Marc Jacobs Martin Hofmann Aptius Astghik Sargsyan Biomarker Ontology (BMONT) 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. 2025-06-20 Version Release: 0.5.8 has close match 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] has close match imported from 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] imported from 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 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label fromOldVersion editor preferred label editor preferred label editor preferred term 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label editor preferred term~editor preferred label 编辑首选术语 编辑首选术语 编辑首选术语~编辑首选标签 编辑首选标签 编辑首选标签 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO:0000112 uberon example_of_usage true example_of_usage example of usage example of usage has curation status 有管理状态 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status 有管理状态 有管理状态 definition definition textual 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. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition. 官方的定义，解释类或属性的含义。应该是亚里士多德式的，形式化和规范化的。 可以通过口语定义进行扩充。 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。 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 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. PERSON:Daniel Schober DEFINITION GROUP:OBI:<http://purl.obolibrary.org/obo/obi> no DEFINITION definition definition textual definition textual definition 定义 定义 文本定义 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。 PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 IAO:0000116 uberon uberon editor_note editor_note 编辑_注释 true editor_note editor_note 编辑_注释 IAO:0000116 IAO:0000116 uberon uberon editor_note editor_note true 1 editor_note editor_note editor note editor note 编者注 编者注 IAO:0000116 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。 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor definition_editor term editor term editor 术语编辑者 术语编辑者 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） OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 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). alternative term alternative term 替代术语 替代术语 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 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> 论OBO-讨论邮件-列表，请参阅http://bit.ly/hgm99w definition source definition source definition_source 定义来源 定义来源 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. PERSON:Alan Ruttenberg PERSON:Melanie Courtot has obsolescence reason curator note An administrative note of use for a curator but of no use for a user PERSON:Alan Ruttenberg IAO:0000232 uberon curator_notes true 1 curator_notes curator note curator note curator notes 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external uberon term_tracker_item true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from imported from expand assertion to 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 . 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:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label 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 Person:Alan Ruttenberg term replaced by 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. A13 Conceptual Entity Related_To_Genetic_Biomarker Related_To_Genetic_Biomarker Related_To_Genetic_Biomarker An association that specifies one of three data types for a particular variable, String, Code or Number. A23 Conceptual Entity Has_PCDC_Data_Type Has_PCDC_Data_Type Has_PCDC_Data_Type An association that indicates a PCDC AML concept is a Authorized Value for a PCDC AML Variable concept. A24 Conceptual Entity Is_PCDC_AML_Authorized_Value_For_Variable Is_PCDC_AML_Authorized_Value_For_Variable Is_PCDC_AML_Authorized_Value_For_Variable An association that indicates a PCDC EWS concept is a Authorized Value for a specific PCDC EWS Variable concept. A28 Conceptual Entity Is_PCDC_EWS_Authorized_Value_For_Variable Is_PCDC_EWS_Authorized_Value_For_Variable Is_PCDC_EWS_Authorized_Value_For_Variable An association that shows which Authorized Values are possible for a specific PCDC EWS Variable concept. A29 Conceptual Entity Has_PCDC_EWS_Authorized_Value Has_PCDC_EWS_Authorized_Value Has_PCDC_EWS_Authorized_Value An association that connects a concept representing a GDC property to its dedicated value concept(s). A31 Conceptual Entity Has_GDC_Value Has_GDC_Value Has_GDC_Value An association that that connects a concept representing a GDC value to any associated GDC property concept(s). A32 Conceptual Entity Is_Value_For_GDC_Property Is_Value_For_GDC_Property Is_Value_For_GDC_Property 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. A33 Conceptual Entity Is_PCDC_GCT_Authorized_Value_For_Variable Is_PCDC_GCT_Permissible_Value_For_Variable Is_PCDC_GCT_Authorized_Value_For_Variable Is_PCDC_GCT_Permissible_Value_For_Variable Is_PCDC_GCT_Authorized_Value_For_Variable Is_PCDC_GCT_Permissible_Value_For_Variable An association that shows which Permissible Values are possible for a specific PCDC GCT Variable. A34 Conceptual Entity Has_PCDC_GCT_Permissible_Value Has_PCDC_GCT_Permissible_Value Has_PCDC_GCT_Permissible_Value An association that indicates a PCDC ALL concept is a Authorized Value for a PCDC ALL Variable concept. A35 Conceptual Entity Is_PCDC_ALL_Authorized_Value_For_Variable Is_PCDC_ALL_Authorized_Value_For_Variable Is_PCDC_ALL_Authorized_Value_For_Variable An association that shows which Permissible Values are possible for a specific SeroNet Variable. A37 Conceptual Entity Has_SeroNet_Permissible_Value Has_SeroNet_Permissible_Value Has_SeroNet_Permissible_Value 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. A38 Conceptual Entity Has_PCDC_OS_Authorized_Value Has_PCDC_OS_Permissible_Value Has_PCDC_OS_Authorized_Value Has_PCDC_OS_Permissible_Value Has_PCDC_OS_Authorized_Value Has_PCDC_OS_Permissible_Value An association that shows which Authorized Values are possible for a specific PCDC HL Variable. A39 Conceptual Entity Has_PCDC_HL_Authorized_Value Has_PCDC_HL_Authorized_Value Has_PCDC_HL_Authorized_Value An association that shows which Authorized Values are possible for a specific DIPG/DMG Variable. A40 Conceptual Entity Has_DIPG_DMG_Authorized_Value Has_DIPG_DMG_Authorized_Value Has_DIPG_DMG_Authorized_Value An association specifying the Values for a specific OORO Prostate Cancer (PC) Attribute. A42 Conceptual Entity Has_OORO_PC_Value Has_OORO_PC_Value Has_OORO_PC_Value true A property representing a concept unique identifier within the NCI Enterprise Vocabulary Service's NCI Thesaurus. NHC0 Conceptual Entity code code code 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. P106 Conceptual Entity Semantic Type Semantic_Type 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. Semantic_Type Semantic_Type A property representing an alternative Preferred Name for use in some NCI systems. Provides an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name 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. P108 Conceptual Entity Preferred Name Preferred_Name Preferred Name Preferred Term Preferred_Name Preferred_Name 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. P207 Conceptual Entity UMLS CUI UMLS_CUI UMLS_CUI UMLS_CUI 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). P208 Conceptual Entity NCI Metathesaurus CUI NCI_META_CUI NCI_META_CUI NCI_META_CUI 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. P317 Conceptual Entity FDA Table FDA_Table FDA_Table FDA_Table 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. P322 Conceptual Entity Contributing Source Contributing_Source Contributing_Source Contributing_Source A property representing the English language definition of a concept from a source other than NCI. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION A property representing the accession number for an miRNA within the Sanger miRBase database. P362 Conceptual Entity miRBase_ID miRBase_ID miRBase_ID true 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. P366 Conceptual Entity Legacy Concept Name Legacy Concept Name Legacy_Concept_Name Legacy Concept Name 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. P375 Conceptual Entity Maps_To Maps_To Maps_To 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. P98 Conceptual Entity DesignNote DesignNote DesignNote DesignNote 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 Person: Alejandra Gonzalez-Beltran Person: Philippe Rocca-Serra ISA tools project (http://isa-tools.org) ISA alternative term IEDB alternative term An alternative term used by the IEDB. PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters IEDB IEDB alternative term the symbol assigned by the nomenclature authority Oliver He, Yue Liu symbol from nomenclature authority the full name assigned by the nomenclature authority Oliver He, Yue Liu full name from nomenclature authority A GeneID in the NCBI Gene database Oliver He, Yue Liu NCBI GeneID the NCBI LocusTag name of a gene Oliver He, Yue Liu NCBI LocusTag the map location of a gene Oliver He, Yue Liu gene map location a date of content modification Oliver He, Yue Liu modification date The NCBITaxon ontology ID of an organism. Oliver He, Yue Liu organism NCBITaxon ID A chromosome ID where a gene is located. Oliver He chromosome ID of gene an annotation property that specifies the type of a gene Oliver He type of gene an annotation property that specifies a nomenclature status Oliver He nomenclature status an annotation property that shows the GO information associated with a specific gene. Yongqun He has GO association An annotation property that represents a gene's association with PubMed publication(s). Yongqun He 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 . } RO:0002161 uberon never_in_taxon true true never_in_taxon never in taxon never_in_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. non-overlapping with shares no parts with 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 . } RO:0002171 uberon mutually_spatially_disjoint_with true true mutually_spatially_disjoint_with mutually spatially disjoint with mutually_spatially_disjoint_with https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern 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 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) } RO:0002175 applicable for taxon uberon present_in_taxon true true present_in_taxon 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 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). RO:0002604 quality is_opposite_of true true is_opposite_of is opposite of is_opposite_of An administrative note of use for a curator but of no use for a user. no organizational term IAO:0000232 editor_notes curator note 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. yes metadata complete - requires restrictions and relationships IAO:0000119 definition source description source 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. metadata complete - requires restrictions and relationships SCDO description adapted from source Description inherent in name (not provided by source) Only label adapted organizational term property has curation status 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. SCDO (Jade Hotchkiss) existence in other ontologies Used to record the identifier that had been used previously but is no longer in use. SCDO (Jade Hotchkiss) previous identifier an alternative term used for STATO statistical ontology and ISA team Alejandra Gonzalez-Beltran Orlaith Burke 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. UBPROP:0000001 uberon external_definition true external_definition This annotation property may be replaced with an annotation property from an external ontology such as IAO external_definition A textual description of an axiom loss in this ontology compared to an external ontology. UBPROP:0000002 uberon axiom_lost_from_external_ontology true axiom_lost_from_external_ontology This annotation property may be replaced with an annotation property from an external ontology such as IAO axiom_lost_from_external_ontology Notes on the homology status of this class. UBPROP:0000003 uberon homology_notes true homology_notes This annotation property may be replaced with an annotation property from an external ontology such as IAO homology_notes 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'. UBPROP:0000007 uberon has_relational_adjective true has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes true taxon_notes taxon_notes Notes on the evolved function of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000009 uberon function_notes true function_notes function_notes Notes on how similar or equivalent classes are represented in other ontologies. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000012 uberon external_ontology_notes true external_ontology_notes external_ontology_notes FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term UBPROP:0000202 uberon fma_set_term true fma_set_term fma_set_term excluded_subClassOf true excluded subClassOf 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. no ready for release 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. http://purl.org/dc/elements/1.1/creator uberon dc-creator true dc-creator An entity primarily responsible for making the content of the resource. Creator creator dc:creator 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. http://purl.org/dc/elements/1.1/description uberon dc-description true dc-description An account of the content of the resource. Description Description description identifier_dc identifier A related resource from which the described class/term's annotations are derived. yes pending vetting by the SCDO developers dc:source http://purl.org/dc/terms/contributor uberon dc-contributor true dc-contributor contributor 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. definition_citation consider Author of the class. created_by Date class was created. creation date creation_date ID of merged class. has_alternative_id An alternative label for a class or property which has a more general meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/18 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. Conceptual Entity xRef metadata complete - requires restrictions and relationships IAO:0100001 SBO:0000554 DbXref Xref database cross-reference database_cross_reference db xref hasDbXref database cross reference database cross reference database_cross_reference database_cross_reference has database cross reference xRef 数据库_交叉_引用 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. Exact 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/20 no pending vetting by the SCDO developers IAO:0100001 FULL_SYN Synonym with Source Data has exact synonym has exact synonym hasExactSynonym has_exact_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/20 An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/19 Name space of the ontology. IAO:0100001 disease_ontology has_obo_namespace has_obo_namespace 有_obo_命名空间 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. https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has synonym An identifier for an individual entity. 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. id An association that connects the concept defining a particular terminology subset with concepts that belong to this subset. In subset. Concept_In_Subset in subset in_subset shorthand IAO:0100001 shorthand shorthand Comment. comment comment Is defined by. is defined by rdfs:isDefinedBy label label A human readable name for this class. A human-readable name for the class/term. yes A human-readable name for the subject. label label rdfs:label 标签 http://www.w3.org/2000/01/rdf-schema#seeAlso seeAlso spatial uberon seeAlso true true seeAlso see_also_rdf_schema see also see also seeAlso change note A note about a modification to a concept. definition 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. has exact match note A general note, for any purpose. This property may be used directly, or as a super-property for more specific note types. A preferred label. yes pending vetting by the SCDO developers preferred label skos:prefLabel The preferred lexical label for a resource, in a given language. scope note A note that helps to clarify the meaning and/or the use of a concept. http://xmlns.com/foaf/0.1/depicted_by uberon depicted_by true depicted_by depicted by alternate name isCandidateBiomarkerFor isPrognosticBiomarkerFor isDiagnosticBiomarkerFor isMonitoringBiomarkerFor isPredictiveBiomarkerFor isDigitalBiomarkerFor isImagingBiomarkerFor isBiomarkerOfAging procedure A procedure is plan containing multiple activities that are intended to be executed in an order following a procedure specification. [Allotrope] procedure 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. https://pubmed.ncbi.nlm.nih.gov/15178952/ total tau A protein that is phosphorylated through post-translational modification. Its accumulation reflects the formation of neurofibrillary tangles, synaptic impairment, and neuronal dysfunction. https://pubmed.ncbi.nlm.nih.gov/32812023/ phosphorylated tau entity Entity 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 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 per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant 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 (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 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]) occurrent Occurrent 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 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. per discussion with Barry Smith 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] ic IndependentContinuant 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 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] s-region SpatialRegion 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 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. per discussion with Barry Smith 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] t-region TemporalRegion 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 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 per discussion with Barry Smith 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] 2d-s-region TwoDimensionalSpatialRegion 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 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] st-region SpatiotemporalRegion 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 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 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] process Process 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 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]) (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] disposition Disposition 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 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] realizable RealizableEntity 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 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] 0d-s-region ZeroDimensionalSpatialRegion 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 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] quality Quality 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 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] sdc SpecificallyDependentContinuant 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 role of being a doctor 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 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. per discussion with Barry Smith (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] role Role 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 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] fiat-object-part FiatObjectPart 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 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] 1d-s-region OneDimensionalSpatialRegion 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 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] object-aggregate ObjectAggregate 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 An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects 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] 3d-s-region ThreeDimensionalSpatialRegion 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 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] site Site 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 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] object Object 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 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]) gdc GenericallyDependentContinuant 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 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] function Function 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 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] p-boundary ProcessBoundary 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 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] 1d-t-region OneDimensionalTemporalRegion 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 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] material MaterialEntity 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 (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] 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] cf-boundary ContinuantFiatBoundary 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 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]) 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. (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] immaterial ImmaterialEntity 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 1d-cf-boundary OneDimensionalContinuantFiatBoundary 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 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] process-profile ProcessProfile 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 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] r-quality RelationalQuality 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. 