Becky Steck Chrysta Lienczewski Deborah Hoshizaki Evren Azeloglu George Oliver John F. Bertram John O'Toole Jonathan Himmelfarb Laura Mariani Matthias Kretzler Michael Todd Valerius Ravi Iyengar Sean Mooney The KPMP Consortium Ulysses Balis Edison Ong Jennifer Schaub Ling Wan Yingtong Liu Yongqun "Oliver" He 2022-02-16 KTAO (Kidney Tissue Atlas Ontology) is a community-based biomedical ontology. Its development is supported by the NIH-NIDDK supported Kidney Precision Medicine Project (KPMP). OWL-DL KTAO: A biomedical ontology that represents kidney tissue atlas. KTAO: Kidney Tissue Atlas Ontology Vision Release: 1.0.102 BFO OWL specification label 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 BFO OWL specification label BFO CLIF 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 BFO CLIF specification label editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) 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 example example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not 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> example of usage example of usage has curation status PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot OBI_0000281 has curation status has curation status definition definition textual definition English language definitions of what NCI means by the concept. These are limited to 1024 characters. They may also include information about the definition's source and attribution in a form that can easily be interpreted by software. 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. 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 GROUP:OBI:<http://purl.obolibrary.org/obo/obi> DEFINITION definition definition textual definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> GROUP:OBI:<http://purl.obofoundry.org/obo/obi> IAO:0000116 uberon editor_note 1 true editor_note editor note editor note definition editor term editor 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 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. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor term editor term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term alternative term definition source Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 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 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> definition source definition source 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 1 curator_notes curator note curator note curator notes term tracker item term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ 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. 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 Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external term_tracker_item true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. The 'tracker item' can associate a tracker with a specific ontology term. term tracker item term tracker item ontology term requester The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'term requester' can credit the person, organization or project who request the ontology term. ontology term requester 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 expression to expand expression to 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 . PERSON:Alan Ruttenberg PERSON:Bjoern Peters PERSON:Chris Mungall PERSON:Melanie Courtot GROUP:OBO Foundry <http://obofoundry.org/> OBO foundry unique label elucidation person:Alan Ruttenberg Person:Barry Smith Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms elucidation elucidation has associated axiom(nl) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom associated with a term expressed using natural language has associated axiom(nl) has associated axiom(nl) has associated axiom(fol) Person:Alan Ruttenberg Person:Alan Ruttenberg An axiom expressed in first order logic using CLIF syntax has associated axiom(fol) has associated axiom(fol) preferred_root term replaced by C3829466 NCIT_C106180 term_mapping_to_UMLS term_mapping_to_NCIT A property created to allow the source NICHD to assign a parent to each concept with the intent of creating a hierarchy that includes only terms in which they are the contributing source. A11 Conceptual Entity Has_NICHD_Parent Has_NICHD_Parent Has_NICHD_Parent true NHC0 code code code 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 Provides an alternative Preferred Name for use in some NCI systems. P107 Conceptual Entity Display Name Display_Name Display Name Display_Name Display_Name 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 Concept Unique Identifiers, or CUIs, are concept numbers 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 Contains a Concept Unique Identifier for those concepts that appear in NCI Metathesaurus but not in the NLM UMLS. P208 Conceptual Entity NCI Metathesaurus CUI NCI_META_CUI NCI_META_CUI NCI_META_CUI An NCI Thesaurus property used to indicate the standing of a concept in relation to currently accepted classifications and concepts. In NCI Thesaurus concept status subtype indicates concepts with unusual and problematic characteristics that should be evaluated by people and/or programs before those concept are used. P310 Conceptual Entity Concept Status Concept_Status Concept_Status Concept_Status This 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 English language definitions of what a source other than NCI means by the concept. These are limited to 1024 characters. They include information about the definition's source in a form that can easily be interpreted by software. P325 Conceptual Entity [source] Definition ALT_DEFINITION ALT_DEFINITION ALT_DEFINITION true 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 P371 Conceptual Entity NICHD_Hierarchy_Term NICHD NICHD_Hierarchy_Term NICHD_Hierarchy_Term 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 has_MedDRA_id has_meddra_id 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 NIAID GSCID-BRC alternative term An alternative term used by the National Institute of Allergy and Infectious Diseases (NIAID) Genomic Sequencing Centers for Infectious Diseases (GSCID) and Bioinformatics Resource Centers (BRC). PERSON: Chris Stoeckert, Jie Zheng NIAID GSCID-BRC metadata working group NIAID GSCID-BRC 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 YH: use the convention: GO_ID (EC: xx; Qualifier: xx; PMID: xxxxx;) where GO_ID is a GO ID, EC is the Evidence Code, Qualifier is a specific association type, and PMID is a PubMed ID of a paper that supports the gene-GO association. has GO association An annotation property that represents a gene's association with PubMed publication(s). Yongqun He YH: use the format: PMID: pmid1, pmid2, ... where pmid1 and pmid2 are specfic PubMed IDs (PMIDs). has PubMed association A subproperty of seeAlso that represents a NCIT identifier mapped to the specified term Oliver He term mapping to NCIT ID A subproperty of seeAlso that represents a UMLS CUI identifier mapped to the specified term Oliver He term mapping to UMLS CUI An annotation property that refers to a code defined by NCIT NCIT code alternative term in Chinese An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context. temporal interpretation temporal interpretation https://code.google.com/p/obo-relations/wiki/ROAndTime https://github.com/oborel/obo-relations/wiki/ROAndTime 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. Chris Mungall ?X DisjointWith RO_0002162 some ?Y Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) RO:0002161 uberon never_in_taxon true true never_in_taxon never in taxon never_in_taxon An assertion that holds between an ontology class and an organism taxon class, which is intepreted to yield some relationship between instances of the ontology class and the taxon. taxonomic class assertion S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T. RO:0002174 uberon dubious_for_taxon 1 1 dubious_for_taxon this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost dubious_for_taxon 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. https://orcid.org/0000-0002-6601-2165 RO:0002175 applicable for taxon uberon present_in_taxon 1 true 1 true present_in_taxon present in taxon present_in_taxon An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL. logical macro assertion https://github.com/oborel/obo-relations/wiki/ShortcutRelations A logical macro assertion whose domain is an IRI for a class The domain for this class can be considered to be owl:Class, but we cannot assert this in OWL2-DL logical macro assertion on a class A logical macro assertion whose domain is an IRI for a property logical macro assertion on a property Used to annotate object properties to describe a logical meta-property or characteristic of the object property. logical macro assertion on an object property logical macro assertion on an annotation property relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q' Chris Mungall is direct form of 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 1 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 1 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 1 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 1 has_relational_adjective has_relational_adjective Notes on the how instances of this class vary across species. UBPROP:0000008 uberon taxon_notes 1 taxon_notes taxon_notes Notes on the structure, composition or histology of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000010 uberon structure_notes 1 structure_notes structure_notes Notes on the ontogenic development of instances of this class. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000011 uberon development_notes 1 development_notes development_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 1 external_ontology_notes external_ontology_notes Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy. This annotation property may be replaced with an annotation property from an external ontology such as IAO UBPROP:0000013 uberon terminology_notes 1 terminology_notes terminology_notes excluded_from_qc_check true excluded from QC check excluded_subClassOf true excluded subClassOf A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy ncbi_taxonomy has_rank Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. http://purl.org/dc/elements/1.1/contributor uberon dc-contributor 1 true dc-contributor An entity responsible for making contributions to the content of the resource. Contributor Contributor contributor 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 creator Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. A date associated with an event in the life cycle of the resource. Date Date 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 Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). The physical or digital manifestation of the resource. Format Format The present resource may be derived from the Source resource in whole or in part. Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system. A reference to a resource from which the present resource is derived. Source Source Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. The topic of the content of the resource. Subject and Keywords Subject and Keywords Typically, a Title will be a name by which the resource is formally known. http://purl.org/dc/elements/1.1/title uberon dc-title true dc-title A name given to the resource. Title Title title Mark Miller 2018-05-11T13:47:29Z http://purl.org/dc/terms/license uberon dcterms-license true dcterms-license license consider has_alternative_id has_broad_synonym database_cross_reference 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. FULL_SYN Synonym with Source Data has exact synonym has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym Used to associate the concept defining a particular terminology subset with concepts that belong to this subset. Concept_In_Subset in subset in_subset shorthand label label label http://www.w3.org/2000/01/rdf-schema#seeAlso uberon seeAlso true true seeAlso see also seeAlso http://xmlns.com/foaf/0.1/depicted_by uberon depicted_by foaf-depicted_by 1 true depicted_by foaf-depicted_by depicted by depicted_by C26 CI_ChemClass C36 CI_with C24 has_Ingredient C28 has_MoA C20 has_PE C32 has_PK C40 induces C38 may_prevent C34 may_treat is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 external quality uberon part_of part_of part of part of part_of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) Q1 has_part Q2 if and only if: every instance of Q1 is a quality_of an entity that has_quality some Q2. a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 external protein quality uberon has_part has_part has part has part has_part BFO_0000052 BFO_0000052s BFO_0000052ed inheres-in_at inheresInAt b inheres_in c at t =Def. b is a dependent continuant & c is an independent continuant that is not a spatial region & b s-depends_on c at t. (axiom label in BFO2 Reference: [051-002]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'inheres in at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'inheres in@en(x,y,t)'. BFO 2 Reference: Inherence is a subrelation of s-depends_on which holds between a dependent continuant and an independent continuant that is not a spatial region. Since dependent continuants cannot migrate from one independent continuant bearer to another, it follows that if b s-depends_on independent continuant c at some time, then b s-depends_on c at all times at which a exists. Inherence is in this sense redundantly time-indexed.For example, consider the particular instance of openness inhering in my mouth at t as I prepare to take a bite out of a donut, followed by a closedness at t+1 when I bite the donut and start chewing. The openness instance is then shortlived, and to say that it s-depends_on my mouth at all times at which this openness exists, means: at all times during this short life. Every time you make a fist, you make a new (instance of the universal) fist. (Every time your hand has the fist-shaped quality, there is created a new instance of the universal fist-shaped quality.) BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (inheresInAt a b t) (and (DependentContinuant a) (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))) // axiom label in BFO2 CLIF: [051-002] inheres in at all times bearer of bearer_of http://purl.obolibrary.org/obo/omrse.owl is bearer of is_bearer_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in http://purl.obolibrary.org/obo/ro.owl [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) BFO:0000054 realized_in realized_in Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realized in BFO_0000055 BFO_0000055s BFO_0000055ed realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes concretized-by_st [copied from inverse property 'concretizes at some time'] You may concretize a piece of software by installing it in your computer [copied from inverse property 'concretizes at some time'] You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. [copied from inverse property 'concretizes at some time'] you may concretize a poem as a pattern of memory traces in your head [copied from inverse property 'concretizes at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) [copied from inverse property 'concretizes at some time'] b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) concretized by at some time concretizes_st concretizesAt You may concretize a piece of software by installing it in your computer You may concretize a recipe that you find in a cookbook by turning it into a plan which exists as a realizable dependent continuant in your head. you may concretize a poem as a pattern of memory traces in your head Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'concretizes at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'concretizes@en'(x,y,t) b concretizes c at t means: b is a specifically dependent continuant & c is a generically dependent continuant & for some independent continuant that is not a spatial region d, b s-depends_on d at t & c g-depends on d at t & if c migrates from bearer d to another bearer e than a copy of b will be created in e. (axiom label in BFO2 Reference: [075-002]) if b g-depends on c at some time t, then there is some d, such that d concretizes b at t and d s-depends_on c at t. (axiom label in BFO2 Reference: [076-001]) (forall (x y t) (if (concretizesAt x y t) (and (SpecificallyDependentContinuant x) (GenericallyDependentContinuant y) (exists (z) (and (IndependentContinuant z) (specificallyDependsOnAt x z t) (genericallyDependsOnAt y z t)))))) // axiom label in BFO2 CLIF: [075-002] (forall (x y t) (if (genericallyDependsOnAt x y t) (exists (z) (and (concretizesAt z x t) (specificallyDependsOnAt z y t))))) // axiom label in BFO2 CLIF: [076-001] concretizes at some time preceded by X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X). x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 is preceded by takes place after external uberon preceded_by preceded_by preceded by preceded by preceded_by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external uberon precedes precedes precedes precedes occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t occurs_in unfolds in unfolds_in BFO:0000066 external occurs_in occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant occurs in occurs in site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t BFO:0000067 uberon contains_process contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant contains process contains process s-depends-on_at specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'specifically depends on at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'specifically depends on@en(x,y,t)'. BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at all times located-at-r_st occupiesSpatialRegionAt Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) BFO2 Reference: independent continuant BFO2 Reference: spatial region b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) every region r is occupies_spatial_region r at all times. (axiom label in BFO2 Reference: [042-002]) if b occupies_spatial_region r at t & b continuant_part_of b at t, then there is some r which is continuant_part_of r at t such that b occupies_spatial_region r at t. (axiom label in BFO2 Reference: [043-001]) (forall (r t) (if (Region r) (occupiesSpatialRegionAt r r t))) // axiom label in BFO2 CLIF: [042-002] (forall (x r t) (if (occupiesSpatialRegionAt x r t) (and (SpatialRegion r) (IndependentContinuant x)))) // axiom label in BFO2 CLIF: [041-002] (forall (x y r_1 t) (if (and (occupiesSpatialRegionAt x r_1 t) (continuantPartOfAt y x t)) (exists (r_2) (and (continuantPartOfAt r_2 r_1 t) (occupiesSpatialRegionAt y r_2 t))))) // axiom label in BFO2 CLIF: [043-001] occupies spatial region at some time exists-at existsAt BFO2 Reference: entity BFO2 Reference: temporal region b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) exists at BFO_0000117 BFO_0000117s BFO_0000117ed o-has-part hasOccurrentPart [copied from inverse property 'part of occurrent'] Mary’s 5th birthday occurrent_part_of Mary’s life [copied from inverse property 'part of occurrent'] The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. [copied from inverse property 'part of occurrent'] the first set of the tennis match occurrent_part_of the tennis match. b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) [copied from inverse property 'part of occurrent'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of occurrent'] BFO2 Reference: occurrent [copied from inverse property 'part of occurrent'] b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) (iff (hasOccurrentPart a b) (occurrentPartOf b a)) // axiom label in BFO2 CLIF: [007-001] has occurrent part o-has-ppart hasProperOccurrentPart [copied from inverse property 'proper part of occurrent'] b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 has proper occurrent part r-location-of_st [copied from inverse property 'occupies spatial region at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'occupies spatial region at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'occupies spatial region@en'(x,y,t) [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: independent continuant [copied from inverse property 'occupies spatial region at some time'] BFO2 Reference: spatial region [copied from inverse property 'occupies spatial region at some time'] b occupies_spatial_region r at t means that r is a spatial region in which independent continuant b is exactly located (axiom label in BFO2 Reference: [041-002]) has spatial occupant at some time has-s-dep_st [copied from inverse property 'specifically depends on at some time'] A pain s-depends_on the organism that is experiencing the pain [copied from inverse property 'specifically depends on at some time'] a gait s-depends_on the walking object. (All at some specific time.) [copied from inverse property 'specifically depends on at some time'] a shape s-depends_on the shaped object [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat [copied from inverse property 'specifically depends on at some time'] one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of buying and the associated process of selling [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas [copied from inverse property 'specifically depends on at some time'] reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball [copied from inverse property 'specifically depends on at some time'] the one-sided dependence of an occurrent on an independent continuant: handwave on a hand [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 [copied from inverse property 'specifically depends on at some time'] the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 [copied from inverse property 'specifically depends on at some time'] the two-sided reciprocal s-dependence of the roles of husband and wife [20 [copied from inverse property 'specifically depends on at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 [copied from inverse property 'specifically depends on at some time'] BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. [copied from inverse property 'specifically depends on at some time'] BFO2 Reference: specifically dependent continuant\; process; process boundary [copied from inverse property 'specifically depends on at some time'] To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 has specific dependent at some time occupied-by [copied from inverse property 'occupies spatiotemporal region'] BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. [copied from inverse property 'occupies spatiotemporal region'] p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) has spatiotemporal occupant occupies occupiesSpatiotemporalRegion BFO 2 Reference: The occupies_spatiotemporal_region and occupies_temporal_region relations are the counterpart, on the occurrent side, of the relation occupies_spatial_region. p occupies_spatiotemporal_region s. This is a primitive relation between an occurrent p and the spatiotemporal region s which is its spatiotemporal extent. (axiom label in BFO2 Reference: [082-003]) occupies spatiotemporal region BFO_0000132 BFO_0000132s BFO_0000132ed o-part-of occurrentPartOf Mary’s 5th birthday occurrent_part_of Mary’s life The process of a footballer’s heart beating