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).
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.
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]
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]
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]
The original source of imported information. [PAV]
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.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred label
editor preferred term
editor preferred term~editor preferred label
编辑首选术语
编辑首选标签
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
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）
PERSON:Daniel Schober
example of usage
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.
has curation status
有管理状态
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
textual definition
定义
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.
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.
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。
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
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。
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.
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。
文本定义
editor note
编者注
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.
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。
uberon
editor_note
编辑_注释
definition editor
term editor
术语编辑者
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
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
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
20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
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。
alternative label
alternative term
替代术语
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.
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
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）
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).
definition source
定义来源
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
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
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
论OBO-讨论邮件-列表，请参阅http://bit.ly/hgm99w
has obsolescence reason
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.
curator note
An administrative note of use for a curator but of no use for a user
term tracker item
the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/
An IRI or similar locator for a request or discussion of an ontology term.
Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg
The 'tracker item' can associate a tracker with a specific ontology term.
imported from
For external terms/classes, the ontology from which the term was imported
OBO foundry unique label
An alternative name for a class or property which is unique across the OBO Foundry.
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 .
PERSON:Bjoern Peters
PERSON:Chris Mungall
GROUP:OBO Foundry <http://obofoundry.org/>
elucidation
has associated axiom(nl)
has associated axiom(fol)
has axiom label
term replaced by
Use on obsolete terms, relating the term to another term that can be used as a substitute
Person:Alan Ruttenberg
Cooper Stansbury
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.
RUBRIC
An association that indicates that a finding or lab test is related to a gene, possibly through a variant or product.
An association that specifies one of three data types for a particular variable, String, Code or Number.
An association that indicates a PCDC AML concept is a Authorized Value for a PCDC AML Variable concept.
An association that indicates a PCDC EWS concept is a Authorized Value for a specific PCDC EWS Variable concept.
An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept.
An association that connects a concept representing a GDC property to its dedicated value concept(s).
An association that that connects a concept representing a GDC value to any associated GDC property concept(s).
An association that indicates a concept is a dedicated Authorized Value concept for a specific PCDC GCT Variable.
An association that indicates a concept is a dedicated Permissible Value concept for a specific PCDC GCT Variable.
An association that shows which Permissible Values are possible for a specific PCDC GCT Variable.
An association that indicates a PCDC ALL concept is a Authorized Value for a PCDC ALL Variable concept.
An association that shows which Permissible Values are possible for a specific SeroNet Variable.
An association that shows which Authorized Values are possible for a specific PCDC OS Variable.
An association that shows which Permissible Values are possible for a specific PCDC OS Variable.
An association that shows which Authorized Values are possible for a specific PCDC HL Variable.
An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable.
An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute.
A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus.
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.
The semantic type describes the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
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.
A property representing an alternative Preferred Name for use in some NCI systems.
Provides an alternative Preferred Name for use in some NCI systems.
A property representing the word or phrase that NCI uses by preference to refer to the concept.
The word or phrase that NCI uses by preference to refer to the concept.
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.
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).
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.
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.
A property representing the English language definition of a concept from a source other than NCI.
A property representing the accession number for an miRNA within the Sanger miRBase database.
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.
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.
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.
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.
ISA alternative term
An alternative term used by the ISA tools project (http://isa-tools.org).
Requested by Alejandra Gonzalez-Beltran https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
ISA tools project (http://isa-tools.org)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
the symbol assigned by the nomenclature authority
symbol from nomenclature authority
the full name assigned by the nomenclature authority
full name from nomenclature authority
NCBI GeneID
NCBI LocusTag
gene map location
modification date
The NCBITaxon ontology ID of an organism.
organism NCBITaxon ID
A chromosome ID where a gene is located.
chromosome ID of gene
an annotation property that specifies the type of a gene
type of gene
an annotation property that specifies a nomenclature status
nomenclature status
an annotation property that shows the GO information associated with a specific gene.
has GO association
An annotation property that represents a gene's association with PubMed publication(s).
has PubMed association
tooth SubClassOf 'never in taxon' value 'Aves'
S never_in_taxon T iff: S SubClassOf in_taxon only not T.
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.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)
Class: ?X DisjointWith: RO_0002162 some ?Y
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 . }
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.
Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: (BFO_0000050 some ?X) and (BFO_0000050 some ?Y)
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 . }
mutually spatially disjoint with
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
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) }
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.
present in taxon
'anterior end of organism' is-opposite-of 'posterior end of organism'
'increase in temperature' is-opposite-of 'decrease in temperature'
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).
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.
metadata complete - requires restrictions and relationships
An assertion of whether or not the term/class description is an adaptation of the description in the description source.
Requested inclusion of this property into RO. Check details here again after inclusion.
Description inherent in name (not provided by source)
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.
Used to record the identifier that had been used previously but is no longer in use.
an alternative term used for STATO statistical ontology and ISA team
Alejandra Gonzalez-Beltran
Philippe Rocca-Serra
STATO alternative term
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.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
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'.
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
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
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.
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.
An entity primarily responsible for making the content of the resource.
Creator
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.
An account of the content of the resource.
Description
identifier_dc
identifier
A related resource from which the described class/term's annotations are derived.
For use in the EMBL-EBI ArrayExpress interface.
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.
An alternative label for a class or property which has a more general meaning than the preferred name/primary label.
has broad synonym
A database cross-reference. An annotation which directs one to information contained within a database.
A property representing a reference to an identical or very similar object in another database.