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 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] 2d-cf-boundary TwoDimensionalContinuantFiatBoundary 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 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] 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary 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 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. requested by Melanie Courtot 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] 0d-t-region ZeroDimensionalTemporalRegion 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 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] history History 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 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]) yes A biomarker of genomic variation in which blocks of DNA are missing or for which multiple copies exist. https://pubmed.ncbi.nlm.nih.gov/22752797/ CNV biomarker copy number variant biomarker https://pubmed.ncbi.nlm.nih.gov/30203254/ yes A biomarker to discriminate between healthy individuals and those in an early stage of the disease. https://pubmed.ncbi.nlm.nih.gov/22752797/ screening marker screening biomarker yes A biomarker that is essential to the efficacy and safety of a corresponding therapeutic product. https://pubmed.ncbi.nlm.nih.gov/22752797/ companion endpoint yes A biomarker that reports interaction of the drug with its target https://pubmed.ncbi.nlm.nih.gov/22752797/ target biomarker yes A biomarker that distinguishes between different stages of chronic disease. https://pubmed.ncbi.nlm.nih.gov/22752797/ disease stage biomarker staging biomarker yes A biomarker that predicts a beneficial effect of a given treatment. https://pubmed.ncbi.nlm.nih.gov/22752797/ efficacy biomarker yes A biomarker that reports to the toxic effect of a drug on an in vitro or in vivo system. https://pubmed.ncbi.nlm.nih.gov/22752797/ toxicity biomarker yes 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. https://www.fda.gov/media/122319/download COU context of use https://pubmed.ncbi.nlm.nih.gov/29110507/ Validation is a process to establish that the performance of a test, tool, or instrument is acceptable for its intended purpose. https://pubmed.ncbi.nlm.nih.gov/33545385/ biomarker validation https://pubmed.ncbi.nlm.nih.gov/20199395/ 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. https://pubmed.ncbi.nlm.nih.gov/33545385/ analitical validation https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. https://pubmed.ncbi.nlm.nih.gov/33545385/ clinical validation https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. https://pubmed.ncbi.nlm.nih.gov/27891226/ clinical specificity 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. https://pubmed.ncbi.nlm.nih.gov/27891226/ CDx companion diagnostics https://pubmed.ncbi.nlm.nih.gov/29110507/ 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 https://pubmed.ncbi.nlm.nih.gov/27891226/ complementary diagnostics A biomarker regulatory entity refers to a regulatory organization responsible for qualification and acceptance of biomarkers for futrher use in pharmaceutical research and development. biomarker regulatory entity 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. https://www.pmda.go.jp/english/about-pmda/outline/0005.html PMDA The Japanese Pharmaceuticals and Medical Device Agency Japan’s Pharmaceuticals and Medical Devices Agency https://pubmed.ncbi.nlm.nih.gov/29110507/ https://www.pmda.go.jp/english/ Biomarkers that represent acute and chronic pain, predisposition to develop chronic pain and , and pain chronification, recovery and treatment outcomes. https://pubmed.ncbi.nlm.nih.gov/32541893/ chronic pain biomarker https://pubmed.ncbi.nlm.nih.gov/30844399/ 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)). https://www.fda.gov/media/133511/download drug development tool https://pubmed.ncbi.nlm.nih.gov/29110507/ 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. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/qualification-medical-device-development-tools Qualification of Medical Device Development Tools Guidance for Industry, Tool Developers, and Food and Drug Administration Staff https://pubmed.ncbi.nlm.nih.gov/29110507/ https://www.fda.gov/media/87134/download 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. https://www.fda.gov/media/133511/download Qualification Process for Drug Development Tools Guidance for Industry and FDA Staff https://pubmed.ncbi.nlm.nih.gov/29110507 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. https://www.fda.gov/regulatory-information/selected-amendments-fdc-act/21st-century-cures-act 21st Century Cures Act https://pubmed.ncbi.nlm.nih.gov/29110507/ 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 https://pubmed.ncbi.nlm.nih.gov/29110507/ https://www.fda.gov/media/71422/download https://www.fda.gov/regulatory-information/search-fda-guidance-documents/pharmacogenetic-tests-and-genetic-tests-heritable-markers 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. https://www.fda.gov/drugs/biomarker-qualification-program/about-biomarkers-and-qualification qualified biomarker https://pubmed.ncbi.nlm.nih.gov/20199395/ 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. https://resources.pkdcure.org/resources/what-is-total-kidney-volume-tkv-and-why-is-it-important-to-me/ TKV total renal volume total kidney volume https://pubmed.ncbi.nlm.nih.gov/35383043/ Urinary total protein (UTP) includes all proteins in urine samples. The presence of some quantities of proteins (<150 mg/day) is considered normal. https://www.human.de/lab-professionals/trends-topics/urinary-total-protein-more-than-just-protein total protein urine total potein 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. https://pubmed.ncbi.nlm.nih.gov/32541893/ out-of-sample testing cross-validation testing 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 multimarker panel multimarker signature composite biomarkers 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 standard https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. generated with ChatGPT version 4,0 on 22․05․24 regulatory guideline https://pubmed.ncbi.nlm.nih.gov/32541893/ Qualification is the evidentiary process of linking a biomarker with biological processes and clinical end points. https://pubmed.ncbi.nlm.nih.gov/20199395/ biomarker qualification yes 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. https://doi.org/10.53347/rID-85803 cardiac function yes Systolic function refers to the heart's ability to throw out a specific amount of blood in a certain amount of time. https://doi.org/10.53347/rID-85803 cardiac systolic function ventricular systolic function systolic function yes A biomarker that measures epigenetic alterations, such as DNA methylation, histone methylation, histone acetylation, microRNAs, or other non-coding RNA. https://pubmed.ncbi.nlm.nih.gov/22122639/ epigenetic biomarker 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. generated with ChatGPT version 3,5 on 02.04.2024 stratification biomarker yes 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. generated with ChatGPT version 3,5 on 02.04.2024 prediction model 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. https://www.ncbi.nlm.nih.gov/mesh/68017270 lipoprotein a Biomarker repurposing, the novel application of existing biomarkers for other purposes. https://pubmed.ncbi.nlm.nih.gov/30044870/ biomarker repurposing 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. https://pubmed.ncbi.nlm.nih.gov/27975230/ candidate biomarker 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. diagnostic biomarker text mining bin A placeholder for diagnostic biomarkers, organized based on the reasoning application 'isDiagnosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases. This class is used for grouping terms and should not be used for logical reasoning. 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. monitoring biomarker text mining bin A placeholder for monitoring biomarkers, organized based on the reasoning application 'isMonitoringBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases. This class is used for grouping terms and should not be used for logical reasoning. 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. prognostic biomarker text minig bin A placeholder for prognostic biomarkers, organized based on the reasoning application 'isPrognosticBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases. This class is used for grouping terms and should not be used for logical reasoning. 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. predictive biomarker text minig bin 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. generated with ChatGPT version 4,0 on 22․05․24 therapeutic biomarker Digital biomarkers are objective, quantifiable, physiological, and behavioral measures that are collected by means of digital devices that are portable, wearable, implantable, or digestible. https://pubmed.ncbi.nlm.nih.gov/32095769/ digital biomarker 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. generated with ChatGPT version 4,0 on 22․05․24 digital device 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. generated with ChatGPT version 4,0 on 22․05․24 wearable device wearable 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. generated with ChatGPT version 4,0 on 22․05․24 smartwatch 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). generated with ChatGPT version 4,0 on 22․05․24 metric Augmentation index is a measure of systemic arterial stiffness derived from the ascending aortic pressure waveform. https://pubmed.ncbi.nlm.nih.gov/10811742/ AIx augmentation index Arterial compliance is a change in dimension in response to a given change in stress. https://pubmed.ncbi.nlm.nih.gov/9549658/ arterial compliance The stiffness index (SI) derived from the analysis of digital volume pulse (DVP) is a noninvasive indirect technique of measuring arterial stiffness peripherally. https://pubmed.ncbi.nlm.nih.gov/18551104/ arterial stiffness index stiffness index 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 activity level 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. generated with ChatGPT version 4,0 on 22․05․24 step count 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. generated with ChatGPT version 4,0 on 22․05․24 distance walked 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. generated with ChatGPT version 4,0 on 22․05․24 distance run 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. generated with ChatGPT version 4,0 on 22․05․24 active minute 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. https://www.ncbi.nlm.nih.gov/mesh/2027898 gait analysis 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). https://pubmed.ncbi.nlm.nih.gov/24842231/ blood volume pulse This class is used for grouping terms and should not be used for logical reasoning. 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. digital biomarker text mining bin A placeholder for digital biomarkers, organized based on the reasoning application 'isDigitalBiomarkerFor some disease', to facilitate text mining and information retrieval for specific diseases. This class is used for grouping terms and should not be used for logical reasoning. 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. imaging biomarker text mining bin 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 heart rate recovery 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. generated with ChatGPT version 3,5 on 03.05.2024 blood lipid level 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. https://pubmed.ncbi.nlm.nih.gov/27923744/ myelin water fraction 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. https://pubmed.ncbi.nlm.nih.gov/9370546/ dynamic susceptibility contrast 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 cerebral blood volume 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. generated with ChatGPT version 3,5 on 07.05.2024 cancer metabolism tumor metabolism 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. https://pubmed.ncbi.nlm.nih.gov/36947181/ lesion burden overall lesion burden lesion load 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. generated with ChatGPT version 3,5 on 07.05.2024 gray matter volume 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 tissue attenuation value tissue attenuation coefficient 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. generated with ChatGPT version 3,5 on 07.05.2024 functional connectivity density 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. https://pubmed.ncbi.nlm.nih.gov/25032494/ BOLD signal blood oxygen level-dependent signal 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. generated with ChatGPT version 3,5 on 07.05.2024 axonal water fraction 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. generated with ChatGPT version 3,5 on 07.05.2024 apparent fiber density 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. generated with ChatGPT version 3,5 on 07.05.2024 fractional anisotropy 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. generated with ChatGPT version 3,5 on 07.05.2024 tau accumulation tau aggregation tau burden tau deposition 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. generated with ChatGPT version 3,5 on 07.05.2024 mean diffusivity 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. generated with ChatGPT version 4,0 on 22․05․24 walking speed gait speed https://pubmed.ncbi.nlm.nih.gov/33971647/ 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. generated with ChatGPT version 4,0 on 22․05․24 gait stride length stride length https://pubmed.ncbi.nlm.nih.gov/33971647/ 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. generated with ChatGPT version 4,0 on 22․05․24 gait cycle time https://pubmed.ncbi.nlm.nih.gov/33971647/ Leukocyte telomere length (LTL) is a complex genetic trait. It shortens with age and is associated with a host of aging-related disorders. https://pubmed.ncbi.nlm.nih.gov/18282113/ LTL WBC telomere length White blood cell telomere length 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 behaviour mitochondrial performance 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. relabel 'tissue'? portion of tissue CARO:0000043 tissue yes A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group. 0 C27H46O InChI=1S/C27H46O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h9,18-19,21-25,28H,6-8,10-17H2,1-5H3/t19-,21+,22+,23-,24+,25+,26+,27-/m1/s1 HVYWMOMLDIMFJA-DPAQBDIFSA-N 386.655 386.35487 C1[C@@]2([C@]3(CC[C@]4([C@]([C@@]3(CC=C2C[C@H](C1)O)[H])(CC[C@@]4([C@H](C)CCCC(C)C)[H])[H])C)[H])C CHEBI:13982 CHEBI:23204 CHEBI:3659 CHEBI:41564 Beilstein:2060565 CAS:57-88-5 DrugBank:DB04540 Gmelin:550297 HMDB:HMDB0000067 KEGG:C00187 KEGG:D00040 KNApSAcK:C00003648 LIPID_MAPS_instance:LMST01010001 MetaCyc:CHOLESTEROL PDBeChem:CLR PMID:10901445 PMID:11412894 PMID:16341241 PMID:24287311 PMID:25308664 PMID:25451949 PMID:25522988 PMID:25658343 PMID:25977713 PMID:4696527 PMID:8838010 Reaxys:2060565 Wikipedia:Cholesterol CHOLESTEROL Cholesterol cholest-5-en-3beta-ol cholesterol chebi_ontology (3beta,14beta,17alpha)-cholest-5-en-3-ol Cholest-5-en-3beta-ol Cholesterin total cholesterol CHEBI:16113 cholesterol 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. 0 (C2H2NOR)nC2H3NOR CHEBI:14753 CHEBI:25906 CHEBI:7990 KEGG:C00012 Peptide peptides chebi_ontology Peptid peptido peptidos CHEBI:16670 peptide yes A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine. 0 C4H7N3O InChI=1S/C4H7N3O/c1-7-2-3(8)6-4(7)5/h2H2,1H3,(H2,5,6,8) DDRJAANPRJIHGJ-UHFFFAOYSA-N 113.11800 113.05891 CN1CC(=O)NC1=N CHEBI:14029 CHEBI:23406 CHEBI:3910 CAS:60-27-5 HMDB:HMDB0000562 KEGG:C00791 KEGG:D03600 MetaCyc:CREATININE PMID:11256540 PMID:11981083 PMID:17190852 PMID:17422601 PMID:18182718 PMID:19236048 PMID:19715855 PMID:19968328 PMID:21775764 PMID:22047975 PMID:22121923 PMID:22166252 PMID:22207347 PMID:22212624 PMID:22223530 PMID:22331238 PMID:22338083 PMID:22349552 PMID:22390548 PMID:22432114 PMID:22441184 PMID:22459582 PMID:22498455 Reaxys:112064 Wikipedia:Creatinine 2-imino-1-methylimidazolidin-4-one Creatinine creatinine chebi_ontology 1-Methylglycocyamidine 1-Methylhydantoin-2-imide 1-methylglycocyamidine 2-Amino-1-methylimidazolin-4-one 2-amino-1,5-dihydro-1-methyl-4H-Imidazol-4-one Creatine anhydride Kreatinin creatinina CHEBI:16737 creatinine yes An aldohexose used as a source of energy and metabolic intermediate. 0 C6H12O6 180.15588 180.06339 CHEBI:14313 CHEBI:24277 CHEBI:33929 CHEBI:5418 CAS:50-99-7 KEGG:C00293 Wikipedia:Glucose Glucose gluco-hexose glucose chebi_ontology DL-glucose Glc Glukose CHEBI:17234 glucose An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.. 0 C19H28O2 InChI=1S/C19H28O2/c1-18-9-7-13(20)11-12(18)3-4-14-15-5-6-17(21)19(15,2)10-8-16(14)18/h11,14-17,21H,3-10H2,1-2H3/t14-,15-,16-,17-,18-,19-/m0/s1 MUMGGOZAMZWBJJ-DYKIIFRCSA-N 288.42440 288.20893 [H][C@@]12CCC3=CC(=O)CC[C@]3(C)[C@@]1([H])CC[C@]1(C)[C@@H](O)CC[C@@]21[H] CHEBI:15214 CHEBI:26883 CHEBI:45798 CHEBI:9461 Beilstein:1915399 Beilstein:3653705 CAS:58-22-0 DrugBank:DB00624 Drug_Central:2607 Gmelin:538843 HMDB:HMDB0000234 KEGG:C00535 KEGG:D00075 KNApSAcK:C00003675 LIPID_MAPS_instance:LMST02020002 PDBeChem:TES PMID:10438974 PMID:11786693 PMID:18900503 PMID:24498482 Reaxys:1915399 Wikipedia:Testosterone 17beta-hydroxyandrost-4-en-3-one TESTOSTERONE Testosterone testosterone chebi_ontology 17beta-Hydroxy-4-androsten-3-one 17beta-hydroxy-4-androsten-3-one 4-androsten-17beta-ol-3-one Androderm Testosteron testosterona testosterone testosteronum CHEBI:17347 testosterone yes Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids. 0 C6H5O6R3 173.10030 173.00861 [*]C(=O)OCC(COC([*])=O)OC([*])=O CHEBI:15255 CHEBI:27085 CHEBI:9664 KEGG:C00422 LIPID_MAPS_class:LMGL0301 PMID:2474544 Triglyceride triglycerides chebi_ontology Triacylglycerol Triglycerid Triglyzerid a triacylglycerol triacylglycerols triglycerides CHEBI:17855 triglyceride yes A L-arginine derivative having two methyl groups both attached to the primary amino moiety of the guanidino group. 0 C8H18N4O2 InChI=1S/C8H18N4O2/c1-12(2)8(10)11-5-3-4-6(9)7(13)14/h6H,3-5,9H2,1-2H3,(H2,10,11)(H,13,14)/t6-/m0/s1 YDGMGEXADBMOMJ-LURJTMIESA-N 202.25428 202.14298 CN(C)C(=N)NCCC[C@H](N)C(O)=O CHEBI:12680 CHEBI:21908 CHEBI:25683 CHEBI:41833 CHEBI:7432 Beilstein:2261521 CAS:30315-93-6 DrugBank:DB01686 KEGG:C03626 PDBeChem:DA2 (2S)-2-amino-5-(N',N'-dimethylcarbamimidamido)pentanoic acid (2S)-2-amino-5-{[(dimethylamino)(imino)methyl]amino}pentanoic acid N(5)-(N,N-dimethylcarbamimidoyl)-L-ornithine N(5)-[(dimethylamino)(imino)methyl]-L-ornithine chebi_ontology ADMA N(5)-((dimethylamino)iminomethyl)-L-ornithine N(G),N(G)-dimethylarginine N(G)-dimethylarginine N(G1),N(G1)-dimethylarginine N,N-dimethylarginine NG,NG-DIMETHYL-L-ARGININE NG,NG-Dimethyl-L-arginine asymmetric dimethylarginine guanidino-N,N-dimethylarginine CHEBI:17929 N(omega),N(omega)-dimethyl-L-arginine yes '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. CHEBI:14517 CHEBI:25054 CHEBI:6486 KEGG:C01356 Lipid lipids chebi_ontology CHEBI:18059 lipid yes Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity chebi_ontology entidad molecular entidades moleculares entite moleculaire molecular entities molekulare Entitaet CHEBI:23367 molecular entity A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17. 0 C18H24O2 InChI=1S/C18H24O2/c1-18-9-8-14-13-5-3-12(19)10-11(13)2-4-15(14)16(18)6-7-17(18)20/h3,5,10,14-17,19-20H,2,4,6-9H2,1H3/t14-,15-,16+,17?,18+/m1/s1 VOXZDWNPVJITMN-WKUFJEKOSA-N 272.38196 272.17763 [H][C@]12CC[C@]3(C)C(O)CC[C@@]3([H])[C@]1([H])CCc1cc(O)ccc21 CHEBI:42364 PMID:10696569 PMID:24084694 Wikipedia:Estradiol estra-1,3,5(10)-triene-3,17-diol chebi_ontology oestradiol CHEBI:23965 estradiol yes A chemical entity is a physical entity of interest in chemistry including molecular entities, parts thereof, and chemical substances. chemical entity chebi_ontology CHEBI:24431 chemical entity A role played by the molecular entity or part thereof within a biological context. chebi_ontology biological function CHEBI:24432 biological role 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. chebi_ontology endocrine hormones CHEBI:24621 hormone yes An oxopurine that is the final oxidation product of purine metabolism. 0 C5H4N4O3 168.11042 168.02834 HMDB:HMDB0000289 Wikipedia:Uric_acid chebi_ontology uric acids CHEBI:27226 uric acid A heteroglycan consisting of a mannan backbone with galactose side groups. CHEBI:24146 CHEBI:5255 PMID:1375195 PMID:2426444 chebi_ontology CHEBI:27680 galactomannan yes 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). 0 Cl2H6N2Pt H6Cl2N2Pt InChI=1S/2ClH.2H3N.Pt/h2*1H;2*1H3;/q;;;;+2/p-2 LXZZYRPGZAFOLE-UHFFFAOYSA-L 300.04452 298.95560 [H][N]([H])([H])[Pt](Cl)(Cl)[N]([H])([H])[H] CHEBI:23314 CHEBI:3722 CAS:15663-27-1 DrugBank:DB00515 Gmelin:2519 HMDB:HMDB0014656 KEGG:C06911 KEGG:D00275 MetaCyc:CPD0-1392 MolBase:25 PMID:10883661 PMID:12537968 PMID:12831510 PMID:12935404 PMID:16327988 PMID:18472761 PMID:1855275 PMID:23554447 PMID:23604226 PMID:23651576 PMID:28494534 Patent:DE2318020 Patent:DE2329485 Reaxys:11324567 Wikipedia:Cisplatin (SP-4-2)-diamminedichloridoplatinum (SP-4-2)-diamminedichloroplatinum Cisplatin cis-diamminedichloridoplatinum(II) cis-diamminedichloroplatinum(II) chebi_ontology Briplatin CDDP Cismaplat Lederplatin Neoplatin Peyrone's chloride Peyrone's salt Platamine Platinex Platinol Randa [PtCl2(NH3)2] cis-DDP cis-Diamminedichloroplatinum(II) cis-[PtCl2(NH3)2] cis-diamminedichloroplatinum cis-diammineplatinum(II) dichloride cis-dichlorodiammineplatinum(II) cis-platin cisplatin cisplatine cisplatino cisplatinum CHEBI:27899 cisplatin yes COMe:PRX000321 hemoglobin chebi_ontology haemoglobin vertebrate haemoglobin CHEBI:35143 hemoglobin 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. 