once is an occurrent part but not a temporal_part of a game of football. the first set of the tennis match occurrent_part_of the tennis match. [copied from inverse property 'has occurrent part'] b has_occurrent_part c = Def. c occurrent_part_of b. (axiom label in BFO2 Reference: [007-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: occurrent b occurrent_part_of c =Def. b is a part of c & b and c are occurrents. (axiom label in BFO2 Reference: [003-002]) occurrent_part_of is antisymmetric. (axiom label in BFO2 Reference: [123-001]) occurrent_part_of is reflexive (every occurrent entity is an occurrent_part_of itself). (axiom label in BFO2 Reference: [113-002]) occurrent_part_of is transitive. (axiom label in BFO2 Reference: [112-001]) occurrent_part_of satisfies unique product. (axiom label in BFO2 Reference: [125-001]) occurrent_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [124-001]) (forall (x y t) (if (and (occurrentPartOf x y t) (not (= x y))) (exists (z) (and (occurrentPartOf z y t) (not (exists (w) (and (occurrentPartOf w x t) (occurrentPartOf w z t)))))))) // axiom label in BFO2 CLIF: [124-001] (forall (x y t) (if (and (occurrentPartOf x y t) (occurrentPartOf y x t)) (= x y))) // axiom label in BFO2 CLIF: [123-001] (forall (x y t) (if (exists (v) (and (occurrentPartOf v x t) (occurrentPartOf v y t))) (exists (z) (forall (u w) (iff (iff (occurrentPartOf w u t) (and (occurrentPartOf w x t) (occurrentPartOf w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [125-001] (forall (x y z) (if (and (occurrentPartOf x y) (occurrentPartOf y z)) (occurrentPartOf x z))) // axiom label in BFO2 CLIF: [112-001] (forall (x) (if (Occurrent x) (occurrentPartOf x x))) // axiom label in BFO2 CLIF: [113-002] part of occurrent o-ppart-of properOccurrentPartOf [copied from inverse property 'has proper occurrent part'] b has_proper_occurrent_part c = Def. c proper_occurrent_part_of b. [XXX-001 b proper_occurrent_part_of c =Def. b occurrent_part_of c & b and c are not identical. (axiom label in BFO2 Reference: [005-001]) (iff (properOccurrentPartOf a b) (and (occurrentPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [005-001] proper part of occurrent t-part-of temporalPartOf the 4th year of your life is a temporal part of your life\. The first quarter of a game of football is a temporal part of the whole game\. The process of your heart beating from 4pm to 5pm today is a temporal part of the entire process of your heart beating.\ The 4th year of your life is a temporal part of your life the process boundary which separates the 3rd and 4th years of your life. your heart beating from 4pm to 5pm today is a temporal part of the process of your heart beating b proper_temporal_part_of c =Def. b temporal_part_of c & not (b = c). (axiom label in BFO2 Reference: [116-001]) b temporal_part_of c =Def.b occurrent_part_of c & & for some temporal region t, b occupies_temporal_region t & for all occurrents d, t (if d occupies_temporal_region t & t? occurrent_part_of t then (d occurrent_part_of a iff d occurrent_part_of b)). (axiom label in BFO2 Reference: [078-003]) if b proper_temporal_part_of c, then there is some d which is a proper_temporal_part_of c and which shares no parts with b. (axiom label in BFO2 Reference: [117-002]) (forall (x y) (if (properTemporalPartOf x y) (exists (z) (and (properTemporalPartOf z y) (not (exists (w) (and (temporalPartOf w x) (temporalPartOf w z)))))))) // axiom label in BFO2 CLIF: [117-002] (iff (properTemporalPartOf a b) (and (temporalPartOf a b) (not (= a b)))) // axiom label in BFO2 CLIF: [116-001] (iff (temporalPartOf a b) (and (occurrentPartOf a b) (exists (t) (and (TemporalRegion t) (occupiesSpatioTemporalRegion a t))) (forall (c t_1) (if (and (Occurrent c) (occupiesSpatioTemporalRegion c t_1) (occurrentPartOf t_1 r)) (iff (occurrentPartOf c a) (occurrentPartOf c b)))))) // axiom label in BFO2 CLIF: [078-003] temporal part of st-projects-onto-s_st projects onto spatial region at some time s-projection-of-st_st spatial projection of spatiotemporal at some time st-projects-onto-t projects onto temporal region t-projection-of-st temporal projection of spatiotemporal spans occupiesTemporalRegion p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) occupies temporal region span-of spanOf [copied from inverse property 'occupies temporal region'] p occupies_temporal_region t. This is a primitive relation between an occurrent p and the temporal region t upon which the spatiotemporal region p occupies_spatiotemporal_region projects. (axiom label in BFO2 Reference: [132-001]) has temporal occupant during-which-exists [copied from inverse property 'exists at'] BFO2 Reference: entity [copied from inverse property 'exists at'] BFO2 Reference: temporal region [copied from inverse property 'exists at'] b exists_at t means: b is an entity which exists at some temporal region t. (axiom label in BFO2 Reference: [118-002]) during which exists bearer-of_at bearerOfAt b bearer_of c at t =Def. c s-depends_on b at t & b is an independent continuant that is not a spatial region. (axiom label in BFO2 Reference: [053-004]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'bearer of at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'bearer of@en(x,y,t)'. BFO2 Reference: independent continuant that is not a spatial region BFO2 Reference: specifically dependent continuant (iff (bearerOfAt a b t) (and (specificallyDependsOnAt b a t) (IndependentContinuant a) (not (SpatialRegion a)) (existsAt b t))) // axiom label in BFO2 CLIF: [053-004] bearer of at all times has-d_at hasDispositionAt a has_disposition b at t =Def. b disposition_of a at t. (axiom label in BFO2 Reference: [069-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has disposition at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has disposition@en(x,y,t)'. (iff (hasDispositionAt a b t) (dispositionOf b a t)) // axiom label in BFO2 CLIF: [069-001] has disposition at all times BFO_0000167 BFO_0000167s BFO_0000167ed has participant at all times has-s-dep_at has specific dependent at all times s-depends-on_st specificallyDependsOn A pain s-depends_on the organism that is experiencing the pain a gait s-depends_on the walking object. (All at some specific time.) a shape s-depends_on the shaped object one-sided s-dependence of a dependent continuant on an independent continuant: an instance of headache s-depends_on some head one-sided s-dependence of a dependent continuant on an independent continuant: an instance of temperature s-depends_on some organism one-sided s-dependence of a process on something: a process of cell death s-depends_on a cell one-sided s-dependence of a process on something: an instance of seeing (a relational process) s-depends_on some organism and on some seen entity, which may be an occurrent or a continuant one-sided s-dependence of one occurrent on another: a process of answering a question is dependent on a prior process of asking a question one-sided s-dependence of one occurrent on another: a process of obeying a command is dependent on a prior process of issuing a command one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of hitting a ball with a cricket bat one-sided s-dependence of one occurrent on multiple independent continuants: a relational process of paying cash to a merchant in exchange for a bag of figs reciprocal s-dependence between occurrents: a process of buying and the associated process of selling reciprocal s-dependence between occurrents: a process of increasing the volume of a portion of gas while temperature remains constant and the associated process of decreasing the pressure exerted by the gas reciprocal s-dependence between occurrents: in a game of chess the process of playing with the white pieces is mutually dependent on the process of playing with the black pieces the one-sided dependence of an occurrent on an independent continuant: football match on the players, the ground, the ball the one-sided dependence of an occurrent on an independent continuant: handwave on a hand the three-sided reciprocal s-dependence of the hue, saturation and brightness of a color [45 the three-sided reciprocal s-dependence of the pitch, timbre and volume of a tone [45 the two-sided reciprocal s-dependence of the roles of husband and wife [20 Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'specifically depends on at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'specifically depends on@en'(x,y,t) BFO 2 Reference: An entity – for example an act of communication or a game of football – can s-depends_on more than one entity. Complex phenomena for example in the psychological and social realms (such as inferring, commanding and requesting) or in the realm of multi-organismal biological processes (such as infection and resistance), will involve multiple families of dependence relations, involving both continuants and occurrents [1, 4, 28 BFO 2 Reference: S-dependence is just one type of dependence among many; it is what, in the literature, is referred to as ‘existential dependence’ [87, 46, 65, 20 BFO 2 Reference: the relation of s-depends_on does not in every case require simultaneous existence of its relata. Note the difference between such cases and the cases of continuant universals defined historically: the act of answering depends existentially on the prior act of questioning; the human being who was baptized or who answered a question does not himself depend existentially on the prior act of baptism or answering. He would still exist even if these acts had never taken place. BFO2 Reference: specifically dependent continuant\; process; process boundary To say that b s-depends_on a at t is to say that b and c do not share common parts & b is of its nature such that it cannot exist unless c exists & b is not a boundary of c and b is not a site of which c is the host [64 If b is s-depends_on something at some time, then b is not a material entity. (axiom label in BFO2 Reference: [052-001]) If b s-depends_on something at t, then there is some c, which is an independent continuant and not a spatial region, such that b s-depends_on c at t. (axiom label in BFO2 Reference: [136-001]) If occurrent b s-depends_on some independent continuant c at t, then b s-depends_on c at every time at which b exists. (axiom label in BFO2 Reference: [015-002]) an entity does not s-depend_on any of its (continuant or occurrent) parts or on anything it is part of. (axiom label in BFO2 Reference: [013-002]) if b s-depends_on c at t & c s-depends_on d at t then b s-depends_on d at t. (axiom label in BFO2 Reference: [054-002]) (forall (x y t) (if (and (Entity x) (or (continuantPartOfAt y x t) (continuantPartOfAt x y t) (occurrentPartOf x y) (occurrentPartOf y x))) (not (specificallyDependsOnAt x y t)))) // axiom label in BFO2 CLIF: [013-002] (forall (x y t) (if (and (Occurrent x) (IndependentContinuant y) (specificallyDependsOnAt x y t)) (forall (t_1) (if (existsAt x t_1) (specificallyDependsOnAt x y t_1))))) // axiom label in BFO2 CLIF: [015-002] (forall (x y t) (if (specificallyDependsOnAt x y t) (exists (z) (and (IndependentContinuant z) (not (SpatialRegion z)) (specificallyDependsOnAt x z t))))) // axiom label in BFO2 CLIF: [136-001] (forall (x y z t) (if (and (specificallyDependsOnAt x y t) (specificallyDependsOnAt y z t)) (specificallyDependsOnAt x z t))) // axiom label in BFO2 CLIF: [054-002] (forall (x) (if (exists (y t) (specificallyDependsOnAt x y t)) (not (MaterialEntity x)))) // axiom label in BFO2 CLIF: [052-001] specifically depends on at some time c-part-of_st continuantPartOfAt Mary’s arm continuant_part_of Mary in the time of her life prior to her operation