma that excludes clotting factors.
imported from: uberon.owl
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

feces
type: Class
subclass of: excreta
definition: Portion of semisolid bodily waste discharged through the anus[MW,modified].
imported from: uberon.owl
external_definition: Excretion in semisolid state processed by the intestine.[FMA]
has_relational_adjective: fecal
has_broad_synonym: excreta
database cross reference: BTO:0000440
database cross reference: CALOHA:TS-2345
database cross reference: ENVO:00002003
database cross reference: FMA:64183
database cross reference: GAID:1199
database cross reference: MA:0002509
database cross reference: MAT:0000053
database cross reference: MESH:D005243
database cross reference: MIAA:0000053
database cross reference: NCIT:C13234
database cross reference: UMLS:C0015733
database cross reference: Wikipedia:Feces
database cross reference: galen:Feces
has exact synonym: faeces
has exact synonym: fecal material
has exact synonym: fecal matter
has exact synonym: piece of shit
has exact synonym: portion of excrement
has exact synonym: portion of faeces
has exact synonym: portion of fecal material
has exact synonym: portion of fecal matter
has exact synonym: portion of feces
has exact synonym: portionem cacas
has exact synonym: stool
has_narrow_synonym: cow dung
has_narrow_synonym: cow pat
has_narrow_synonym: dung
has_narrow_synonym: fewmet
has_narrow_synonym: frass
has_narrow_synonym: guano
has_narrow_synonym: portion of dung
has_narrow_synonym: portion of guano
has_narrow_synonym: portion of scat
has_narrow_synonym: scat
has_narrow_synonym: spraint
has_obo_namespace: uberon
has_related_synonym: droppings
has_related_synonym: excrement
has_related_synonym: ordure
has_related_synonym: spoor
id: UBERON:0001988
in subset: pheno slim
in subset: uberon slim

liver
type: Class
subclass of: organ
fromOldVersion: yes
definition: An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
imported from: uberon.owl
present_in_taxon: NCBITaxon 9606
external_definition: Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
axiom_lost_from_external_ontology: relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
homology_notes: All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
has_relational_adjective: hepatic
taxon_notes: An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
taxon_notes: The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
function_notes: secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
external_ontology_notes: Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
database cross reference: AAO:0010111
database cross reference: BTO:0000759
database cross reference: CALOHA:TS-0564
database cross reference: EFO:0000887
database cross reference: EHDAA2:0000997
database cross reference: EHDAA:2197
database cross reference: EMAPA:16846
database cross reference: EV:0100089
database cross reference: FMA:7197
database cross reference: GAID:288
database cross reference: MA:0000358
database cross reference: MAT:0000097
database cross reference: MESH:D008099
database cross reference: MIAA:0000097
database cross reference: NCIT:C12392
database cross reference: SCTID:181268008
database cross reference: TAO:0000123
database cross reference: UMLS:C0023884
database cross reference: VHOG:0000257
database cross reference: Wikipedia:Liver
database cross reference: XAO:0000133
database cross reference: ZFA:0000123
database cross reference: galen:Liver
has_obo_namespace: uberon
has_related_synonym: iecur
has_related_synonym: jecur
id: UBERON:0002107
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

kidney
type: Class
subclass of: organ
fromOldVersion: yes
definition: A paired organ of the urinary tract which has the production of urine as its primary function.
imported from: uberon.owl
mutually_spatially_disjoint_with: UBERON_0000160
present_in_taxon: NCBITaxon 9606
external_definition: One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
has_relational_adjective: renal
fma_set_term: FMA_264815
database cross reference: AAO:0000250
database cross reference: BTO:0000671
database cross reference: CALOHA:TS-0510
database cross reference: EFO:0000929
database cross reference: EMAPA:17373
database cross reference: EV:0100096
database cross reference: FMA:7203
database cross reference: GAID:423
database cross reference: MA:0000368
database cross reference: MAT:0000119
database cross reference: MESH:D007668
database cross reference: MIAA:0000119
database cross reference: NCIT:C12415
database cross reference: SCTID:181414000
database cross reference: UMLS:C0022646
database cross reference: Wikipedia:Kidney
database cross reference: XAO:0003267
database cross reference: galen:Kidney
has_narrow_synonym: reniculate kidney
has_obo_namespace: uberon
id: UBERON:0002113
in subset: efo slim
in subset: human reference atlas
in subset: major organ
in subset: organ slim
in subset: pheno slim
in subset: uberon slim
in subset: vertebrate core

integumental system
type: Class
subclass of: anatomical system
definition: Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle.
imported from: uberon.owl
homology_notes: (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]
contributor: cmungall
contributor: tfhayamizu
has_alternative_id: UBERON:0007029
database cross reference: AEO:0000154
database cross reference: BILA:0000118
database cross reference: CALOHA:TS-1299
database cross reference: CARO:0002001
database cross reference: EFO:0000807
database cross reference: EHDAA2:0000836
database cross reference: EHDAA2_RETIRED:0003154
database cross reference: EHDAA:6520
database cross reference: EMAPA:17524
database cross reference: EV:0100151
database cross reference: FBbt:00004969
database cross reference: FMA:72979
database cross reference: HAO:0000421
database cross reference: MA:0000014
database cross reference: MAT:0000033
database cross reference: MESH:D034582
database cross reference: MIAA:0000033
database cross reference: NCIT:C12907
database cross reference: SCTID:361692004
database cross reference: TADS:0000108
database cross reference: UMLS:C0037267
database cross reference: VHOG:0000403
database cross reference: Wikipedia:Integumentary_system
database cross reference: XAO:0000176
database cross reference: galen:Surface
has exact synonym: integumentary system
has_obo_namespace: uberon
has_related_synonym: body surface
has_related_synonym: dermal system
has_related_synonym: external covering of organism
has_related_synonym: integumentum commune
has_related_synonym: organism surface
has_related_synonym: surface
id: UBERON:0002416
in subset: efo slim
in subset: grouping class
in subset: pheno slim

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.
imported from: uberon.owl
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

hair of head
type: Class
subclass of: integumental system
definition: A strand of hair that is part of a head.
imported from: uberon.owl
has_broad_synonym: hair
database cross reference: FMA:54241
has exact synonym: head hair
has_narrow_synonym: hair of scalp
has_obo_namespace: uberon
id: UBERON:0016446
in subset: pheno slim

juvenile stage
type: Class
subclass of: biological_process
definition: The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity.
imported from: uberon.owl
contributor: ANiknejad
contributor: cmungall
has_obo_namespace: uberon
id: UBERON:0034919

voice analysis
type: Class
subclass of: process
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: The process of examining the acoustic properties of a person's voice to extract meaningful information. This can include pitch, tone, volume, speech patterns, and other vocal features.
definition source: generated with ChatGPT version 4,0 on 22․05․24

knee extension strength
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT version 4,0 on 19.06.2025
definition: Knee extension strength refers to the amount of force that the muscles on the front of the thigh—primarily the quadriceps—can generate to straighten (extend) the knee joint.

biomarker of aging text mining bin
type: Class
equivalent class: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
subclass of: biomarker text-mining category
editor note: This class is used for grouping terms and should not be used for logical reasoning.
description: The concept of the 'biomarker of aging TM_BIN' allows for the compilation of diverse concepts related to aging biomarkersusinga the axiom 'isDiagnosticBiomarkerFor some disease'. This enables the adaptation of the ontology for text mining purposes, facilitating the retrieval and extraction of information related to diagnostic biomarkers within a specific disease.
definition: A placeholder for aging biomarkers, organized based on the reasoning application 'isBiomarkerOfAging some disease', to facilitate text mining and information retrieval for aging research.

brain aging
type: Class
subclass of: aging
definition: Brain aging is a complex process that affects everything from the subcellular to the organ level, begins early in life, and accelerates with age. Morphologically, brain aging is primarily characterized by brain volume loss, cortical thinning, white matter degradation, loss of gyrification, and ventricular enlargement. Pathophysiologically, brain aging is associated with neuron cell shrinking, dendritic degeneration, demyelination, small vessel disease, metabolic slowing, microglial activation, and the formation of white matter lesions.
definition source: https://pubmed.ncbi.nlm.nih.gov/34600936/

epigenetic clock
type: Class
subclass of: age estimator
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Epigenetic clocks are mathematically derived age estimators that are based on combinations of methylation values that change with age at specific CpGs in the genome.
definition source: https://pubmed.ncbi.nlm.nih.gov/37034474/

proteomic clock
type: Class
subclass of: age estimator
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A proteomic aging clock is a biological tool that estimates an individual's biological age based on the levels of specific proteins in the body. These proteins serve as biomarkers of aging, reflecting underlying processes such as inflammation, metabolism, immune function, and cellular repair mechanisms.
definition: generated with ChatGPT version 4,0 on 19․08․24
has exact synonym: protein-based aging clock

hannum clock
type: Class
subclass of: epigenetic clock
definition: The Hannum Clock is one of the early and widely recognized epigenetic clocks designed to estimate biological age by analyzing DNA methylation patterns. It was developed by Dr. Gregory Hannum and his colleagues in 2013 and represents a key advancement in the field of aging research.
definition source: generated with ChatGPT version 4,0 on 19․08․24

horvath clock
type: Class
subclass of: epigenetic clock
definition: The Horvath Clock, developed by Dr. Steve Horvath in 2013, is a groundbreaking epigenetic clock that estimates biological age based on DNA methylation patterns. This clock is widely regarded as one of the most accurate and versatile tools for measuring biological aging across different tissues and cell types. The Horvath Clock uses the methylation levels at specific CpG sites (regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide) to estimate an individual’s biological age. Methylation at these sites tends to correlate strongly with chronological age, but it can also reveal biological age, reflecting an individual's health status and aging rate.
definition source: https://pubmed.ncbi.nlm.nih.gov/38486063/

DNAm PhenoAge
type: Class
subclass of: epigenetic clock
definition: DNAm PhenoAge is an epigenetic clock that allows for an estimate of phenotypic age from a single array, obviating the need for multiple assays to measure the nine blood-based components of phenotypic age.
definition: https://pubmed.ncbi.nlm.nih.gov/31780646/
has exact synonym: Levine clock
has exact synonym: PhenoAge clock

phenotypic age
type: Class
subclass of: age
definition: Phenotypic age refers to an individual’s biological age, which is determined by their physical characteristics and functioning rather than their chronological age
definition source: https://pubmed.ncbi.nlm.nih.gov/38486063/
has exact synonym: PhenoAge