Reference database or publication source.
database cross reference
database_cross_reference
has database cross reference
数据库_交叉_引用
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.
An alias in which the alias exhibits true synonymy. Example: ornithine cycle is an exact synonym of urea cycle.
An alternative label for a class or property which has the exact same meaning than the preferred name/primary label.
An alternative label for a given entity such as a commonly used abbreviation or synonym.
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.
has exact synonym
An alternative label for a class or property which has a more specific meaning than the preferred name/primary label.
has narrow synonym
has_obo_namespace
有_obo_命名空间
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.
has related synonym
has synonym
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.
An association that connects the concept defining a particular terminology subset with concepts that belong to this subset.
shorthand
comment
label
A human-readable name for the class/term.
A human-readable name for the subject.
see_also_rdf_schema
see also
A note about a modification to a concept.
A statement or formal explanation of the meaning of a concept.
A skos concept mapping used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably.
This property may be used directly, or as a super-property for more specific note types.
The preferred lexical label for a resource, in a given language.
A note that helps to clarify the meaning and/or the use of a concept.
alternate name
isBiomarkerOfAging
A procedure is plan containing multiple activities that are intended to be executed in an order following a procedure specification. [Allotrope]
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.
A protein that is phosphorylated through post-translational modification. Its accumulation reflects the formation of neurofibrillary tangles, synaptic impairment, and neuronal dysfunction.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
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
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
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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
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
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])
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])
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])
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])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
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
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.
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.
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.
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])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
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])
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])
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])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(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]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
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.
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])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
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
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])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
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])
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)
(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]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
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.
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])
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])
(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]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(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]
(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]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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])
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])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(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]
quality
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
of one-sided specifically dependent continuants: the mass of this tomato
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.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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])
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.
(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]
specifically dependent continuant
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.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
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])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
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
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
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])
(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]
fiat object part
an edge of a cube-shaped portion of space.
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])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a collection of cells in a blood biobank.
a swarm of bees is an aggregate of members who are linked together through natural bonds
a symphony orchestra
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)
defined by fiat: the aggregate of members of an organization
defined through physical attachment: the aggregate of atoms in a lump of granite
defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container
defined via attributive delimitations such as: the patients in this hospital
the aggregate of bearings in a constant velocity axle joint
the aggregate of blood cells in your body
the nitrogen atoms in the atmosphere
the restaurants in Palo Alto
your collection of Meissen ceramic plates.
An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects
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).
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.
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])
(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]
object aggregate
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
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])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
atom
cell
cells and organisms
engineered artifacts
grain of sand
molecule
organelle
organism
planet
solid portions of matter
star
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.
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).
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
BFO 2 Reference: an object is a maximal causally unified material entity
BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74
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])
object
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.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
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.
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])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the boundary between the 2nd and 3rd year of your life.
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])
Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])
(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002]
(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001]
process boundary
the temporal region during which a process occurs.
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).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
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
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.
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.
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])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(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]
(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]
material entity
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])
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.
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
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.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(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]
continuant fiat boundary
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
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
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])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
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
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.
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.
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])
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])
(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]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
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])
(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]
relational quality
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])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
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.
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])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
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])
history
A biomarker of genomic variation in which blocks of DNA are missing or for which multiple copies exist.
A biomarker to discriminate between healthy individuals and those in an early stage of the disease.
A biomarker that is essential to the efficacy and safety of a corresponding therapeutic product.
A biomarker that reports interaction of the drug with its target
A biomarker that distinguishes between different stages of chronic disease.
A biomarker that predicts a beneficial effect of a given treatment.
A biomarker that reports to the toxic effect of a drug on an in vitro or in vivo system.
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.
generated with ChatGPT version 3,5 on 07.05.2024
COX proportional hazards regression model
The context of use is a concise description of a biomarker's specified use in drug developement.
Validation is a process to establish that the performance of a test, tool, or instrument is acceptable for its intended purpose.
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.
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.
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.
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.
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
A biomarker regulatory entity refers to a regulatory organization responsible for qualification and acceptance of biomarkers for futrher use in pharmaceutical research and development.
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.
The Japanese Pharmaceuticals and Medical Device Agency
Japan’s Pharmaceuticals and Medical Devices Agency
Biomarkers that represent acute and chronic pain, predisposition to develop chronic pain and , and pain chronification, recovery and treatment outcomes.
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)).
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.
Qualification of Medical Device Development Tools Guidance for Industry, Tool Developers, and Food and Drug Administration Staff
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.
Qualification Process for Drug Development Tools Guidance for Industry and FDA Staff
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.
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.
Pharmacogenetic Tests and Genetic Tests for Heritable Markers Guidance for Industry and FDA Staff
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.
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.
Urinary total protein (UTP) includes all proteins in urine samples. The presence of some quantities of proteins (<150 mg/day) is considered normal.
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.
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.
generated with ChatGPT version 3,5 on 02.04.2024
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.
generated with ChatGPT version 4,0 on 22․05․24
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.
Qualification is the evidentiary process of linking a biomarker with biological processes and clinical end points.
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.
Systolic function refers to the heart's ability to throw out a specific amount of blood in a certain amount of time.
A biomarker that measures epigenetic alterations, such as DNA methylation, histone methylation, histone acetylation, microRNAs, or other non-coding RNA.
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.
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.
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.
Biomarker repurposing, the novel application of existing biomarkers for other purposes.
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.
This class is used for grouping terms and should not be used for logical reasoning.
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.
A placeholder for diagnostic biomarkers, organized based on the reasoning application 'isDiagnosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
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.