the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. [copied from inverse property 'has continuant part at some time'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. BFO2 Reference: continuant BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'has continuant part at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) continuant_part_of is antisymmetric. (axiom label in BFO2 Reference: [120-001]) continuant_part_of is reflexive (every continuant entity is a continuant_part_of itself). (axiom label in BFO2 Reference: [111-002]) continuant_part_of is transitive. (axiom label in BFO2 Reference: [110-001]) continuant_part_of satisfies unique product. (axiom label in BFO2 Reference: [122-001]) continuant_part_of satisfies weak supplementation. (axiom label in BFO2 Reference: [121-001]) if b continuant_part_of c at t and b is an independent continuant, then b is located_in c at t. (axiom label in BFO2 Reference: [047-002]) (forall (x t) (if (Continuant x) (continuantPartOfAt x x t))) // axiom label in BFO2 CLIF: [111-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (IndependentContinuant x)) (locatedInAt x y t))) // axiom label in BFO2 CLIF: [047-002] (forall (x y t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y x t)) (= x y))) // axiom label in BFO2 CLIF: [120-001] (forall (x y t) (if (and (continuantPartOfAt x y t) (not (= x y))) (exists (z) (and (continuantPartOfAt z y t) (not (exists (w) (and (continuantPartOfAt w x t) (continuantPartOfAt w z t)))))))) // axiom label in BFO2 CLIF: [121-001] (forall (x y t) (if (exists (v) (and (continuantPartOfAt v x t) (continuantPartOfAt v y t))) (exists (z) (forall (u w) (iff (iff (continuantPartOfAt w u t) (and (continuantPartOfAt w x t) (continuantPartOfAt w y t))) (= z u)))))) // axiom label in BFO2 CLIF: [122-001] (forall (x y z t) (if (and (continuantPartOfAt x y t) (continuantPartOfAt y z t)) (continuantPartOfAt x z t))) // axiom label in BFO2 CLIF: [110-001] (iff (ImmaterialEntity a) (and (IndependentContinuant a) (not (exists (b t) (and (MaterialEntity b) (continuantPartOfAt b a t)))))) // axiom label in BFO2 CLIF: [028-001] part of continuant at some time c-has-part_st hasContinuantPartAt [copied from inverse property 'part of continuant at some time'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at some time'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'has continuant part at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'has continuant part@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance level, relation. The BFO reading of the binary relation 'part of continuant at some time@en' is: exists t, exists_at(x,t) & exists_at(y,t) & 'part of continuant@en'(x,y,t) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at some time'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at some time'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at some time'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) (iff (hasContinuantPartAt a b t) (continuantPartOfAt b a t)) // axiom label in BFO2 CLIF: [006-001] has continuant part at some time c-part-of-object_at [copied from inverse property 'has continuant part at all times'] b has_continuant_part c at t = Def. c continuant_part_of b at t. (axiom label in BFO2 Reference: [006-001]) forall(t) exists_at(y,t) -> exists_at(x,t) and 'part of continuant'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'has continuant part at all times' [copied from inverse property 'has continuant part at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'has continuant part at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'has continuant part@en(x,y,t)'. part of continuant at all times that whole exists c-has-part-object_at [copied from inverse property 'part of continuant at all times'] Mary’s arm continuant_part_of Mary in the time of her life prior to her operation [copied from inverse property 'part of continuant at all times'] the Northern hemisphere of the planet Earth is a part of the planet Earth at all times at which the planet Earth exists. forall(t) exists_at(y,t) -> exists_at(x,t) and 'has continuant part'(x,y,t) This is a binary version of a ternary time-indexed, instance level, relation. Unlike the rest of the temporalized relations which temporally quantify over existence of the subject of the relation, this relation temporally quantifies over the existence of the object of the relation. The relation is provided tentatively, to assess whether the GO needs such a relation. It is inverse of 'part of continuant at all times' [copied from inverse property 'part of continuant at all times'] Alan Ruttenberg: This is a binary version of a ternary time-indexed, instance-level, relation. The BFO reading of the binary relation 'part of continuant at all times@en' is: forall(t) exists_at(x,t) -> exists_at(y,t) and 'part of continuant@en(x,y,t)'. [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: Immaterial entities are in some cases continuant parts of their material hosts. Thus the hold of a ship, for example, is a part of the ship; it may itself have parts, which may have names (used for example by ship stow planners, customs inspectors, and the like). Immaterial entities under both 1. and 2. can be of zero, one, two or three dimensions. We define:a(immaterial entity)[Definition: a is an immaterial entity = Def. a is an independent continuant that has no material entities as parts. (axiom label in BFO2 Reference: [028-001]) [copied from inverse property 'part of continuant at all times'] BFO 2 Reference: a (continuant or occurrent) part of itself. We appreciate that this is counterintuitive for some users, since it implies for example that President Obama is a part of himself. However it brings benefits in simplifying the logical formalism, and it captures an important feature of identity, namely that it is the limit case of mereological inclusion. [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuant [copied from inverse property 'part of continuant at all times'] BFO2 Reference: continuantThe range for ‘t’ (as in all cases throughout this document unless otherwise specified) is: temporal region. [copied from inverse property 'part of continuant at all times'] b continuant_part_of c at t =Def. b is a part of c at t & t is a time & b and c are continuants. (axiom label in BFO2 Reference: [002-001]) has continuant part at all times that part exists x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer. cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. caudal_to posterior_to x proximal_to y iff x is closer to the point of attachment with the body than y. proximal_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. in_left_side_of X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. in_right_side_of X posterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the posterior portion. in_posterior_side_of X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. in_anterior_side_of X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure. BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y. BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of This relation holds when both the deep_to and ajdacent_to relationship similarly hold. immediately_deep_to X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y. BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of GOREL:0002004 external results_in_fission_of results_in_fission_of results_in_fission_of has measurement unit label This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r person:Alan Ruttenberg Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes relates a process to a time-measurement-datum that represents the duration of the process Person:Alan Ruttenberg is duration of A shortcut object property that represents a relation between a biological entity and a material entity inside a human patient where the biological entity is susceptible to be differentially regulated in the material entity (e.g., cell or anatomic entity) of a human patient with a specific disease. Oliver He, Edison Ong susceptible to be differentially regulated in human disease A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be differentially regulated in a cell of a chronical kidney disease (CKD) patient. Oliver He, Edison Ong susceptible to be differentially regulated in CKD in cell A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be up-regulated in a cell of a chronical kidney disease (CKD) patient Oliver He, Edison Ong susceptible to be up-regulated in CKD in cell A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be down-regulated in a cell of a chronical kidney disease (CKD) patient Oliver He, Edison Ong susceptible to be down-regulated in CKD in cell A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be differentially regulated in a cell in an acute kidney injury (AKI) patient. Oliver He susceptible to be differentially regulated in AKI in cell A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be differentially regulated in the anatomic location of a chronical kidney disease (CKD) patient. Oliver He susceptible to be differentially regulated in CKD in anatomic location A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be up-regulated in the anatomic location of a chronical kidney disease (CKD) patient. Oliver He susceptible to be up-regulated in CKD in anatomic location A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be down-regulated in the anatomic location of a chronical kidney disease (CKD) patient. Oliver He susceptible to be down-regulated in CKD in anatomic location A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be differentially regulated in the anatomic location of an acute kidney injury (AKI) patient. Oliver He, Edison Ong susceptible to be differentially regulated in AKI in anatomic location A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be up-regulated in a cell of an acute kidney injury (AKI) patient Oliver He, Edison Ong susceptible to be up-regulated in AKI in cell A shortcut object property that represents a relation between a biological entity and a cell where the entity is susceptible to be down-regulated in a cell of an acute kidney injury (AKI) patient Oliver He, Edison Ong susceptible to be down-regulated in AKI in cell A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be down-regulated in the anatomic location of an acute kidney injury (AKI) patient. Oliver He susceptible to be down-regulated in AKI in anatomic location A shortcut object property that represents a relation between a biological entity and an anatomic location where the entity is susceptible to be down-regulated in the anatomic location of an acute kidney injury (AKI) patient. Oliver He susceptible to be up-regulated in AKI in anatomic location An object property that represents a relation between a gene and a cell type where the gene is the gene marker of the cell type Oliver He, Yingtong Liu is gene marker of cell An object property that represents a relation between a celltype and a gene where the cell has the gene as its gene marker Oliver He, Yingtong Liu cell has gene marker Oliver He, Yingtong Liu An object property that represents a relation between a disease and a biomarker where the disease has the biomarker. disease has biomarker An object property that represents a relation between a disease and a gene where the disease has the gene as a biomarker. Oliver He, Yingtong Liu disease has gene biomarker An object property that represents a relation between a disease and a protein where the disease has the protein as a biomarker. Oliver He, Yingtong Liu disease has protein biomarker An object property that represents a relation between a