GrimAge clock
type: Class
subclass of: epigenetic clock
definition: An epigenetic clock called DNA methylation GrimAge (DNAmGrimAge) was specifically designed to connect the relationship between “grim” events such as death and biological age and its derivation was based on smoking pack-years and multiple inflammatory proteins associated with mortality.
definition source: https://pubmed.ncbi.nlm.nih.gov/35944348/
has exact synonym: DNA methylation GrimAge
has exact synonym: DNAm GrimAge

mitotic clock
type: Class
subclass of: age estimator
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: A mitotic clock refers to a biological mechanism that tracks the number of times a cell has divided (or undergone mitosis) during its lifespan. This concept is primarily based on the idea that each cell has a finite number of divisions it can undergo, which is associated with cellular aging, senescence, and the potential for cancer development.
definition source: generated with ChatGPT version 4,0 on 19․08․24

decline in stem cell function
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The decline in stem cell function is a well-established feature of the aging process and plays a crucial role in the overall degeneration of tissues and organs as we age. Stem cells are responsible for tissue regeneration, repair, and maintaining homeostasis in the body. As we age, the function of these stem cells diminishes, leading to impaired tissue repair, reduced regeneration capacity, and an increased risk of age-related diseases.
definition source: generated with ChatGPT version 4,0 on 19․08․24

stem cell quantity
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The decline in stem cell function is a well-established feature of the aging process and plays a crucial role in the overall degeneration of tissues and organs as we age. Stem cells are responsible for tissue regeneration, repair, and maintaining homeostasis in the body. As we age, the function of these stem cells diminishes, leading to impaired tissue repair, reduced regeneration capacity, and an increased risk of age-related diseases.
definition source: generated with ChatGPT version 4,0 on 19․08․24

regenerative capacity
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Regenerative capacity is a complex trait dependent on the ability to access high-fidelity morphogenetic programmes after injury. It is distributed unequally among species and, within individuals, among their tissues.
definition source: generated with ChatGPT version 4,0 on 19․08․24

ELOVL2 hypermethilation
type: Class
subclass of: biological feature
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: ELOVL2 hypermethylation refers to an increase in DNA methylation at the ELOVL2 gene, which has been consistently associated with aging. The ELOVL2 gene encodes an enzyme involved in the elongation of very long-chain fatty acids. It has emerged as one of the most reliable epigenetic biomarkers of aging.
definition source: generated with ChatGPT version 4,0 on 19․08․24

hayflick limit
type: Class
subclass of: biological principle
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The Hayflick limit refers to the discovery by Leonard Hayflick that normal human cells grown in culture can only divide a finite number of times before entering a state of senescence, where they cease to divide. It describes a limit on the process of cell division and is related to the concept of cellular senescence.
definition source: https://pubmed.ncbi.nlm.nih.gov/11413492/

BloodAge
type: Class
subclass of: age estimator
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
definition: BloodAge refers to a biological age estimation method that uses a blood-based proteomic signature to assess how old a person is biologically, as opposed to their chronological age. By analyzing the levels of specific proteins in the blood, this method predicts a person's biological aging and potential risk for age-related diseases.

biological age
type: Class
subclass of: age
definition source: https://pubmed.ncbi.nlm.nih.gov/37944549/
has exact synonym: bAge
definition: Biological age is a measure of health that offers insights into ageing.

age estimator
type: Class
subclass of: Model
definition source: generated with ChatGPT version 4,0 on 19.06.2024
definition: A computational or biological tool, model, or marker used to estimate the chronological or biological age of an organism based on measurable features such as genetic, epigenetic, physiological, or imaging data.

biological principle
type: Class
subclass of: independent continuant
definition source: generated with ChatGPT version 3,5 on 23.08.24
definition: A biological principle is a fundamental concept or theory that underpins and explains biological phenomena and processes. It provides a foundational understanding of how biological systems function and guides research, experimentation, and interpretation in the field of biology.

GrimAge2
type: Class
subclass of: epigenetic clock
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: DNA methylation GrimAge version 2
has exact synonym: DNAm GrimAge2
definition: GrimAge2 is an updated version of the original GrimAge, which is a DNA methylation-based biological clock developed to estimate biological age and predict mortality risk.

DNA methylation risk score
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: DNAmRS
definition: DNA methylation-based risk score is a relatively recent metric used in research to assess biological age and associated health risks based on DNA methylation patterns. It evaluates the methylation levels at specific sites in the genome that are linked to various health outcomes, effectively providing a score that reflects the biological age of an individual as opposed to their chronological age.

pace of aging computed from the epigenome
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: DNAm pace of aging
has exact synonym: DunedinPACE
has exact synonym: epigenetic aging rate
has exact synonym: pace of aging
has exact synonym: rate of epigenetic aging
definition: Pace of Aging Computed from the Epigenome is a biomarker developed to assess the biological aging process based on DNA methylation patterns. Unlike other aging measures that focus on chronological age, DunedinPACE specifically evaluates how quickly or slowly an individual is aging by analyzing chemical tags (methylation marks) on DNA in white blood cells.

MetaboHealth score
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: M-metabo-score
definition: The MetaboHealth score is a metabolomics-based health assessment that utilizes a panel of serum metabolic markers to evaluate an individual's metabolic health and its association with health outcomes.

MetaboAge score
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
definition: The MetaboAge score is a biological age predictor based on metabolomic biomarkers. It is calculated using a model that analyzes 63 metabolites in the blood, allowing researchers to estimate an individual’s biological age as opposed to their chronological age. A key feature of MetaboAge is the difference between the predicted metabolomic age and the actual chronological age (referred to as ΔMetaboAge). A positive ΔMetaboAge may suggest accelerated biological aging and a higher risk of mortality. This score has been validated in various studies and is often used to study aging and its relation to mortality and other health outcomes​.

integrative biomarker
type: Class
subclass of: biomarker
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
definition: An integrative biomarker refers to a biological marker that combines multiple types of data or molecular measurements to provide a more comprehensive assessment of a biological process, disease state, or health outcome. These biomarkers integrate data from various domains, such as genomics, proteomics, metabolomics, and epigenetics, along with clinical and demographic information. The goal is to create a more holistic view of an individual's health status, particularly for complex conditions such as aging, cancer, cardiovascular diseases, or metabolic disorders.

intrinsic epigenetic age acceleration
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: IEAA
definition: Intrinsic Epigenetic Age Acceleration refers to a metric used to assess biological aging, independent of age-related changes in blood cell composition. It is calculated using DNA methylation data and reflects "cell-intrinsic" aging processes. This measure is derived by regressing DNA methylation age (calculated through Horvath's epigenetic clock) on chronological age, but without factoring in shifts in blood cell types that typically occur with age. Because IEAA does not include these immune system-related factors, it is considered a measure of fundamental, internal cellular aging.

extrinsic epigenetic age acceleration
type: Class
subclass of: metric
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT-4 on 09․10․24
has exact synonym: EEAA
definition: Extrinsic Epigenetic Age Acceleration is a metric used to estimate biological aging by incorporating both DNA methylation patterns and changes in blood cell composition. This measure reflects the combined effects of intrinsic cellular aging (similar to IEAA) and the aging of the immune system, which involves shifts in certain immune cell types, such as T cells and B cells.

handgrip strength
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: https://pubmed.ncbi.nlm.nih.gov/34233405/
definition: Handgrip strength (HGS) is a simple and reliable measurement of maximum voluntary muscle strength. It is an important tool for diagnosing sarcopenia and is widely used as a single indicator to represent overall muscle strength. HGS can predict not only muscle mass and physical activity, but also the incidence of chronic diseases, nutritional status, quality of life, independence of daily life, length of hospital stay, and even mortality.

cortical thinning
type: Class
subclass of: pathologic process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT version 4,0 on 19.06.2024
definition: Cortical thinning is the gradual reduction in the thickness of the brain’s cerebral cortex—the outer layer of neural tissue involved in functions such as perception, memory, and decision-making. It is commonly measured using neuroimaging techniques like MRI and is associated with normal aging, neurodegenerative diseases (e.g., Alzheimer’s), and certain psychiatric conditions.

functional connectivity decline
type: Class
subclass of: pathologic process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition source: generated with ChatGPT version 4,0 on 19.06.2024
definition: Functional connectivity decline refers to a reduction in the coordinated activity or communication between different regions of the brain over time. It typically indicates weakened synchronization in neural signals, often observed in aging, neurodegenerative diseases (like Alzheimer’s), or brain injury. This decline can affect cognitive functions such as memory, attention, and executive processing.

biomarker text-mining category
type: Class
subclass of: information content entity
editor note: This class is used for grouping terms and should not be used for logical reasoning.
definition: A placeholder for grouping classes for biomarker text-minig purposes.

process quality
type: Class
subclass of: quality
imported from: sio.owl
description: A process quality is quality that is associated with a process.

mathematical entity
type: Class
subclass of: information content entity
imported from: sio.owl
description: A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
subset: math+

parameter
type: Class
subclass of: information content entity
fromOldVersion: yes
imported from: sio.owl
description: A parameter is variable whose value changes the characteristics of a system or a function.

normality
type: Class
subclass of: quality
imported from: sio.owl
description: normality is the quality in which the value may differ from normal or average

normal
type: Class
subclass of: normality
imported from: sio.owl
description: A quality that has a value that is normal or average.
equivalent to: PATO:0000461

abnormal
type: Class
subclass of: normality
imported from: sio.owl
description: A quality that has a value that is outside normal or average.

increased
type: Class
subclass of: abnormal
imported from: sio.owl
description: A quality that has a value that is increased compared to normal or average.
equivalent to: PATO:0002300

decreased
type: Class
subclass of: abnormal
imported from: sio.owl
description: A quality that has a value that is decreased compared to normal or average.
equivalent to: PATO:0002301

correlation
type: Class
subclass of: mathematical entity
imported from: sio.owl
description: A correlation is a statistical relationship involving dependence between two random variables or datasets.

severe
type: Class
subclass of: quality
imported from: sio.owl
description: severe is a qualitative intensity value that is more intense than strong, but less intense than fatal.