A placeholder for monitoring biomarkers, organized based on the reasoning application 'isMonitoringBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
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.
A placeholder for prognostic biomarkers, organized based on the reasoning application 'isPrognosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
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.
A placeholder for predictive biomarkers, organized based on the reasoning application 'isPredictiveBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
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.
Digital biomarkers are objective, quantifiable, physiological, and behavioral measures that are collected by means of digital devices that are portable, wearable, implantable, or digestible.
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.
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.
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.
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).
Augmentation index is a measure of systemic arterial stiffness derived from the ascending aortic pressure waveform.
Arterial compliance is a change in dimension in response to a given change in stress.
The stiffness index (SI) derived from the analysis of digital volume pulse (DVP) is a noninvasive indirect technique of measuring arterial stiffness peripherally.
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.
generated with ChatGPT version 4,0 on 22.05.2024
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.
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.
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.
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.
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.
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).
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.
A placeholder for digital biomarkers, organized based on the reasoning application 'isDigitalBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
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.
A placeholder for imaging biomarkers, organized based on the reasoning application 'isImagingBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases.
The rate at which the heart rate returns to baseline after physical activity, indicative of cardiovascular fitness and recovery capacity.
generated with ChatGPT version 3,5 on 03.05.2024
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.
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.
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.
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.
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 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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Leukocyte telomere length (LTL) is a complex genetic trait. It shortens with age and is associated with a host of aging-related disorders.
leukocyte telomere length
Mitochondrial function refers to the various vital processes performed by mitochondria, which are the energy-producing organelles in cells.
generated with ChatGPT version 4,0 on 19․08․24
mitochondrial function
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.
A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group.
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.
A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine.
An aldohexose used as a source of energy and metabolic intermediate.
An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5..
Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids.
A L-arginine derivative having two methyl groups both attached to the primary amino moiety of the guanidino group.
(2S)-2-amino-5-(N',N'-dimethylcarbamimidamido)pentanoic acid
(2S)-2-amino-5-{[(dimethylamino)(imino)methyl]amino}pentanoic acid
'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.
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17.
A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances.
A role played by the molecular entity or part thereof within a biological context.
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.
An oxopurine that is the final oxidation product of purine metabolism.
A heteroglycan consisting of a mannan backbone with galactose side groups.
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).
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.
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.
hydroxymethylglutaryl-CoA reductase inhibitor
hydroxymethylglutaryl-CoA reductase inhibitors
EC 1.1.1.34/EC 1.1.1.88 (hydroxymethylglutaryl-CoA reductase) inhibitor
Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL).
Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL).
Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc.
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.
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).
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.
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.
The study of the interaction of a sample with radiation or particles for measurement or detection.
Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance.
A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one).
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
A leukocyte with abundant granules in the cytoplasm.
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.
Editors note: consider adding taxon constraint to vertebrata (PMID:18025161)
Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells.
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.
An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue.
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.
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.
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.
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).
Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time.
The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity.
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.
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.
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
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.
clinical trial
A disease that involving errors in metabolic processes of building or degradation of molecules.
metabolic disease
An intestinal disease characterized by inflammation located in all parts of digestive tract.
Xref MGI. OMIM mapping confirmed by DO. [SN].
An artery disease that is characterized by build up of plaque in the arteries that carry blood to your head, organs, and limbs.
A vascular disease caused by the formation of a blood clot inside a blood vessel, obstructing the flow of blood through the circulatory system.
thrombosis
A male reproductive organ cancer that is located_in the prostate.
NGP - new growth of prostate
hereditary prostate cancer
malignant tumor of the prostate
prostate cancer, familial
prostate neoplasm
prostatic cancer
prostatic neoplasm
tumor of the prostate
A stomach cancer that is located_in the gastric fundus.
Ca fundus - stomach
malignant neoplasm of fundus of stomach
malignant tumor of fundus of stomach
A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy.
gestational hypertension
hypertension induced by pregnancy
pre-eclamptic toxaemia
preeclampsia
preeclampsia/eclampsia
pregnancy associated hypertension
pregnancy toxemia
proteinuric hypertension of pregnancy
toxaemia of pregnancy
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.
celiac sprue
coeliac disease
idiopathic steatorrhea
An artery disease characterized by chronic elevated blood pressure in the arteries.
HTN
hyperpiesia
vascular hypertensive disorder
hypertensive disease
A cardiovascular system disease that involves the heart.
An ovarian dysfunction that is characterized by hyperandrogenism, polycystic ovaries, hirsutism, oligomenorrhea or amenorrhea, anovulation and excessive body weight.
Multicystic ovaries
PCOS
Polycystic Ovarian disease
Polycystic ovaries
Stein-Leventhal synd.
Stein-Leventhal syndrome
polycystic ovary
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.
Huntington disease
Huntington's chorea
A disease of anatomical entity which occurs in the blood, heart, blood vessels or the lymphatic system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells or lymph to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis.
disease of subdivision of hemolymphoid system
A respiratory system cancer that is located_in the lung.
lung neoplasm
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.
Alpha-galactosidase A deficiency
Angiokeratoma Corporis Diffusum
Fabry's disease
alpha galactosidase deficiency
deficiency of melibiase
A musculoskeletal system disease that involves inflammation or pain in the muscles, joints, or fibrous tissue.
A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm.