0 C19H31R 259.450 259.24258 C12C(C3C(C(CC3)*)(C)CC1)CCC4C2(CCCC4)C CHEBI:13687 CHEBI:26768 CHEBI:9263 KEGG:C00377 MetaCyc:Steroids Steroid steroids chebi_ontology a steroid CHEBI:35341 steroid yes 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. PMID:1464741 PMID:15531285 PMID:20467214 Wikipedia:HMG-CoA_reductase chebi_ontology HMG-CoA reductase inhibitor HMG-CoA reductase inhibitors hydroxymethylglutaryl-CoA reductase inhibitor hydroxymethylglutaryl-CoA reductase inhibitors CHEBI:35664 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). chebi_ontology LDL cholesterol LDL-C beta-lipoprotein cholesterol CHEBI:47774 low-density lipoprotein cholesterol Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL). chebi_ontology HDL cholesterol HDL-C alpha-lipoprotein cholesterol CHEBI:47775 high-density lipoprotein cholesterol yes Anything used in a scientific experiment to indicate the presence of a substance or quality, change in a body, etc. chebi_ontology Indikator prognostic indicator CHEBI:47867 indicator 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. 0 C257H383N65O77S6 InChI=1S/C257H383N65O77S6/c1-29-131(23)205(313-193(339)104-259)252(393)317-204(130(21)22)248(389)288-159(75-82-200(349)350)217(358)282-156(71-78-189(263)335)221(362)308-183-116-403-404-117-184-243(384)305-178(111-324)240(381)294-162(88-123(7)8)225(366)295-168(95-140-53-61-146(329)62-54-140)228(369)283-154(69-76-187(261)333)218(359)290-161(87-122(5)6)223(364)285-158(74-81-199(347)348)220(361)302-174(101-190(264)336)235(376)298-170(97-142-57-65-148(331)66-58-142)231(372)309-182(242(383)304-176(255(396)397)103-192(266)338)115-402-401-114-181(214(355)273-107-194(340)278-153(72-79-197(343)344)216(357)281-151(51-42-84-271-257(267)268)212(353)272-108-195(341)279-166(93-138-46-36-32-37-47-138)227(368)297-167(94-139-48-38-33-39-49-139)230(371)299-171(98-143-59-67-149(332)68-60-143)238(379)320-208(135(27)327)254(395)322-85-43-52-186(322)246(387)286-152(50-40-41-83-258)222(363)321-209(136(28)328)256(398)399)311-250(391)203(129(19)20)316-236(377)164(90-125(11)12)292-229(370)169(96-141-55-63-147(330)64-56-141)296-224(365)160(86-121(3)4)289-210(351)133(25)277-215(356)157(73-80-198(345)346)287-247(388)202(128(17)18)315-237(378)165(91-126(13)14)293-233(374)173(100-145-106-270-120-276-145)301-239(380)177(110-323)280-196(342)109-274-213(354)180(113-400-405-118-185(310-244(183)385)245(386)319-207(134(26)326)253(394)306-179(112-325)241(382)318-206(132(24)30-2)251(392)312-184)307-226(367)163(89-124(9)10)291-232(373)172(99-144-105-269-119-275-144)300-219(360)155(70-77-188(262)334)284-234(375)175(102-191(265)337)303-249(390)201(127(15)16)314-211(352)150(260)92-137-44-34-31-35-45-137/h31-39,44-49,53-68,105-106,119-136,150-186,201-209,323-332H,29-30,40-43,50-52,69-104,107-118,258-260H2,1-28H3,(H2,261,333)(H2,262,334)(H2,263,335)(H2,264,336)(H2,265,337)(H2,266,338)(H,269,275)(H,270,276)(H,272,353)(H,273,355)(H,274,354)(H,277,356)(H,278,340)(H,279,341)(H,280,342)(H,281,357)(H,282,358)(H,283,369)(H,284,375)(H,285,364)(H,286,387)(H,287,388)(H,288,389)(H,289,351)(H,290,359)(H,291,373)(H,292,370)(H,293,374)(H,294,381)(H,295,366)(H,296,365)(H,297,368)(H,298,376)(H,299,371)(H,300,360)(H,301,380)(H,302,361)(H,303,390)(H,304,383)(H,305,384)(H,306,394)(H,307,367)(H,308,362)(H,309,372)(H,310,385)(H,311,391)(H,312,392)(H,313,339)(H,314,352)(H,315,378)(H,316,377)(H,317,393)(H,318,382)(H,319,386)(H,320,379)(H,321,363)(H,343,344)(H,345,346)(H,347,348)(H,349,350)(H,396,397)(H,398,399)(H4,267,268,271)/t131-,132-,133-,134+,135+,136+,150-,151-,152-,153-,154-,155-,156-,157-,158-,159-,160-,161-,162-,163-,164-,165-,166-,167-,168-,169-,170-,171-,172-,173-,174-,175-,176-,177-,178-,179-,180-,181-,182-,183-,184-,185-,186-,201-,202-,203-,204-,205-,206-,207-,208-,209-/m0/s1 PBGKTOXHQIOBKM-FHFVDXKLSA-N 5807.630 5803.63765 CC[C@H](C)[C@H](NC(=O)CN)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@H]1CSSC[C@@H]2NC(=O)[C@@H](NC(=O)[C@H](CO)NC(=O)[C@@H](NC(=O)[C@H](CSSC[C@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CC3=CNC=N3)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CC(N)=O)NC(=O)[C@@H](NC(=O)[C@@H](N)CC3=CC=CC=C3)C(C)C)C(=O)NCC(=O)N[C@@H](CO)C(=O)N[C@@H](CC3=CNC=N3)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CC3=CC=C(O)C=C3)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H](CSSC[C@H](NC(=O)[C@H](CC3=CC=C(O)C=C3)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](CC3=CC=C(O)C=C3)NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CO)NC2=O)C(=O)N[C@@H](CC(N)=O)C(O)=O)C(=O)NCC(=O)N[C@@H](CCC(O)=O)C(=O)N[C@@H](CCCNC(N)=N)C(=O)NCC(=O)N[C@@H](CC2=CC=CC=C2)C(=O)N[C@@H](CC2=CC=CC=C2)C(=O)N[C@@H](CC2=CC=C(O)C=C2)C(=O)N[C@@H]([C@@H](C)O)C(=O)N2CCC[C@H]2C(=O)N[C@@H](CCCCN)C(=O)N[C@@H]([C@@H](C)O)C(O)=O)NC1=O)[C@@H](C)O)[C@@H](C)CC CAS:11061-68-0 DrugBank:DB00030 KEGG:C00723 KEGG:D00085 PMID:22249812 PMID:22617471 PMID:22715632 PMID:22843207 PMID:31301295 PMID:31821343 PMID:31876563 PMID:32208558 PMID:32398693 PMID:32629793 PMID:32797824 PMID:8019699 chebi_ontology Exubera Insulin Insulin recombinant human insulin insulin (recombinant) insulin human insulina humana insuline humaine insulinum humanum CHEBI:5931 insulin (human) 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). CHEBI:53002 KEGG:C16514 KEGG:C16515 PMID:21892760 PMID:22226401 PMID:22457725 PMID:22459190 PMID:22561032 PMID:22569063 Wikipedia:Beta_amyloid chebi_ontology amyloid beta beta amyloid beta-amyloid beta-amyloids CHEBI:64645 amyloid-beta 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. 0 C194H295N53O58S InChI=1S/C194H295N53O58S/c1-25-102(19)158(188(299)211-87-143(256)218-124(67-94(3)4)174(285)228-123(62-66-306-24)172(283)241-152(96(7)8)186(297)209-83-140(253)206-84-145(258)240-154(98(11)12)191(302)245-157(101(17)18)193(304)305)247-192(303)159(103(20)26-2)246-162(273)104(21)215-141(254)85-207-164(275)116(47-36-38-63-195)223-181(292)133(77-139(199)252)234-185(296)137(90-249)220-144(257)88-210-187(298)153(97(9)10)242-184(295)135(79-151(269)270)235-170(281)121(56-60-147(261)262)222-161(272)106(23)217-173(284)127(69-107-41-30-27-31-42-107)231-177(288)129(71-109-45-34-29-35-46-109)237-189(300)156(100(15)16)244-183(294)125(68-95(5)6)229-166(277)117(48-37-39-64-196)224-168(279)119(54-58-138(198)251)226-178(289)130(73-111-80-202-91-212-111)233-180(291)132(75-113-82-204-93-214-113)238-190(301)155(99(13)14)243-171(282)122(57-61-148(263)264)227-175(286)126(72-110-50-52-114(250)53-51-110)219-142(255)86-208-165(276)136(89-248)239-182(293)134(78-150(267)268)236-179(290)131(74-112-81-203-92-213-112)232-167(278)118(49-40-65-205-194(200)201)225-176(287)128(70-108-43-32-28-33-44-108)230-169(280)120(55-59-146(259)260)221-160(271)105(22)216-163(274)115(197)76-149(265)266/h27-35,41-46,50-53,80-82,91-106,115-137,152-159,248-250H,25-26,36-40,47-49,54-79,83-90,195-197H2,1-24H3,(H2,198,251)(H2,199,252)(H,202,212)(H,203,213)(H,204,214)(H,206,253)(H,207,275)(H,208,276)(H,209,297)(H,210,298)(H,211,299)(H,215,254)(H,216,274)(H,217,284)(H,218,256)(H,219,255)(H,220,257)(H,221,271)(H,222,272)(H,223,292)(H,224,279)(H,225,287)(H,226,289)(H,227,286)(H,228,285)(H,229,277)(H,230,280)(H,231,288)(H,232,278)(H,233,291)(H,234,296)(H,235,281)(H,236,290)(H,237,300)(H,238,301)(H,239,293)(H,240,258)(H,241,283)(H,242,295)(H,243,282)(H,244,294)(H,245,302)(H,246,273)(H,247,303)(H,259,260)(H,261,262)(H,263,264)(H,265,266)(H,267,268)(H,269,270)(H,304,305)(H4,200,201,205)/t102-,103-,104-,105-,106-,115-,116-,117-,118-,119-,120-,121-,122-,123-,124-,125-,126-,127-,128-,129-,130-,131-,132-,133-,134-,135-,136-,137-,152-,153-,154-,155-,156-,157-,158-,159-/m0/s1 FEWOUVRMGWFWIH-ILZZQXMPSA-N 4329.80300 4327.14843 CC[C@H](C)[C@H](NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)CNC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)CNC(=O)[C@H](CO)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C)NC(=O)[C@@H](N)CC(O)=O)C(C)C)C(C)C)C(C)C)[C@@H](C)CC)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](C(C)C)C(=O)NCC(=O)NCC(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C(C)C)C(O)=O KEGG:C16514 PMID:11444969 PMID:15541300 PMID:16137568 PMID:17446087 PMID:18571334 Reaxys:21949886 L-alpha-aspartyl-L-alanyl-L-alpha-glutamyl-L-phenylalanyl-L-arginyl-L-histidyl-L-alpha-aspartyl-L-serylglycyl-L-tyrosyl-L-alpha-glutamyl-L-valyl-L-histidyl-L-histidyl-L-glutaminyl-L-lysyl-L-leucyl-L-valyl-L-phenylalanyl-L-phenylalanyl-L-alanyl-L-alpha-glutamyl-L-alpha-aspartyl-L-valylglycyl-L-seryl-L-asparaginyl-L-lysylglycyl-L-alanyl-L-isoleucyl-L-isoleucylglycyl-L-leucyl-L-methionyl-L-valylglycylglycyl-L-valyl-L-valine chebi_ontology 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 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV beta-amyloid 40 beta-amyloid polypeptide 40 beta-amyloid protein 40 CHEBI:64646 amyloid-beta polypeptide 40 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. 0 C203H311N55O60S InChI=1S/C203H311N55O60S/c1-28-106(20)164(195(310)220-91-149(267)228-130(71-98(4)5)181(296)238-129(66-70-319-27)179(294)251-158(100(8)9)193(308)218-87-146(264)215-88-151(269)250-160(102(12)13)198(313)255-163(105(18)19)199(314)258-165(107(21)29-2)200(315)227-112(26)202(317)318)257-201(316)166(108(22)30-3)256-169(284)109(23)224-147(265)89-216-171(286)122(51-40-42-67-204)233-188(303)139(81-145(208)263)244-192(307)143(94-260)230-150(268)92-219-194(309)159(101(10)11)252-191(306)141(83-157(280)281)245-177(292)127(60-64-153(272)273)232-168(283)111(25)226-180(295)133(73-113-45-34-31-35-46-113)241-184(299)135(75-115-49-38-33-39-50-115)247-196(311)162(104(16)17)254-190(305)131(72-99(6)7)239-173(288)123(52-41-43-68-205)234-175(290)125(58-62-144(207)262)236-185(300)136(77-117-84-211-95-221-117)243-187(302)138(79-119-86-213-97-223-119)248-197(312)161(103(14)15)253-178(293)128(61-65-154(274)275)237-182(297)132(76-116-54-56-120(261)57-55-116)229-148(266)90-217-172(287)142(93-259)249-189(304)140(82-156(278)279)246-186(301)137(78-118-85-212-96-222-118)242-174(289)124(53-44-69-214-203(209)210)235-183(298)134(74-114-47-36-32-37-48-114)240-176(291)126(59-63-152(270)271)231-167(282)110(24)225-170(285)121(206)80-155(276)277/h31-39,45-50,54-57,84-86,95-112,121-143,158-166,259-261H,28-30,40-44,51-53,58-83,87-94,204-206H2,1-27H3,(H2,207,262)(H2,208,263)(H,211,221)(H,212,222)(H,213,223)(H,215,264)(H,216,286)(H,217,287)(H,218,308)(H,219,309)(H,220,310)(H,224,265)(H,225,285)(H,226,295)(H,227,315)(H,228,267)(H,229,266)(H,230,268)(H,231,282)(H,232,283)(H,233,303)(H,234,290)(H,235,298)(H,236,300)(H,237,297)(H,238,296)(H,239,288)(H,240,291)(H,241,299)(H,242,289)(H,243,302)(H,244,307)(H,245,292)(H,246,301)(H,247,311)(H,248,312)(H,249,304)(H,250,269)(H,251,294)(H,252,306)(H,253,293)(H,254,305)(H,255,313)(H,256,284)(H,257,316)(H,258,314)(H,270,271)(H,272,273)(H,274,275)(H,276,277)(H,278,279)(H,280,281)(H,317,318)(H4,209,210,214)/t106-,107-,108-,109-,110-,111-,112-,121-,122-,123-,124-,125-,126-,127-,128-,129-,130-,131-,132-,133-,134-,135-,136-,137-,138-,139-,140-,141-,142-,143-,158-,159-,160-,161-,162-,163-,164-,165-,166-/m0/s1 DZHSAHHDTRWUTF-SIQRNXPUSA-N 4514.03900 4511.26960 CC[C@H](C)[C@H](NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)CNC(=O)[C@H](CCCCN)NC(=O)[C@H](CC(N)=O)NC(=O)[C@H](CO)NC(=O)CNC(=O)[C@@H](NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](NC(=O)[C@H](CC(C)C)NC(=O)[C@H](CCCCN)NC(=O)[C@H](CCC(N)=O)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@@H](NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)CNC(=O)[C@H](CO)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](Cc1c[nH]cn1)NC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCC(O)=O)NC(=O)[C@H](C)NC(=O)[C@@H](N)CC(O)=O)C(C)C)C(C)C)C(C)C)[C@@H](C)CC)C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](C(C)C)C(=O)NCC(=O)NCC(=O)N[C@@H](C(C)C)C(=O)N[C@@H](C(C)C)C(=O)N[C@@H]([C@@H](C)CC)C(=O)N[C@@H](C)C(O)=O KEGG:C16515 L-alpha-aspartyl-L-alanyl-L-alpha-glutamyl-L-phenylalanyl-L-arginyl-L-histidyl-L-alpha-aspartyl-L-serylglycyl-L-tyrosyl-L-alpha-glutamyl-L-valyl-L-histidyl-L-histidyl-L-glutaminyl-L-lysyl-L-leucyl-L-valyl-L-phenylalanyl-L-phenylalanyl-L-alanyl-L-alpha-glutamyl-L-alpha-aspartyl-L-valylglycyl-L-seryl-L-asparaginyl-L-lysylglycyl-L-alanyl-L-isoleucyl-L-isoleucylglycyl-L-leucyl-L-methionyl-L-valylglycylglycyl-L-valyl-L-valyl-L-isoleucyl-L-alanine chebi_ontology 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 DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIA beta-amyloid 42 beta-amyloid polypeptide 42 beta-amyloid protein 42 CHEBI:64647 amyloid-beta polypeptide 42 The study of the interaction of a sample with radiation or particles for measurement or detection. spectrometry CHMO:0000228 spectroscopy Spectrometry where the sample is converted into gaseous ions which are characterised by their mass-to-charge ratio and relative abundance. MS mass spectroscopy CHMO:0000470 mass spectrometry yes 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. CALOHA:TS-2035 FBbt:00007002 FMA:68646 GO:0005623 KUPO:0000002 MESH:D002477 VHOG:0001533 WBbt:0004017 XAO:0003012 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). cell yes A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. BTO:0000782 CALOHA:TS-1001 FMA:62870 MESH:D013601 VHOG:0001479 T lymphocyte T-cell T-lymphocyte immature T cell mature T cell T cell A leukocyte with abundant granules in the cytoplasm. BTO:0000539 BTO:0001026 CALOHA:TS-0422 FMA:62854 granular leucocyte granular leukocyte polymorphonuclear leukocyte granulocyte 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. BTO:0000775 CALOHA:TS-0583 FMA:62863 MESH:D008214 VHOG:0001535 Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte yes Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 CALOHA:TS-0638 FMA:62864 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. monocyte An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 CALOHA:TS-0549 FMA:62852 MESH:D007962 leucocyte white blood cell immune cell leukocyte yes 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. PMN poly polymorphonuclear leucocyte polymorphonuclear leukocyte polymorphonuclear neutrophil polynuclear neutrophilic leucocyte polynuclear neutrophilic leukocyte BTO:0000130 CALOHA:TS-0688 FMA:62860 MESH:D009504 neutrocyte neutrophil leucocyte neutrophil leukocyte neutrophilic leucocyte neutrophilic leukocyte neutrophil 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. clinical_measurement_ontology CMO:0000000 clinical measurement 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. mshimoyama 2009-12-17T10:41:54Z glucose measurement EFO:0004465 EFO:0004468 fasting blood glucose measurement clinical_measurement_ontology CMO:0000046 blood glucose level 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). JSmith 2012-03-28T10:49:24Z CHEBI:16737 EFO:0007934 CrCl creatinine clearance measurement clinical_measurement_ontology CMO:0000765 creatinine clearance Renal blood flow (RBF) is the volume of blood delivered to or exiting from the kidneys per unit time. JSmith 2012-07-11T10:38:08Z clinical_measurement_ontology CMO:0000907 renal blood flow rate The amount of oxygen bound to hemoglobin in the blood expressed as a percentage of the maximal binding capacity. JSmith 2013-01-09T16:37:31Z oxygen saturation measurement EFO:0005682 blood oxygen saturation percent oxygen saturation clinical_measurement_ontology CMO:0001324 oxygen saturation 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. sjwang 2018-11-13T15:12:25Z EFO:0008003 PMID:26063669 HRV RR variability cycle length variability heart rate variability measurement clinical_measurement_ontology CMO:0002812 heart rate variability 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. slaulede 2021-05-20T15:30:59Z EFO:0004517 EFO:0004724 PMID:32088716 Carotid–femoral PWV PWV arterial stiffness measurement carotid-femoral pulse wave velocity clinical_measurement_ontology CMO:0003717 pulse wave velocity 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 slaulede 2021-07-29T16:36:46Z EFO:0007980 PMID:27403447 PMID:29498562 CBF rate cerebral blood flow measurement clinical_measurement_ontology CMO:0003815 cerebral blood flow rate 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. Oliver He, Asiyah Yu Lin, Qingliang Li interventional trial https://clinicaltrials.gov/ct2/search/map https://en.wikipedia.org/wiki/Clinical_trial https://prsinfo.clinicaltrials.gov/definitions.html https://www.who.int/ictrp/en/ clinical trial A disease that involving errors in metabolic processes of building or degradation of molecules. ICD10CM:E88.9 ICD9CM:277.9 MESH:D008659 NCI:C3235 SNOMEDCT_US_2022_09_01:75934005 UMLS_CUI:C0025517 metabolic disease metabolic disorder disease_ontology DOID:0014667 disease of metabolism yes An intestinal disease characterized by inflammation located in all parts of digestive tract. EFO:0003767 KEGG:05321 MESH:D015212 NCI:C3138 OMIM:PS266600 SNOMEDCT_US_2022_09_01:155759008 UMLS_CUI:C0021390 disease_ontology DOID:0050589 Xref MGI. OMIM mapping confirmed by DO. [SN]. inflammatory bowel disease yes An artery disease that is characterized by build up of plaque in the arteries that carry blood to your head, organs, and limbs. lschriml 2014-02-18T12:41:09Z MESH:D058729 peripheral arterial disease disease_ontology DOID:0050830 peripheral artery disease A vascular disease caused by the formation of a blood clot inside a blood vessel, obstructing the flow of blood through the circulatory system. MESH:D013927 disease_ontology DOID:0060903 thrombosis yes A male reproductive organ cancer that is located_in the prostate. DOID:514 ICD10CM:C61 ICD9CM:185 KEGG:05215 MESH:D011471 NCI:C3343 NCI:C7378 OMIM:176807 OMIM:300147 OMIM:300704 OMIM:601518 OMIM:602759 OMIM:608656 OMIM:608658 OMIM:609299 OMIM:609558 OMIM:610321 OMIM:610997 OMIM:611100 OMIM:611868 OMIM:611928 OMIM:611955 OMIM:611958 OMIM:611959 ORDO:1331 SNOMEDCT_US_2022_09_01:126906006 SNOMEDCT_US_2022_09_01:93974005 UMLS_CUI:C0033578 UMLS_CUI:C0376358 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 disease_ontology DOID:10283 Xref MGI. OMIM mapping confirmed by DO. [SN]. prostate cancer yes A stomach cancer that is located_in the gastric fundus. ICD10CM:C16.1 ICD9CM:151.3 SNOMEDCT_US_2022_09_01:93809003 UMLS_CUI:C0153420 Ca fundus - stomach malignant neoplasm of fundus of stomach malignant tumor of fundus of stomach disease_ontology DOID:10538 gastric fundus cancer yes A hypertension occurring during pregnancy characterized by large amounts of protein in the urine (proteinuria) and edema, usually by the last trimester of pregnancy. DOID:12684 ICD10CM:O14 MESH:D011225 NCI:C85021 OMIM:189800 OMIM:609402 OMIM:609403 OMIM:609404 OMIM:614592 ORDO:275555 SNOMEDCT_US_2022_09_01:6758009 UMLS_CUI:C0032914 gestational hypertension hypertension induced by pregnancy pre-eclamptic toxaemia preeclampsia preeclampsia/eclampsia pregnancy associated hypertension pregnancy toxemia proteinuric hypertension of pregnancy toxaemia of pregnancy disease_ontology DOID:10591 Xref MGI. OMIM mapping confirmed by DO. [SN]. pre-eclampsia yes 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. EFO:0001060 GARD:11998 ICD10CM:K90.0 ICD9CM:579.0 MESH:D002446 NCI:C26714 OMIM:607202 OMIM:609754 OMIM:611598 OMIM:612005 OMIM:612006 OMIM:612007 OMIM:612008 OMIM:612009 OMIM:612011 ORDO:555 SNOMEDCT_US_2022_09_01:197477005 UMLS_CUI:C0007570 celiac sprue coeliac disease idiopathic steatorrhea disease_ontology DOID:10608 Xref MGI. OMIM mapping confirmed by DO. [SN]. celiac disease yes An artery disease characterized by chronic elevated blood pressure in the arteries. EFO:0000537 ICD10CM:I10 ICD9CM:401-405.99 MESH:D006973 NCI:C3117 SNOMEDCT_US_2022_09_01:38341003 UMLS_CUI:C0020538 HTN hyperpiesia vascular hypertensive disorder disease_ontology hypertensive disease DOID:10763 hypertension yes A cardiovascular system disease that involves the heart. ICD10CM:I51.9 ICD9CM:429.9 MESH:D006331 NCI:C3079 SNOMEDCT_US_2022_09_01:194707003 UMLS_CUI:C0018799 disease_ontology DOID:114 heart disease yes An ovarian dysfunction that is characterized by hyperandrogenism, polycystic ovaries, hirsutism, oligomenorrhea or amenorrhea, anovulation and excessive body weight. EFO:0000660 ICD10CM:E28.2 ICD9CM:256.4 MESH:D011085 NCI:C26862 OMIM:184700 SNOMEDCT_US_2022_09_01:69878008 UMLS_CUI:C0032460 Multicystic ovaries PCOS Polycystic Ovarian disease Polycystic ovaries Stein-Leventhal synd. Stein-Leventhal syndrome polycystic ovary disease_ontology DOID:11612 OMIM mapping confirmed by DO. [SN]. polycystic ovary syndrome yes 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. GARD:6677 ICD10CM:G10 ICD9CM:333.4 KEGG:05016 MESH:D006816 NCI:C82342 OMIM:143100 SNOMEDCT_US_2022_09_01:58756001 UMLS_CUI:C0020179 HD Huntington disease Huntington's chorea disease_ontology DOID:12858 Huntington's disease yes 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. DOID:73 ICD9CM:429.2 MESH:D002318 NCI:C2931 SNOMEDCT_US_2022_09_01:266275004 UMLS_CUI:C0007222 disease of subdivision of hemolymphoid system disease_ontology DOID:1287 cardiovascular system disease yes A respiratory system cancer that is located_in the lung. DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 SNOMEDCT_US_2022_09_01:187860004 SNOMEDCT_US_2022_09_01:187864008 SNOMEDCT_US_2022_09_01:187868006 SNOMEDCT_US_2022_09_01:187874006 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493 disease_ontology lung neoplasm DOID:1324 lung cancer yes 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. GARD:6400 ICD10CM:E75.21 MESH:D000795 NCI:C84701 OMIM:301500 SNOMEDCT_US_2022_09_01:16652001 UMLS_CUI:C0002986 Alpha-galactosidase A deficiency Angiokeratoma Corporis Diffusum Fabry Disease, Cardiac Variant Fabry's disease alpha galactosidase deficiency deficiency of melibiase disease_ontology DOID:14499 OMIM mapping confirmed by DO. [SN]. Fabry disease yes A musculoskeletal system disease that involves inflammation or pain in the muscles, joints, or fibrous tissue. disease_ontology DOID:1575 rheumatic disease yes A disease of anatomical entity that located_in the respiratory system which extends from the nasal sinuses to the diaphragm. DOID:3226 ICD10CM:J98 ICD9CM:519 SNOMEDCT_US_2022_09_01:155603009 UMLS_CUI:C0029582 respiratory disease disease_ontology DOID:1579 respiratory system disease yes A thoracic cancer that originates in the mammary gland. DOID:1648 DOID:4241 ICD10CM:C50 MESH:D001943 NCI:C9335 OMIM:114480 SNOMEDCT_US_2022_09_01:254837009 UMLS_CUI:C0006142 breast tumor malignant neoplasm of breast malignant tumor of the breast mammary cancer mammary tumor primary breast cancer disease_ontology mammary neoplasm DOID:1612 Xref MGI. OMIM