male
type: Class
subclass of: physical object quality
fromOldVersion: yes
imported from: sio.owl
description: male is a biological sex of an individual with male sexual organs.
equivalent to: PATO:0000384

female
type: Class
subclass of: physical object quality
fromOldVersion: yes
imported from: sio.owl
description: female is a biological sex of an individual with female sexual organs.

metabolic syndrome
type: Class
subclass of: disease of metabolism
fromOldVersion: yes
definition: A cluster of metabolic risk factors for CARDIOVASCULAR DISEASES and TYPE 2 DIABETES MELLITUS. The major components of metabolic syndrome X include excess ABDOMINAL FAT; atherogenic DYSLIPIDEMIA; HYPERTENSION; HYPERGLYCEMIA; INSULIN RESISTANCE; a proinflammatory state; and a prothrombotic (THROMBOSIS) state. (from AHA/NHLBI/ADA Conference Proceedings, Circulation 2004; 109:551-556)
definition editor: James Malone
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: DOID:14221
database cross reference: ICD9:277.7
database cross reference: MeSH:D024821
database cross reference: MedDRA:10052066
database cross reference: NCIt:C84442
database cross reference: OMIM:605552
database cross reference: OMIM:615812
database cross reference: SNOMEDCT:237602007
has exact synonym: Cardiovascular Syndrome, Metabolic
has exact synonym: Cardiovascular Syndromes, Metabolic
has exact synonym: Dysmetabolic Syndrome X
has exact synonym: Insulin Resistance Syndrome X
has exact synonym: MetS
has exact synonym: Metabolic Cardiovascular Syndrome
has exact synonym: Metabolic Syndrome X
has exact synonym: Metabolic X Syndrome
has exact synonym: Reaven Syndrome X
has exact synonym: Syndrome X, Dysmetabolic
has exact synonym: Syndrome X, Insulin Resistance
has exact synonym: Syndrome X, Metabolic
has exact synonym: Syndrome X, Reaven
has exact synonym: Syndrome, Metabolic Cardiovascular
has exact synonym: Syndrome, Metabolic X
has exact synonym: X Syndrome, Metabolic

antibody
type: Class
subclass of: protein
fromOldVersion: yes
definition: An antibody function (or antigen binding function) is an infection-fighting protein molecule in blood or secretory fluids that tags, neutralizes, and helps destroy pathogenic microorganisms such as bacteria, viruses and toxins.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: efo.owl
database cross reference: MO:833
database cross reference: MeSH:D000906
database cross reference: NCIt:C16295
database cross reference: NIFSTD:birnlex_2110
database cross reference: SNOMEDCT:68498002
has exact synonym: antibodies

cardiovascular disease
type: Class
subclass of: cardiovascular system disease
definition: A body system disease 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.
definition: A disease involving the cardiovascular system.
definition: A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma. -- 2003
definition: A non-neoplastic or neoplastic disorder affecting the heart or the vessels (arteries, veins and lymph vessels). Representative examples of non-neoplastic cardiovascular disorders are endocarditis and hypertension. Representative examples of neoplastic cardiovascular disorders are endocardial myxoma and angiosarcoma.
definition: Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM.
definition editor: James Malone
imported from: efo.owl
exact match: D002318
exact match: http://identifiers.org/snomedct/49601007
exact match: http://linkedlifedata.com/resource/umls/id/C0007222
exact match: cardiovascular system disease
exact match: NCIT C2931
gwas trait: true
database cross reference: DOID:1287
database cross reference: ICD10:I98
database cross reference: ICD10:I99
database cross reference: ICD9:390-459.99
database cross reference: ICD9:420-429.99
database cross reference: ICD9:423
database cross reference: ICD9:423.8
database cross reference: ICD9:424
database cross reference: ICD9:429
database cross reference: ICD9:429.2
database cross reference: ICD9:429.7
database cross reference: ICD9:429.8
database cross reference: ICD9:429.81
database cross reference: ICD9:429.89
database cross reference: ICD9:459.89
database cross reference: ICD9:459.9
database cross reference: MESH:D002318
database cross reference: MONDO:0004995
database cross reference: MeSH:D002318
database cross reference: MedDRA:10007648
database cross reference: NCIT:C2931
database cross reference: NCIt:C2931
database cross reference: SCTID:49601007
database cross reference: SNOMEDCT:105980002
database cross reference: SNOMEDCT:49601007
database cross reference: UMLS:C0007222
has exact synonym: ASCVD
has exact synonym: CARDIOVASC DIS
has exact synonym: CIRCULATORY DISEASE NOS
has exact synonym: CVD
has exact synonym: CVD, NOS
has exact synonym: CVS disease
has exact synonym: Cardiovascular Disease (CVD)
has exact synonym: Cardiovascular Diseases
has exact synonym: Cardiovascular Disorder
has exact synonym: Cardiovascular Disorders
has exact synonym: Cardiovascular disease, NOS
has exact synonym: Cardiovascular disease, unspecified
has exact synonym: Cardiovascular disorder, NOS
has exact synonym: Cardiovascular system disease
has exact synonym: Certain sequelae of myocardial infarction, not elsewhere classified
has exact synonym: Circulatory system disease NOS
has exact synonym: Circulatory system disease NOS (disorder)
has exact synonym: DISEASES OF THE CIRCULATORY SYSTEM
has exact synonym: Disease affecting entire cardiovascular system
has exact synonym: Disease affecting entire cardiovascular system (disorder)
has exact synonym: Disease of cardiovascular system
has exact synonym: Disease of cardiovascular system (disorder)
has exact synonym: Disease of cardiovascular system, NOS
has exact synonym: Disease, Cardiovascular
has exact synonym: Diseases, Cardiovascular
has exact synonym: Disorder of cardiovascular system
has exact synonym: Disorder of cardiovascular system (disorder)
has exact synonym: Disorder of circulatory system
has exact synonym: Disorder of circulatory system, NOS
has exact synonym: Disorder of the circulatory system
has exact synonym: ILL-DEFINED HRT DIS NEC
has exact synonym: Ill-defined descriptions and complications of heart disease
has exact synonym: OTHER SEQUELAE OF MI NEC
has exact synonym: Other diseases of endocardium
has exact synonym: Other diseases of endocardium (disorder)
has exact synonym: Other diseases of pericardium
has exact synonym: Other diseases of pericardium (disorder)
has exact synonym: Other disorders of papillary muscle
has exact synonym: Other forms of heart disease

Crohn's disease
type: Class
subclass of: inflammatory bowel disease
fromOldVersion: yes
definition: A chronic transmural inflammation that may involve any part of the DIGESTIVE TRACT from MOUTH to ANUS, mostly found in the ILEUM, the CECUM, and the COLON. In Crohn disease, the inflammation, extending through the intestinal wall from the MUCOSA to the serosa, is characteristically asymmetric and segmental. Epithelioid GRANULOMAS may be seen in some patients.
definition: A gastrointestinal disorder characterized by chronic inflammation involving all layers of the intestinal wall, noncaseating granulomas affecting the intestinal wall and regional lymph nodes, and transmural fibrosis. Crohn disease most commonly involves the terminal ileum; the colon is the second most common site of involvement.
definition editor: James Malone
definition editor: Tomasz Adamusiak
imported from: efo.owl
exact match: D003424
exact match: http://identifiers.org/snomedct/7620006
exact match: http://linkedlifedata.com/resource/umls/id/C0010346
exact match: CN043071
exact match: DOID 8778
exact match: NCIT C2965
gwas trait: true
database cross reference: DOID:8778
database cross reference: ICD10:K50
database cross reference: ICD9:555.1
database cross reference: MESH:D003424
database cross reference: MONDO:0005011
database cross reference: MeSH:D003424
database cross reference: MedDRA:10011401
database cross reference: NCIT:C2965
database cross reference: NCIt:C27837
database cross reference: NCIt:C2965
database cross reference: OMIM:266600
database cross reference: Orphanet:206
database cross reference: SCTID:34000006
database cross reference: SCTID:7620006
database cross reference: SNOMEDCT:34000006
database cross reference: UMLS:C0010346
database cross reference: UMLS:CN043071
has exact synonym: CROHN DIS
has exact synonym: CROHNS DIS
has exact synonym: Colitis, Granulomatous
has exact synonym: Crohn Disease
has exact synonym: Crohn disease
has exact synonym: Crohn's associated gastritis
has exact synonym: Crohn's disease
has exact synonym: Crohn's disease of colon
has exact synonym: Crohn's disease of large bowel
has exact synonym: Crohns Disease
has exact synonym: Enteritis, Granulomatous
has exact synonym: Enteritis, Regional
has exact synonym: Gastritis Associated with Crohn Disease
has exact synonym: Gastritis Associated with Crohn's Disease
has exact synonym: Ileitis, Regional
has exact synonym: Ileitis, Terminal
has exact synonym: Ileocolitis
has exact synonym: granulomatous colitis
has exact synonym: paediatric Crohn's disease
has exact synonym: pediatric Crohn's disease
has exact synonym: regional enteritis
id: EFO:0000384
in subset: orphanet rare
in subset: rare