A thoracic cancer that originates in the mammary gland.
breast tumor
malignant neoplasm of breast
malignant tumor of the breast
mammary cancer
mammary tumor
primary breast cancer
mammary neoplasm
A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis.
malignant neoplasm
malignant tumor
primary cancer
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.
vascular tissue disease
disorder of iron metabolism
iron disorder
iron metabolism disease
A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells.
anaemia
A female reproductive organ cancer that is located_in the ovary.
malignant Ovarian tumor
malignant tumour of ovary
ovarian neoplasm
ovary neoplasm
primary ovarian cancer
tumor of the Ovary
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.
Exercise induced asthma
bronchial hyperreactivity
chronic obstructive asthma
chronic obstructive asthma with acute exacerbation
chronic obstructive asthma with status asthmaticus
exercise-induced asthma
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.
ILD
A mood disorder that involves alternating periods of mania and depression.
Manic Bipolar Affective disorder
Manic Depressive disorder
Manic bipolar I disorder
bipolar depression
bipolar disorder manic phase
manic depression
manic disorder
mixed bipolar disorder
Depressive-manic psych.
A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth.
disease of supporting structures of teeth
periodontium disorder
An integumentary system disease that is located_in skin.
Genodermatosis
skin and subcutaneous tissue disease
A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma.
NSCLC
Non-small cell lung cancer
non-small cell lung carcinoma
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.
disorder of liver
hepatic disorder
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.
autoimmune hypersensitivity disease
hypersensitivity reaction type II disease
A pancreas disease that is characterized by inflammation of the pancreas.
pancreatitis
Cirrhosis
cirrhosis of liver
A urinary system disease that is located_in the kidney.
nephropathy
A kidney disease that is characterized by the presence of excess proteins in the urine.
A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia.
Myocardial infarct
heart attack
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.
CHF
Cardiac Failure Congestive
Congestive heart disease
Weak heart
An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain.
CVA
cerebrovascular disorder
stroke
A liver carcinoma that has_material_basis_in undifferentiated hepatocytes and located_in the liver.
Hepatoma
A kidney failure that is characterized by the gradual loss of kidney function.
CKD
CRF
chronic kidney failure
chronic renal disease
chronic renal failure syndrome
renal failure - chronic
A lower respiratory tract disease in which the function of the lungs is adversely affected by narrowing or blockage of the airways resulting in poor air flow, a loss of elasticity in the lungs that produces a decrease in the total volume of air that the lungs are able to hold, and clotting, scarring, or inflammation of the blood vessels that affect the ability of the lungs to take up oxygen and to release carbon dioxide.
Updating out dated CUI and removing lung abscess as a synonym.
A skin disease that is characterized by patches of thick red skin and silvery scales.
Xref MGI. Update outdated UMLS CUI from C00295134 to C0033860.
A large intestine cancer that is located_in the colon and/or located_in the rectum.
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.
A diabetes mellitus that is characterized by high blood sugar, insulin resistance, and relative lack of insulin.
NIDDM
non-insulin-dependent diabetes mellitus
type 2 diabetes
type II diabetes mellitus
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.
Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
blood vessel formation from pre-existing blood vessels
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.
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.
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
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.
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.
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.
metabolic process resulting in cell growth
multicellular organism metabolic process
Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions.
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.
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.
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.
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
Cessation of menstruation, occurring in (e.g.) the human female usually around the age of 50.
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).
A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging.
A person who makes a donation.
donor
donors
Analyses regarding statistical data.
statistical analysis
statistical analyses
This is the root of the phenotypic abnormality subontology of the HPO.
Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia).
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.
Abnormal calcification of the vasculature.
Partial or complete wasting (loss) of brain tissue that was once present.
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.
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.
Applies to a sign, symptom or manifestation that occurs multiple times separated by intervals in which the sign, symptom, or manifestation is not present.
An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements.
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
Data items include counts of things, analyte concentrations, and statistical summaries.
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.
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.
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.
2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/
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
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
PERSON: Jonathan Rees
data
information content entity
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
A generically dependent continuant that is about some thing.
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).
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.
measurement datum
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,}.
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.
2/2/2009 is_specified_output of some assay?
person:Chris Stoeckert
textual entity
Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities
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.
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.
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.
PERSON: Lawrence Hunter
text
hypothesis textual entity
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
A textual entity that expresses an assertion that is intended to be tested.
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
A document that either prescribes actions or prescribes the permissions, obligations, restrictions, or protections relating to public or legal policy.
Rules, legal specifications, guidelines (both categorical and hypothetical), that exist together in one regulatory document. Regulations may contain a single, or multiple rules.
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.
regulatory document
A process that is a systemic inflammatory response to infection.
sepsis
A clinically prescribed procedure, therapy, intervention, or recommendation.
medical action
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.
An action or administration of therapeutic agents to produce an effect that is intended to alter or stop a pathologic process.
therapeutic procedure
Any procedure or test to diagnose a disease or disorder.
diagnostic procedure
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.
surgical procedure
A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly.
biomarker analysis
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.
genetic testing
The use of synthetic or naturally-occurring chemicals for the treatment of diseases.
treatment with a chemotherapeutic medication
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.
chemotherapy
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.
eye movement measurement
The use of ultrasound to produce images of structures in the heart.
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
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.
An impairment of the structure or function of the blood vessels which carry blood away from the heart.
A primary or metastatic malignant neoplasm involving the stomach.
gastric cancer risk after h. pylori infection
malignant neoplasm of lesser curve of stomach
malignant tumor of greater curve of stomach
malignant tumor of lesser curve of stomach
malignant tumour of greater curve of stomach
malignant tumour of lesser curve of stomach
Any disease in which the causes of the disease is a perturbation of the kidney leading to its dysfunction.