mapping confirmed by DO. [SN]. breast cancer yes A disease of cellular proliferation that is malignant and primary, characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. ICD10CM:C80.1 ICD9CM:199 ICDO:8000/3 MESH:D009369 NCI:C9305 SNOMEDCT_US_2022_09_01:269513004 UMLS_CUI:C0006826 malignant neoplasm malignant tumor primary cancer disease_ontology DOID:162 Updating out dated UMLS CUI. cancer yes 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. DOID:0000405 DOID:2403 DOID:2869 DOID:324 DOID:325 DOID:45 ICD10CM:I72.9 ICD9CM:442.9 MESH:D000783 MESH:D014652 MESH:D020758 MESH:D020760 NCI:C26693 NCI:C35117 SNOMEDCT_US_2022_09_01:27550009 SNOMEDCT_US_2022_09_01:371029002 SNOMEDCT_US_2022_09_01:432119003 UMLS_CUI:C0002940 UMLS_CUI:C0042373 UMLS_CUI:C0752127 UMLS_CUI:C0752130 vascular tissue disease disease_ontology DOID:178 vascular disease ICD10CM:E83.1 ICD9CM:275.0 MESH:D019189 SNOMEDCT_US_2023_03_01:30913008 UMLS_CUI:C0012715 disorder of iron metabolism iron disorder disease_ontology DOID:2351 iron metabolism disease yes A hematopoietic system disease that is characterized by a decrease in the normal number of red blood cells. EFO:0004272 ICD10CM:D64.9 ICD9CM:285.9 MESH:D000740 NCI:C2869 SNOMEDCT_US_2022_09_01:64593003 UMLS_CUI:C0002871 anaemia disease_ontology DOID:2355 PRISM. anemia MESH:D000740 yes A female reproductive organ cancer that is located_in the ovary. DOID:0060070 DOID:2144 DOID:9595 GARD:7295 ICD10CM:C56 ICD9CM:183.0 MESH:D010051 NCI:C4984 NCI:C7431 OMIM:167000 OMIM:607893 ORDO:213500 ORDO:213517 SNOMEDCT_US_2022_09_01:123843001 SNOMEDCT_US_2022_09_01:372117006 SNOMEDCT_US_2022_09_01:93934004 UMLS_CUI:C0919267 UMLS_CUI:C1140680 UMLS_CUI:C1299247 malignant Ovarian tumor malignant tumour of ovary ovarian neoplasm ovary neoplasm primary ovarian cancer tumor of the Ovary disease_ontology DOID:2394 Xref MGI. OMIM mapping confirmed by DO. [SN]. ovarian cancer yes 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. DOID:12703 DOID:13829 DOID:13830 DOID:2840 DOID:5783 EFO:0000270 GARD:10246 ICD10CM:J45 ICD9CM:493 KEGG:05310 MESH:D001249 NCI:C28397 OMIM:600807 SNOMEDCT_US_2022_09_01:187687003 UMLS_CUI:C0004096 Exercise induced asthma bronchial hyperreactivity chronic obstructive asthma chronic obstructive asthma with acute exacerbation chronic obstructive asthma with status asthmaticus exercise-induced asthma disease_ontology DOID:2841 Xref MGI. asthma MESH:D001249 yes 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. GARD:13336 ICD10CM:J84.9 MESH:D017563 NCI:C164315 SNOMEDCT_US_2022_09_01:64667001 UMLS_CUI:C0206062 ILD disease_ontology DOID:3082 interstitial lung disease yes A mood disorder that involves alternating periods of mania and depression. DOID:3311 DOID:9554 DOID:9555 EFO:0000289 GARD:10249 ICD10CM:F31 ICD9CM:296.40 ICD9CM:296.60 ICD9CM:296.80 MESH:D001714 NCI:C34423 NCI:C34424 NCI:C34805 SNOMEDCT_US_2022_09_01:16506000 SNOMEDCT_US_2022_09_01:191627008 SNOMEDCT_US_2022_09_01:192355004 SNOMEDCT_US_2022_09_01:68569003 UMLS_CUI:C0005586 UMLS_CUI:C0005587 UMLS_CUI:C0024713 UMLS_CUI:C0236780 Manic Bipolar Affective disorder Manic Depressive disorder Manic bipolar I disorder bipolar depression bipolar disorder manic phase manic depression manic disorder mixed bipolar disorder disease_ontology Depressive-manic psych. DOID:3312 bipolar disorder yes A mouth disease that is relating to or affecting the structures surrounding and supporting the teeth. ICD10CM:K05.6 MESH:D010510 NCI:C63743 SNOMEDCT_US_2022_09_01:196354003 UMLS_CUI:C0031090 disease of supporting structures of teeth periodontium disorder disease_ontology DOID:3388 periodontal disease yes An integumentary system disease that is located_in skin. DOID:1576 DOID:1698 DOID:187 DOID:6486 DOID:8948 ICD9CM:702 MESH:D012871 MESH:D012873 NCI:C156032 NCI:C3371 SNOMEDCT_US_2022_09_01:201095006 SNOMEDCT_US_2022_09_01:5613003 SNOMEDCT_US_2022_09_01:95320005 UMLS_CUI:C0029574 UMLS_CUI:C0037274 UMLS_CUI:C0037277 Genodermatosis skin and subcutaneous tissue disease disease_ontology DOID:37 skin disease yes A lung carcinoma that is characterized as any type of epithelial lung cancer other than small cell lung carcinoma. EFO:0003060 KEGG:05223 MESH:D002289 NCI:C2926 SNOMEDCT_US_2022_09_01:254637007 UMLS_CUI:C0007131 NSCLC Non-small cell lung cancer non-small cell lung carcinoma disease_ontology DOID:3908 lung non-small cell carcinoma yes 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. MESH:D004194 NCI:C2991 SNOMEDCT_US_2022_09_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease yes DOID:2164 DOID:2165 DOID:46 ICD10CM:K76.9 ICD9CM:573.9 MESH:D008107 NCI:C3196 SNOMEDCT_US_2022_09_01:62857009 UMLS_CUI:C0023895 disorder of liver hepatic disorder disease_ontology fatty liver disease DOID:409 liver disease yes 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 disease ICD9CM:720 OMIM:109100 UMLS_CUI:C0003089 autoimmune hypersensitivity disease hypersensitivity reaction type II disease disease_ontology DOID:417 Xref MGI. autoimmune disease A pancreas disease that is characterized by inflammation of the pancreas. EFO:0000278 ICD10CM:K85.9 MESH:D010195 NCI:C3306 OMIM:167800 SNOMEDCT_US_2023_03_01:393591004 UMLS_CUI:C0030305 disease_ontology DOID:4989 pancreatitis yes EFO:0001422 ICD10CM:K74.60 MESH:D008103 NCI:C2951 SNOMEDCT_US_2022_09_01:19943007 UMLS_CUI:C0023890 Cirrhosis cirrhosis of liver disease_ontology liver fibrosis DOID:5082 liver cirrhosis yes A urinary system disease that is located_in the kidney. DOID:11705 EFO:0003086 ICD10CM:N08 MESH:D007674 NCI:C3149 SNOMEDCT_US_2022_09_01:266612003 UMLS_CUI:C0022658 impaired renal function disease nephropathy renal disease disease_ontology DOID:557 kidney disease yes A kidney disease that is characterized by the presence of excess proteins in the urine. ICD10CM:R80 ICD9CM:791.0 MESH:D011507 NCI:C38012 SNOMEDCT_US_2022_09_01:144515004 UMLS_CUI:C0033687 disease_ontology DOID:576 proteinuria yes A coronary artery disease characterized by myocardial cell death (myocardial necrosis) due to prolonged ischaemia. EFO:0000612 ICD10CM:I21 MESH:D009203 NCI:C27996 OMIM:608557 SNOMEDCT_US_2022_09_01:66514008 UMLS_CUI:C0027051 Myocardial infarct acute myocardial infarction heart attack disease_ontology DOID:5844 Xref MGI. myocardial infarction yes 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. DOID:395 ICD10CM:I50 ICD10CM:I50.9 ICD9CM:428 ICD9CM:428.0 MESH:D006333 NCI:C3080 NCI:C50577 SNOMEDCT_US_2022_09_01:155374007 SNOMEDCT_US_2022_09_01:195108009 UMLS_CUI:C0018801 UMLS_CUI:C0018802 CHF Cardiac Failure Congestive Congestive heart disease Weak heart disease_ontology DOID:6000 congestive heart failure yes An vascular disease that is characterized by dysfunction of the blood vessels supplying the brain. DOID:12214 DOID:3455 DOID:8231 EFO:0000712 ICD10CM:I67.9 ICD9CM:437.9 MESH:D002561 NCI:C2938 SNOMEDCT_US_2022_09_01:266312006 UMLS_CUI:C0007820 CVA cerebrovascular disorder stroke disease_ontology DOID:6713 OMIM mapping confirmed by DO. [SN]. cerebrovascular disease yes A liver carcinoma that has_material_basis_in undifferentiated hepatocytes and located_in the liver. DOID:5005 EFO:0000182 ICD10CM:C22.0 ICDO:8170/3 MESH:D006528 NCI:C3099 OMIM:114550 ORDO:88673 SNOMEDCT_US_2022_09_01:154469006 UMLS_CUI:C2239176 Hepatoma disease_ontology DOID:684 OMIM mapping confirmed by DO. [SN]. hepatocellular carcinoma yes A kidney failure that is characterized by the gradual loss of kidney function. ICD10CM:N18.9 ICD9CM:585.6 MESH:D007676 NCI:C9438 SNOMEDCT_US_2022_09_01:155856009 UMLS_CUI:C0022661 CKD CKD CRF chronic kidney failure chronic renal disease chronic renal failure syndrome renal failure - chronic disease_ontology DOID:784 chronic kidney disease yes 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. DOID:11894 DOID:11895 DOID:29 DOID:766 ICD10CM:J98.4 MESH:D008171 NCI:C3198 SNOMEDCT_US_2022_09_01:266374002 UMLS_CUI:C0024115 disease_ontology DOID:850 Updating out dated CUI and removing lung abscess as a synonym. lung disease yes A skin disease that is characterized by patches of thick red skin and silvery scales. EFO:0000676 GARD:10262 ICD10CM:L40 MESH:D011565 NCI:C3346 OMIM:PS177900 SNOMEDCT_US_2022_09_01:156369008 UMLS_CUI:C0033860 disease_ontology DOID:8893 Xref MGI. Update outdated UMLS CUI from C00295134 to C0033860. psoriasis yes A large intestine cancer that is located_in the colon and/or located_in the rectum. ICD10CM:C18.9 KEGG:05210 MESH:D015179 NCI:C2956 NCI:C4978 OMIM:114500 SNOMEDCT_US_2022_09_01:126837005 SNOMEDCT_US_2022_09_01:93854002 UMLS_CUI:C0009404 UMLS_CUI:C0346629 disease_ontology DOID:9256 Xref MGI. OMIM mapping confirmed by DO. [SN]. colorectal cancer yes 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. DOID:0081062 ICD10CM:E08-E13 ICD9CM:250 MESH:D003920 NCI:C2985 SNOMEDCT_US_2022_09_01:267467004 UMLS_CUI:C0011849 diabetes disease_ontology DOID:9351 diabetes mellitus yes A diabetes mellitus that is characterized by high blood sugar, insulin resistance, and relative lack of insulin. EFO:0001360 ICD10CM:E11 KEGG:04930 MESH:D003924 NCI:C26747 OMIM:125853 OMIM:601283 OMIM:601407 OMIM:603694 OMIM:608036 SNOMEDCT_US_2022_09_01:44054006 UMLS_CUI:C0011860 NIDDM T2DM insulin resistance non-insulin-dependent diabetes mellitus type 2 diabetes type II diabetes mellitus disease_ontology DOID:9352 Xref MGI. OMIM mapping confirmed by DO. [SN]. type 2 diabetes mellitus yes 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. EFO:0001073 ICD10CM:E66.9 ICD9CM:278.00 MESH:D009765 NCI:C159658 OMIM:601665 SNOMEDCT_US_2022_09_01:5476005 UMLS_CUI:C0028754 disease_ontology DOID:9970 OMIM mapping confirmed by DO. [SN]. obesity Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels. Wikipedia:Angiogenesis blood vessel formation from pre-existing blood vessels biological_process GO:0001525 angiogenesis yes 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. fibrinogen fibrinogen alpha chain fibrinogen beta chain fibrinogen gamma chain cellular_component GO:0005577 fibrinogen complex 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. inflammation Wikipedia:Inflammation biological_process GO:0006954 inflammatory response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. biological_process GO:0006955 immune response 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. https://github.com/geneontology/go-ontology/issues/24968 jl 2012-09-19T15:05:24Z GO:0000004 GO:0007582 GO:0044699 Wikipedia:Biological_process biological process physiological process biological_process single organism process single-organism process GO:0008150 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. biological_process 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. https://github.com/geneontology/go-ontology/issues/26424 jl 2012-10-17T15:46:40Z GO:0044236 GO:0044710 Wikipedia:Metabolism metabolism metabolic process resulting in cell growth metabolism resulting in cell growth multicellular organism metabolic process biological_process single-organism metabolic process GO:0008152 Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. metabolic process 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. jl 2012-12-11T16:56:55Z GO:0008151 GO:0044763 GO:0050875 cell physiology cellular physiological process cell growth and/or maintenance biological_process single-organism cellular process GO:0009987 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. cellular process 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. https://github.com/geneontology/go-ontology/issues/22557 Wikipedia:Gene_expression biological_process GO:0010467 gene expression 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. GO:0043234 macromolecular complex macromolecule complex protein containing complex protein complex protein-protein complex cellular_component GO:0032991 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. protein-containing complex Cessation of menstruation, occurring in (e.g.) the human female usually around the age of 50. Wikipedia:Menopause biological_process GO:0042697 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). menopause A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest. https://github.com/geneontology/go-ontology/issues/22788 tb 2011-01-05T02:27:08Z biological_process GO:0090398 cellular senescence A cell aging process associated with the dismantling of a cell as a response to telomere shortening and/or cellular aging. https://github.com/geneontology/go-ontology/issues/22788 tb 2011-01-05T02:32:29Z biological_process GO:0090399 replicative senescence A person who makes a donation. http://homosaurus.org/v2/donors https://homosaurus.org/terms/donors donor donor donors Analyses regarding statistical data. https://en.wikipedia.org/wiki/Category:Statistical_analysis https://www.wikidata.org/wiki/Q12718609 statistical analysis statistical analyses A phenotypic abnormality. UMLS:C4021819 Organ abnormality HP:0000118 This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality yes Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). MSH:D058186 SNOMEDCT_US:14350001000004108 SNOMEDCT_US:14669001 UMLS:C0022660 UMLS:C2609414 Acute kidney failure Acute renal failure HP:0001919 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. Acute kidney injury SNOMEDCT_US:22631008 SNOMEDCT_US:394616008 UMLS:C0231686 Gait instability Unsteady walk HP:0002317 Unsteady gait Abnormal calcification of the vasculature. MSH:D061205 SNOMEDCT_US:237897009 UMLS:C0342649 HP:0004934 Vascular calcification Partial or complete wasting (loss) of brain tissue that was once present. 2013-11-23T02:46:15Z SNOMEDCT_US:278849000 SNOMEDCT_US:418143002 SNOMEDCT_US:52522001 UMLS:C0154671 UMLS:C0235946 Brain degeneration Brain wasting whole brain volume loss HP:0012444 Brain atrophy 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. 2014-06-06T06:34:24Z HP:0000004 UMLS:C4021064 Phenotypic modifier HP:0012823 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. Clinical modifier Applies to a sign, symptom or manifestation that occurs multiple times separated by intervals in which the sign, symptom, or manifestation is not present. 2018-02-25T14:40:47Z Intermittent Recurrent An abnormality of movement with a neurological basis characterized by changes in coordination and speed of voluntary movements. 2010-05-28T11:48:50Z HP:0001294 SNOMEDCT_US:60342002 UMLS:C0026650 Abnormality of movement Movement disorder Unusual movement HP:0100022 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. Abnormality of movement yes 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 data item yes 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. PERSON: Chris Stoeckert OBI_0000142 information content entity yes 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 OBI_0000305 group:OBI measurement datum yes 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 textual entity yes 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 Person:Alan Ruttenberg hypothesis textual entity A document that either prescribes actions or prescribes the permissions, obligations, restrictions, or protections relating to public or legal policy. Cooper Stansbury 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. Albert Goldfain Alexander Diehl Lindsay Cowell sepsis A clinically prescribed procedure, therapy, intervention, or recommendation. 2018-11-16T20:07:28Z OGMS:0000096 health care process 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. 2018-11-16T20:08:29Z NCIT:C25218 NCIT:C49236 OAE:0000094 OGMS:0000112 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. 2018-11-16T20:10:20Z NCIT:C18020 OGMS:0000104 diagnostic technique procedure diagnostic testing 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. 2018-11-16T20:10:35Z ERO:0000378 NCIT:C15329 NCIT:C17173 NCRO:0000228 OAE:0000067 SCDO:1000017 operation surgery surgical intervention surgical operation surgical procedure A broad subcategory of medical signs or objective indications of medical state which can be measured accurately and reproducibly. 2018-11-16T20:22:04Z NCIT:C63333 biomarker assessment biomarker measurement biomarker test 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. 2019-01-20T00:46:22Z NCIT:C15709 genetic analysis genetic testing The use of synthetic or naturally-occurring chemicals for the treatment of diseases. 2020-06-02T13:10:41Z NCIT:C15632 OGMS:0000113 chemotherapeutic agent treatment chemotherapeutic drug treatment treatment with a chemotherapeutic agent treatment with a chemotherapeutic drug 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. 2023-02-24T19:31:14Z NCIT:C162707 eye movement assessment eye movement measurement The use of ultrasound to produce images of structures in the heart. 2020-01-24T20:39:14Z http://orcid.org/0000-0001-7941-2961 cardiac echo procedure echo procedure echocardiogram procedure heart diagnostic sonography heart medical ultrasound heart sonography heart ultrasound examination heart ultrasound imaging procedure heart ultrasound procedure sonography of heart ultrasonography of heart echocardiography Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences. PSI-MI MI:0252 biological feature 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. mshimoyama 2010-08-05T01:56:02Z OGTT measurement_method_ontology MMO:0000113 oral glucose tolerance test yes An impairment of the structure or function of the blood vessels which carry blood away from the heart. DOID:0050828 ICD9:447.8 ICD9:447.9 NCIT:C35317 SCTID:359557001 UMLS:C0852949 arterial disease arterial disorder arteriopathy artery disease artery disease or disorder disease of artery disease or disorder of artery disorder of artery MONDO:0000473 arterial disorder A primary or metastatic malignant neoplasm involving the stomach. https://github.com/monarch-initiative/mondo/issues/4521 gastric neoplasm DOID:10534 ICD10CM:C16 ICD9:151 ICD9:151.4 ICD9:151.5 ICD9:151.6 ICD9:151.9 NCIT:C9331 OMIM:613659 Orphanet:63443 Ca lesser curvature - stomach cancer of stomach gastric cancer gastric cancer risk after h. pylori infection gastric cancer, somatic malignant gastric neoplasm malignant gastric tumor malignant gastric tumour malignant neoplasm of lesser curve of stomach malignant neoplasm of stomach malignant neoplasm of the stomach malignant stomach neoplasm malignant tumor of body of stomach malignant tumor of greater curve of stomach malignant tumor of lesser curve of stomach malignant tumor of stomach malignant tumor of the stomach malignant tumour of body of stomach malignant tumour of greater curve of stomach malignant tumour of lesser curve of stomach malignant tumour of stomach malignant tumour of the stomach stomach cancer Ca body - stomach ca greater curvature of stomach malignant neoplasm of body of stomach gastric cancer, intestinal MONDO:0001056 gastric cancer Any disease in which the causes of the disease is a perturbation of the kidney leading to its dysfunction. disease of kidney kidney disease DOID:11705 ICD10CM:N25 ICD9:588.8 ICD9:588.89 ICD9:588.9 SCTID:197663003 MONDO:0001343 impaired renal function disease yes A disease or disorder that involves the digestive system. DOID:77 EFO:0000405 ICD10CM:K00-K95 ICD9:520-579.99 ICD9:V47.3 MESH:D005767 NCIT:C2990 SCTID:53619000 alimentary system disease digestive disease digestive system disease digestive system disease or disorder digestive system disorder disease of digestive system disease or disorder of digestive system disorder of digestive system gastroenterological system disease gastroenterological system disorder gastroenteropathy gastrointestinal disease gastrointestinal disorder gastrointestinal system disease gastrointestinal system disorder git disease stomach or intestinal disorder MONDO:0004335 digestive system disorder yes 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. https://github.com/monarch-initiative/mondo/issues/4013 DOID:10652 EFO:0000249 GARD:0000632 HP:0002511 ICD10CM:G30 ICD9:290.1 ICD9:331.0 MESH:D000544 NCIT:C2866 NIFSTD:birnlex_2092 Orphanet:238616 SCTID:142811000119104 UMLS:C0002395 AD Alzheimer dementia Alzheimer disease Alzheimer's dementia Alzheimer's disease Alzheimers dementia Alzheimers disease presenile and senile dementia Alzheimer disease, familial MONDO:0004975 Alzheimer disease yes 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. DOID:3083 EFO:0000341 ICD9:490-496.99 ICD9:496 MESH:D029424 NCIT:C3199 OMIM:606963 SCTID:13645005 COPD COPD, chronic obstructive pulmonary disease chronic obstructive airway disease chronic obstructive airways disease chronic obstructive lung disease chronic obstructive pulmonary disease (COPD) chronic obstructive pulmonary disease, (COPD) cold cold (chronic obstructive lung disease) disease (COPD), chronic obstructive obstructive lung disease, chronic obstructive pulmonary disease (COPD), chronic pulmonary disease (COPD), chronic obstructive MONDO:0005002 chronic obstructive pulmonary disease 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. neoplasm (disease) cell process disease DOID:14566 EFO:0000616 HP:0002664 ICD10CM:C00-D49 ICD10CM:C7A-C7A ICD10CM:C7B-C7B ICD9:140-239.99 ICD9:239.8 ICD9:239.9 MESH:D009369 NCIT:C3262 ONCOTREE:OTHER SCTID:55342001 UMLS:CN236628 disease of cellular proliferation neoplasia neoplasm neoplasm (disease) neoplastic disease neoplastic growth tumor tumor disease other neoplasm MONDO:0005070 neoplasm A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. DOID:863 EFO:0000618 ICD10CM:G00-G99 ICD9:349.89 ICD9:349.9 MESH:D009422 NCIT:C26835 SCTID:118940003 UMLS:C0027765 Wikipedia:Nervous_system_disease disease of nervous system disease or disorder of nervous system disorder of nervous system nervous system disease nervous system disease or disorder nervous system disorder neurologic disease neurologic disorder neurological disease neurological disorder MONDO:0005071 '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. nervous system disorder An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections. DOID:104 EFO:0000771 ICD9:040.89 ICD9:041.89 ICD9:041.9 MESH:D001424 NCIT:C2890 SCTID:87628006 UMLS:C0004623 Bacteria caused disease or disorder Bacteria disease or disorder Bacteria infectious disease bacterial disease bacterial disorder bacterial