disease and a RNA where the disease has the mRNA as a biomarker. Oliver He, Yingtong Liu disease has RNA biomarker An object property that represents a relation between a biomarker and a disease where the biomarker serves as a biomarker role for the disease Yingtong Liu, Oliver He biomarker of disease An object property that represents a relation between a gene and a disease where the gene is a biomarkder of the disease. Yingtong Liu, Oliver He gene biomarker of disease An object property that represents a relation between a protein and a disease where the protein is a biomarkder of the disease. Yingtong Liu, Oliver He protein biomarker of disease An object property that represents a relation between a RNA of a gene and a disease where the mRNA expression of the gene is a biomarkder of the disease. Yingtong Liu, Oliver He RNA biomarker of disease biomarker related is biomarker of cell An adverse event has a participant quality, such as a hyperkalemia AE has a participatn quality blood potassium increased. an object property that represents a relation between a process and a quality, in which the process has a participant that has the quality. This is a shortcut relation of the following full version: 'has participant' some (participant 'has quality' ) in: process 'has participant' some (participant 'has quality' some quality) Yongqun He has participant quality a 'occurs in' relation that is applied at the adverse event setting and indicates where an adverse event occurs in. Yongqun He adverse event occurs in AE occurs in a specific 'preceded by' object property that has a domain of an adverse event. Yongqun He adverse event preceded by is_supported_by_data The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of is_manufactured_by http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. Alan Ruttenberg Liju Fan has_make has_manufacturer is_manufactured_by is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by has organization member has value specification A relation between an information content entity and a value specification that specifies its value. PERSON: James A. Overton OBI has value specification a 'part of continuant at some time' relation that incides a genome belongs to a organism. Yongqun He, Bin Zhao is genome of organism a relation between a gene and the organism where this gene belongs to the organism in nature. It does not include a foreign gene that is transferred to an organism by a genetic engineering method. Oliver He, Yue Liu is gene of organism BFO relation takes precedence. We anticipate BFO 2.0 including and defining this relation. When it does, we will obsolete this property and declare it equivalent to the BFO 2.0 relation. is-aggregate-of true A kidney biopsy protocol is executed in a kidney biopsy process. A shortcut relation that is concretized and realized in some process. Jie Zheng, Oliver He executed in A 'has part' object property that has the range of a textual question Oliver He has question form generated by An object property that indicates a relation between a question and an answer has answer to question has answer An object property that represents a relation between a form and a question where the question sets up an exclusion criterion. Specifically, when the answer to the question is Yes, the candidate becomes ineligible for the participation of a study. Fred Dowd, Oliver He has exclusion question An object property that represents a relation between a form and a question where the question sets up an inclusion criterion. Specifically, when the answer to the question is Yes, then the candidate fulfills a criterion for being eligible for participating in a study. Note that there might be other criteria that the candidate also need to meet in order to be fully eligible. Meanwhile, if the answer is No, the candidate may still be eligible depending on the other restriction. Fred Dowd, Oliver He has inclusion question has process quality An object property that represents a relation between a person with a biological sex and a process where the person has a specific susceptbility to a process Anthony Huffman, Oliver He has sex-specific susceptibility to An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding male population Anthony Huffman, Oliver He has increased susceptibility compared to male to Male has increased susceptibility to death due to COVID-19 infection compared to female. Note that in this case, the male can mean one single male individual. however, the female here means the whole female population. It is reported that the ratio of deaths in COVID-19 infected males to females is 1·21:1 in high-income countries, but 2·8:1 in low-income countries (Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8023692/). An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to corresponding female population Anthony Huffman, Oliver He has increased susceptibility compared to female to An object property that represents a relation between a person with a biological sex and a process where the person has an increased susceptbility to a process compared to the whole population with all sexes included Anthony Huffman, Oliver He has increased sex-specific susceptibility compared to sex baseline to A care_site has a care_site_id (OMOP: http://ohdsi.github.io/CommonDataModel/cdm54.html#CARE_SITE) An object property that represents a relation between an entity and its corresponding identifier that is owned by the entity. Oliver He, Long Tran has identifier A patient was admitted to the hospital from home or a long-term care facility. An object property that represents a relation between a patient and a site from which the patient was admitted. Long Tran, Oliver He http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE admitted from After a visit, a person was discharged to home or a long-term care site. Typically this applies only to visits that have a length of stay of a day or more. An object property that represents a relation between a patient and a site to which the patient was discharged after a visit. http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_OCCURRENCE discharged to inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. 'inheres in at all times' inheres_in http://purl.obolibrary.org/obo/ro.owl Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer of bearer_of is bearer of RO:0000053 external uberon bearer_of bearer_of bearer of bearer of bearer_of has characteristic is bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in RO:0000056 external uberon participates_in participates_in participates in participates in participates_in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://purl.obolibrary.org/obo/ro.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant has_participant has participant has participant has_participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as concretizes A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. http://purl.obolibrary.org/obo/obi.owl It is recommended to not use this if possible in OMRSE. According to OntoBee this relation has been obsoleted and replaced with 'concretization of at all times'. As of Dec. 2, 2013 iao-main still uses this relation. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality RO:0000086 protein uberon has_quality false has_quality has quality has quality has_quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has role has_role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from this parent cell derives into this cell (cell division) this parent nucleus derives into this nucleus (nuclear division) a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. derives_into derives into is location of my head is the location of my brain this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime location_of RO:0001015 uberon location_of location_of location of location_of located in my brain is located in my head this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime located_in http://www.obofoundry.org/ro/#OBO_REL:located_in RO:0001025 file:/Users/michaelashburner/Desktop/gaz/gaz.oboInOwl uberon located_in located_in located in located_in located_in (type level) my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. David Osumi-Sutherland has boundary has_2D_boundary RO:0002002 uberon has_boundary has_boundary has 2D boundary has boundary David Osumi-Sutherland http://www.ncbi.nlm.nih.gov/pubmed/22402613 RO:0002005 nerve supply uberon innervated_by innervated_by http://code.google.com/p/obo-relations/issues/detail?id=6 innervated_by innervated_by X outer_layer_of Y iff: . X :continuant that bearer_of some PATO:laminar . X part_of Y . exists Z :surface . X has_boundary Z . Z boundary_of Y has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 David Osumi-Sutherland RO:0002007 external uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of bounding layer of dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity David Osumi-Sutherland <= Primitive instance level timing relation between events before or simultaneous with Relation between occurrents, shares start and end boundaries. David Osumi-Sutherland RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) simultaneous with simultaneous_with David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y). David Osumi-Sutherland starts_at_end_of A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of external uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by immediately_preceded_by David Osumi-Sutherland ends_at_start_of meets RO:0002090 external immediately_precedes immediately_precedes X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes immediately_precedes David Osumi-Sutherland io X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)) starts during David Osumi-Sutherland d during X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y)) happens during David Osumi-Sutherland o overlaps X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y). ends during ends_during Relation between a neuron and an anatomical structure that its soma is part of. David Osumi-Sutherland <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) has soma location Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. Alexander Diehl Chris Mungall Lindsay Cowell <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) has plasma membrane part A overlaps B if they share some part in common. x overlaps y if and only if there exists some z such that x has part z and z part of y BFO_0000051 some (BFO_0000050 some ?Y) http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) RO:0002131 external uberon overlaps overlaps overlaps overlaps Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. David Osumi-Sutherland <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) RO:0002134 uberon innervates innervates http://code.google.com/p/obo-relations/issues/detail?id=6 innervates innervates X continuous_with Y if and only if X and Y share a fiat boundary. David Osumi-Sutherland connected to The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) RO:0002150 uberon continuous_with continuous_with continuous with continuous_with FMA:85972 lactation SubClassOf 'only in taxon' some 'Mammalia' S only_in_taxon T iff: S SubClassOf in_taxon only T. U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon. x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria Chris Mungall RO:0002160 never_outside_taxon specific_to specific_to_taxon protein uberon only_in_taxon false only_in_taxon Down-propagates. The original name for this in the paper is 'specific_to'. Applicable to genes because some genes are lost in sub-species (strains) of a species. only in taxon only_in_taxon x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. Chris Mungall Jennifer Deegan RO:0002162 uberon in_taxon in_taxon Connects a biological entity to its taxon of origin. in taxon A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. Chris Mungall Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern The M8 connects Glasgow and Edinburgh a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. attached to part of (anatomical structure to anatomical structure) RO:0002177 uberon attaches_to_part_of attaches_to_part_of attached to part of attaches_to_part_of Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. relation between an artery and the structure is supplies with blood. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies supplies Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure RO:0002179 drains blood from drains from uberon drains drains source: Wikipedia drains drains w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. RO:0002180 external uberon has_component has_component has component has component has_component A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype). has phenotype inverse of has phenotype phenotype of x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y Chris Mungall David Osumi-Sutherland Melissa Haendel Terry Meehan RO:0002202 uberon develops_from develops_from This is the transitive form of the develops from relation develops from develops from develops_from inverse of develops from Chris Mungall David Osumi-Sutherland Terry Meehan RO:0002203 uberon develops_into develops_into develops into develops_into 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process Chris Mungall expressed in Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. Chris Mungall David Osumi-Sutherland has developmental precursor FBbt RO:0002207 uberon directly_develops_from directly_develops_from TODO - add child relations from DOS directly develops from directly_develops_from inverse of directly develops from developmental precursor of directly develops into process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2. We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit Chris Mungall David Hill Tanya Berardini GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false RO:0002211 external regulates regulates has_component regulates regulates regulates (processual) Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall negatively regulates (process to process) RO:0002212 external negatively_regulates negatively_regulates negatively regulates negatively regulates Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2. Chris Mungall positively regulates (process to process) RO:0002213 external positively_regulates positively_regulates positively regulates positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. Chris Mungall has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO_0000053 some (RO_0000054 only ?Y) RO:0002215 external uberon capable_of capable_of capable of capable of capable_of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. Chris Mungall has function in RO_0000053 some (RO_0000054 only (BFO_0000050 some ?Y)) RO:0002216 external uberon capable_of_part_of capable_of_part_of capable of part of capable of part of 'heart development' has active participant some Shh protein x has participant y if and only if x realizes some active role that inheres in y This may be obsoleted and replaced by the original 'has agent' relation Chris Mungall has agent has active participant x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y. Chris Mungall RO:0002219 uberon surrounded_by surrounded_by surrounded by surrounded by surrounded_by A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. The epidermis layer of a vertebrate is adjacent to the dermis. The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. x adjacent to y if and only if x and y share a boundary. x adjacent_to y iff: x and y share a boundary x adjacent_to y iff: x and y share a boundary. This relation acts as a join point with BSPO Chris Mungall RO:0002220 external uberon adjacent_to adjacent_to adjacent to adjacent to adjacent_to inverse of surrounded by inverse of surrounded_by inverse of surrounded_by. Chris Mungall RO:0002221 uberon surrounds surrounds surrounds surrounds Chris Mungall Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to Relation between occurrents, shares a start boundary with. inverse of starts with Chris Mungall Allen RO:0002223 uberon starts starts starts starts Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall started by RO:0002224 external uberon starts_with starts_with starts with starts with x develops from part of y if and only if there exists some z such that x develops from z and z is part of y Chris Mungall RO:0002225 uberon develops_from_part_of develops_from_part_of develops from part of develops_from_part_of Relation between occurrents, shares an end boundary with. inverse of ends with Chris Mungall RO:0002229 finishes uberon ends ends ends ends x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. Chris Mungall finished by RO:0002230 external uberon ends_with ends_with ends with ends with x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y Chris Mungall starts with process that occurs in RO:0002231 external has_start_location has_start_location has start location has start location x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y Chris Mungall ends with process that occurs in RO:0002232 external has_end_location has_end_location has end location has end location p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p. p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. Chris Mungall consumes RO:0002233 external has_input has_input has input has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p. p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. Chris Mungall produces RO:0002234 external has_output has_output has output has output Any relationship between an exposure event or process and any other entity. related via exposure to Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] x has developmental contribution from y iff x has some part z such that z develops from y Chris Mungall RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from has developmental contribution from inverse of has developmental contribution from Chris Mungall RO:0002255 uberon developmentally_contributes_to developmentally_contributes_to developmentally contributes to developmentally_contributes_to t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor anatomical structure type T to T', where T' develops_from T Chris Mungall David Osumi-Sutherland Melissa Haendel induced by Developmental Biology, Gilbert, 8th edition, figure 6.5(F) GO:0001759 We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally induced by developmentally_induced_by Inverse of developmentally induced by Chris Mungall developmentally induces Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false Chris Mungall In general you should not use this relation to make assertions - use one of the more specific relations below this one RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by developmentally preceded by x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage Chris Mungall replaces RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally replaces developmentally_replaces Inverse of developmentally preceded by Chris Mungall developmentally succeeded by Inverse of 'expressed in' Chris Mungall expresses p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. Chris Mungall RO:0002295 external results_in_developmental_progression_of results_in_developmental_progression_of results in developmental progression of results in developmental progression of every flower development (GO:0009908) results in development of some flower (PO:0009046) p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. Chris Mungall http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of results_in_development_of results in development of results in development of an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) Chris Mungall GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of results_in_formation_of results in formation of results in formation of an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. Chris Mungall GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of results_in_morphogenesis_of results in morphogenesis of results in morphogenesis of cjm RO:0002304 external causally_upstream_of,_positive_effect causally_upstream_of,_positive_effect holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect cjm RO:0002305 external causally_upstream_of,_negative_effect causally_upstream_of,_negative_effect holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y causally upstream of, negative effect A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event. has exposure stimulus Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c. Chris Mungall regulates localization of RO:0002313 external transports_or_maintains_localization_of transports_or_maintains_localization_of transports or maintains localization of transports or maintains localization of q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of Because part_of is transitive, inheres in is a sub-relation of inheres in part of Chris Mungall inheres in part of characteristic of part of inheres in part of an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity Chris Mungall GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of results_in_acquisition_of_features_of results in acquisition of features of results in acquisition of features of A relationship that holds via some environmental process Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to A relationship that is mediated in some way by the environment or environmental feature (ENVO:00002297) ecologically related to A mereological relationship or a topological relationship Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to A relationship that holds between entities participating in some developmental process (GO:0032502) Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to a particular instances of akt-2 enables some instance of protein kinase activity Chris Mungall catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. Chris Mungall This is a grouping relation that collects relations used for the purpose of connecting structure and function RO:0002328 uberon functionally_related_to functionally_related_to functionally related to functionally related to holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c Chris Mungall regulates levels of (process to entity) RO:0002332 external regulates_levels_of regulates_levels_of regulates levels of regulates levels of inverse of enables Chris Mungall enabled by inverse of regulates Chris Mungall regulated by (processual) RO:0002334 external regulated_by regulated_by regulated by regulated by inverse of negatively regulates Chris Mungall RO:0002335 external negatively_regulated_by negatively_regulated_by negatively regulated by negatively regulated by inverse of positively regulates Chris Mungall RO:0002336 external positively_regulated_by positively_regulated_by positively regulated by positively regulated by A relationship that holds via some process of localization Chris Mungall Do not use this relation directly. It is a grouping relation. related via localization to This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. Chris Mungall RO:0002338 external has_target_start_location has_target_start_location has target start location has target start location This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. Chris Mungall RO:0002339 external has_target_end_location