A disease or disorder that involves the digestive system.
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.
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.
COPD, chronic obstructive pulmonary disease
chronic obstructive pulmonary disease (COPD)
chronic obstructive pulmonary disease, (COPD)
obstructive pulmonary disease (COPD), chronic
pulmonary disease (COPD), chronic obstructive
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.
A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves.
'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.
An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections.
Build-up of fatty material and calcium deposition in the arterial wall resulting in partial or complete occlusion of the arterial lumen.
Note that NCIT distinguishes between atherosclerotic cardiovascular disease and atherosclerosis - we merge these here
rare bone disease related to a common gene or pathway defect
The spread of a malignant neoplasm to the lymph nodes.
metastatic malignant neoplasm to the lymph nodes
metastatic malignant neoplasm in the lymph nodes
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.
A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function.
central nervous system degenerative disorder
central nervous system neurodegenerative disorder
degenerative disorder of central nervous system
Editor notes: DO treats this as two diseases
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.
systemic lupus erythematosus susceptibility to
systemic lupus erythematosus, susceptibility to
excess lymphocyte low molecular weight DNA
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.
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).
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.
A brain disease that is characterized by brain dysfunction caused by an outside force, usually a violent blow to the head.
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.
Extracellular deposition of amyloid protein.
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.
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
increased reactive oxygen species production
diminished effectiveness of insulin in lowering plasma glucose levels
The determination of the amount of kidney injury molecule-1 present in a sample.
A measurement of the kidney injury molecule-1 (Kim-1) in a biological specimen.
Hepatitis A Virus Cellular Receptor 1 Measurement
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.
The determination of the amount of human epidermal growth factor receptor 2 present in a sample.
Human Epidermal Growth Factor Receptor 2 Measurement
A measurement of HER2 protein in a biological specimen.
Human Epidermal Growth Factor Receptor 2
Receptor Tyrosine-Protein Kinase erbB-2 Measurement
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.
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.
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.
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.
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.
A measurement of the magnitude of diffusion of water molecules within tissue.
A technique used to measure the diameter of the pupil in response to stimuli.
An isoenzyme complex comprised of a heterodimer of creatine kinase M-type and B-type.
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.
Perfusion-Weighted Magnetic Resonance Imaging
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.
A public health agency based in London that is responsible for the scientific evaluation, supervision, and safety monitoring of medicines in the European Union.
In a clinical trial, an assessment of an intervention's effects that takes the place of a patient-based conclusion.
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.]
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.
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.
Systematic investigation into the causes of cancer and development of strategies for prevention, diagnosis, treatment, and cure.
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.
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.
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.
Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance
Detection and measurement of the resonant spectra of molecular species in a tissue or sample.
A type of spectroscopy that detects and measures the resonant spectra of molecular species in a tissue or sample.
Spectroscopy, Nuclear Magnetic Resonance
A representation of something, often idealized or modified to make it conceptually easier to understand.
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]
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.
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.
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.
Medical Imaging, Positron Emission Tomography
Positron emission tomography (procedure)
proton magnetic resonance spectroscopic imaging
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.
A series of detailed pictures of areas inside the body; the pictures are created by a computer linked to an x-ray machine.
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.
Computerized axial tomography (procedure)
The use of high-frequency sound waves to generate images of the body.
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.
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.
2-Dimensional Grayscale Ultrasound Imaging
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.
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.
The United States regulatory authority charged with, among other responsibilities, granting IND and NDA approvals.
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.
A method of producing pictures of areas inside the body.
Method of imaging used to visualize and aspect of the patient for use in diagnosis or treatment.
A measurement of the temperature of the body.
Temperature measured in Celsius or Fahrenheit
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.
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.
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.
An assigned tumor grade based on a defined scoring system.
A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable.
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]
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).
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).
Used here to organize a wide variety of concepts that are characterized by writing or text
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)
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)
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)
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)
Changes in the regulation of the expression of gene activity without alteration of genetic structure.
A fibrillar protein present in blood plasma; it converts to fibrin during the process of blood clot formation.
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.
Multiplying or increasing in number. In biology, cell proliferation occurs by a process known as cell division.
Pertaining to the state of proliferation, in which the entity is actively multiplying or increasing in number.
A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood.
A condition of abnormal blood clotting or bleeding.
A radiographic procedure using the emission of x-rays to form an image of the structure penetrated by the radiation.
A radiographic procedure using the emission of x-rays, a type of penetrating energy wave.
Radiographic imaging procedure (procedure)
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.
Positive Predictive Value of Diagnostic Test
The likelihood that an individual with a positive test result truly has the particular gene and/or disease in question.
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.
Negative Predictive Value of Diagnostic Test
The likelihood that an individual with a negative test result is truly unaffected and/or does not have the particular gene mutation in question.
The act of observing something (and sometimes keeping a record of it).
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.
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).
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.
A type of MRI technique that maps the diffusion of water in three dimensions.
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.
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.
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.)
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.
Information or variable that supports a probabilistic estimate of future events.
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.
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.
Center for Devices and Radiological Health
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.
A laboratory test used for the measurement of creatinine levels in the serum to determine the glomerular filtration rate.
A healthy subject that is matched with an affected individual in a trial.
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.
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).
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.
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.
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'.
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.
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.
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.
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.
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.
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'.