diabetic nephropathy
type: Class
subclass of: kidney disease
definition: Diabetic nephropathy (sometimes called Kimmelstiel-Wilson syndrome) is a progressive kidney disorder caused by vascular damage to the glomerular capillaries, in patients with diabetes mellitus. It is usually manifested with nephritic syndrome and glomerulosclerosis.
definition: Progressive kidney disorder caused by vascular damage to the glomerular capillaries, in patients with diabetes mellitus. It is usually manifested with nephritic syndrome and glomerulosclerosis.
definition editor: James Malone
definition editor: Tomasz Adamusiak
imported from: efo.owl
exact match: D003928
exact match: http://identifiers.org/snomedct/127013003
exact match: NCIT C84417
gwas trait: true
database cross reference: DOID:11503
database cross reference: EFO:0004996
database cross reference: EFO:0004997
database cross reference: ICD9:250.4
database cross reference: ICD9:250.40
database cross reference: ICD9:583.81
database cross reference: MESH:D003928
database cross reference: MONDO:0005016
database cross reference: MeSH:D003928
database cross reference: MedDRA:10061835
database cross reference: NCIT:C84417
database cross reference: NCIt:C84417
database cross reference: OMIM:612624
database cross reference: OMIM:612628
database cross reference: OMIM:612634
database cross reference: SCTID:127013003
database cross reference: SCTID:50620007
database cross reference: SNOMEDCT:127013003
database cross reference: SNOMEDCT:197605007
database cross reference: SNOMEDCT:311366001
database cross reference: SNOMEDCT:38542009
database cross reference: SNOMEDCT:54181000
database cross reference: SNOMEDCT:707221002
has exact synonym: DKD
has exact synonym: DMII RENAL UNCNTRLD
has exact synonym: DMII RENL NT ST UNCNTRLD
has exact synonym: Diabetes with renal manifestations
has exact synonym: Diabetes with renal manifestations (disorder)
has exact synonym: Diabetes-nephrosis syndrome
has exact synonym: Diabetes-nephrosis syndrome (disorder)
has exact synonym: Diabetic Glomerulosclerosis
has exact synonym: Diabetic Kidney Disease
has exact synonym: Diabetic Kidney Diseases
has exact synonym: Diabetic Nephropathies
has exact synonym: Diabetic renal disease
has exact synonym: Diabetic renal disease (disorder)
has exact synonym: Glomerulosclerosis, Diabetic
has exact synonym: Glomerulosclerosis, Nodular
has exact synonym: Intracapillary Glomerulosclerosis
has exact synonym: Kidney Disease, Diabetic
has exact synonym: Kidney Diseases, Diabetic
has exact synonym: Kimmelstiel - Wilson disease
has exact synonym: Kimmelstiel Wilson Disease
has exact synonym: Kimmelstiel Wilson Syndrome
has exact synonym: Kimmelstiel-Wilson Disease
has exact synonym: Kimmelstiel-Wilson Syndrome
has exact synonym: Nephropathies, Diabetic
has exact synonym: Nephropathy, Diabetic
has exact synonym: Nephrotic syndrome due to diabetes mellitus
has exact synonym: Nephrotic syndrome in diabetes mellitus
has exact synonym: Nephrotic syndrome in diabetes mellitus (disorder)
has exact synonym: Nodular Glomerulosclerosis
has exact synonym: Renal disorder associated with diabetes mellitus
has exact synonym: Syndrome, Kimmelstiel-Wilson
has exact synonym: diabetic kidney disease
has exact synonym: diabetic nephropathy
has_narrow_synonym: type 1 diabetes nephropathy
has_narrow_synonym: type 2 diabetes nephropathy
id: EFO:0000401

genotype
type: Class
subclass of: genomic measurement
definition: The total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: efo.owl
database cross reference: MO:51
database cross reference: MeSH:D005838
database cross reference: NCIt:C16631
database cross reference: NIFSTD:birnlex_2023
comment: Information, making the distinction between the actual physical material (e.g. a cell) and the information about the genetic content (genotype).

survival time
type: Class
subclass of: measurement
definition: Time of survival is an information entity which is about the length of time a material entity has survived after some adverse event, such as infection from a disease.
definition editor: James Malone
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D013534
database cross reference: NCIt:C17177
database cross reference: PERSON: James Malone
database cross reference: SNOMEDCT:445320007
has exact synonym: survival
has exact synonym: time of survival

pulmonary arterial hypertension
type: Class
subclass of: hypertension
definition: A syndrome with pathological changes in the pulmonary arteries and impaired PULMONARY CIRCULATION that can be the result of PULMONARY HYPERTENSION. Ayerza syndrome is characterized by slowly developing ASTHMA; BRONCHITIS; DYSPNEA; and CYANOSIS in association with POLYCYTHEMIA.
definition: Increased VASCULAR RESISTANCE in the PULMONARY CIRCULATION, usually secondary to HEART DISEASES or LUNG DISEASES.
definition: Pulmonary arterial hypertension (PAH) is a group of diseases characterized by mean pulmonary artery pressure >20 mmHg and elevated pulmonary arterial resistance leading to right heart failure. PAH is progressive and potentially fatal. PAH may be idiopathic and/ or familial, have overt features of venous/capillary involvement (pulmonary veno-occlusive disease, PVOD/pulmonary capillary hemangiomatosis, PCH), induced by drug or toxin (drug-or toxin-induced PAH), or associated with other diseases like congenital heart disease, connective tissue disease, HIV, schistosomiasis, portal hypertension (PAH associated with other disease).
definition editor: James Malone
term tracker item: https://github.com/monarch-initiative/mondo/issues/5537
term tracker item: https://github.com/monarch-initiative/mondo/issues/5781
imported from: efo.owl
close match: http://identifiers.org/meddra/10064911
exact match: http://identifiers.org/mesh/D000081029
exact match: http://identifiers.org/snomedct/11399002
exact match: http://linkedlifedata.com/resource/umls/id/C2973725
exact match: Orphanet_182090
gwas trait: true
database cross reference: DOID:6432
database cross reference: GARD:7501
database cross reference: MESH:D000081029
database cross reference: MONDO:0015924
database cross reference: MeSH:D006976
database cross reference: MedDRA:10064911
database cross reference: NCIt:C3120
database cross reference: NORD:1634
database cross reference: OMIM:615371
database cross reference: Orphanet:182090
database cross reference: SCTID:11399002
database cross reference: SNOMEDCT:70995007
database cross reference: UMLS:C2973725
has exact synonym: Ayerza Arrilaga Syndrome
has exact synonym: Ayerza Syndrome
has exact synonym: Ayerza's Syndrome
has exact synonym: Ayerza-Arrilaga Syndrome
has exact synonym: Ayerzas Syndrome
has exact synonym: HYPERTENSION PULM
has exact synonym: Hypertension, Pulmonary
has exact synonym: PAH
has exact synonym: PHT - Pulmonary hypertension
has exact synonym: PPH1
has exact synonym: PULM HYPERTENSION
has exact synonym: Pulmonary hypertension, NOS
has exact synonym: Syndrome, Ayerza
has exact synonym: Syndrome, Ayerza-Arrilaga
has exact synonym: pulmonary arterial hypertension
has exact synonym: pulmonary hypertension
has exact synonym: pulmonary hypertension (disorder)
has exact synonym: pulmonary hypertension, primary, 1
has_narrow_synonym: PAH with overt features of venous/capillaries involvement
has_narrow_synonym: PVOD/PCH
has_related_synonym: PPH
has_related_synonym: idiopathic pulmonary hypertension
id: EFO:0001361
in subset: disease grouping
in subset: gard rare
in subset: nord rare
in subset: ordo group of disorders
in subset: orphanet rare
in subset: rare

cross sectional design
type: Class
subclass of: clinical trial
fromOldVersion: yes
definition: A study in which participants are examined at only a single time for characteristics of a disease.
definition editor: James Malone
definition editor: Natalja Kurbatova
definition editor: Tomasz Adamusiak
imported from: efo.owl
database cross reference: NCIt:C53310
has exact synonym: Cross-Sectional Study

measurement
type: Class
subclass of: information content entity
definition: A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
definition editor: James Malone
definition editor: Jie Zheng
definition editor: Tomasz Adamusiak
imported from: efo.owl
branch class: true
database cross reference: MO:144
database cross reference: NCIt:C25209
database cross reference: NIFSTD:sao279801585
database cross reference: SNOMEDCT:122869004

pancreatic carcinoma
type: Class
subclass of: cancer
definition: A carcinoma that arises from epithelial cells of the exocrine pancreas
imported from: efo.owl
exact match: http://identifiers.org/snomedct/372142002
exact match: http://linkedlifedata.com/resource/umls/id/C0235974
exact match: DOID 4905
exact match: NCIT C3850
conforms to: carcinoma.yaml
gwas trait: true
has_broad_synonym: cancer of pancreas
has_broad_synonym: cancer of the pancreas
has_broad_synonym: exocrine cancer
has_broad_synonym: pancreas cancer
has_broad_synonym: pancreatic cancer
database cross reference: DOID:4905
database cross reference: EFO:0002618
database cross reference: MONDO:0005192
database cross reference: NCIT:C3850
database cross reference: OMIM:260350
database cross reference: SCTID:372142002
database cross reference: UMLS:C0235974
has exact synonym: carcinoma of exocrine pancreas
has exact synonym: carcinoma of pancreas
has exact synonym: carcinoma of the pancreas
has exact synonym: exocrine pancreas carcinoma
has exact synonym: exocrine pancreatic carcinoma
has exact synonym: pancreas carcinoma
has exact synonym: pancreatic cancer (not islets)
has exact synonym: pancreatic carcinoma
has_related_synonym: pancreatic carcinoma, familial
id: EFO:0002618

postmenopausal
type: Class
subclass of: process
fromOldVersion: yes
definition editor: James Malone
imported from: efo.owl
database cross reference: NCIt:C15421

pregnancy
type: Class
subclass of: biological_process
definition: The state or condition of having a developing embryo or fetus in the body (uterus), after union of an ovum and spermatozoon, during the period from conception to birth.
definition: The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: ICD10:Z34
database cross reference: MeSH:D011247
database cross reference: MedDRA:10036556
database cross reference: NCIt:C25742
database cross reference: SNOMEDCT:289908002
has exact synonym: Gestation
has exact synonym: PREGN
has exact synonym: Pregnancies