infection bacterial infectious disease infection, bacterial infections, bacterial MONDO:0005113 bacterial infectious disease yes Build-up of fatty material and calcium deposition in the arterial wall resulting in partial or complete occlusion of the arterial lumen. DOID:1936 EFO:0003914 ICD10CM:I70 ICD9:440 ICD9:440.8 MESH:D050197 NCIT:C35768 NCIT:C35771 SCTID:441574008 atherosclerosis of artery atherosclerotic cardiovascular disease atherosclerosis artery MONDO:0005311 Note that NCIT distinguishes between atherosclerotic cardiovascular disease and atherosclerosis - we merge these here atherosclerosis Diseases of bones. DOID:0080001 EFO:0004260 ICD10CM:M80-M85 ICD9:731.8 ICD9:733.99 MESH:D001847 Orphanet:364803 SCTID:76069003 UMLS:C0005940 UMLS:CN204768 bone element disease bone element disease or disorder disease of bone element disease or disorder of bone element disorder of bone element rare bone disease related to a common gene or pathway defect skeletal disease MONDO:0005381 bone disorder yes The spread of a malignant neoplasm to the lymph nodes. EFO:0004906 NCIT:C4904 UMLS:C0686619 Metastases to lymph nodes lymph node metastasis metastasis to lymph node metastatic malignant neoplasm to the lymph nodes metastatic neoplasm to the lymph node metastatic tumor to lymph node MONDO:0005438 metastatic malignant neoplasm in the lymph nodes yes 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. EFO:0005672 MESH:D054058 NCIT:C53652 SCTID:394659003 UMLS:C0948089 acute coronary syndrome acute coronary syndromes coronary syndrome, acute coronary syndromes, acute syndrome, acute coronary syndromes, acute coronary MONDO:0005542 acute coronary syndrome yes A disorder of the central nervous system characterized by gradual and progressive loss of neural tissue and neurologic function. degenerative disease DOID:1289 EFO:0005772 ICD9:349.89 MESH:D019636 NCIT:C4802 SCTID:80690008 brain degeneration central nervous system degenerative disorder central nervous system neurodegenerative disorder degenerative disorder of central nervous system neurodegenerative disease cerebral degeneration disease MONDO:0005559 Editor notes: DO treats this as two diseases neurodegenerative disease yes 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. https://github.com/monarch-initiative/mondo/issues/4521 systemic lupus erythematosus (disease) DOID:9074 EFO:0002690 HP:0002725 ICD9:710.0 MESH:D008180 NCIT:C3201 OMIM:152700 Orphanet:536 SCTID:55464009 SLE SLE - lupus erythematosus, systemic disseminated lupus erythematosus lupus erythematosus, systemic systemic lupus erythematosus systemic lupus erythematosus (disease) systemic lupus erythematosus susceptibility to systemic lupus erythematosus, susceptibility to excess LMW-DNA excess lymphocyte low molecular weight DNA lupus nephritis, susceptibility to MONDO:0007915 systemic lupus erythematosus yes 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. https://github.com/monarch-initiative/mondo/issues/4521 https://github.com/monarch-initiative/mondo/issues/6094 atrophic arthritis DOID:7148 EFO:0000685 HP:0001370 ICD9:714.0 MESH:D001172 NCIT:C2884 OMIM:180300 Orphanet:284130 SCTID:69896004 UMLS:C0003873 RA arthritis or polyarthritis, rheumatic arthritis, rheumatoid autoimmune arthritis rheumatoid arthritis rheumatoid arthritis, progression of rheumatoid arthritis, susceptibility to MONDO:0008383 rheumatoid arthritis 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). EFO:1001375 ICD10CM:I20-I25 MESH:D017202 NCIT:C50625 SCTID:414545008 UMLS:C0151744 IHD ischemic disease of myocardium ischemic heart disease myocardium ischemic disease disease, ischemic heart diseases, ischemic heart heart disease, ischemic heart diseases, ischemic ischemia, myocardial ischemias, myocardial ischemic heart diseases myocardial Ischemias MONDO:0024644 myocardial ischemia 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. MESH:D001930 Orphanet:90056 brain injury injury of brain brain Traumas brain trauma MONDO:0043510 brain injury A brain disease that is characterized by brain dysfunction caused by an outside force, usually a violent blow to the head. DOID:0081292 MONDO:0858950 traumatic brain injury Pathological structure or process mouse_pathology.ontology MPATH:0 pathological entity 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. mouse_pathology.ontology programmed cell death MPATH:3 apoptosis Extracellular deposition of amyloid protein. mouse_pathology.ontology Amyloidosis MPATH:34 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. amyloid deposition yes 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 MPheno.ontology increased ROS production increased reactive oxygen species production MP:0003674 oxidative stress yes diminished effectiveness of insulin in lowering plasma glucose levels MPheno.ontology MP:0005331 insulin resistance The determination of the amount of kidney injury molecule-1 present in a sample. C100433 Laboratory Procedure Kidney Injury Molecule-1 Measurement Kidney Injury Molecule-1 Measurement C2681921 CDISC CTRP A measurement of the kidney injury molecule-1 (Kim-1) in a biological specimen. HAVCR1 Measurement HAVcr-1 Measurement Hepatitis A Virus Cellular Receptor 1 Hepatitis A Virus Cellular Receptor 1 Measurement KIM-1 KIM-1 Measurement KIM1 KIM1 Measurement Kidney Injury Molecule 1 Measurement Kidney Injury Molecule-1 Kidney Injury Molecule-1 Measurement Kidney Injury Molecule-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. C106407 Nucleic Acid, Nucleoside, or Nucleotide MicroRNA 124 MicroRNA 124 C2743231 CTRP MIMAT0000422 MIR124 MIRN124 MicroRNA 124 hsa-miR-124 hsa-miR-124-3p hsa-miR-124a miR-124 MicroRNA 124 The determination of the amount of human epidermal growth factor receptor 2 present in a sample. C112312 Laboratory Procedure Human Epidermal Growth Factor Receptor 2 Measurement C3810543 CDISC A measurement of HER2 protein in a biological specimen. ERBB2 HER2 HER2/NEU Human Epidermal Growth Factor Receptor 2 Human Epidermal Growth Factor Receptor 2 Measurement Receptor Tyrosine-Protein Kinase erbB-2 Measurement Human Epidermal Growth Factor Receptor 2 Measurement yes 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. C113609 Disease or Syndrome Chronic Liver Disease C0341439 CPTAC MedDRA NICHD SeroNet 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. Chronic liver disease Chronic Liver Disease Chronic_Liver_Disease Chronic Liver Disease 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. C116021 Nucleic Acid, Nucleoside, or Nucleotide MicroRNA 181 MicroRNA 181 C3898411 CTRP 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. MIR181 MIRN181 MicroRNA 181 hsa-mir-181 mir-181 MicroRNA 181 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. C116401 Nucleic Acid, Nucleoside, or Nucleotide MicroRNA 9 MicroRNA 9 C3884166 CTRP MIPF0000014 MIR9 MIRN9 MicroRNA 9 hsa-miR-9-5p hsa-mir-9 miR-9 miRNA 9 miRNA-9 miRNA9 MicroRNA 9 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. C116487 Diagnostic Procedure Diffusion Kurtosis Imaging Diffusion Kurtosis Imaging CL433731 CTRP DKI Diffusion Kurtosis Imaging Diffusion Kurtosis Imaging A measurement of the magnitude of diffusion of water molecules within tissue. C116753 Conceptual Entity Apparent Diffusion Coefficient C3890194 ADC Apparent Diffusion Coefficient Effective Diffusion Coefficient Apparent Diffusion Coefficient A technique used to measure the diameter of the pupil in response to stimuli. C120540 Diagnostic Procedure Pupillometry C0260180 Pupillometry Pupillometry An isoenzyme complex comprised of a heterodimer of creatine kinase M-type and B-type. C122778 Amino Acid, Peptide, or Protein Creatine Kinase MB Creatine Kinase MB C0010290 CTRP CK-MB CKMB CPK-MB Creatine Kinase MB Creatine Kinase-MB Creatine Phosphokinase-MB MM-CK Creatine Kinase MB 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. C128056 Diagnostic Procedure Perfusion-Weighted Magnetic Resonance Imaging Perfusion-Weighted Magnetic Resonance Imaging C0879554 CTRP PWI Perfusion-Weighted MR Perfusion-Weighted MRI Perfusion-Weighted Magnetic Resonance Imaging 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. C129416 Nucleic Acid, Nucleoside, or Nucleotide MicroRNA 16 CL512801 MIMAT0000069 MIR16 MIRN16 MiR-16 MiRNA16 MicroRNA 16 hsa-miR-16 hsa-miR-16-5p MicroRNA 16 A public health agency based in London that is responsible for the scientific evaluation, supervision, and safety monitoring of medicines in the European Union. C142543 Organization European Medicines Agency CL541263 CDISC-GLOSS The regulatory agency for the EU. EMA European Medicines Agency European Medicines Agency (EMA) European Medicines Agency In a clinical trial, an assessment of an intervention's effects that takes the place of a patient-based conclusion. C142724 Functional Concept Surrogate Marker C0086589 CDISC-GLOSS 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.] Surrogate Marker surrogate biomarker surrogate marker Surrogate Marker 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. C15367 Health Care Activity Risk Assessment Risk Assessment C0086930 CTRP 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. Risk_Assessment Risk Assessment risk assessment Risk Assessment Systematic investigation into the causes of cancer and development of strategies for prevention, diagnosis, treatment, and cure. C16199 Research Activity Cancer Research C1516225 Cancer_Research_Project Cancer Research Cancer Research Programs Cancer Research Project Cancer Research C16234 Qualitative Concept Clinical Sensitivity C1516631 Clinical_Sensitivity Clinical Sensitivity Clinical Sensitivity 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. C16809 Diagnostic Procedure Magnetic Resonance Imaging Magnetic Resonance Imaging C0024485 CDISC CTRP DIPG/DMG FDA GDC OORO PCDC mCode 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. Magnetic_Resonance_Imaging MRI MR MR Imaging MRI MRI Scan Magnetic Resonance Magnetic Resonance Imaging Magnetic Resonance Imaging Scan Magnetic resonance imaging (procedure) Medical Imaging, Magnetic Resonance / Nuclear Magnetic Resonance NMR Imaging NMRI Nuclear Magnetic Resonance Imaging magnetic resonance imaging nuclear magnetic resonance imaging Magnetic Resonance Imaging Detection and measurement of the resonant spectra of molecular species in a tissue or sample. C16810 Diagnostic Procedure Magnetic Resonance Spectroscopy C0024487 CDISC A type of spectroscopy that detects and measures the resonant spectra of molecular species in a tissue or sample. Magnetic_Resonance_Spectroscopy Magnetic Resonance Spectroscopy NMR Spectroscopy NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY Spectroscopy, MR Spectroscopy, NMR Spectroscopy, Nuclear Magnetic Resonance Magnetic Resonance Spectroscopy yes A representation of something, often idealized or modified to make it conceptually easier to understand. C16866 Intellectual Product Model C3161035 CDISC-GLOSS 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] Model_System Model Model System Modeling System Models model Model 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. C17007 Diagnostic Procedure Positron Emission Tomography Positron Emission Tomography C0032743 CDISC CTRP GDC OORO PCDC mCode 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. Positron_Emission_Tomography PET Medical Imaging, Positron Emission Tomography PET PET SCAN PET Scan PET scan PT Pet Scan Positron Emission Tomography Positron Emission Tomography Scan Positron emission tomography (procedure) Positron-Emission Tomography positron emission tomography scan proton magnetic resonance spectroscopic imaging Positron Emission Tomography 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. C17204 Diagnostic Procedure Computed Tomography Computed Tomography C0040405 CDISC CTRP DIPG/DMG FDA GDC OORO PCDC mCode 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. Computed_Tomography CT Scan CAT CAT Scan CAT scan CT CT SCAN CT Scan CT scan Computed Axial Tomography Computed Tomography Computerized Axial Tomography Computerized Tomography Computerized axial tomography (procedure) computed tomography computerized axial tomography computerized tomography tomography Computed Tomography The use of high-frequency sound waves to generate images of the body. C17230 Health Care Activity Ultrasonography Ultrasound Imaging C0041618 CDISC CTRP NICHD OORO 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. Ultrasound_Imaging 2-Dimensional Grayscale Ultrasound Imaging 2-Dimensional Ultrasound Imaging 2D-US ULTRASOUND US Ultrasonography Ultrasound Ultrasound Imaging Ultrasound Test Ultrasound, Medical ultrasonography ultrasound 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. C17237 Health Care Related Organization Food and Drug Administration C0041714 CDISC-GLOSS FDA 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. Food_and_Drug_Administration FDA Food and Drug Administration Food and Drug Administration (FDA) Food and Drug Administration 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. C17369 Diagnostic Procedure Imaging Technique Imaging Technique C0079595 CTRP DIPG/DMG GDC OORO PCDC mCode 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. Imaging_Technique Imaging Diagnostic Imaging Technique IMAGING_METHOD Image Type Imaging Imaging (procedure) Imaging Procedures Imaging Technique Medical Imaging Type of imaging imaging imaging modality imaging procedure imaging type imaging_type Imaging Technique A measurement of the temperature of the body. C174446 Quantitative Concept Body Temperature C0005903 CDISC ICDC OORO A measurement of the temperature of the body. Temperature measured in Celsius or Fahrenheit Body Temperature TEMP Temperature Temperature in Celsius or Fahrenheit body temperature body_temperature Body Temperature 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. C175504 Manufactured Object Smartphone Smartphone C3204335 CTRP Smartphone Smartphone 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. C18000 Qualitative Concept Histologic Grade C0919553 CDISC CPTAC ICDC NAACCR PCDC 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. Histopathologic_Grade Grade Grade (high/low) Grading HISTOLOGY_GRADE Histologic Grade Histopathologic Grade Histopathology Grade OVLTGRD Overall Tumor Grade Tumor Grade Tumor_Grade grade grading histological grade histological_grade Histologic Grade A physical object, or electronic counterpart, that is characterized by containing writing which is meant to be human-readable. C19498 Intellectual Product Document CL414404 BRIDG CDISC-GLOSS 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). Document_Type Used here to organize a wide variety of concepts that are characterized by writing or text DOC Document Document Type documentation Document 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) C201303 Functional Concept Response Biomarker CDISC 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) Exposure Response Biomarker Response Biomarker Response Biomarker 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) C201362 Functional Concept Monitoring Biomarker CL1920311 CDISC 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) Exposure Monitoring Biomarker Monitoring Biomarker Monitoring Biomarker 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) C201365 Functional Concept Pharmacodynamic Biomarker CL1920306 CDISC 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) Pharmacodynamic Biomarker Pharmacodynamic Biomarker 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) C201367 Functional Concept Safety Biomarker CL1920308 CDISC 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) Exposure Safety Biomarker Safety Biomarker Safety Biomarker Changes in the regulation of the expression of gene activity without alteration of genetic structure. C21051 Genetic Function Epigenetic Process Epigenetic Process C1516924 CTRP Epigenetic_Process Epigenetic Change Epigenetic Mechanism Epigenetic Process Epigenetics Epigenetic Process A fibrillar protein present in blood plasma; it converts to fibrin during the process of blood clot formation. C25736 Amino Acid, Peptide, or Protein Fibrinogen Fibrinogen C0016006 CTRP Fibrinogen Fibrinogen Fibrinogen yes C28234 Quantitative Concept Progression-free Survival C0242792 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. Progression-free_Survival PFS Progression-free Survival progression-free survival Progression-free Survival Multiplying or increasing in number. C28378 Conceptual Entity Proliferation C1514485 CDISC 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. Proliferating Proliferation PROLIFERATING Proliferating Proliferation proliferating Proliferation A condition in which there is a deviation from or interruption of the normal coagulation properties of the blood. C2902 Disease or Syndrome Coagulation Disorder C4229995 Patient Code (Appendix B) CPTAC FDA MedDRA NICHD mCode 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. Coagulation_Disorder Coagulopathy IMDRF:E0302 Coagulation Defect Coagulation Disorder Coagulation defect, unspecified Coagulopathy Coagulopathy, specify Coagulation Disorder A radiographic procedure using the emission of x-rays to form an image of the structure penetrated by the radiation. C38101 Diagnostic Procedure Radiography X-Ray Imaging C0043299 CDISC CTRP OORO PCDC mCode A radiographic procedure using the emission of x-rays, a type of penetrating energy wave. Radiography Conventional X-Ray Diagnostic Radiology Medical Imaging, X-Ray Plain film radiographs RG Radiographic Imaging Radiographic imaging procedure (procedure) Radiography Static X-Ray X-RAY X-Ray X-Ray Imaging X-Ray Imaging 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. C41389 Quantitative Concept Positive Predictive Value of Diagnostic Test C1514243 The likelihood that an individual with a positive test result truly has the particular gene and/or disease in question. Positive_Predictive_Value_of_Diagnostic_Test PPV Positive Predictive Value of Diagnostic Test positive predictive value Positive Predictive Value of Diagnostic Test https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. C41390 Quantitative Concept Negative Predictive Value of Diagnostic Test C1513918 The likelihood that an individual with a negative test result is truly unaffected and/or does not have the particular gene mutation in question. Negative_Predictive_Value_of_Diagnostic_Test NPV Negative Predictive Value of Diagnostic Test negative predictive value Negative Predictive Value of Diagnostic Test https://pubmed.ncbi.nlm.nih.gov/32541893/ C53249 Quantitative Concept Spearman Correlation Test C1710141 Spearman_Correlation Spearman Correlation Spearman Correlation Test Spearman Correlation Test The act of observing something (and sometimes keeping a record of it). C61256 Activity Monitoring Monitoring C1283169 CDISC-GLOSS CTRP 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). Monitoring Monitoring monitor monitoring Monitoring 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. C64862 Diagnostic Procedure Diffusion Tensor Imaging Diffusion Tensor Imaging C1537007 CDISC CTRP DIPG/DMG A type of MRI technique that maps the diffusion of water in three dimensions. Diffusion_Tensor_Imaging DIFFUSION TENSOR MRI DT-MRI DTI Diffusion Tensor Imaging Diffusion Tensor Imaging 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. C686 Amino Acid, Peptide, or Protein Neuropeptide C0027895 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. Neuropeptide Neuropeptide neuropeptide Neuropeptide C68763 Indicator, Reagent, or Diagnostic Aid Valid Biomarker C2349100 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.) Valid_Biomarker Valid Biomarker Valid Biomarker yes 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. C68771 Clinical Attribute Clinical Endpoint C2347784 Clinical_Endpoint Clinical Endpoint primary endpoint Clinical Endpoint Information or variable that supports a probabilistic estimate of future events. C75944 Clinical Attribute Predictor C2698872 Predictor Predictor Predictor 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. C82669 Professional or Occupational Group Center for Drug Evaluation and Research C2826368 Center_for_Drug_Evaluation_and_Research CDER Center for Drug Evaluation and Research Center for Drug Evaluation and Research 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. C82670 Professional or Occupational Group Center for Devices and Radiological Health C2826369 Center_for_Devices_and_Radiological_Health CDRH Center for Devices and Radiological Health 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. C88164 Classification Cardiorespiratory Fitness C2981722 Cardiorespiratory Fitness Cardiorespiratory Fitness A laboratory test used for the measurement of creatinine levels in the serum to determine the glomerular filtration rate. C88227 Laboratory Procedure Serum Creatinine Assay C2981751 Serum Creatinine Assay Serum Creatinine Assay A healthy subject that is matched with an affected individual in a trial. C94342 Qualitative Concept Healthy Control Healthy Control C2986479 CTRP 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. Healthy Control healthy control Healthy Control C94416 Temporal Concept Sleep Stage C0037319 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). Sleep Stage sleep stage Sleep Stage The volume of tumor. C94515 Quantitative Concept Tumor Volume C0475276 ICDC PCDC 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. TUMOR_VOLUME Tumor Volume tumor volume volume of tumor volume_of_tumor Tumor Volume 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'. Yongqun He AE adverse reaction 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/. adverse event An inferential statistical data analysis that is used to analyze data that arises from more than one variable Yongqun He, Jie Zheng MVA WEB: http://www.camo.com/multivariate_analysis.html multivariate analysis An inferential statistical data analysis that has only one independent variable Yongqun He univariate analysis yes 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. Yongqun He WEB: http://www.uptodate.com/contents/glossary-of-common-biostatistical-and-epidemiological-terms STATO_0000182 odds ratio planned process 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. Bjoern Peters branch derived 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) planned process 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 study investigation 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 OBI branch derived study assay any method assay yes diagnosis textual entity diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. Jennifer Fostel diagnosis textual entity yes patient role 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 patient 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 OBI 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 placebo 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 placebo 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 yes 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 p-value imaging assay An assay that produces a picture of an entity. PlanAndPlannedProcess Branch OBI branch derived imaging assay disease stage 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 PERSON: Bjoern peters disease stage blood specimen blood drawn from a human for glucose assay a material entity derived from a portion of blood collected from an organism Bjoern Peters Bjoern Peters blood specimen enzyme-linked immunosorbent assay 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. IEDB ELISA IEDB enzyme-linked immunosorbent assay statistical hypothesis test A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test. James Malone PERSON: James Malone statistical hypothesis test yes center value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. PERSON: James Malone PERSON: Monnie McGee median center value western blot assay 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. IEDB Philippe Rocca-Serra IEDB Philippe Rocca-Serra western blot assay flow cytometry assay 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. IEDB FACS IEDB flow cytometry assay yes device 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. PERSON: Helen Parkinson instrument OBI development call 2012-12-17. device yes 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 Group: OBI group genotype information immunohistochemistry 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. IEDB IEDB immunohistochemistry biopsy Biopsy of a potentially cancerous mole. 