WEB: http://en.wikipedia.org/wiki/Adverse_event
WEB: http://www.fda.gov/Safety/MedWatch/HowToReport/ucm053087.htm
WEB: http://www.ncbi.nlm.nih.gov/pubmed/25093068
The OAE official website is: http://www.oae-ontology.org/.
An inferential statistical data analysis that is used to analyze data that arises from more than one variable
WEB: http://www.camo.com/multivariate_analysis.html
An inferential statistical data analysis that has only one independent variable
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.
WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms
planned process
Injecting mice with a vaccine in order to test its efficacy
A process that realizes a plan which is the concretization of a plan specification.
'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.)
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.
6/11/9: Edited at workshop. Used to include: is initiated by an agent
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)
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
Bjoern Peters
OBI branch derived
Could add specific objective specification
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
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
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.
PlanAndPlannedProcess Branch
measuring
scientific observation
diagnosis textual entity
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
Jennifer Fostel
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
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
GROUP:Role Branch
OBI, CDISC
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
patient role
study subject role
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.
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.
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.
GROUP: Role Branch
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
participant under investigation role
Pill consisting of inert materials
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
Person:Jennifer Fostel
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.
placebo role
p-value
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).
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.
May be outside the scope of OBI long term, is needed so is retained
PERSON:Chris Stoeckert
WEB: http://en.wikipedia.org/wiki/P-value
An assay that produces a picture of an entity.
Stage II breast cancer, The timepoint of recovery from a disease
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
disease stage
blood drawn from a human for glucose assay
a material entity derived from a portion of blood collected from an organism
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.
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.
statistical hypothesis test
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
PERSON: James Malone
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
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.
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.
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.
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.
A voltmeter is a measurement device which is intended to perform some measure function.
An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure.
A material entity that is designed to perform a function in a scientific investigation, but is not a reagent.
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 role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay.
genotype information
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
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.
discussed on San Diego OBI workshop, March 2011
Group: OBI group
Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques.
An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section.
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.
blood serum specimen
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.
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PERSON: Maura Gasparetto
PERSON: Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Blood_plasma
specimen
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
A material entity that has the specimen role.
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.
GROUP: OBI Biomaterial Branch
multiple linear regression analysis
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.
Tina Hernandez-Boussard
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.
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.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
staining
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
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
validation
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.
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.
abnormal, harmful processes caused by or associated with a disease
IEDB
pathologic process
A gene is a material entity that represents the entire DNA sequence required for synthesis of a functional protein or RNA molecule.
WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/
gene
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.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
The totality of all processes through which a given disease instance is realized.
The representation of a conclusion of a diagnostic process.
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
A hypothesis about some future part of a disease course.
A disease stage which is characterized by the lack of a manifestation of a disease
A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased.
Albert Goldfain Richard Scheuermann Sagar Jain
remission
A therapeutic procedure in which a body part is transferred into a organism
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.
Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization.
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).
A change in electrical resistance of the skin, occurring in emotion and in certain other conditions.
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.
Pressure within the cranial cavity. It is influenced by brain mass, the circulatory system, CSF dynamics, and skull rigidity.
Blood tests that are used to evaluate how well a patient's liver is working and also to help diagnose liver conditions.
Exfoliate neoplastic cells circulating in the blood and associated with metastasizing tumors.
The study of chance processes or the relative frequency characterizing a chance process.
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).
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.
Peroxidase catalyzed oxidation of lipids using hydrogen peroxide as an electron acceptor.
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.
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.
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.
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.
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.
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.
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.
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.
musculoaponeurotic fibrosarcoma oncogene homolog
v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog
v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
Measurable indicator including genetic or acquired host factors and intrinsic factors, influencing the response of an individual to a (dietary) exposure.
susceptibility biomarker
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.
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.
Yingtong Liu, Anthony Huffman, Oliver He
biomarker
A biomarker that is indicative of an immune response
immune biomarker
cytokine biomarker
inflammatory cytokine biomarker
A biomarker that is indicative of a disease
disease biomarker
A biomarker that is an indicator of a cell lineage or cell type
cell lineage biomarker
molecular biomarker
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.
cellular biomarker
imaging biomarker
A biomarker that can predict clincal outcome.
predictive biomarker
A biomarker that provides information about the patient's overall outcome, regardless of therapy.
prognostic biomarker
A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients.
diagnostic biomarker
A molecular biomarker at the DNA gene level
DNA biomarker
RNA biomarker
A biomarker that is indicative of a disease and achieved through imaging.
imaging disease biomarker
imaging disease biomarkers by magnetic resonance imaging
imaging disease biomarkers by MRI
A biomarker that is indicative of the presence of cancer in the body
cancer marker
A time quality inhering in a bearer by virtue of how long the bearer has existed.
A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance.
A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time.
A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
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.
An age quality that exists by virtue of the time (years and months) that the bearer has existed.
A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time.
A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize.
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof.
The definition above excludes protein complexes, which some also consider a protein. Those who wish to refer to a class representing both senses of the word are directed to CHEBI:36080. Note that the definition allows for experimentally-manipulated genes, and allows for artifically-produced derivatives that mimic those found naturally. Proteins (in the sense defined here) that descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic [PRO:WCB].
A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof.
A Bcl-2-like apoptosis inhibitor that is a translation product of the human BCL2 gene or a 1:1 ortholog thereof.
A trypsin that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TP53 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof.
30 kDa adipocyte complement-related protein
adipocyte complement-related 30 kDa protein
adipocyte, C1q and collagen domain-containing protein
adipose most abundant gene transcript 1 protein
A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof.