hepatitis C virus infection
type: Class
subclass of: liver disease
definition: A Hepacivirus infectious disease and is_a viral hepatitis that results_in inflammation located_in liver, has_agent Hepatitis C virus, which is transmitted_by blood from an infected person enters the body of an uninfected person. The infection has_symptom fever, has_symptom fatigue, has_symptom loss of appetite, has_symptom nausea, has_symptom vomiting, has_symptom abdominal pain, has_symptom clay-colored bowel movements, has_symptom joint pain, and has_symptom jaundice.
definition: A Hepacivirus infectious disease which is a chronic bloodborne infectious disease caused by Hepatitis C virus. The symptoms include fever, fatigue, loss of appetite, nausea, vomiting, abdominal pain, clay-colored bowel movements, joint pain and jaundice.
definition: A viral hepatitis and is_a Hepacivirus infectious disease, that results_in inflammation located_in liver, has_agent Hepatitis C virus, which is transmitted_by blood from an infected person enters the body of an uninfected person. The infection has_symptom fever, has_symptom fatigue, has_symptom loss of appetite, has_symptom nausea, has_symptom vomiting, has_symptom abdominal pain, has_symptom clay-colored bowel movements, has_symptom joint pain, and has_symptom jaundice.
definition: A viral infection caused by the hepatitis C virus.
definition editor: Tomasz Adamusiak
imported from: efo.owl
exact match: D006526
exact match: http://identifiers.org/snomedct/128302006
exact match: http://linkedlifedata.com/resource/umls/id/C0019196
exact match: DOID 1883
exact match: NCIT C3098
excluded subClassOf: MONDO_0005093
gwas trait: true
database cross reference: DOID:1883
database cross reference: ICD9:070.41
database cross reference: ICD9:070.54
database cross reference: ICD9:070.7
database cross reference: MESH:D006526
database cross reference: MONDO:0005231
database cross reference: NCIT:C3098
database cross reference: NCIt:C3098
database cross reference: SCTID:128302006
database cross reference: SNOMEDCT:50711007
database cross reference: UMLS:C0019196
has exact synonym: HCV infection
has exact synonym: Hepatitis C (disorder)
has exact synonym: Hepatitis C virus caused hepatitis
has exact synonym: Hepatitis C virus hepatitis
has exact synonym: Hepatitis non-A non-B (disorder)
has exact synonym: NANBH
has exact synonym: Viral hepatitis C
has exact synonym: Viral hepatitis C (disorder)
has exact synonym: acute hepatitis C with hepatic coma
has exact synonym: hepatitis C
has exact synonym: hepatitis C infection
has exact synonym: hepatitis C virus infection
has exact synonym: hepatitis Nona nonB
has exact synonym: hepatitis nonA nonB
has exact synonym: hepatitis type C
has exact synonym: non-A, non-B Hepatitis
has exact synonym: viral hepatitis C
has_narrow_synonym: chronic hepatitis C
id: EFO:0003047

heart failure
type: Class
subclass of: heart disease
definition: Inability of the heart to pump blood at an adequate rate to meet tissue metabolic requirements. Clinical symptoms of heart failure include: unusual dyspnea on light exertion, recurrent dyspnea occurring in the supine position, fluid retention or rales, jugular venous distension, pulmonary edema on physical exam, or pulmonary edema on chest x-ray presumed to be cardiac dysfunction.
definition editor: Catherine Leroy
definition editor: Tomasz Adamusiak
imported from: efo.owl
exact match: D006333
exact match: http://identifiers.org/snomedct/84114007
exact match: http://linkedlifedata.com/resource/umls/id/C0018801
exact match: NCIT C50577
gwas trait: true
database cross reference: ICD10:I50
database cross reference: ICD9:428
database cross reference: ICD9:428.9
database cross reference: MESH:D006333
database cross reference: MONDO:0005252
database cross reference: MeSH:D006333
database cross reference: MedDRA:10007554
database cross reference: MedDRA:10007564
database cross reference: MedDRA:10019279
database cross reference: MedDRA:10019284
database cross reference: MedDRA:10019285
database cross reference: NCIT:C50577
database cross reference: NCIt:C50577
database cross reference: SCTID:84114007
database cross reference: SNOMEDCT:84114007
database cross reference: UMLS:C0018801
has exact synonym: Heart failure (disorder)
has exact synonym: Heart failure NOS
has exact synonym: Heart failure NOS (disorder)
has exact synonym: Heart failure, unspecified
has exact synonym: Heart: [weak] or [failure NOS]
has exact synonym: Weak heart
has exact synonym: cardiac dysfunction
has exact synonym: cardiac failure
has exact synonym: cardiac insufficiency
has exact synonym: failure, heart
has exact synonym: heart failure
has exact synonym: insufficiency, Cardiac
id: EFO:0003144

tumor necrosis factor-alpha
type: Class
subclass of: cytokine
definition: Tumor necrosis factor (TNF, cachexin or cachectin formerly known as tumor necrosis factor-alpha or TNF-α) is a cytokine involved in systemic inflammation and is a member of a group of cytokines that stimulate the acute phase reaction. It is produced chiefly by activated macrophages, although it can be produced by other cell types as well.
definition editor: Ele Holloway
definition editor: James Malone
definition editor: Tomasz Adamusiak
imported from: efo.owl
definition_citation: http://en.wikipedia.org/wiki/Tumour_necrosis_factor-alpha
database cross reference: CASRN:308079-78-9
database cross reference: DSSTox_CID:40634
database cross reference: MeSH:D014409
database cross reference: OMIM:191160
has exact synonym: TNF-alpha; tumor necrosis factor
has exact synonym: TNF-α

vascular endothelial growth factor
type: Class
subclass of: protein
definition: Vascular endothelial growth factor (VEGF) is a signal protein produced by cells that stimulates vasculogenesis and angiogenesis. It is part of the system that restores the oxygen supply to tissues when blood circulation is inadequate. Serum concentration of VEGF is high in bronchial asthma and low in diabetes mellitus. VEGF's normal function is to create new blood vessels during embryonic development, new blood vessels after injury, muscle following exercise, and new vessels (collateral circulation) to bypass blocked vessels. When VEGF is overexpressed, it can contribute to disease. Solid cancers cannot grow beyond a limited size without an adequate blood supply; cancers that can express VEGF are able to grow and metastasize. Overexpression of VEGF can cause vascular disease in the retina of the eye and other parts of the body. Drugs such as bevacizumab can inhibit VEGF and control or slow those diseases. VEGF is a sub-family of growth factors, to be specific, the platelet-derived growth factor family of cystine-knot growth factors. They are important signaling proteins involved in both vasculogenesis (the de novo formation of the embryonic circulatory system) and angiogenesis (the growth of blood vessels from pre-existing vasculature).
definition editor: Ele Holloway
definition editor: James Malone
definition editor: Tomasz Adamusiak
imported from: efo.owl
definition_citation: http://en.wikipedia.org/wiki/Vascular_endothelial_growth_factor
database cross reference: CASRN:127464-60-2
database cross reference: DSSTox_Generic_SID:40639
database cross reference: OMIM:192240
database cross reference: SNOMEDCT:417324009
has exact synonym: VEGF

vitamin D deficiency
type: Class
subclass of: disease
definition: A nutritional condition produced by a deficiency of VITAMIN D in the diet, insufficient production of vitamin D in the skin, inadequate absorption of vitamin D from the diet, or abnormal conversion of vitamin D to its bioactive metabolites. It is manifested clinically as RICKETS in children and OSTEOMALACIA in adults. (From Cecil Textbook of Medicine, 19th ed, p1406)
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: ICD10:E55
database cross reference: ICD9:268
database cross reference: MeSH:D014808
database cross reference: MedDRA:10047626
database cross reference: NCIt:C114830
database cross reference: SNOMEDCT:34713006
has exact synonym: Avitaminosis D
has exact synonym: Avitaminosis D, NOS
has exact synonym: DEFIC VITAMIN D
has exact synonym: Deficiencies, Vitamin D
has exact synonym: Deficiency, Vitamin D
has exact synonym: VITAMIN D DEFIC
has exact synonym: Vitamin D Deficiencies
has exact synonym: Vitamin D deficiency (disorder)
has exact synonym: Vitamin D deficiency, NOS
has exact synonym: Vitamin D insufficiency

cytokine
type: Class
subclass of: protein
imported from: efo.owl
database cross reference: NCIt:C20464
database cross reference: SNOMEDCT:75777003

pulmonary function measurement
type: Class
subclass of: measurement
definition: Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc.
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D012129
database cross reference: NCIt:C38081
has exact synonym: FUNCTION TEST PULM
has exact synonym: FUNCTION TESTS PULM
has exact synonym: Function Test, Lung
has exact synonym: Function Test, Pulmonary
has exact synonym: Function Test, Respiratory
has exact synonym: Function Tests, Lung
has exact synonym: Function Tests, Pulmonary
has exact synonym: Function Tests, Respiratory
has exact synonym: Lung Function Test
has exact synonym: Lung Function Tests
has exact synonym: PULM FUNCTION TEST
has exact synonym: PULM FUNCTION TESTS
has exact synonym: Pulmonary Function Tests
has exact synonym: Respiratory Function Test
has exact synonym: Respiratory Function Tests
has exact synonym: TEST PULM FUNCTION
has exact synonym: TESTS PULM FUNCTION
has exact synonym: Test, Lung Function
has exact synonym: Test, Pulmonary Function
has exact synonym: Test, Respiratory Function
has exact synonym: Tests, Lung Function
has exact synonym: Tests, Pulmonary Function
has exact synonym: Tests, Respiratory Function
has exact synonym: pulmonary function test

risk factor
type: Class
subclass of: disposition
definition: An aspect of personal behavior or lifestyle, environmental exposure, or inborn or inherited characteristic, which, on the basis of epidemiologic evidence, is known to be associated with a health-related condition considered important to prevent.
definition: Any aspect of an individual's life, behavior, an environmental exposure, or an inborn or inherited characteristic that increases the likelihood of a disease, condition or injury.
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D012307
database cross reference: NCIt:C17103
database cross reference: SNOMEDCT:80943009
has exact synonym: Factor, Risk
has exact synonym: Factors, Risk
has exact synonym: Risk Factors

bone density
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The amount of mineral per square centimeter of BONE. This is the definition used in clinical practice. Actual bone density would be expressed in grams per milliliter. It is most frequently measured by X-RAY ABSORPTIOMETRY or TOMOGRAPHY, X RAY COMPUTED. Bone density is an important predictor for OSTEOPOROSIS.
definition editor: Tomasz Adamusiak
imported from: efo.owl
gwas trait: true
database cross reference: ICD10:M85
database cross reference: MeSH:D015519
database cross reference: NCIt:C96950
has exact synonym: BMD
has exact synonym: Bone Densities
has exact synonym: Bone Mineral Densities
has exact synonym: Bone Mineral Density
has exact synonym: Density, Bone
has exact synonym: Density, Bone Mineral
has exact synonym: aBMD
has exact synonym: areal bone mineral density

interleukin
type: Class
subclass of: cytokine
definition: An interleukin is a multifunctional cytokine produced by leukocytes for regulating immune responses.
definition editor: James Malone
imported from: efo.owl
database cross reference: NCIt:C20497
database cross reference: SNOMEDCT:38476002