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. Damion Dooley Nicole Vasilevsky https://en.wikipedia.org/wiki/Biopsy biopsy 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 PERSON: Philippe Rocca-Serra WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen 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. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen 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 WEB:http://en.wikipedia.org/wiki/Linear_regression multiple linear regression analysis staining 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. Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining staining validation 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 Philippe Rocca-Serra adapted from wordnet (wkipedia) validation yes microarray 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. Daniel Schober PERSON: Chris Stoeckert microarray pathologic process abnormal, harmful processes caused by or associated with a disease IEDB 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. Oliver He WEB: http://www.ncbi.nlm.nih.gov/books/NBK21640/ gene Bin Zhao, Yue Liu, Oliver He SIR2L1 WEB: http://www.ncbi.nlm.nih.gov/gene SIRT1 sirtuin 1 23411 RP11-57G10.3 10q21.3 20140408 9606 10 protein-coding Official from a nomenclature committee GO_0000012 (EC: IMP); GO_0000122 (EC: IDA, PMID: 12535671); GO_0000122 (EC: IMP); GO_0000183 (EC: IDA, PMID: 18485871); GO_0000720 (EC: IMP); GO_0000731 (EC: ISS); GO_0000790 (EC: IDA, PMID: 17505061); GO_0001525 (EC: IDA); GO_0001542 (EC: IEA); GO_0001678 (EC: ISS); GO_0001934 (EC: ISS); GO_0002039 (EC: IPI, PMID: 11672523); GO_0002821 (EC: IDA); GO_0003714 (EC: IDA, PMID: 12535671); GO_0003714 (EC: ISS); GO_0003950 (EC: TAS, Qualifier: NOT, PMID: 17456799); GO_0004407 (EC: IDA); GO_0005515 (EC: IPI, PMID: 11672523); GO_0005634 (EC: IDA); GO_0005635 (EC: IDA, PMID: 15469825); GO_0005637 (EC: IDA, PMID: 15469825); GO_0005654 (EC: IDA, PMID: 16079181); GO_0005677 (EC: IDA, PMID: 18485871); GO_0005719 (EC: IDA, PMID: 15469825); GO_0005720 (EC: IDA, PMID: 15469825); GO_0005730 (EC: IDA, PMID: 15469825); GO_0005730 (EC: IDA, Qualifier: NOT); GO_0005737 (EC: IDA); GO_0005737 (EC: IDA, Qualifier: NOT, PMID: 15469825); GO_0005739 (EC: IDA); GO_0006260 (EC: TAS, PMID: 17317627); GO_0006281 (EC: TAS, PMID: 17317627); GO_0006342 (EC: TAS, PMID: 10381378); GO_0006343 (EC: IDA, PMID: 15469825); GO_0006344 (EC: IMP, PMID: 15469825); GO_0006346 (EC: TAS); GO_0006351 (EC: IEA); GO_0006364 (EC: IEA); GO_0006471 (EC: TAS, Qualifier: NOT, PMID: 17456799); GO_0006476 (EC: IDA, PMID: 18203716); GO_0006476 (EC: IMP, PMID: 11672523); GO_0006642 (EC: ISS); GO_0006974 (EC: IDA, PMID: 18203716); GO_0006979 (EC: IDA, PMID: 14976264); GO_0007283 (EC: IEA); GO_0007346 (EC: IDA, PMID: 15692560); GO_0007517 (EC: IEA); GO_0007569 (EC: TAS, PMID: 11672523); GO_0008022 (EC: IPI, PMID: 18203716); GO_0008284 (EC: IMP); GO_0009267 (EC: ISS); GO_0010875 (EC: ISS); GO_0010906 (EC: ISS); GO_0016032 (EC: IEA); GO_0016239 (EC: IDA, PMID: 18296641); GO_0016567 (EC: IDA); GO_0016575 (EC: IDA, PMID: 12006491); GO_0016605 (EC: IDA, PMID: 12006491); GO_0017136 (EC: IDA, PMID: 12006491); GO_0018394 (EC: IMP, PMID: 18004385); GO_0019213 (EC: IDA, PMID: 18203716); GO_0030308 (EC: IMP, PMID: 17505061); GO_0030512 (EC: ISS); GO_0031393 (EC: ISS); GO_0031648 (EC: ISS); GO_0031937 (EC: IMP, PMID: 15469825); GO_0032007 (EC: IMP); GO_0032071 (EC: IMP, PMID: 19934257); GO_0032088 (EC: IDA, PMID: 15152190); GO_0032868 (EC: ISS); GO_0033158 (EC: IMP, PMID: 18203716); GO_0033553 (EC: IDA, PMID: 18485871); GO_0033558 (EC: IDA, PMID: 19934257); GO_0034391 (EC: ISS); GO_0034979 (EC: IDA); GO_0034979 (EC: IMP, PMID: 11672523); GO_0034983 (EC: IDA, PMID: 15469825); GO_0035098 (EC: IDA, Qualifier: colocalizes_with, PMID: 15684044); GO_0035356 (EC: ISS); GO_0035358 (EC: ISS); GO_0042127 (EC: IMP, PMID: 12006491); GO_0042326 (EC: IMP, PMID: 17612497); GO_0042393 (EC: IPI, PMID: 15469825); GO_0042542 (EC: IDA, PMID: 19934257); GO_0042632 (EC: ISS); GO_0042771 (EC: IMP); GO_0042802 (EC: IPI, PMID: 15469825); GO_0043065 (EC: IDA, PMID: 15152190); GO_0043065 (EC: IMP, PMID: 19047049); GO_0043066 (EC: IMP, PMID: 16892051); GO_0043124 (EC: IDA, PMID: 17680780); GO_0043161 (EC: IMP); GO_0043280 (EC: IMP, PMID: 19047049); GO_0043398 (EC: IPI, PMID: 12535671); GO_0043425 (EC: IPI, PMID: 12535671); GO_0043433 (EC: IDA, PMID: 11672523); GO_0043433 (EC: IMP, PMID: 17505061); GO_0043518 (EC: IDA, PMID: 11672523); GO_0045348 (EC: IDA); GO_0045599 (EC: ISS); GO_0045739 (EC: IMP, PMID: 19934257); GO_0045892 (EC: IDA, PMID: 11672523); GO_0045944 (EC: IDA); GO_0046628 (EC: IDA); GO_0046872 (EC: IEA); GO_0046969 (EC: ISS); GO_0050872 (EC: ISS); GO_0051019 (EC: IPI); GO_0051097 (EC: IDA, PMID: 18203716); GO_0051898 (EC: IMP); GO_0055089 (EC: ISS); GO_0060766 (EC: IMP, PMID: 17505061); GO_0070301 (EC: IDA); GO_0070403 (EC: IEA); GO_0070857 (EC: ISS); GO_0070932 (EC: IDA); GO_0070932 (EC: IMP, PMID: 17505061); GO_0071356 (EC: IDA, PMID: 15152190); GO_0071456 (EC: IMP); GO_0071479 (EC: ISS); GO_1902166 (EC: ISS, PMID: 11672522); GO_1902176 (EC: IMP, PMID: 17317627); GO_2000111 (EC: ISS); GO_2000480 (EC: IDA); GO_2000481 (EC: IMP, PMID: 18687677); GO_2000655 (EC: IMP, PMID: 17505061); GO_2000757 (EC: IDA); GO_2000773 (EC: IDA); GO_2000774 (EC: IDA, PMID: 18687677) PMID: 10381378; 10873683; 11230166; 11672522; 11672523; 12006491; 12297502; 12413881; 12477932; 12535671; 12930829; 12939617; 14702039; 14976264; 14980222; 15126506; 15152190; 15164054; 15175761; 15205477; 15302935; 15469825; 15489334; 15632193; 15639232; 15640142; 15684044; 15692560; 15719057; 15744310; 15749705; 15780941; 16079181; 16154098; 16166628; 16183991; 16207712; 16257164; 16269335; 16288004; 16328012; 16344560; 16354677; 16385451; 16628003; 16751189; 16892051; 16923962; 16959573; 16964243; 16998474; 16998810; 17041012; 17081983; 17098745; 17099246; 17112576; 17172643; 17180656; 17213307; 17283066; 17317627; 17334224; 17373700; 17456799; 17487425; 17505061; 17516504; 17581637; 17601350; 17612497; 17624472; 17638871; 17680780; 17785417; 17806102; 17895433; 17901049; 17916362; 17934453; 17936707; 17937892; 17964266; 17996922; 18004385; 18029348; 18174544; 18184747; 18193082; 18203716; 18230337; 18235501; 18235502; 18296641; 18329615; 18342601; 18344999; 18414679; 18438697; 18482975; 18485871; 18485895; 18556572; 18563176; 18573234; 18636124; 18660489; 18662546; 18662547; 18681908; 18687677; 18689793; 18704159; 18723829; 18724249; 18755897; 18774777; 18800364; 18820948; 18821472; 18823944; 18829436; 18829956; 18834855; 18835033; 18838864; 18850005; 18922603; 18957417; 18977241; 19008647; 19014491; 19017485; 19047049; 19060927; 19071085; 19075016; 19104446; 19132007; 19149601; 19166820; 19167483; 19188449; 19218236; 19220062; 19229036; 19236849; 19244234; 19267881; 19285077; 19286634; 19289152; 19322201; 19343720; 19364925; 19376817; 19377286; 19404850; 19430421; 19433578; 19478080; 19491102; 19498162; 19509139; 19553684; 19555662; 19568959; 19578370; 19581416; 19615732; 19643082; 19649206; 19664641; 19680556; 19690166; 19713122; 19714620; 19716821; 19720090; 19741164; 19786632; 19819989; 19883617; 19887452; 19895790; 19923004; 19934257; 19934264; 19995796; 19996091; 20027304; 20033348; 20041875; 20042607; 20060806; 20068143; 20071779; 20089851; 20100829; 20102704; 20103737; 20107110; 20131294; 20157519; 20160399; 20167603; 20203304; 20217115; 20225204; 20335544; 20360068; 20375098; 20379614; 20412117; 20421294; 20426787; 20431927; 20439735; 20448046; 20451257; 20463039; 20479254; 20484414; 20488443; 20493163; 20503258; 20506278; 20555380; 20595232; 20617556; 20620956; 20627091; 20631301; 20633545; 20668205; 20668706; 20670893; 20689156; 20693263; 20702418; 20733005; 20803525; 20812964; 20813124; 20817729; 20819794; 20844277; 20869593; 20941378; 20955178; 20956937; 20966076; 20972425; 20977650; 20978007; 21030595; 21056897; 21067862; 21074897; 21098725; 21108727; 21118843; 21130087; 21139048; 21144831; 21149449; 21149730; 21163946; 21176092; 21212262; 21241768; 21245135; 21245319; 21277951; 21289058; 21329659; 21331741; 21337390; 21345792; 21349544; 21390332; 21414717; 21454709; 21471201; 21474819; 21501079; 21502801; 21502975; 21504832; 21505241; 21527554; 21533107; 21543634; 21555002; 21556116; 21567102; 21596753; 21604001; 21636977; 21697093; 21698133; 21700104; 21701047; 21703114; 21713995; 21719763; 21720722; 21745208; 21746786; 21760635; 21775285; 21778425; 21789216; 21807113; 21810449; 21813271; 21832856; 21852339; 21865267; 21871827; 21882241; 21890473; 21906983; 21915620; 21920899; 21947282; 21956116; 21963094; 21968188; 21972126; 21987377; 22000456; 22013015; 22017869; 22038097; 22050448; 22073865; 22094255; 22094256; 22121772; 22124156; 22133824; 22137654; 22146883; 22149272; 22152608; 22157007; 22157016; 22159506; 22169038; 22178470; 22190034; 22190494; 22197555; 22198152; 22200427; 22207735; 22219708; 22228742; 22230810; 22245592; 22249256; 22266962; 22272724; 22302044; 22306819; 22308024; 22312127; 22322739; 22328728; 22330808; 22333659; 22340598; 22355666; 22363646; 22364258; 22370592; 22378745; 22385246; 22389628; 22406815; 22410779; 22446626; 22448750; 22465953; 22479397; 22493485; 22510409; 22537175; 22542455; 22552445; 22553202; 22554968; 22564731; 22584570; 22586264; 22590959; 22613205; 22623155; 22628222; 22640743; 22661383; 22674476; 22683003; 22683888; 22689577; 22696478; 22700961; 22703651; 22728651; 22732402; 22735644; 22740055; 22773876; 22780949; 22789853; 22796962; 22807441; 22824213; 22833338; 22836009; 22863883; 22867969; 22885181; 22893703; 22902550; 22902626; 22934845; 22935421; 22939629; 22980663; 22986535; 22986747; 22990118; 22995302; 23024800; 23038275; 23045412; 23050959; 23056314; 23070058; 23075334; 23079621; 23133645; 23135526; 23137540; 23143889; 23169992; 23178529; 23209300; 23224247; 23224434; 23238746; 23247197; 23247634; 23248098; 23255128; 23257246; 23262029; 23267107; 23276927; 23305113; 23332867; 23340254; 23349863; 23354305; 23357110; 23361587; 23363613; 23365135; 23370328; 23382074; 23382833; 23390957; 23395904; 23417673; 23449222; 23450480; 23453030; 23473037; 23474493; 23475622; 23483263; 23505545; 23548308; 23561972; 23583951; 23602568; 23613875; 23661372; 23673452; 23702379; 23704280; 23754392; 23760629; 23768087; 23770291; 23797802; 23800577; 23814050; 23827175; 23855981; 23877372; 23892437; 23897426; 23922917; 23952905; 23993977; 24039251; 24126058; 24141423; 24147777; 24184811; 24211209; 24211575; 24218438; 24507186 sirtuin 1 Ensembl:ENSG00000096717 HGNC:14929 HPRD:08381 MIM:604479 Vega:OTTHUMG00000018340 SIRT1 Bin Zhao, Yue Liu, Oliver He SIR2L7 WEB: http://www.ncbi.nlm.nih.gov/gene SIRT7 sirtuin 7 51547 17q25 20140408 9606 17 protein-coding Official from a nomenclature committee GO_0000122 (EC: IDA); GO_0003682 (EC: IDA); GO_0005515 (EC: IPI, PMID: 19174463); GO_0005730 (EC: IDA, PMID: 16079181); GO_0005731 (EC: IDA, PMID: 19174463); GO_0005737 (EC: IEA); GO_0007072 (EC: IMP, PMID: 19174463); GO_0009303 (EC: IMP, PMID: 19174463); GO_0046872 (EC: IEA); GO_0070403 (EC: IEA); GO_0070932 (EC: IDA); GO_0070933 (EC: IDA); GO_0097372 (EC: IDA) PMID: 9776767; 10873683; 11953824; 12454780; 12477932; 14702039; 15489334; 16079181; 16169070; 16525639; 16618798; 17003781; 19174463; 20375098; 21832049; 22147730; 22586326; 22722849; 23079745; 23680022; 23750001; 24207024; 24250222 sirtuin 7 Ensembl:ENSG00000187531 HGNC:14935 HPRD:12094 MIM:606212 Vega:OTTHUMG00000177957 SIRT7 yes 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. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T11:13:49Z phenotype yes A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:39:44Z disorder The totality of all processes through which a given disease instance is realized. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:55:44Z disease course The representation of a conclusion of a diagnostic process. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z diagnosis 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 Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z treatment yes A hypothesis about some future part of a disease course. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T12:42:23Z prognosis 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 http://code.google.com/p/ogms/issues/detail?id=73 10 NOV 2015 remission A therapeutic procedure in which a body part is transferred into a organism transplantation yes 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. https://www.ncbi.nlm.nih.gov/mesh/2009893 Trastuzumab Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization. https://www.ncbi.nlm.nih.gov/mesh/?term=calcium+metabolism+disorders Calcium Metabolism Disorders 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). https://www.ncbi.nlm.nih.gov/mesh/68004035 Diet Therapy A change in electrical resistance of the skin, occurring in emotion and in certain other conditions. https://www.ncbi.nlm.nih.gov/mesh/?term=galvanic+skin+response skin conductance Galvanic Skin Response 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. https://www.ncbi.nlm.nih.gov/mesh/?term=growth+disorder growth disorder Growth Disorders Pressure within the cranial cavity. It is influenced by brain mass, the circulatory system, CSF dynamics, and skull rigidity. https://www.ncbi.nlm.nih.gov/mesh/68007427 Intracranial Pressure Blood tests that are used to evaluate how well a patient's liver is working and also to help diagnose liver conditions. https://www.ncbi.nlm.nih.gov/mesh/?term=liver+function+tests Liver Function Tests yes Exfoliate neoplastic cells circulating in the blood and associated with metastasizing tumors. https://www.ncbi.nlm.nih.gov/mesh/?term=Neoplastic+Cells%2C+Circulating Neoplastic Cells, Circulating yes The study of chance processes or the relative frequency characterizing a chance process. https://www.ncbi.nlm.nih.gov/mesh/68011336 Probability 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). https://www.ncbi.nlm.nih.gov/mesh/?term=Prostatectomy Prostatectomy yes 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. https://www.ncbi.nlm.nih.gov/mesh/?term=roc+curve ROC Curve Peroxidase catalyzed oxidation of lipids using hydrogen peroxide as an electron acceptor. https://www.ncbi.nlm.nih.gov/mesh/68015227 Lipid Peroxidation 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. https://www.ncbi.nlm.nih.gov/mesh/68019394 Ki-67 Antigen yes 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. https://www.ncbi.nlm.nih.gov/mesh/?term=Natriuretic+Peptide%2C+Brain Natriuretic Peptide, Brain https://www.ncbi.nlm.nih.gov/mesh/?term=Leukoaraiosis white matter hyperintensity Leukoaraiosis 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. yes 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. https://www.ncbi.nlm.nih.gov/mesh/?term=Dyslipidemias Dyslipidemias yes 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. https://www.ncbi.nlm.nih.gov/mesh/68054392 adipokine Adipokines 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. https://www.ncbi.nlm.nih.gov/mesh/?term=elastic+modulus Elastic Modulus 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. https://www.ncbi.nlm.nih.gov/mesh/68055436 Growth Differentiation Factor 15 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). https://www.ncbi.nlm.nih.gov/mesh/68004035 Biochemical Processes 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. https://www.ncbi.nlm.nih.gov/mesh/68063646 Carcinogenesis Entrez:383 arginase 1 ARG1 Entrez:3820 killer cell lectin like receptor B1 KLRB1 Entrez:4094 musculoaponeurotic fibrosarcoma oncogene homolog v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog MAF Entrez:4097 v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G MAFG Entrez:8460 tyrosylprotein sulfotransferase 1 TPST1 Entrez:8644 aldo-keto reductase family 1, member C3 AKR1C3 Entrez:55841 KIBRA WWC family member 3 WWC3 Measurable indicator including genetic or acquired host factors and intrinsic factors, influencing the response of an individual to a (dietary) exposure. ENPADASI_WP4 https://www.ncbi.nlm.nih.gov/pubmed/28974991 susceptibility biomarker yes 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 https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell) https://en.wikipedia.org/wiki/Biomarker_(medicine) biological marker biomarker Anthony Huffman, Oliver He A biomarker that is indicative of an immune response https://pubmed.ncbi.nlm.nih.gov/22072636/ https://pubmed.ncbi.nlm.nih.gov/32286245/ immune biomarker Anthony Huffman, Oliver He cytokine biomarker Anthony Huffman, Oliver He inflammatory cytokine biomarker A biomarker that is indicative of a disease Yingtong Liu, Anthony Huffman, Oliver He https://en.wikipedia.org/wiki/Biomarker_(medicine) disease marker marker of disease disease biomarker A biomarker that is an indicator of a cell lineage or cell type Yingtong Liu, Anthony Huffman, Oliver He cell marker cell type marker https://en.wikipedia.org/wiki/Biomarker_(medicine) cell lineage biomarker Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers 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. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Cellular_Biomarkers cellular biomarker Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Imaging_Biomarkers imaging biomarker yes A biomarker that can predict clincal outcome. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker predictive marker predictive biomarker yes A biomarker that provides information about the patient's overall outcome, regardless of therapy. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker prognostic biomarker yes A biomarker that can serve a role in narrowing down diagnosis, which can lead to diagnosis that is significantly more specific to individual patients. Oliver He, Yingtong Liu https://en.wikipedia.org/wiki/Biomarker diagnostic marker diagnostic biomarker A molecular biomarker at the DNA gene level Oliver He, Yingtong Liu genomic biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers DNA biomarker A molecular biomarker at the RNA level Oliver He, Yingtong Liu transcriptomic biomarker https://en.wikipedia.org/wiki/Biomarker_(cell)#Molecular_Biomarkers RNA biomarker A biomarker that is indicative of a disease and achieved through imaging. https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI) imaging disease biomarker Oliver He imaging disease biomarkers by magnetic resonance imaging https://en.wikipedia.org/wiki/Biomarker_(medicine)#Imaging_disease_biomarkers_by_magnetic_resonance_imaging_(MRI) imaging disease biomarkers by MRI yes Oliver He A biomarker that is indicative of the presence of cancer in the body https://en.wikipedia.org/wiki/Cancer_biomarker cancer biomarker tumor biomarker tumour marker cancer marker yes A time quality inhering in a bearer by virtue of how long the bearer has existed. quality PATO:0000011 age A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance. concentration quality PATO:0000033 concentration of A physical quality which inheres in a bearer by virtue of the number of the bearer's repetitive actions in a particular time. quality PATO:0000044 frequency yes A quality inhering in a bearer by virtue of the bearer's disposition to detect or perceive external stimulation. sensitivity quality PATO:0000085 sensitivity toward yes A quality which inheres in a continuant. PATO:0001237 PATO:0001238 snap:Quality monadic quality of a continuant multiply inhering quality of a physical entity quality of a continuant quality of a single physical entity quality of an object quality of continuant monadic quality of an object monadic quality of continuant quality PATO:0001241 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. physical object quality An age quality that exists by virtue of the time (years and months) that the bearer has existed. quality PATO:0001486 chronological age A quality of a single process inhering in a bearer by virtue of the bearer's increasing over time. quality PATO:0001818 progressive yes A disposition inhering in a tumour by virtue of the bearer's disposition not to progress, invade surrounding tissues or metastasize. 