A neurotrophin that is a translation product of the human BDNF gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CHI3L1 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CLU gene or a 1:1 ortholog thereof.
testosterone-repressed prostate message 2
A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human CST3 gene or a 1:1 ortholog thereof.
An EGF receptor type tyrosine-protein kinase that is a translation product of the human EGFR gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human ESR1 gene or a 1:1 ortholog thereof.
nuclear receptor subfamily 3 group A member 1
A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof.
25 kDa alpha-2-microglobulin-related subunit of MMP-9
neutrophil gelatinase-associated lipocalin
A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human NRGN gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human SPP1 gene or a 1:1 ortholog thereof.
calcium oxalate crystal growth inhibitor protein
A protein that is a translation product of the human TFF3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TNNI3 gene or a 1:1 ortholog thereof.
A protein that is a translation product of the human TNNT2 gene or a 1:1 ortholog thereof.
A protein-containing complex that is the remnant of fibrin mesh degradation (fibrinolysis) by plasmin in human.
Category=organism-complex. Requested by=MAxO.
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.
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.
The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute.
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.
the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria
type II error rate
false negative rate
prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size.
adapted from: https://www.health.ny.gov/diseases/chronic/basicstat.htm
prevalence
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.
Rand accuracy
Rand index
adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016
accuracy
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)
positive predictive value
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.
precision
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.
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.
A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease.
A pain that is characterized by ranging from mild to severe and which continues beyond the expected healing phase.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
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.
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
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.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
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.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
Excretion that is the output of a kidney.
kidney excreta from some taxa (e.g. in aves) may not be liquid
A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord.
many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]
Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]
In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]
EHDAA2 models this as developing from CP, which is wrong
the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations.
A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions.
We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin
The liquid component of blood, in which erythrocytes are suspended.
The portion of blood plasma that excludes clotting factors.
Portion of semisolid bodily waste discharged through the anus[MW,modified].
Excretion in semisolid state processed by the intestine.[FMA]
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].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
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]
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).
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.
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].
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.
A paired organ of the urinary tract which has the production of urine as its primary function.
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]
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.
(...) 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]
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
A strand of hair that is part of a head.
The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity.
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.
generated with ChatGPT version 4,0 on 19.06.2025
knee extension strength
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.
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.
biomarker of aging text mining bin
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 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.
brain aging
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.
epigenetic clock
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.
proteomic clock
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.
hannum clock
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.
horvath clock
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.
DNAm PhenoAge
Phenotypic age refers to an individual’s biological age, which is determined by their physical characteristics and functioning rather than their chronological age
phenotypic age
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.
GrimAge clock
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.
mitotic clock
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.
decline in stem cell function
stem cell quantity
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.
regenerative capacity
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.
ELOVL2 hypermethilation
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.
hayflick limit
BloodAge
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
Biological age is a measure of health that offers insights into ageing.
generated with ChatGPT version 4,0 on 19.06.2024
age estimator
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.
generated with ChatGPT version 3,5 on 23.08.24
biological principle
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
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
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
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
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
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
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
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
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
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
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
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
A placeholder for grouping classes for biomarker text-minig purposes.
A process quality is quality that is associated with a process.
process quality
A mathematical entity is an information content entity that are components of a mathematical system or can be defined in mathematical terms.
mathematical entity
A parameter is variable whose value changes the characteristics of a system or a function.
parameter
normality is the quality in which the value may differ from normal or average
normality
A quality that has a value that is normal or average.
normal
A quality that has a value that is outside normal or average.
abnormal
A quality that has a value that is increased compared to normal or average.
increased
A quality that has a value that is decreased compared to normal or average.
decreased
A correlation is a statistical relationship involving dependence between two random variables or datasets.
correlation
severe is a qualitative intensity value that is more intense than strong, but less intense than fatal.
severe
male is a biological sex of an individual with male sexual organs.
male
female is a biological sex of an individual with female sexual organs.
female
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)
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.
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.
A disease involving the cardiovascular system.
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
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.
Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM.
Certain sequelae of myocardial infarction, not elsewhere classified
Circulatory system disease NOS (disorder)
Disease affecting entire cardiovascular system
Disease affecting entire cardiovascular system (disorder)
Disease of cardiovascular system (disorder)
Disorder of cardiovascular system (disorder)
Ill-defined descriptions and complications of heart disease
Other diseases of endocardium (disorder)
Other diseases of pericardium (disorder)
Other ill-defined heart disease (disorder)
Other ill-defined heart disease NOS (disorder)
Other pericardial disease NOS (disorder)
Other sequelae of myocardial infarction, not elsewhere classified
Other specified pericardial disease NOS (disorder)
[X]Cardiovascular disease, unspecified (disorder)
[X]Other forms of heart disease (disorder)
[X]Other ill-defined heart diseases (disorder)
[X]Other specified diseases of pericardium
[X]Other specified diseases of pericardium (disorder)
cardiovascular system disease or disorder
disease or disorder of cardiovascular system
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.
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.
Gastritis Associated with Crohn's Disease
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.
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.
Diabetes with renal manifestations (disorder)
Nephrotic syndrome due to diabetes mellitus
Nephrotic syndrome in diabetes mellitus (disorder)
Renal disorder associated with diabetes mellitus
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.
Information, making the distinction between the actual physical material (e.g. a cell) and the information about the genetic content (genotype).
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.
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.
Increased VASCULAR RESISTANCE in the PULMONARY CIRCULATION, usually secondary to HEART DISEASES or LUNG DISEASES.
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).