tumor size
type: Class
subclass of: metric
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: The physical size of a tumor.
definition editor: James Malone
imported from: efo.owl
database cross reference: NCIt:C120284
database cross reference: SNOMEDCT:263605001
has exact synonym: size of tumor

hepatitis B virus infection
type: Class
subclass of: liver disease
definition: A viral infection caused by the hepatitis B virus.
definition: INFLAMMATION of the LIVER in humans caused by a member of the ORTHOHEPADNAVIRUS genus, HEPATITIS B VIRUS. It is primarily transmitted by parenteral exposure, such as transfusion of contaminated blood or blood products, but can also be transmitted via sexual or intimate personal contact.
definition editor: Dani Welter
imported from: efo.owl
exact match: D006509
exact match: http://identifiers.org/snomedct/66071002
exact match: http://linkedlifedata.com/resource/umls/id/C0019163
exact match: DOID 2043
exact match: NCIT C3097
excluded subClassOf: MONDO_0005093
gwas trait: true
database cross reference: DOID:2043
database cross reference: ICD10:B16
database cross reference: ICD9:070.30
database cross reference: MESH:D006509
database cross reference: MONDO:0005344
database cross reference: MeSH:D019694
database cross reference: NCIT:C3097
database cross reference: NCIt:C3097
database cross reference: SCTID:66071002
database cross reference: UMLS:C0019163
has exact synonym: HBV infection
has exact synonym: Hepatitis B
has exact synonym: Hepatitis B infection
has exact synonym: Hepatitis B virus caused hepatitis
has exact synonym: Hepatitis B virus hepatitis
has exact synonym: hepatitis B infection
has exact synonym: hepatitis B virus infection
has exact synonym: hepatitis B, chronic
has exact synonym: hepatitis type B
has exact synonym: viral Hepatitis B
has exact synonym: viral hepatitis B
has_narrow_synonym: chronic hepatitis B
has_related_synonym: serum hepatitis
id: EFO:0004197

nephrotic syndrome
type: Class
subclass of: kidney disease
definition: A collection of symptoms that include severe edema, proteinuria, and hypoalbuminemia; it is indicative of renal dysfunction.
definition: A condition characterized by severe PROTEINURIA, greater than 3.5 g/day in an average adult. The substantial loss of protein in the urine results in complications such as HYPOPROTEINEMIA; generalized EDEMA; HYPERTENSION; and HYPERLIPIDEMIAS. Diseases associated with nephrotic syndrome generally cause chronic kidney dysfunction.
definition editor: Dani Welter
imported from: efo.owl
exact match: D009404
exact match: http://identifiers.org/snomedct/52254009
exact match: http://linkedlifedata.com/resource/umls/id/C0027726
exact match: DOID 1184
exact match: NCIT C34845
narrow match: Orphanet_564127
gwas trait: true
database cross reference: DOID:1184
database cross reference: ICD10:N04
database cross reference: ICD9:581
database cross reference: ICD9:581.9
database cross reference: MESH:D009404
database cross reference: MONDO:0005377
database cross reference: MeSH:D009404
database cross reference: MedDRA:10029164
database cross reference: NCIT:C34845
database cross reference: NCIt:C34845
database cross reference: OMIM:615861
database cross reference: OMIM:617783
database cross reference: OMIM:618176
database cross reference: OMIM:618177
database cross reference: OMIM:618178
database cross reference: OMIM:618594
database cross reference: Orphanet:564127
database cross reference: SCTID:52254009
database cross reference: SNOMEDCT:52254009
database cross reference: UMLS:C0027726
has exact synonym: nephrotic syndrome
has exact synonym: nephrotic syndrome (acquired)
has exact synonym: nephrotic syndromes
has exact synonym: syndrome, nephrotic
has exact synonym: syndromes, nephrotic
has_related_synonym: nephrosis
id: EFO:0004255

albuminuria
type: Class
subclass of: phenotype
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: The presence of albumin in the urine, an indicator of KIDNEY DISEASES.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: HP:0012592
database cross reference: MeSH:D000419
database cross reference: MedDRA:10001580
database cross reference: SNOMEDCT:274769005
has exact synonym: urinary albumin excretion

venous thromboembolism
type: Class
subclass of: vascular disease
definition: Obstruction of a vein or VEINS (embolism) by a blood clot ( THROMBUS) in the blood stream.
definition: Occlusion of the lumen of a vein by a thrombus that has migrated from a distal site via the blood stream.
definition editor: Dani Welter
imported from: efo.owl
exact match: D054556
exact match: http://linkedlifedata.com/resource/umls/id/C1861172
exact match: NCIT C99537
gwas trait: true
database cross reference: ICD10:I74
database cross reference: ICD10:I82
database cross reference: MESH:D054556
database cross reference: MONDO:0005399
database cross reference: MeSH:D054556
database cross reference: MedDRA:10066899
database cross reference: NCIT:C99537
database cross reference: NCIt:C99537
database cross reference: UMLS:C1861172
has exact synonym: VTE
has exact synonym: venous thromboembolism
id: EFO:0004286

vital capacity
type: Class
subclass of: pulmonary function measurement
definition: The volume of air that is exhaled by a maximal expiration following a maximal inspiration.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D014797
database cross reference: MedDRA:10047579
database cross reference: NCIt:C111361
database cross reference: SNOMEDCT:268379003
has exact synonym: FVC
has exact synonym: forced vital capacity

maximal midexpiratory flow rate
type: Class
subclass of: pulmonary function measurement
definition: Measurement of rate of airflow over the middle half of a FORCED VITAL CAPACITYÂ determination (from the 25 percent level to the 75 percent level). Common abbreviations are MMFRÂ and FEF 25%-75%.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D008450
has exact synonym: FEF25-75%

forced expiratory volume
type: Class
subclass of: pulmonary function measurement
definition: Measure of the maximum amount of air that can be expelled in a given number of seconds during a FORCED VITAL CAPACITYÂ determination . It is usually given as FEVÂ followed by a subscript indicating the number of seconds over which the measurement is made, although it is sometimes given as a percentage of forced vital capacity.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D005541
database cross reference: MedDRA:10016984
database cross reference: NCIt:C120933
has exact synonym: FEV1
has exact synonym: FEVt
has exact synonym: timed vital capacity

blood pressure
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: PRESSURE of the BLOOD on the ARTERIES and other BLOOD VESSELS.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D001794
database cross reference: MedDRA:10005727
database cross reference: NCIt:C54706
database cross reference: SNOMEDCT:75367002

body weight
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D001835
database cross reference: NCIt:C81328
database cross reference: SNOMEDCT:27113001
has exact synonym: weight

waist circumference
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: The measurement around the body at the level of the ABDOMEN and just above the hip bone. The measurement is usually taken immediately after exhalation.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D055105
database cross reference: MedDRA:10074998
database cross reference: NCIt:C100948
database cross reference: SNOMEDCT:276361009

neuroimaging measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Non-invasive methods of visualizing and measuring the CENTRAL NERVOUS SYSTEM, especially the brain, by various imaging modalities e.g. CT scan
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
has exact synonym: brain imaging
comment: is about MeSH:D059906

mortality
type: Class
subclass of: measurement
fromOldVersion: yes
definition: Quantification of the number of deaths in a population.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D009026
database cross reference: MeSH:Q000401
database cross reference: NCIt:C16880
database cross reference: SNOMEDCT:409651001
has exact synonym: mortality measurement
has exact synonym: mortality rate

insulin sensitivity measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: An insulin sensitivity measurement is a measurement of insulin metabolism, which can be measured in a number of ways, for example using the HOMA model or via a glucose tolerance test.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: insulin sensitivity test
has_related_synonym: insulin sensitivity

HOMA-IR
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: The HOMA-IR measurement employs the homeostatic model assessment (HOMA) to quantify insulin resistance.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: homeostasis model assessment insulin resistance

telomere length
type: Class
subclass of: genomic measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A measurement of telomere length measures the number of TTAGGG repeats at the end of the chromosome. As cell division proceeds telomeres shorten, telomere length is measure of cellular aging.
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370421/
gwas trait: true

muscle measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A muscle mass measurement is the quantification of the mass of a muscle e.g. skeletal muscle for an individual.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: muscle mass
has exact synonym: muscle mass measurement

arterial stiffness measurement
type: Class
subclass of: metric
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
fromOldVersion: yes
definition: An Arterial stiffness measurement is the information output of a non invasive pulse wave velocity assay. Arterial stiffness is a predictor of cardiovascular mortality
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: arterial stiffness

genomic measurement
type: Class
subclass of: measurement
definition: Is a quantification of some aspect of the genome, e.g. copy number variation at some locus.
definition editor: Helen Parkinson
imported from: efo.owl

total cholesterol measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
definition: A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
database cross reference: SNOMEDCT:121868005
has exact synonym: cholesterol, total
has exact synonym: total cholesterol
has exact synonym: total cholesterol levels

interleukin 18 (Homo sapiens)
type: Class
subclass of: interleukin
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Interleukin-18 (IL18, also known as interferon-gamma inducing factor) is a protein which in humans is encoded by the IL18 gene.[1][2] The protein encoded by this gene is a proinflammatory cytokine.
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://en.wikipedia.org/wiki/Interleukin_18
definition_citation: http://www.uniprot.org/uniprot/Q14116
has exact synonym: IL-18
has exact synonym: interleukin 18

FEV/FVC ratio
type: Class
subclass of: pulmonary function measurement
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: Is the measurement of the ratio of forced expiratory volume (FEV) to forced vital capacity (FVC), used as a measure of pulmonary function.
gwas trait: true
has exact synonym: FEV/FEC ratio
has exact synonym: FEV/FVC
has exact synonym: FEV1/FVC