2009-10-05T12:47:14Z quality benign PATO:0002096 neoplastic, non-malignant yes An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof. natural protein native protein protein PR:000000001 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]. protein yes A protein that is a translation product of the human IL6 gene or a 1:1 ortholog thereof. PIRSF:PIRSF001935 B-cell hybridoma growth factor B-cell stimulatory factor 2 BSF-2 CDF CTL differentiation factor IFN-beta-2 IL-6 IL6 hybridoma growth factor interferon beta-2 interleukin HP-1 protein IFNB2 PR:000001393 Category=gene. interleukin-6 yes A Bcl-2-like apoptosis inhibitor that is a translation product of the human BCL2 gene or a 1:1 ortholog thereof. IUPHARobj:2844 BCL2 protein Bcl-2 PR:000002307 Category=gene. apoptosis regulator Bcl-2 yes A trypsin that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof. IUPHARobj:2373 KLK3 P-30 antigen gamma-seminoprotein kallikrein-3 semenogelase seminin protein APS PSA PR:000003015 Category=gene. prostate-specific antigen yes A protein that is a translation product of the human TP53 gene or a 1:1 ortholog thereof. PIRSF:PIRSF002089 TP53 antigen NY-CO-13 antigen p53 phosphoprotein p53 tumor suppressor p53 protein P53 Trp53 PR:000003035 Category=gene. cellular tumor antigen p53 yes A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof. 30 kDa adipocyte complement-related protein ADIPOQ adipocyte complement-related 30 kDa protein adipocyte, C1q and collagen domain-containing protein adipocyte-specific protein AdipoQ adipose most abundant gene transcript 1 protein apM-1 gelatin-binding protein protein ACDC ACRP30 APM1 GBP28 PR:000003777 Category=gene. adiponectin A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof. ALB serum albumin protein Alb-1 Alb1 GIG20 GIG42 PRO0903 PRO1708 PRO2044 PRO2619 PRO2675 UNQ696/PRO1341 PR:000003918 Category=gene. albumin A neurotrophin that is a translation product of the human BDNF gene or a 1:1 ortholog thereof. BDNF abrineurin protein PR:000004716 Category=gene. brain-derived neurotrophic factor A protein that is a translation product of the human CHI3L1 gene or a 1:1 ortholog thereof. 39 kDa synovial protein BRP39 protein CGP-39 CHI3L1 GP-39 YKL-40 cartilage glycoprotein 39 protein Brp39 PR:000005423 Category=gene. chitinase-3-like protein 1 A protein that is a translation product of the human CLU gene or a 1:1 ortholog thereof. CLU Ku70-binding protein 1 NA1/NA2 SGP-2 TRPM-2 aging-associated gene 4 protein apo-J apolipoprotein J clustrin complement cytolysis inhibitor complement-associated protein SP-40,40 sulfated glycoprotein 2 testosterone-repressed prostate message 2 protein AAG4 APOJ CLI KUB1 Msgp-2 PR:000005615 Category=gene. clusterin yes A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof. CRP protein PTX1 PR:000005897 Category=gene. C-reactive protein yes A protein that is a translation product of the human CST3 gene or a 1:1 ortholog thereof. CST3 cystatin-3 gamma-trace neuroendocrine basic polypeptide post-gamma-globulin protein PR:000005965 Category=gene. cystatin-C yes An EGF receptor type tyrosine-protein kinase that is a translation product of the human EGFR gene or a 1:1 ortholog thereof. IUPHARobj:1797 EGFR proto-oncogene c-ErbB-1 receptor tyrosine-protein kinase erbB-1 protein ERBB ERBB1 HER1 PR:000006933 Category=gene. epidermal growth factor receptor yes A protein that is a translation product of the human ESR1 gene or a 1:1 ortholog thereof. IUPHARobj:620 ER ER-alpha ESR1 estradiol receptor nuclear receptor subfamily 3 group A member 1 protein ESR Estr Estra NR3A1 PR:000007204 Category=gene. estrogen receptor A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof. GFAP protein PR:000007939 Category=gene. Requested by=CL. glial fibrillary acidic protein yes A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof. p25 25 kDa alpha-2-microglobulin-related subunit of MMP-9 LCN2 SV-40-induced 24P3 protein lipocalin-2 oncogene 24p3 protein HNL NGAL PR:000009725 Category=gene. Requested by=CL. neutrophil gelatinase-associated lipocalin yes A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof. LEP obese protein obesity factor protein OB OBS PR:000009758 Category=gene. leptin A protein that is a translation product of the human NRGN gene or a 1:1 ortholog thereof. NRGN Ng RC3 protein PR:000011426 Category=gene. neurogranin A protein that is a translation product of the human SPP1 gene or a 1:1 ortholog thereof. 2AR SPP-1 SPP1 bone sialoprotein 1 calcium oxalate crystal growth inhibitor protein early T-lymphocyte activation 1 protein minopontin nephropontin secreted phosphoprotein 1 urinary stone protein uropontin protein BNSP Eta-1 OPN Op PSEC0156 PR:000015561 Category=gene. osteopontin A protein that is a translation product of the human TFF3 gene or a 1:1 ortholog thereof. P1.B TFF3 intestinal trefoil factor polypeptide P1.B protein ITF TFI PR:000016276 Category=gene. trefoil factor 3 yes A protein that is a translation product of the human TNNI3 gene or a 1:1 ortholog thereof. TNNI3 cTnI cardiac troponin I troponin I protein TNNC1 PR:000016506 Category=gene. troponin I, cardiac muscle A protein that is a translation product of the human TNNT2 gene or a 1:1 ortholog thereof. TNNT2 TnTc cTnT cardiac muscle troponin T protein PR:000016509 Category=gene. troponin T, cardiac muscle A protein-containing complex that is the remnant of fibrin mesh degradation (fibrinolysis) by plasmin in human. D-dimer hFDP/D-dimer protein PR:000050369 Category=organism-complex. Requested by=MAxO. D-dimer (human) yes 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. glycated hemoglobin glycohemoglobin HbA1c HgbA1c protein PR:000050469 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. hemoglobin A1c The number of times an organism breathes with the lungs (respiration) per unit time, usually per minute. Sufficient SCDO:0000993 MESH:D056152 Breathing Frequency Pulmonary Ventilation Rate Respiration Rate Respiratory Rate Damage inflicted on the intestine. Few but definitions not available SCDO (Jade Hotchkiss) Intestinal Damage Intestinal Injury yes 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. SO:0000649 INSDC_feature:ncRNA http://en.wikipedia.org/wiki/MiRNA http://en.wikipedia.org/wiki/StRNA INSDC_qualifier:miRNA micro RNA microRNA small temporal RNA stRNA sequence SO:0000276 miRNA the false negative rate is a data item which denotes the proportion of missed detection of elements known to be meeting the detection criteria Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra STATO, adapted from type II error rate β probability of false negatives false negative rate yes prevalence is a ratio formed by the number of subjects diagnosed with a disease divided by the total population size. Philippe Rocca-Serra 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. Philippe Rocca-Serra 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) Philippe Rocca-Serra positive predictive value adapted from wikipedia: https://en.wikipedia.org/wiki/Accuracy_and_precision#In_binary_classification last accessed: May 2016 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 https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. https://pubmed.ncbi.nlm.nih.gov/32541893/ 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. symptoms SYMP:0000061 inflammation 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. SYMP:0000476 ICD9CM_2005:783.21 UMLS_CUI:C0043096 UMLS_ICD9CM_2005_AUI:A1605347 loss of weight symptoms SYMP:0000178 weight loss A symptom is a perceived change in function, sensation, loss, disturbance or appearance reported by a patient indicative of a disease. symptoms SYMP:0000462 symptom A pain that is characterized by ranging from mild to severe and which continues beyond the expected healing phase. symptoms SYMP:0000837 chronic pain Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 SCTID:362889002 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 http://dbpedia.org/ontology/AnatomicalStructure biological structure connected biological structure uberon UBERON:0000061 anatomical structure yes 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 BIRNLEX:4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 SCTID:272625005 UMLS:C0178784 WBbt:0003760 Wikipedia:Organ_(anatomy) uberon anatomical unit body organ element UBERON:0000062 organ 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. UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta 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] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 TAO:0000007 UMLS:C0005767 VHOG:0000224 Wikipedia:Blood XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood 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. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BIRNLEX:14 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 SCTID:278195005 TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 Wikipedia:Organ_system XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system 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. AAO:0010841 AEO:0000000 BILA:0000000 BIRNLEX:6 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity Excretion that is the output of a kidney. kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 EMAPA:36554 ENVO:00002047 FMA:12274 GAID:1189 MA:0002545 MAT:0000058 MESH:D014556 MIAA:0000058 NCIT:C13283 UMLS:C0042036 Wikipedia:Urine galen:Urine uberon UBERON:0001088 urine yes 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. BIRNLEX:1798 BTO:0000237 CALOHA:TS-0130 EFO:0000329 EHDAA2:0004441 ENVO:02000029 EV:0100311 FMA:20935 GAID:1181 MA:0002503 MAT:0000499 MESH:D002555 NCIT:C12692 TAO:0002184 UMLS:C0007806 VHOG:0001278 Wikipedia:Cerebrospinal_fluid ZFA:0001626 CSF cerebral spinal fluid uberon liquor cerebrospinalis spinal fluid UBERON:0001359 cerebrospinal fluid A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions. salivary 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 BTO:0001202 CALOHA:TS-0891 EMAPA:36536 ENVO:02000036 FMA:59862 GAID:1167 MA:0002507 MAT:0000444 MESH:D012463 NCIT:C13275 UMLS:C0036087 Wikipedia:Saliva galen:Saliva salivary gland secretion uberon sailva normalis saliva atomaris saliva molecularis UBERON:0001836 saliva The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 UMLS:C0032105 Wikipedia:Blood_plasma blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma The portion of blood plasma that excludes clotting factors. BTO:0000133 BTO:0001239 CALOHA:TS-0923 EHDAA2:0004728 EMAPA:35770 FMA:63083 MA:0002502 MESH:D044967 NCIT:C13325 UMLS:C0229671 Wikipedia:Serum_(blood) serum uberon UBERON:0001977 blood serum Portion of semisolid bodily waste discharged through the anus[MW,modified]. Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 UMLS:C0015733 Wikipedia:Feces galen:Feces faeces fecal material fecal matter piece of shit portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces yes 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] hepatic 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. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 SCTID:181268008 TAO:0000123 UMLS:C0023884 VHOG:0000257 Wikipedia:Liver XAO:0000133 ZFA:0000123 galen:Liver uberon iecur jecur UBERON:0002107 liver https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg yes 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] renal AAO:0000250 BTO:0000671 CALOHA:TS-0510 EFO:0000929 EMAPA:17373 EV:0100096 FMA:7203 GAID:423 MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 NCIT:C12415 SCTID:181414000 UMLS:C0022646 Wikipedia:Kidney XAO:0003267 galen:Kidney reniculate kidney uberon UBERON:0002113 kidney 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] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 SCTID:361692004 TADS:0000108 UMLS:C0037267 VHOG:0000403 Wikipedia:Integumentary_system XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid BIRNLEX:20 EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 Wikipedia:Body_fluid galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid A strand of hair that is part of a head. hair FMA:54241 head hair hair of scalp uberon UBERON:0016446 hair of head The stage of being no more dependent of the nest and/or from caregivers for subsistence while having not reach sexual maturity. uberon UBERON:0034919 juvenile stage 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 22․05․24 voice analysis 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. This class is used for grouping terms and should not be used for logical reasoning. 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. https://pubmed.ncbi.nlm.nih.gov/34600936/ 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. https://pubmed.ncbi.nlm.nih.gov/37034474/ 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. generated with ChatGPT version 4,0 on 19․08․24 protein-based aging clock 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. generated with ChatGPT version 4,0 on 19․08․24 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. https://pubmed.ncbi.nlm.nih.gov/38486063/ 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. https://pubmed.ncbi.nlm.nih.gov/31780646/ Levine clock PhenoAge clock 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 https://pubmed.ncbi.nlm.nih.gov/38486063/ PhenoAge 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. https://pubmed.ncbi.nlm.nih.gov/35944348/ DNA methylation GrimAge DNAm GrimAge 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. generated with ChatGPT version 4,0 on 19․08․24 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. generated with ChatGPT version 4,0 on 19․08․24 decline in stem cell function 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. generated with ChatGPT version 4,0 on 19․08․24 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. generated with ChatGPT version 4,0 on 19․08․24 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. generated with ChatGPT version 4,0 on 19․08․24 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. https://pubmed.ncbi.nlm.nih.gov/11413492/ hayflick limit generated with ChatGPT-4 on 09․10․24 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. https://pubmed.ncbi.nlm.nih.gov/37944549/ bAge 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. generated with ChatGPT-4 on 09․10․24 DNA methylation GrimAge version 2 DNAm GrimAge2 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. generated with ChatGPT-4 on 09․10․24 DNAmRS 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. generated with ChatGPT-4 on 09․10․24 DNAm pace of aging DunedinPACE epigenetic aging rate pace of aging rate of epigenetic aging 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. generated with ChatGPT-4 on 09․10․24 M-metabo-score 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. generated with ChatGPT-4 on 09․10․24 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​. generated with ChatGPT-4 on 09․10․24 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. generated with ChatGPT-4 on 09․10․24 IEAA 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. generated with ChatGPT-4 on 09․10․24 EEAA 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. https://pubmed.ncbi.nlm.nih.gov/34233405/ 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. generated with ChatGPT version 4,0 on 19.06.2024 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. generated with ChatGPT version 4,0 on 19.06.2024 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. This class is used for grouping terms and should not be used for logical reasoning. 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. math+ mathematical entity yes 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. PATO:0000461 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. PATO:0002300 increased A quality that has a value that is decreased compared to normal or average. PATO:0002301 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 yes male is a biological sex of an individual with male sexual organs. PATO:0000384 male yes female is a biological sex of an individual with female sexual organs. female yes 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) James Malone Tomasz Adamusiak true DOID:14221 ICD9:277.7 MeSH:D024821 MedDRA:10052066 NCIt:C84442 OMIM:605552 OMIM:615812 SNOMEDCT:237602007 Cardiovascular Syndrome, Metabolic Cardiovascular Syndromes, Metabolic Dysmetabolic Syndrome X Insulin Resistance Syndrome X MetS Metabolic Cardiovascular Syndrome Metabolic Syndrome X Metabolic X Syndrome Reaven Syndrome X Syndrome X, Dysmetabolic Syndrome X, Insulin Resistance Syndrome X, Metabolic Syndrome X, Reaven Syndrome, Metabolic Cardiovascular Syndrome, Metabolic X X Syndrome, Metabolic metabolic syndrome yes 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. James Malone Jie Zheng Tomasz Adamusiak MO:833 MeSH:D000906 NCIt:C16295 NIFSTD:birnlex_2110 SNOMEDCT:68498002 antibodies antibody 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. James Malone true DOID:1287 ICD10:I98 ICD10:I99 ICD9:390-459.99 ICD9:420-429.99 ICD9:423 ICD9:423.8 ICD9:424 ICD9:429 ICD9:429.2 ICD9:429.7 ICD9:429.8 ICD9:429.81 ICD9:429.89 ICD9:459.89 ICD9:459.9 MESH:D002318 MONDO:0004995 MeSH:D002318 MedDRA:10007648 NCIT:C2931 NCIt:C2931 SCTID:49601007 SNOMEDCT:105980002 SNOMEDCT:49601007 UMLS:C0007222 ASCVD CARDIOVASC DIS CIRCULATORY DISEASE NOS CVD CVD, NOS CVS disease Cardiovascular Disease (CVD) Cardiovascular Diseases Cardiovascular Disorder Cardiovascular Disorders Cardiovascular disease, NOS Cardiovascular disease, unspecified Cardiovascular disorder, NOS Cardiovascular system disease Certain sequelae of myocardial infarction, not elsewhere classified Circulatory system disease NOS Circulatory system disease NOS (disorder) DISEASES OF THE CIRCULATORY SYSTEM Disease affecting entire cardiovascular system Disease affecting entire cardiovascular system (disorder) Disease of cardiovascular system Disease of cardiovascular system (disorder) Disease of cardiovascular system, NOS Disease, Cardiovascular Diseases, Cardiovascular Disorder of cardiovascular system Disorder of cardiovascular system (disorder) Disorder of circulatory system Disorder of circulatory system, NOS Disorder of the circulatory system ILL-DEFINED HRT DIS NEC Ill-defined descriptions and complications of heart disease OTHER SEQUELAE OF MI NEC Other diseases of endocardium Other diseases of endocardium (disorder) Other diseases of pericardium Other diseases of pericardium (disorder) Other disorders of papillary muscle Other forms of heart disease Other forms of heart disease (disorder) Other heart disease Other heart disease (disorder) Other heart disease NOS Other heart disease NOS (disorder) Other ill-defined heart disease Other ill-defined heart disease (disorder) Other ill-defined heart disease NOS Other ill-defined heart disease NOS (disorder) Other ill-defined heart diseases Other pericardial disease NOS Other pericardial disease NOS (disorder) Other sequelae of myocardial infarction, not elsewhere classified Other specified diseases of pericardium Other specified pericardial disease NOS Other specified pericardial disease NOS (disorder) PAPILLARY MUSCLE DIS NEC PERICARDIAL DISEASE NEC Unspecified circulatory system disorder [X]Cardiovascular disease, unspecified [X]Cardiovascular disease, unspecified (disorder) [X]Other forms of heart disease [X]Other forms of heart disease (disorder) [X]Other ill-defined heart diseases [X]Other ill-defined heart diseases (disorder) [X]Other specified diseases of pericardium [X]Other specified diseases of pericardium (disorder) cardiovascular disease cardiovascular disease (CVD) cardiovascular disorder cardiovascular system disease cardiovascular system disease or disorder circulatory system disease disease of cardiovascular system disease of subdivision of hemolymphoid system disease or disorder of cardiovascular system disorder of cardiovascular system circulatory system disease EFO:0000319 cardiovascular disease yes 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. James Malone Tomasz Adamusiak true DOID:8778 ICD10:K50 ICD9:555.1 MESH:D003424 MONDO:0005011 MeSH:D003424 MedDRA:10011401 NCIT:C2965 NCIt:C27837 NCIt:C2965 OMIM:266600 Orphanet:206 SCTID:34000006 SCTID:7620006 SNOMEDCT:34000006 UMLS:C0010346 UMLS:CN043071 CROHN DIS CROHNS DIS Colitis, Granulomatous Crohn Disease Crohn disease Crohn's associated gastritis Crohn's disease Crohn's disease of colon Crohn's disease of large bowel Crohns Disease Enteritis, Granulomatous Enteritis, Regional Gastritis Associated with Crohn Disease Gastritis Associated with Crohn's Disease Ileitis, Regional Ileitis, Terminal Ileocolitis granulomatous colitis paediatric Crohn's disease pediatric Crohn's disease regional enteritis EFO:0000384 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. James Malone Tomasz Adamusiak true DOID:11503 EFO:0004996 EFO:0004997 ICD9:250.4 ICD9:250.40 ICD9:583.81 MESH:D003928 MONDO:0005016 MeSH:D003928 MedDRA:10061835 NCIT:C84417 NCIt:C84417 OMIM:612624 OMIM:612628 OMIM:612634 SCTID:127013003 SCTID:50620007 SNOMEDCT:127013003 SNOMEDCT:197605007 SNOMEDCT:311366001 SNOMEDCT:38542009 SNOMEDCT:54181000 SNOMEDCT:707221002 DKD DMII RENAL UNCNTRLD DMII RENL NT ST UNCNTRLD Diabetes with renal manifestations Diabetes with renal manifestations (disorder) Diabetes-nephrosis syndrome Diabetes-nephrosis syndrome (disorder) Diabetic Glomerulosclerosis Diabetic Kidney Disease Diabetic Kidney Diseases Diabetic Nephropathies Diabetic renal disease Diabetic renal disease (disorder) Glomerulosclerosis, Diabetic Glomerulosclerosis, Nodular Intracapillary Glomerulosclerosis Kidney Disease, Diabetic Kidney Diseases, Diabetic Kimmelstiel - Wilson disease Kimmelstiel Wilson Disease Kimmelstiel Wilson Syndrome Kimmelstiel-Wilson Disease Kimmelstiel-Wilson Syndrome Nephropathies, Diabetic Nephropathy, Diabetic Nephrotic syndrome due to diabetes mellitus Nephrotic syndrome in diabetes mellitus Nephrotic syndrome in diabetes mellitus (disorder) Nodular Glomerulosclerosis Renal disorder associated with diabetes mellitus Syndrome, Kimmelstiel-Wilson diabetic kidney disease diabetic nephropathy type 1 diabetes nephropathy type 2 diabetes nephropathy EFO:0000401 diabetic nephropathy 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. James Malone Jie Zheng Tomasz Adamusiak MO:51 MeSH:D005838 NCIt:C16631 NIFSTD:birnlex_2023 Information, making the distinction between the actual physical material (e.g. a cell) and the information about the genetic content (genotype). 