has_target_end_location has target end location has target end location Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l Chris Mungall RO:0002341 external results_in_transport_along results_in_transport_along results in transport along results in transport along 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) Chris Mungall RO:0002344 external results_in_transport_to_from_or_in results_in_transport_to_from_or_in results in transport to from or in results in transport to from or in An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO RO:0002351 uberon has_member has_member has member has member inverse of has input Chris Mungall RO:0002352 uberon input_of input_of input of input of inverse of has output Chris Mungall RO:0002353 external protein uberon output_of false output_of output of output of output_of Chris Mungall formed as result of a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a Chris Mungall attached to (anatomical structure to anatomical structure) RO:0002371 uberon attaches_to attaches_to attached to attaches_to A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) in branching relationship with https://github.com/obophenotype/uberon/issues/170 Deschutes River tributary_of Columbia River inferior epigastric vein tributary_of external iliac vein x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. Chris Mungall drains into drains to tributary channel of http://en.wikipedia.org/wiki/Tributary http://www.medindia.net/glossary/venous_tributary.htm This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) RO:0002376 uberon drains into tributary_of tributary_of tributary of tributary_of http://en.wikipedia.org/wiki/Tributary x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y we need to check if FMA branch_of implies part_of. the relation we intend to use here should - for example, see vestibulocochlear nerve Chris Mungall RO:0002380 uberon branching_part_of branching_part_of branching part of branching_part_of FMA:85994 x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). Chris Mungall has developmental potential involving x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y. Chris Mungall RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to has potential to developmentally contribute to x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y Chris Mungall has potential to developmentally induce x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y x has the potential to develop into y iff x develops into y or if x is capable of developing into y. Chris Mungall RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into has potential to develop into x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y. Chris Mungall RO:0002388 uberon has_potential_to_directly_develop_into has_potential_to_directly_develop_into has potential to directly develop into has potential to directly develop into This relation groups causal relations between material entities and causal relations between processes This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain Chris Mungall RO:0002411 external causally_upstream_of causally_upstream_of causally upstream of causally upstream of p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q. Chris Mungall RO:0002412 external immediately_causally_upstream_of immediately_causally_upstream_of immediately causally upstream of immediately causally upstream of p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 Chris Mungall influences (processual) RO:0002418 external affects causally_upstream_of_or_within causally_upstream_of_or_within causally upstream of or within inverse of causally upstream of or within Chris Mungall RO:0002427 external causally_downstream_of_or_within causally_downstream_of_or_within causally downstream of or within p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. Chris Mungall RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of A relationship that holds between a disease and organism RO:0002451 transmitted_by transmitted_by transmitted by 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. x composed_primarily_of y iff: more than half of the mass of x is made from parts of y x composed_primarily_of y iff: more than half of the mass of x is made from parts of y. Chris Mungall UBREL:0000002 RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. Chris Mungall has part that occurs in Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). Chris Mungall BFO:0000068 RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant and occurrent, such that c comes into existence at the start of p. x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). Chris Mungall RO:0002489 uberon existence_starts_with existence_starts_with existence starts with x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) Chris Mungall The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) Chris Mungall RO:0002491 exists during uberon existence_starts_and_ends_during existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). Chris Mungall BFO:0000069 RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during Relation between continuant and occurrent, such that c ceases to exist at the end of p. x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). Chris Mungall RO:0002493 uberon existence_ends_with existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships Chris Mungall RO:0002494 transforms from uberon transformation_of transformation_of transformation of x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t Chris Mungall RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). Chris Mungall RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. Chris Mungall RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q. Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes Chris Mungall depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Chris Mungall Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entities A coral reef environment is determined by a particular coral reef s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s. The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future Chris Mungall determined by (system to material entity) Chris Mungall Pier Buttigieg RO:0002507 uberon has_material_contribution_from has_material_contribution_from determined by has material contribution from inverse of determined by Chris Mungall determines (material entity to system) determines s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w. Chris Mungall determined by part of Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. Chris Mungall has supporting framework The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton Chris Mungall causally influenced by (material entity to material entity) causally influenced by Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c Chris Mungall RO:0002565 external results_in_movement_of results_in_movement_of results in movement of Holds between materal entities a and b if the activity of a is causally upstream of the activity of b, or causally upstream of a an activity that modifies b Chris Mungall causally influences (material entity to material entity) causally influences A relation that holds between elements of a musculoskeletal system or its analogs. Chris Mungall Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to inverse of branching part of Chris Mungall RO:0002569 uberon has_branching_part has_branching_part has branching part x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. Chris Mungall GOC:cjm RO:0002571 uberon lumen_of lumen_of lumen of s is luminal space of x iff s is lumen_of x and s is an immaterial entity Chris Mungall RO:0002572 uberon luminal_space_of luminal_space_of luminal space of A relation that holds between an attribute or a qualifier and another attribute. RO:0002573 has_modifier has_modifier has modifier inverse of has skeleton Chris Mungall RO:0002576 uberon skeleton_of skeleton_of skeleton of Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. Chris Mungall directly regulates (processual) directly regulates p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p results in breakdown of RO:0002588 external results_in_assembly_of results_in_assembly_of results in assembly of results_in_assembly_of RO:0002590 external results_in_disassembly_of results_in_disassembly_of results in disassembly of results_in_disassembly_of p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c RO:0002592 external results_in_organization_of results_in_organization_of results in organization of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. Chris Mungall causal relation between material entity and a process Inverse of 'causal agent in process' Inverse of 'causal agent in' RO:0002608 external process_has_causal_agent process_has_causal_agent has causal agent process has causal agent A relationship that holds between two entities, where the relationship holds based on the presence or absence of statistical dependence relationship. The entities may be statistical variables, or they may be other kinds of entities such as diseases, chemical entities or processes. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. related via dependence to a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. Melissa Haendel RO:0003000 external uberon produces produces Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. produces produces a produced_by b iff some process that occurs_in b has_output a. Melissa Haendel RO:0003001 external uberon produced_by produced_by produced by produced by produced_by p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c. cjm 2018-12-13T11:26:17Z RO:0004007 external has_primary_input_or_output has_primary_input_or_output has primary input or output p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c. cjm 2018-12-13T11:26:32Z RO:0004008 external has_primary_output has_primary_output has primary output realizable has basis in is basis for realizable disease has basis in A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function. RO:0004020 disease_has_basis_in_dysfunction_of disease_has_basis_in_dysfunction_of disease has basis in dysfunction of A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process. RO:0004021 disease_has_basis_in_disruption_of disease_has_basis_in_disruption_of Editor note: TODO property chain: disease_has_location <- dhbido o occurs_in disease caused by disruption of disease has basis in disruption of A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature. RO:0004022 disease_arises_from_feature disease_arises_from_feature disease arises from feature disease has basis in feature causal relationship with disease as subject A relationship between a disease and a process where the disease process disrupts the execution of the process. RO:0004024 disease_disrupts disease_disrupts disease causes disruption of disease disrupts RO:0004025 disease_causes_dysfunction_of disease_causes_dysfunction_of disease causes dysfunction of A relationship between a disease and an anatomical entity where the disease has one or more features that are located in that entity. RO:0004026 disease_has_location disease_has_location disease has location A relationship between a disease and an anatomical entity where the disease is triggered by an inflammatory response to stimuli occurring in the anatomical entity RO:0004027 disease_has_inflammation_site disease_has_inflammation_site disease has inflammation site A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M. RO:0004028 realized_in_response_to_stimulus realized_in_response_to_stimulus realized in response to stimulus A relationship between a disease and some feature of that disease, where the feature is either a