NT-proBNP measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
fromOldVersion: yes
definition: Is a quantification of NT-proBNP (N-terminal prohormone of brain natriuretic peptide) which is associated with acute congestive heart failure.
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://en.wikipedia.org/wiki/NT-proBNP
gwas trait: true
has exact synonym: N-Terminal Pro-B-Type Natriuretic Peptide
has exact synonym: NT-proBNP

copy number variation
type: Class
subclass of: genomic measurement
definition: A quantification of a genomic variation that increases or decreases the copy number of a given region.
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://purl.org/obo/owl/SO#SO_0001019

short sleep
type: Class
subclass of: sleep measurement
definition: Is a quantification of sleep time in humans where average sleep time was less than five hours.
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://www.ncbi.nlm.nih.gov/pubmed/22322875
gwas trait: true

genetic variation
type: Class
subclass of: genomic measurement
definition: The genetic variation of individuals in a population.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D014644
database cross reference: NCIt:C17248
database cross reference: SNOMEDCT:64195000

cortical thickness
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Is a quantification of the thickness of brain cortex, e.g. measured by MRI, used in the diagnosis of Alzheimer's disease and other neurological conditions
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: http://www.ncbi.nlm.nih.gov/pubmed/21810643
gwas trait: true

recombination rate
type: Class
subclass of: recombination measurement
definition: Is the genome wide recombination rate.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true

sleep measurement
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Is a quantification of some sleep parameter.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true

inflammatory biomarker measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Is a quantification of any molecule involved in the process of inflammatory response.
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: inflammatory marker measurement
has_related_synonym: inflammatory biomarker
comment: A container class for inflammatory biomarker measurements, populated by selecting all human proteins annotated with inflammatory response, or a child term, and including measurements of these proteins in this class. Only protein-GO term associations with a curated evidence code were considered, so IEA for e.g. were excluded.

maximal oxygen uptake measurement
type: Class
subclass of: pulmonary function measurement
definition: Is the quantification of is the maximum capacity of an individual's body to transport and use oxygen during incremental exercise, and is used as an indicator of physical fitness
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
has exact synonym: VO2 max
has exact synonym: maximal aerobic capacity
has exact synonym: maximal oxygen consumption
has exact synonym: maximal oxygen uptake
has exact synonym: peak oxygen uptake

disease recurrence
type: Class
subclass of: measurement
fromOldVersion: yes
definition: The recurrence of a disease after treatment
definition editor: Helen Parkinson
imported from: efo.owl
gwas trait: true
database cross reference: MedDRA:10061819
has exact synonym: relapse

somatic genotype
type: Class
subclass of: genotype
definition: The total sum of the genetic information of an organism's somatic cells
definition editor: Helen Parkinson
imported from: efo.owl

germline genotype
type: Class
subclass of: genotype
definition: The total sum of the genetic information of an organism's germline
definition editor: Helen Parkinson
imported from: efo.owl

microbiome
type: Class
subclass of: material entity
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: A collection or collectivity of microorganisms.
definition editor: Helen Parkinson
imported from: efo.owl
database cross reference: NCIt:C68564

hippocampal volume
type: Class
subclass of: metric
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isMonitoringBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isPredictiveBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Measurement of the volume of the hippocampus
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

wild type genotype
type: Class
subclass of: genotype
imported from: efo.owl

glomerular filtration rate
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
definition: measurement of the flow rate of filtered fluid through the kidney, calculated either by comparative measurements of substances in the blood and urine, or estimated from a blood test
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MeSH:D005919
database cross reference: MedDRA:10018355
database cross reference: NCIt:C90505
database cross reference: SNOMEDCT:80274001
has exact synonym: GFR

sleep duration
type: Class
subclass of: sleep measurement
definition: duration of sleep, measured either via a self-reporting questionnaire, interview or through obversation in a sleep lab
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

sleep quality
type: Class
subclass of: biological feature
definition: quantification of some aspect of sleep quality, such as number of awakenings during a sleep interval or time taken to get to sleep. Sleep quality can be evaluated either through self-reporting, observation in a sleep lab or using a sleep monitoring device
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: NCIt:C121705

sleep depth
type: Class
subclass of: sleep measurement
definition: self-reported assessment of how difficult an individual is to wake
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

sleep time
type: Class
subclass of: sleep measurement
definition: measurement of the time at which sleep begins
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

sleep latency
type: Class
subclass of: sleep measurement
definition: amount of time, usually recorded in minutes, between going to bed and falling asleep
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

ejection fraction measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isPrognosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
definition: quantification of the volumetric fraction of blood pumped out of the left and right ventricle with each heartbeat or cardiac cycle
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

white matter hyperintensity measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: quantification of white matter hyperintensity, usually measured by MRI
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
has exact synonym: white matter hyperintensity

oxygen saturation measurement
type: Class
subclass of: pulmonary function measurement
definition: quantification of the relative amount of oxygen that is dissolved or carried in a given medium
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: NCIt:C60832
database cross reference: SNOMEDCT:104847001

calcium metabolic disease
type: Class
subclass of: disease of metabolism
definition: Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization.
definition: Disorders of calcium metabolism occur when the body has too little or too much calcium. The serum level of calcium is closely regulated within a fairly limited range in the human body. In a healthy physiology, extracellular calcium levels are maintained within a tight range through the actions of parathyroid hormone, vitamin D and the calcium sensing receptor.[1] Disorders in calcium metabolism can lead to hypocalcemia, decreased plasma levels of calcium or hypercalcemia, elevated plasma calcium levels.
definition editor: Helen Parkinson
imported from: efo.owl
exact match: D002128
exact match: http://identifiers.org/snomedct/71638002
exact match: http://linkedlifedata.com/resource/umls/id/C0006705
exact match: DOID_10575
definition_citation: DOID:10575
definition_citation: http://en.wikipedia.org/wiki/Disorders_of_calcium_metabolism
gwas trait: true
database cross reference: DOID:10575
database cross reference: ICD9:275.4
database cross reference: ICD9:275.40
database cross reference: ICD9:275.49
database cross reference: ICD9CM:275.4
database cross reference: ICD9CM:275.40
database cross reference: MESH:D002128
database cross reference: MONDO:0005557
database cross reference: MeSH:D002128
database cross reference: SCTID:71638002
database cross reference: SNOMEDCT:190863003
database cross reference: SNOMEDCT:190874007
database cross reference: SNOMEDCT:267442002
database cross reference: SNOMEDCT:71638002
database cross reference: UMLS:C0006705
has exact synonym: Calcium Metabolism Disorders
has exact synonym: calcium metabolic disease
has exact synonym: calcium metabolic disorder
has exact synonym: calcium metabolism disease
has exact synonym: calcium metabolism disorder
has exact synonym: disorder of calcium metabolism
has_related_synonym: calcium metabolism disease
has_related_synonym: calcium metabolism disorder
id: EFO:0005769
comment: Consider relocating this as a sibling of metabolic disease.
comment: Defined in terms of GO calcium ion homeostatis. Also consistent with HPO. Note advice from GO as calcium ions are neither created or destroyed is not metabolic process in terms of go, but name retained for purposes of consistency with e.g. Snomed and Mesh
comment: Defined in terms of GO calcium ion homeostatis. Also consistent with HPO. Note advice from GO as calcium ions are neither created or destroyed is not metabolic process in terms of go, but name retained for purposes of consistency with e.g. Snomed and Mesh, Consider relocating this as a sibling of metabolic disease.

recombination measurement
type: Class
subclass of: genomic measurement
definition: quantification of any recombination-related factor, such as hotspot usage, African enchrichment and recombination rate
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

FEV change measurement
type: Class
subclass of: pulmonary function measurement
definition: quantification of the rate of change in FEV of an individual over the course of time, used as an indicator of improvement or decay of pulmonary function
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
has exact synonym: FEV1 change measurement

systolic blood pressure
type: Class
subclass of: blood pressure
definition: The blood pressure during the contraction of the left ventricle of the heart.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: MedDRA:10042955
database cross reference: NCIt:C25298
database cross reference: SNOMEDCT:271649006
has exact synonym: SYSBP
has exact synonym: systolic pressure

malignant
type: Class
subclass of: quality
definition: Refers to abnormal cell activity manifested by decreased control over growth and function, causing tumor growth or spread into surrounding tissue and adverse effects to the host
definition editor: Helen Parkinson
imported from: efo.owl
definition_citation: C14143
database cross reference: NCIt:C14143
database cross reference: SNOMEDCT:21594007

electrodermal activity measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isDigitalBiomarkerFor
  some values from: disease
definition: quantification of the change in the heat and electricity passed through the skin by nerves and sweat. Skin conduction increases in certain emotional states and during hot flashes that happen with menopause.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:25387706
has exact synonym: galvanic skin response measurement

fibrosis
type: Class
subclass of: neoplasm
definition: the formation of excess fibrous connective tissue in an organ or tissue in a reparative or reactive process. This can be a reactive, benign, or pathological state.
definition editor: Sirarat Sarntivijai
imported from: efo.owl
gwas trait: true
database cross reference: MedDRA:10016642
database cross reference: NCIt:C3044
database cross reference: Wikipedia:Fibrosis

airway responsiveness measurement
type: Class
subclass of: pulmonary function measurement
definition: quantification of airway responsiveness, calculated as the concentration of methacholine at which a greater than 20% decresase in FEV1 is achieved during a bronchial challenge test
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:25514360

airway wall thickness measurement
type: Class
subclass of: pulmonary function measurement
definition: Quantification of the thickness of the walls of different parts of the respiratory tract, calculated from cross-sectional CT images. This measure can be used as an indicator of airway obstruction severity in COPD.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:25517131

lipoprotein A measurement
type: Class
subclass of: measurement
definition: quantification of some lipoprotein A in a sample
definition editor: Dani Welter
imported from: efo.owl
definition_citation: PMID:25575512
gwas trait: true
has exact synonym: Lp(a) measurement

chromatid break measurement
type: Class
subclass of: genomic measurement
definition: Quantification of the level of DNA strand breaks in a cell, for example induced by an antineoplastic agent such a bleomycin. Chromatid breaks can be assessed under the microscope in dividing cells during metaphase.
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

seasonal gut microbiome measurement
type: Class
subclass of: gut microbiome measurement
definition: quantification of some aspect of the seasonal variation in the micrbiome of the gut
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

mosaic loss of chromosome Y measurement
type: Class
subclass of: genomic measurement
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

nighttime rest measurement
type: Class
subclass of: sleep measurement
definition: quantification of some aspect of nighttime rest such as duration or quality
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:27126917

daytime rest measurement
type: Class
subclass of: sleep measurement
definition: quantification of some aspect of daytime rest such as duration, frequency or quality
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:27126917

gut microbiome measurement
type: Class
subclass of: microbiome measurement
definition: quantification of some aspect of an individual's micrbiome of the gut
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
has_related_synonym: gut microbiome