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. James Malone true MeSH:D013534 NCIt:C17177 PERSON: James Malone SNOMEDCT:445320007 survival time of survival survival time 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). James Malone https://github.com/monarch-initiative/mondo/issues/5537 https://github.com/monarch-initiative/mondo/issues/5781 true DOID:6432 GARD:7501 MESH:D000081029 MONDO:0015924 MeSH:D006976 MedDRA:10064911 NCIt:C3120 NORD:1634 OMIM:615371 Orphanet:182090 SCTID:11399002 SNOMEDCT:70995007 UMLS:C2973725 Ayerza Arrilaga Syndrome Ayerza Syndrome Ayerza's Syndrome Ayerza-Arrilaga Syndrome Ayerzas Syndrome HYPERTENSION PULM Hypertension, Pulmonary PAH PHT - Pulmonary hypertension PPH1 PULM HYPERTENSION Pulmonary hypertension, NOS Syndrome, Ayerza Syndrome, Ayerza-Arrilaga pulmonary arterial hypertension pulmonary hypertension pulmonary hypertension (disorder) pulmonary hypertension, primary, 1 PAH with overt features of venous/capillaries involvement PVOD/PCH PPH idiopathic pulmonary hypertension EFO:0001361 pulmonary arterial hypertension yes A study in which participants are examined at only a single time for characteristics of a disease. James Malone Natalja Kurbatova Tomasz Adamusiak NCIt:C53310 Cross-Sectional Study cross sectional design A measurement is an information entity that is a recording of the output of a measurement such as produced by an instrument. James Malone Jie Zheng Tomasz Adamusiak true MO:144 NCIt:C25209 NIFSTD:sao279801585 SNOMEDCT:122869004 measurement A carcinoma that arises from epithelial cells of the exocrine pancreas true cancer of pancreas cancer of the pancreas exocrine cancer pancreas cancer pancreatic cancer DOID:4905 EFO:0002618 MONDO:0005192 NCIT:C3850 OMIM:260350 SCTID:372142002 UMLS:C0235974 carcinoma of exocrine pancreas carcinoma of pancreas carcinoma of the pancreas exocrine pancreas carcinoma exocrine pancreatic carcinoma pancreas carcinoma pancreatic cancer (not islets) pancreatic carcinoma pancreatic carcinoma, familial EFO:0002618 pancreatic carcinoma yes James Malone NCIt:C15421 postmenopausal 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. Tomasz Adamusiak true ICD10:Z34 MeSH:D011247 MedDRA:10036556 NCIt:C25742 SNOMEDCT:289908002 Gestation PREGN Pregnancies pregnancy 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. Tomasz Adamusiak true DOID:1883 ICD9:070.41 ICD9:070.54 ICD9:070.7 MESH:D006526 MONDO:0005231 NCIT:C3098 NCIt:C3098 SCTID:128302006 SNOMEDCT:50711007 UMLS:C0019196 HCV infection Hepatitis C (disorder) Hepatitis C virus caused hepatitis Hepatitis C virus hepatitis Hepatitis non-A non-B (disorder) NANBH Viral hepatitis C Viral hepatitis C (disorder) acute hepatitis C with hepatic coma hepatitis C hepatitis C infection hepatitis C virus infection hepatitis Nona nonB hepatitis nonA nonB hepatitis type C non-A, non-B Hepatitis viral hepatitis C chronic hepatitis C EFO:0003047 hepatitis C virus infection 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. Catherine Leroy Tomasz Adamusiak true ICD10:I50 ICD9:428 ICD9:428.9 MESH:D006333 MONDO:0005252 MeSH:D006333 MedDRA:10007554 MedDRA:10007564 MedDRA:10019279 MedDRA:10019284 MedDRA:10019285 NCIT:C50577 NCIt:C50577 SCTID:84114007 SNOMEDCT:84114007 UMLS:C0018801 Heart failure (disorder) Heart failure NOS Heart failure NOS (disorder) Heart failure, unspecified Heart: [weak] or [failure NOS] Weak heart cardiac dysfunction cardiac failure cardiac insufficiency failure, heart heart failure insufficiency, Cardiac EFO:0003144 heart failure 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. Ele Holloway James Malone Tomasz Adamusiak http://en.wikipedia.org/wiki/Tumour_necrosis_factor-alpha CASRN:308079-78-9 DSSTox_CID:40634 MeSH:D014409 OMIM:191160 TNF-alpha; tumor necrosis factor TNF-α tumor necrosis factor-alpha 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). Ele Holloway James Malone Tomasz Adamusiak http://en.wikipedia.org/wiki/Vascular_endothelial_growth_factor CASRN:127464-60-2 DSSTox_Generic_SID:40639 OMIM:192240 SNOMEDCT:417324009 VEGF vascular endothelial growth factor 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) Tomasz Adamusiak true ICD10:E55 ICD9:268 MeSH:D014808 MedDRA:10047626 NCIt:C114830 SNOMEDCT:34713006 Avitaminosis D Avitaminosis D, NOS DEFIC VITAMIN D Deficiencies, Vitamin D Deficiency, Vitamin D VITAMIN D DEFIC Vitamin D Deficiencies Vitamin D deficiency (disorder) Vitamin D deficiency, NOS Vitamin D insufficiency vitamin D deficiency NCIt:C20464 SNOMEDCT:75777003 cytokine Measurement of the various processes involved in the act of respiration: inspiration, expiration, oxygen and carbon dioxide exchange, lung volume and compliance, etc. Tomasz Adamusiak true MeSH:D012129 NCIt:C38081 FUNCTION TEST PULM FUNCTION TESTS PULM Function Test, Lung Function Test, Pulmonary Function Test, Respiratory Function Tests, Lung Function Tests, Pulmonary Function Tests, Respiratory Lung Function Test Lung Function Tests PULM FUNCTION TEST PULM FUNCTION TESTS Pulmonary Function Tests Respiratory Function Test Respiratory Function Tests TEST PULM FUNCTION TESTS PULM FUNCTION Test, Lung Function Test, Pulmonary Function Test, Respiratory Function Tests, Lung Function Tests, Pulmonary Function Tests, Respiratory Function pulmonary function test pulmonary function measurement 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. Tomasz Adamusiak true MeSH:D012307 NCIt:C17103 SNOMEDCT:80943009 Factor, Risk Factors, Risk Risk Factors risk factor 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. Tomasz Adamusiak true ICD10:M85 MeSH:D015519 NCIt:C96950 BMD Bone Densities Bone Mineral Densities Bone Mineral Density Density, Bone Density, Bone Mineral aBMD areal bone mineral density bone density An interleukin is a multifunctional cytokine produced by leukocytes for regulating immune responses. James Malone NCIt:C20497 SNOMEDCT:38476002 interleukin yes The physical size of a tumor. James Malone NCIt:C120284 SNOMEDCT:263605001 size of tumor tumor size 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. Dani Welter true DOID:2043 ICD10:B16 ICD9:070.30 MESH:D006509 MONDO:0005344 MeSH:D019694 NCIT:C3097 NCIt:C3097 SCTID:66071002 UMLS:C0019163 HBV infection Hepatitis B Hepatitis B infection Hepatitis B virus caused hepatitis Hepatitis B virus hepatitis hepatitis B infection hepatitis B virus infection hepatitis B, chronic hepatitis type B viral Hepatitis B viral hepatitis B chronic hepatitis B serum hepatitis EFO:0004197 hepatitis B virus infection 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. Dani Welter true DOID:1184 ICD10:N04 ICD9:581 ICD9:581.9 MESH:D009404 MONDO:0005377 MeSH:D009404 MedDRA:10029164 NCIT:C34845 NCIt:C34845 OMIM:615861 OMIM:617783 OMIM:618176 OMIM:618177 OMIM:618178 OMIM:618594 Orphanet:564127 SCTID:52254009 SNOMEDCT:52254009 UMLS:C0027726 nephrotic syndrome nephrotic syndrome (acquired) nephrotic syndromes syndrome, nephrotic syndromes, nephrotic nephrosis EFO:0004255 nephrotic syndrome yes The presence of albumin in the urine, an indicator of KIDNEY DISEASES. Dani Welter true HP:0012592 MeSH:D000419 MedDRA:10001580 SNOMEDCT:274769005 urinary albumin excretion albuminuria 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. Dani Welter true ICD10:I74 ICD10:I82 MESH:D054556 MONDO:0005399 MeSH:D054556 MedDRA:10066899 NCIT:C99537 NCIt:C99537 UMLS:C1861172 VTE venous thromboembolism EFO:0004286 venous thromboembolism The volume of air that is exhaled by a maximal expiration following a maximal inspiration. Dani Welter true MeSH:D014797 MedDRA:10047579 NCIt:C111361 SNOMEDCT:268379003 FVC forced vital capacity vital capacity Measurement of rate of airflow over the middle half of a FORCED VITAL CAPACITY determination (from the 25 percent level to the 75 percent level). Common abbreviations are MMFR and FEF 25%-75%. Dani Welter true MeSH:D008450 FEF25-75% maximal midexpiratory flow rate Measure of the maximum amount of air that can be expelled in a given number of seconds during a FORCED VITAL CAPACITY determination . It is usually given as FEV 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. Dani Welter true MeSH:D005541 MedDRA:10016984 NCIt:C120933 FEV1 FEVt timed vital capacity forced expiratory volume yes PRESSURE of the BLOOD on the ARTERIES and other BLOOD VESSELS. Dani Welter true MeSH:D001794 MedDRA:10005727 NCIt:C54706 SNOMEDCT:75367002 blood pressure The mass or quantity of heaviness of an individual. It is expressed by units of pounds or kilograms. Dani Welter true MeSH:D001835 NCIt:C81328 SNOMEDCT:27113001 weight body weight yes 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. Dani Welter true MeSH:D055105 MedDRA:10074998 NCIt:C100948 SNOMEDCT:276361009 waist circumference Non-invasive methods of visualizing and measuring the CENTRAL NERVOUS SYSTEM, especially the brain, by various imaging modalities e.g. CT scan Dani Welter true brain imaging is about MeSH:D059906 neuroimaging measurement yes Quantification of the number of deaths in a population. Dani Welter true MeSH:D009026 MeSH:Q000401 NCIt:C16880 SNOMEDCT:409651001 mortality measurement mortality rate mortality 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. Helen Parkinson true insulin sensitivity test insulin sensitivity insulin sensitivity measurement yes The HOMA-IR measurement employs the homeostatic model assessment (HOMA) to quantify insulin resistance. Helen Parkinson true homeostasis model assessment insulin resistance HOMA-IR 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. Helen Parkinson http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3370421/ true telomere length A muscle mass measurement is the quantification of the mass of a muscle e.g. skeletal muscle for an individual. Helen Parkinson true muscle mass muscle mass measurement muscle measurement yes An Arterial stiffness measurement is the information output of a non invasive pulse wave velocity assay. Arterial stiffness is a predictor of cardiovascular mortality Helen Parkinson true arterial stiffness arterial stiffness measurement Is a quantification of some aspect of the genome, e.g. copy number variation at some locus. Helen Parkinson genomic measurement A total cholesterol measurement is the quantification of cholesterol in blood, total cholesterol is defined as the sum of HDL, LDL, and VLDL. Helen Parkinson true SNOMEDCT:121868005 cholesterol, total total cholesterol total cholesterol levels total cholesterol measurement 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. Helen Parkinson http://en.wikipedia.org/wiki/Interleukin_18 http://www.uniprot.org/uniprot/Q14116 IL-18 interleukin 18 interleukin 18 (Homo sapiens) Helen Parkinson Is the measurement of the ratio of forced expiratory volume (FEV) to forced vital capacity (FVC), used as a measure of pulmonary function. true FEV/FEC ratio FEV/FVC FEV1/FVC FEV/FVC ratio yes Is a quantification of NT-proBNP (N-terminal prohormone of brain natriuretic peptide) which is associated with acute congestive heart failure. Helen Parkinson http://en.wikipedia.org/wiki/NT-proBNP true N-Terminal Pro-B-Type Natriuretic Peptide NT-proBNP NT-proBNP measurement A quantification of a genomic variation that increases or decreases the copy number of a given region. Helen Parkinson http://purl.org/obo/owl/SO#SO_0001019 copy number variation Is a quantification of sleep time in humans where average sleep time was less than five hours. Helen Parkinson http://www.ncbi.nlm.nih.gov/pubmed/22322875 true short sleep The genetic variation of individuals in a population. Helen Parkinson true MeSH:D014644 NCIt:C17248 SNOMEDCT:64195000 genetic variation 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 Helen Parkinson http://www.ncbi.nlm.nih.gov/pubmed/21810643 true cortical thickness Is the genome wide recombination rate. Helen Parkinson true recombination rate Is a quantification of some sleep parameter. Helen Parkinson true sleep measurement Is a quantification of any molecule involved in the process of inflammatory response. Helen Parkinson true inflammatory marker measurement inflammatory biomarker 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. inflammatory biomarker measurement 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 Helen Parkinson true VO2 max maximal aerobic capacity maximal oxygen consumption maximal oxygen uptake peak oxygen uptake maximal oxygen uptake measurement yes The recurrence of a disease after treatment Helen Parkinson true MedDRA:10061819 relapse disease recurrence The total sum of the genetic information of an organism's somatic cells Helen Parkinson somatic genotype The total sum of the genetic information of an organism's germline Helen Parkinson germline genotype A collection or collectivity of microorganisms. Helen Parkinson NCIt:C68564 microbiome Measurement of the volume of the hippocampus Dani Welter true hippocampal volume wild type genotype 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 Dani Welter true MeSH:D005919 MedDRA:10018355 NCIt:C90505 SNOMEDCT:80274001 GFR glomerular filtration rate duration of sleep, measured either via a self-reporting questionnaire, interview or through obversation in a sleep lab Dani Welter true sleep duration 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 Dani Welter true NCIt:C121705 sleep quality self-reported assessment of how difficult an individual is to wake Dani Welter true sleep depth measurement of the time at which sleep begins Dani Welter true sleep time amount of time, usually recorded in minutes, between going to bed and falling asleep Dani Welter true sleep latency quantification of the volumetric fraction of blood pumped out of the left and right ventricle with each heartbeat or cardiac cycle Dani Welter true ejection fraction measurement quantification of white matter hyperintensity, usually measured by MRI Dani Welter true white matter hyperintensity white matter hyperintensity measurement quantification of the relative amount of oxygen that is dissolved or carried in a given medium Dani Welter true NCIt:C60832 SNOMEDCT:104847001 oxygen saturation measurement Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization. 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. Helen Parkinson DOID:10575 http://en.wikipedia.org/wiki/Disorders_of_calcium_metabolism true DOID:10575 ICD9:275.4 ICD9:275.40 ICD9:275.49 ICD9CM:275.4 ICD9CM:275.40 MESH:D002128 MONDO:0005557 MeSH:D002128 SCTID:71638002 SNOMEDCT:190863003 SNOMEDCT:190874007 SNOMEDCT:267442002 SNOMEDCT:71638002 UMLS:C0006705 Calcium Metabolism Disorders calcium metabolic disease calcium metabolic disorder calcium metabolism disease calcium metabolism disorder disorder of calcium metabolism calcium metabolism disease calcium metabolism disorder EFO:0005769 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. calcium metabolic disease quantification of any recombination-related factor, such as hotspot usage, African enchrichment and recombination rate Dani Welter true recombination measurement 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 Dani Welter true FEV1 change measurement FEV change measurement The blood pressure during the contraction of the left ventricle of the heart. Dani Welter true MedDRA:10042955 NCIt:C25298 SNOMEDCT:271649006 SYSBP systolic pressure systolic blood pressure 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 Helen Parkinson C14143 NCIt:C14143 SNOMEDCT:21594007 malignant 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. Dani Welter true PMID:25387706 galvanic skin response measurement electrodermal activity measurement 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. Sirarat Sarntivijai true MedDRA:10016642 NCIt:C3044 Wikipedia:Fibrosis fibrosis 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 Dani Welter true PMID:25514360 airway responsiveness measurement 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. Dani Welter true PMID:25517131 airway wall thickness measurement quantification of some lipoprotein A in a sample Dani Welter PMID:25575512 true Lp(a) measurement lipoprotein A measurement 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. Dani Welter true chromatid break measurement quantification of some aspect of the seasonal variation in the micrbiome of the gut Dani Welter true seasonal gut microbiome measurement Dani Welter true mosaic loss of chromosome Y measurement quantification of some aspect of nighttime rest such as duration or quality Dani Welter true PMID:27126917 nighttime rest measurement quantification of some aspect of daytime rest such as duration, frequency or quality Dani Welter true PMID:27126917 daytime rest measurement quantification of some aspect of an individual's micrbiome of the gut Dani Welter true gut microbiome gut microbiome measurement quantification of excessive daytime sleepiness such as how often it occurs and its severity Dani Welter true excessive daytime sleepiness measurement quantification of insomnia such as how often it occurs and its severity Dani Welter true insomnia measurement quantification of some aspect of an individual's microbiome Dani Welter microbiome measurement quantification of the taxonomic variation in a microbiome sample Dani Welter true taxonomic microbiome measurement quantification of the functional variation in a microbiome Dani Welter functional microbiome measurement quantification of some aspect of chronotype such as ease of getting up in the morning Dani Welter true chronotype measurement quantification of some aspect of snoring such as frequency or severity Dani Welter true PMID:28604731 snoring measurement quantification of some aspect of the deposition of amyloid proteins in an organ Dani Welter amyloid deposition measurement Qunatification of the maximum volume of air that an organism can breathe in and out during a specified period of time, often 1 minute. Annalisa Buniello true MedDRA:10026958 PMID:29095316 maximal voluntary ventilation Quantification of a glucose metabolic process. Annalisa Buniello true PMID:29130521 glucose metabolism measurement 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. Laura Harris true PMID:30049742 carbon monoxide diffusing capacity pulmonary diffusing capacity 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. MeSH:D009362 MedDRA:10062194 NCIt:C19151 cancer metastasis neoplasm metastasis tumor cell migration tumor metastasis metastasis 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. ICDO:8000/6 MONDO:0024883 NCIT:C3261 metastatic disease metastatic neoplasm metastatic tumor EFO:0009709 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. metastatic neoplasm 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 ] Maria Cerezo true NCIt:C41372 PMID:30804560 PEF peak expiratory flow Frequency of chromosomal aberrations in human peripheral blood. Joannella Morales true PMID:30368896 CA chromosomal aberration frequency Frequency of chromosome-type chromosomal aberrations in human peripheral blood (typically resulting in damage to both chromatids). Joannella Morales true PMID:30368896 CSA chromosome-type aberration frequency Frequency of chromatid-type chromosomal aberrations in human peripheral blood (typically resulting in damage to a single chromatid). Joannella Morales true PMID:30368896 CTA chromatid-type aberration frequency 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. Laura Harris true PMID:31557306 forced vital capacity change meaurement FVC change measurement Quantification of some aspect of an individual's microbiome of the vagina. Aoife McMahon true PMID:32723796 vaginal flora measurement vaginal microbiota measurement 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. Zoe May Pendlington 2024-03-08T09:27:59Z SNOMED:248280005 aging The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. Zoe May Pendlington 2024-04-12T13:21:16Z MeSH:D019175 NCIt:C17961 Wikipedia:DNA_methylation DNA methylation It is the most common clonal somatic alteration in leukocytes of female individuals. Zoe May Pendlington 2024-08-14T09:43:25Z mLOX mosaic loss of chromosome X measurement Quantification of some aspect of an individual's microbiome of the skin. true PMID:36261456 skin microbiota measurement skin microbiome measurement Quantification of some aspect of an individual's oral microbiome. true PMID:34875929 oral microbiota measurement salivary microbiome measurement oral microbiome measurement A measurement of the sum of durations of wakefulness episodes throughout the night, not including the wakefulness before sleep onset. Santhi Ramachandran true NCIt:C156554 WASO wake after sleep onset A relative measurement of the time spent asleep to the total time spent in bed. Santhi Ramachandran true NCIt:C156553 sleep efficiency A disease involving the thyroid gland. 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. Sirarat Sarntivijai true DOID:50 ICD10:E06 ICD10:E07 ICD10CM:E00-E07 ICD9:240-246.99 ICD9:246.8 ICD9:246.9 MESH:D013959 MONDO:0003240 MedDRA:10043778 MedDRA:10043785 NCIT:C26893 SCTID:14304000 UMLS:C4317107 Wikipedia:Thyroid_disease Thyroiditis disease of thyroid gland disease or disorder of thyroid gland disorder of thyroid gland thyroid disease thyroid gland disease thyroid gland disease or disorder thyroid gland diseases thyroid gland disorder thyroid gland disorders EFO:1000627 thyroid disease yes 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. Gautier Koscielny MedDRA:10048554 Wikipedia:Endothelial_dysfunction endothelial dysfunction