PAH with overt features of venous/capillaries involvement
A study in which participants are examined at only a single time for characteristics of a disease.
A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument.
A carcinoma that arises from epithelial cells of the exocrine pancreas
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.
The status during which female mammals carry their developing young (EMBRYOS or FETUSES) in utero before birth, beginning from FERTILIZATION to BIRTH.
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.
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.
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.
A viral infection caused by the hepatitis C virus.
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.
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.
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).
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)
Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc.
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.
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.
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.
An interleukin is a multifunctional cytokine produced by leukocytes for regulating immune responses.
A viral infection caused by the hepatitis B virus.
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.
A collection of symptoms that include severe edema, proteinuria, and hypoalbuminemia; it is indicative of renal dysfunction.
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.
The presence of albumin in the urine, an indicator of KIDNEY DISEASES.
Obstruction of a vein or VEINS (embolism) by a blood clot ( THROMBUS) in the blood stream.
Occlusion of the lumen of a vein by a thrombus that has migrated from a distal site via the blood stream.
The volume of air that is exhaled by a maximal expiration following a maximal inspiration.
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%.
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.
PRESSURE of the BLOOD on the ARTERIES and other BLOOD VESSELS.
The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms.
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.
Non-invasive methods of visualizing and measuring the CENTRAL NERVOUS SYSTEM, especially the brain, by various imaging modalities e.g. CT scan
Quantification of the number of deaths in a population.
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.
The HOMA-IR measurement employs the homeostatic model assessment (HOMA) to quantify insulin resistance.
homeostasis model assessment insulin resistance
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.
A muscle mass measurement is the quantification of the mass of a muscle e.g. skeletal muscle for an individual.
An Arterial stiffness measurement is the information output of a non invasive pulse wave velocity assay. Arterial stiffness is a predictor of cardiovascular mortality
Is a quantification of some aspect of the genome, e.g. copy number variation at some locus.
A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL.
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.
Is the measurement of the ratio of forced expiratory volume (FEV) to forced vital capacity (FVC), used as a measure of pulmonary function.
Is a quantification of NT-proBNP (N-terminal prohormone of brain natriuretic peptide) which is associated with acute congestive heart failure.
N-Terminal Pro-B-Type Natriuretic Peptide
A quantification of a genomic variation that increases or decreases the copy number of a given region.
Is a quantification of sleep time in humans where average sleep time was less than five hours.
The genetic variation of individuals in a population.
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
Is a quantification of some sleep parameter.
Is a quantification of any molecule involved in the process of inflammatory response.
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.
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
The recurrence of a disease after treatment
The total sum of the genetic information of an organism's somatic cells
The total sum of the genetic information of an organism's germline
A collection or collectivity of microorganisms.
Measurement of the volume of the hippocampus
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
duration of sleep, measured either via a self-reporting questionnaire, interview or through obversation in a sleep lab
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
self-reported assessment of how difficult an individual is to wake
measurement of the time at which sleep begins
amount of time, usually recorded in minutes, between going to bed and falling asleep
quantification of the volumetric fraction of blood pumped out of the left and right ventricle with each heartbeat or cardiac cycle
quantification of white matter hyperintensity, usually measured by MRI
quantification of the relative amount of oxygen that is dissolved or carried in a given medium
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.
Consider relocating this as a sibling of metabolic disease.
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
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.
quantification of any recombination-related factor, such as hotspot usage, African enchrichment and recombination rate
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
The blood pressure during the contraction of the left ventricle of the heart.
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
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.
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.
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
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.
quantification of some lipoprotein A in a sample
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.
quantification of some aspect of the seasonal variation in the micrbiome of the gut
quantification of some aspect of nighttime rest such as duration or quality
quantification of some aspect of daytime rest such as duration, frequency or quality
quantification of some aspect of an individual's micrbiome of the gut
quantification of excessive daytime sleepiness such as how often it occurs and its severity
excessive daytime sleepiness measurement
quantification of insomnia such as how often it occurs and its severity
quantification of some aspect of an individual's microbiome
quantification of the taxonomic variation in a microbiome sample
quantification of the functional variation in a microbiome
quantification of some aspect of chronotype such as ease of getting up in the morning
quantification of some aspect of snoring such as frequency or severity
quantification of some aspect of the deposition of amyloid proteins in an organ
Qunatification of the maximum volume of air that an organism can breathe in and out during a specified period of time, often 1 minute.
Quantification of a glucose metabolic process.
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.
transfer factor of the lung for carbon monoxide
diffusing capacity of the lung for carbon monoxide
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 ]
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.
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.
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.
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.
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 ]
Frequency of chromosomal aberrations in human peripheral blood.
Frequency of chromosome-type chromosomal aberrations in human peripheral blood (typically resulting in damage to both chromatids).
Frequency of chromatid-type chromosomal aberrations in human peripheral blood (typically resulting in damage to a single chromatid).
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.
FVC change measurement
Quantification of some aspect of an individual's microbiome of the vagina.
vaginal microbiome measurement
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.
aging
The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
DNA methylation
It is the most common clonal somatic alteration in leukocytes of female individuals.
mosaic loss of chromosome X measurement
Quantification of some aspect of an individual's microbiome of the skin.
skin microbiome measurement
Quantification of some aspect of an individual's oral microbiome.
oral microbiome measurement
A measurement of the sum of durations of wakefulness episodes throughout the night, not including the wakefulness before sleep onset.
wake after sleep onset
A relative measurement of the time spent asleep to the total time spent in bed.
sleep efficiency
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.
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.