excessive daytime sleepiness measurement
type: Class
subclass of: sleep measurement
definition: quantification of excessive daytime sleepiness such as how often it occurs and its severity
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

insomnia measurement
type: Class
subclass of: sleep measurement
definition: quantification of insomnia such as how often it occurs and its severity
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

microbiome measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: quantification of some aspect of an individual's microbiome
definition editor: Dani Welter
imported from: efo.owl

taxonomic microbiome measurement
type: Class
subclass of: microbiome measurement
definition: quantification of the taxonomic variation in a microbiome sample
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

functional microbiome measurement
type: Class
subclass of: microbiome measurement
definition: quantification of the functional variation in a microbiome
definition editor: Dani Welter
imported from: efo.owl

chronotype measurement
type: Class
subclass of: sleep measurement
definition: quantification of some aspect of chronotype such as ease of getting up in the morning
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true

snoring measurement
type: Class
subclass of: sleep measurement
definition: quantification of some aspect of snoring such as frequency or severity
definition editor: Dani Welter
imported from: efo.owl
gwas trait: true
database cross reference: PMID:28604731

amyloid deposition measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isDiagnosticBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
definition: quantification of some aspect of the deposition of amyloid proteins in an organ
definition editor: Dani Welter
imported from: efo.owl

maximal voluntary ventilation
type: Class
subclass of: pulmonary function measurement
definition: Qunatification of the maximum volume of air that an organism can breathe in and out during a specified period of time, often 1 minute.
definition editor: Annalisa Buniello
imported from: efo.owl
gwas trait: true
database cross reference: MedDRA:10026958
database cross reference: PMID:29095316

glucose metabolism measurement
type: Class
subclass of: measurement
subclass of: Restriction
  on property: isImagingBiomarkerFor
  some values from: disease
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Quantification of a glucose metabolic process.
definition editor: Annalisa Buniello
imported from: efo.owl
gwas trait: true
database cross reference: PMID:29130521

diffusing capacity of the lung for carbon monoxide
type: Class
subclass of: pulmonary function measurement
definition: A measurement of carbon monoxide (CO) transfer from inspired gas to pulmonary capillary blood. During the test, the subject inspires a gas containing CO and one or more tracer gases to allow determination of the gas exchanging capability of the lungs.
definition editor: Laura Harris
imported from: efo.owl
gwas trait: true
database cross reference: PMID:30049742
has exact synonym: carbon monoxide diffusing capacity
has exact synonym: pulmonary diffusing capacity
has exact synonym: transfer factor of the lung for carbon monoxide

metastasis
type: Class
subclass of: pathologic process
definition: The spread or migration of cancer cells from one part of the body (where they first appeared) to another. The secondary tumor contains cells that are like those in the original (primary) tumor. [ NCI ]
editor note: A tumor formed by cells that have spread is referred to as a "metastatic tumor" or a "metastasis", but, strictly speaking, “metastasis” refers to the process of cancer cell migration, not to the tumor mass itself.
imported from: efo.owl
database cross reference: MeSH:D009362
database cross reference: MedDRA:10062194
database cross reference: NCIt:C19151
has exact synonym: cancer metastasis
has exact synonym: neoplasm metastasis
has exact synonym: tumor cell migration
has exact synonym: tumor metastasis

metastatic neoplasm
type: Class
subclass of: neoplasm
definition: A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology.
imported from: efo.owl
exact match: NCIT C3261
database cross reference: ICDO:8000/6
database cross reference: MONDO:0024883
database cross reference: NCIT:C3261
has exact synonym: metastatic disease
has exact synonym: metastatic neoplasm
has exact synonym: metastatic tumor
id: EFO:0009709
comment: Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future.

peak expiratory flow
type: Class
subclass of: pulmonary function measurement
definition: The maximum rate of gas flow, beginning at the point of peak inspiratory capacity, that can be sustained during forced exhalation for a defined period of time.
definition: The maximum rate of gas flow, beginning at the point of peak inspiratory capacity, that can be sustained during forced exhalation for a defined period of time. This test is most often used in combination with other studies of lung function to diagnose and monitor obstructive and restrictive lung disease(s). [ NCI ]
definition editor: Maria Cerezo
imported from: efo.owl
gwas trait: true
database cross reference: NCIt:C41372
database cross reference: PMID:30804560
has exact synonym: PEF

chromosomal aberration frequency
type: Class
subclass of: genomic measurement
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: Frequency of chromosomal aberrations in human peripheral blood.
definition editor: Joannella Morales
imported from: efo.owl
gwas trait: true
database cross reference: PMID:30368896
has exact synonym: CA

chromosome-type aberration frequency
type: Class
subclass of: chromosomal aberration frequency
definition: Frequency of chromosome-type chromosomal aberrations in human peripheral blood (typically resulting in damage to both chromatids).
definition editor: Joannella Morales
imported from: efo.owl
gwas trait: true
database cross reference: PMID:30368896
has exact synonym: CSA

chromatid-type aberration frequency
type: Class
subclass of: chromosomal aberration frequency
definition: Frequency of chromatid-type chromosomal aberrations in human peripheral blood (typically resulting in damage to a single chromatid).
definition editor: Joannella Morales
imported from: efo.owl
gwas trait: true
database cross reference: PMID:30368896
has exact synonym: CTA

FVC change measurement
type: Class
subclass of: pulmonary function measurement
definition: Quantification of the rate of change in forced vital capacity of an individual over the course of time, used as an indicator of improvement or decay of pulmonary function.
definition editor: Laura Harris
imported from: efo.owl
gwas trait: true
database cross reference: PMID:31557306
has exact synonym: forced vital capacity change meaurement

vaginal microbiome measurement
type: Class
subclass of: microbiome measurement
definition: Quantification of some aspect of an individual's microbiome of the vagina.
definition editor: Aoife McMahon
imported from: efo.owl
gwas trait: true
database cross reference: PMID:32723796
has exact synonym: vaginal flora measurement
has exact synonym: vaginal microbiota measurement

aging
type: Class
subclass of: biological_process
definition: A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation.
imported from: efo.owl
creator: Zoe May Pendlington
date: 2024-03-08T09:27:59Z
database cross reference: SNOMED:248280005

DNA methylation
type: Class
subclass of: Epigenetic Process
subclass of: Restriction
  on property: isBiomarkerOfAging
  some values from: disease
definition: The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
imported from: efo.owl
creator: Zoe May Pendlington
date: 2024-04-12T13:21:16Z
database cross reference: MeSH:D019175
database cross reference: NCIt:C17961
database cross reference: Wikipedia:DNA_methylation

mosaic loss of chromosome X measurement
type: Class
subclass of: genomic measurement
definition: It is the most common clonal somatic alteration in leukocytes of female individuals.
imported from: efo.owl
creator: Zoe May Pendlington
date: 2024-08-14T09:43:25Z
has exact synonym: mLOX

skin microbiome measurement
type: Class
subclass of: microbiome measurement
definition: Quantification of some aspect of an individual's microbiome of the skin.
imported from: efo.owl
gwas trait: true
database cross reference: PMID:36261456
has exact synonym: skin microbiota measurement

oral microbiome measurement
type: Class
subclass of: microbiome measurement
definition: Quantification of some aspect of an individual's oral microbiome.
imported from: efo.owl
gwas trait: true
database cross reference: PMID:34875929
has exact synonym: oral microbiota measurement
has exact synonym: salivary microbiome measurement

wake after sleep onset
type: Class
subclass of: sleep measurement
definition: A measurement of the sum of durations of wakefulness episodes throughout the night, not including the wakefulness before sleep onset.
definition editor: Santhi Ramachandran
imported from: efo.owl
gwas trait: true
database cross reference: NCIt:C156554
has exact synonym: WASO

sleep efficiency
type: Class
subclass of: sleep measurement
definition: A relative measurement of the time spent asleep to the total time spent in bed.
definition editor: Santhi Ramachandran
imported from: efo.owl
gwas trait: true
database cross reference: NCIt:C156553

thyroid disease
type: Class
subclass of: disease
definition: A disease involving the thyroid gland.
definition: A thyroid disease is a medical condition impairing the function of the thyroid. Different thyroid diseases include Hashimoto's thyroiditis, hyperthyroidism and hypothyroidism. These diseases have a large range of symptoms and affect all ages.
definition editor: Sirarat Sarntivijai
imported from: efo.owl
exact match: D013959
exact match: http://identifiers.org/snomedct/14304000
exact match: http://linkedlifedata.com/resource/umls/id/C4317107
exact match: E00-E07
exact match: DOID 50
exact match: NCIT C26893
gwas trait: true
database cross reference: DOID:50
database cross reference: ICD10:E06
database cross reference: ICD10:E07
database cross reference: ICD10CM:E00-E07
database cross reference: ICD9:240-246.99
database cross reference: ICD9:246.8
database cross reference: ICD9:246.9
database cross reference: MESH:D013959
database cross reference: MONDO:0003240
database cross reference: MedDRA:10043778
database cross reference: MedDRA:10043785
database cross reference: NCIT:C26893
database cross reference: SCTID:14304000
database cross reference: UMLS:C4317107
database cross reference: Wikipedia:Thyroid_disease
has exact synonym: Thyroiditis
has exact synonym: disease of thyroid gland
has exact synonym: disease or disorder of thyroid gland
has exact synonym: disorder of thyroid gland
has exact synonym: thyroid disease
has exact synonym: thyroid gland disease
has exact synonym: thyroid gland disease or disorder
has exact synonym: thyroid gland diseases
has exact synonym: thyroid gland disorder
has exact synonym: thyroid gland disorders
id: EFO:1000627

endothelial dysfunction
type: Class
subclass of: cardiovascular system disease
fromOldVersion: yes
definition: In vascular diseases, endothelial dysfunction is a systemic pathological state of the endothelium (the inner lining of blood vessels) and can be broadly defined as an imbalance between vasodilating and vasoconstricting substances produced by (or acting on) the endothelium. Normal functions of endothelial cells include mediation of coagulation, platelet adhesion, immune function and control of volume and electrolyte content of the intravascular and extravascular spaces.
definition editor: Gautier Koscielny
imported from: efo.owl
database cross reference: MedDRA:10048554
database cross reference: Wikipedia:Endothelial_dysfunction