phenotype or an isolated disease. RO:0004029 disease_has_feature disease_has_feature disease has feature A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure. RO:0004030 disease_arises_from_structure disease_arises_from_structure disease arises from structure cjm 2018-03-13T23:55:05Z causally upstream of or within, negative effect cjm 2018-03-13T23:55:19Z causally upstream of or within, positive effect r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r. RO:0009501 triggered by process realized_in_response_to realized_in_response_to realized in response to realized in response to p acts on population of c iff c' is a collection, has members of type c, and p has participant c pg 2020-06-08T17:21:33Z RO:0012003 external acts_on_population_of acts_on_population_of acts on population of acts on population of pg 2021-02-26T07:28:29Z RO:0012008 external results_in_fusion_of results_in_fusion_of results in fusion of results in fusion of This relation groups relations between diseases and any other kind of entity. disease relationship p has anatomical participant c iff p has participant c, and c is an anatomical entity cjm 2018-09-26T01:08:58Z results in changes to anatomical or cellular structure a object property that specifies a relation between a vaccine and a vaccine allergen YH has vaccine allergen a shortcut relation that equals to: 'processed material' and (is_specified_output_of some 'vaccine preparation') and ('has function' some ('vaccine function' and ('is realized by' only ('vaccine immunization' and (realizes some ('vaccine host role' and (role_of some 'organism')))))))). The domain of this relation is a vaccine. The range of this relation is a organism. YL Yongqun He vaccine immunization for host a shortcut relation that equals to: processed material and (is_specified_output_of some vaccine preparation) and (has function some (vaccine function and (is realized by only (vaccine immunization and (realizes some ('immunization target role' and (role_of some 'MICROBE')))))))) The domain of this relation is a vaccine. The range of this relation is a microbe (a bacterium, a virus, a fungus, and a parasite) Yongqun He vaccine immunization against microbe has parent hydride is conjugate acid of is conjugate base of is substituent group from has_completed A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_high_plasma_membrane_amount A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. For the formal definition, see Masci et al (PMID:19243617). has_low_plasma_membrane_amount has_not_completed http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 ?Y lacks_part http://purl.obolibrary.org/obo/BFO_0000051 exactly 0 (http://purl.obolibrary.org/obo/GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y) lacks_plasma_membrane_part interacts_with interacts_with_an_exposure_receptor_via interacts_with_an_exposure stressor_via disease_causes_feature disease causes feature disease_has_basis_in_development_of disease_has_basis_in_development_of disease_has_major_feature disease has major feature disease_responds_to disease responds to disease_shares_features_of disease shares features of predisposes_towards predisposes towards q1 decreased_in_magnitude_relative_to q2 if and only if magnitude(q1) < magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality decreased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'decreased strength', relative to the parent type, 'strength'. decreased_in_magnitude_relative_to q1 different_in_magnitude_relative_to q2 if and only if magnitude(q1) NOT =~ magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality different_in_magnitude_relative_to different_in_magnitude_relative_to s3 has_cross_section s3 if and only if : there exists some 2d plane that intersects the bearer of s3, and the impression of s3 upon that plane has shape quality s2. quality has_cross_section Example: a spherical object has the quality of being spherical, and the spherical quality has_cross_section round. has_cross_section q1 increased_in_magnitude_relative_to q2 if and only if magnitude(q1) > magnitude(q2). Here, magnitude(q) is a function that maps a quality to a unit-invariant scale. quality increased_in_magnitude_relative_to This relation is used to determine the 'directionality' of relative qualities such as 'increased strength', relative to the parent type, 'strength'. increased_in_magnitude_relative_to protein has_gene_template false has_gene_template Inverse of part_of. has_part has_quality member_of X part_of Y if X is a subregion of Y. part_of x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. anteriorly connected to carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. distally connected to uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. posteriorly connected to uberon protects protects x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to c site_of p if c is the bearer of a disposition that is realized by a process that has p as part. uberon capable_of_has_part site_of site_of uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of . transitively anteriorly connected to uberon transitively_connected_to transitively_connected to . transitively distally connected to . uberon transitively_proximally_connected_to transitively proximally connected to http://purl.org/obo/owl/relationship OBO_REL:0000007 relationship has_proper_part has_proper_part Ingredient Ingredient Strength Packaged Product VA Class VA Product Active Inactive has measurement value The data type "last 4 digits of social security number" has digit number of 4. A data property that represents a relation between a data type and a number of integer digits that the data type has. Oliver He has digit number quality measured by year Chemical Ingredients N0000000002 991181 C178 Chemical Ingredients [Chemical/Ingredient] Clinical Kinetics N0000000003 1030853 C1373163 C180 Clinical Kinetics [PK] Diseases, Manifestations or Physiologic States N0000000004 989348 C1373233 C182 Diseases, Manifestations or Physiologic States [Disease/Finding] Mental Disorders and Manifestations N0000000006 984721 C2916796 C190 Mental Disorders and Manifestations [Disease/Finding] Infectious Diseases N0000000007 1023583 189822004 190563008 191415002 40733004 C0009450 C192 Infectious Diseases [Disease/Finding] Elimination N0000000022 986944 C0221102 C222 Elimination [PK] Metabolism N0000000023 1023904 C0025519 C224 Metabolism [PK] Site of Metabolism N0000000024 988808 C1373176 C226 Site of Metabolism [PK] Hepatic Metabolism N0000000026 984512 C1373178 C230 Hepatic Metabolism [PK] Route of Excretion N0000000041 987962 C1373186 C260 Route of Excretion [PK] Renal Excretion N0000000042 986666 C1373187 C262 Renal Excretion [PK] Physiochemical Activity N0000000065 989958 C1372991 C308 Physiochemical Activity [MoA] Small Ion Transport Pump Interactions N0000000066 986087 C1373107 C310 Small Ion Transport Pump Interactions [MoA] Active Transporter Interactions N0000000072 1031287 C1373104 C322 Active Transporter Interactions [MoA] Immunologic Factors D007155 Immunologic Factors N0000000082 993127 C2757006 C342 Immunologic Factors [MoA] Receptor Interactions N0000000085 988560 C1372999 C348 Receptor Interactions [MoA] Reverse Transcriptase Inhibitors D018894 Reverse Transcriptase Inhibitors N0000000103 993157 C2757067 C384 Reverse Transcriptase Inhibitors [MoA] Dopamine Agonists D018491 Dopamine Agonists N0000000117 992714 Dopaminergic Agonist C2757007 C412 Dopamine Agonists [MoA] Adrenergic Agonists D000322 Adrenergic Agonists N0000000122 1029285 C2757025 C422 Adrenergic Agonists [MoA] Enzyme Inhibitors D004791 Enzyme Inhibitors N0000000133 1032544 C2756995 C444 Enzyme Inhibitors [MoA] Biological Macromolecular Activity N0000000142 988641 C2267218 C462 Biological Macromolecular Activity [MoA] G-Protein-linked Receptor Interactions N0000000152 984725 G-Protein-linked Receptor-Effector Interactions C2916797 C482 G-Protein-linked Receptor Interactions [MoA] Adrenergic Receptor Interactions N0000000153 987972 C1373072 C484 Adrenergic Receptor Interactions [MoA] Enzyme Interactions N0000000163 988200 C1373066 C504 Enzyme Interactions [MoA] Cytokine Receptor Superfamily Interactions N0000000175 984937 C1373058 C528 Cytokine Receptor Superfamily Interactions [MoA] Ion Channel Interactions N0000000193 988382 C1373047 C564 Ion Channel Interactions [MoA] Cholinergic Nicotinic Receptor Interactions N0000000199 985201 C2267220 C576 Cholinergic Nicotinic Receptor Interactions [MoA] beta Lactamase Inhibitors N0000000202 989759 beta-Lactamase Inhibitors C1373040 C582 beta Lactamase Inhibitors [MoA] Dopamine Receptor Interactions N0000000203 985948 C1373039 C584 Dopamine Receptor Interactions [MoA] Electrolyte Activity N0000000220 984201 C2267221 C618 Electrolyte Activity [MoA] Cellular or Molecular Interactions N0000000223 986459 C1373094 C624 Cellular or Molecular Interactions [MoA] Acid-Base Activity N0000000226 985379 C2267222 C630 Acid-Base Activity [MoA] Cholinergic Nicotinic Antagonists N0000000227 989668 C1373090 C632 Cholinergic Nicotinic Antagonists [MoA] Structural Macromolecules N0000000228 984803 C1373089 C634 Structural Macromolecules [MoA] Nucleic Acid Synthesis Inhibitors D019384 Nucleic Acid Synthesis Inhibitors N0000000233 993166 C2757009 C644 Nucleic Acid Synthesis Inhibitors [MoA] Adrenergic beta-Agonists D000318 Adrenergic beta-Agonists N0000000245 992727 Beta-adrenergic Agonist C2757043 C668 Adrenergic beta-Agonists [MoA] Polycationic Channel Interactions N0000000253 990209 C1373076 C684 Polycationic Channel Interactions [MoA] Immunologic and Biological Factors D007151 Immunologic and Biological Factors N0000000254 1032698 C0021048 C686 Immunologic and Biological Factors [MoA] Congenital Abnormalities M0000013 D000013 Malformations of organs or body parts during development in utero. Congenital Abnormalities N0000000264 1021840 276654001 276655000 276720006 Abnormalities, Congenital Birth Defects Congenital Defects Defects, Congenital Deformities C0000768 C706 Congenital Abnormalities [Disease/Finding] Abnormalities, Drug-Induced M0000014 D000014 Congenital abnormalities caused by medicinal substances or drugs of abuse given to or taken by the mother, or to which she is inadvertently exposed during the manufacture of such substances. The concept excludes abnormalities resulting from exposure to non-medicinal chemicals in the environment. Abnormalities, Drug-Induced N0000000265 989962 Drug-Induced Abnormalities C0000771 C708 Abnormalities, Drug-Induced [Disease/Finding] Acid-Base Imbalance M0000212 D000137 Disturbances in the ACID-BASE EQUILIBRIUM of the body. Acid-Base Imbalance N0000000282 1026879 C0001118 C742 Acid-Base Imbalance [Disease/Finding] Acidosis M0000213 D000138 A pathologic condition of acid accumulation or depletion of base in the body. The two main types are RESPIRATORY ACIDOSIS and metabolic acidosis, due to metabolic acid build up. Acidosis N0000000283 1023565 51387008 C0001122 C744 Acidosis [Disease/Finding] Alcohol Withdrawal Delirium M0000652 D000430 An acute organic mental disorder induced by cessation or reduction in chronic alcohol consumption. Clinical characteristics include CONFUSION; DELUSIONS; vivid HALLUCINATIONS; TREMOR; agitation; insomnia; and signs of autonomic hyperactivity (e.g., elevated blood pressure and heart rate, dilated pupils, and diaphoresis). This condition may occasionally be fatal. It was formerly called delirium tremens. (From Adams et al., Principles of Neurology, 6th ed, p1175) Alcohol Withdrawal Delirium N0000000351 1023188 8635005 Alcohol Withdrawal-Induced Delirium Tremens Delirium Tremens Delirium Tremens, Alcohol Withdrawal Induced C0001957 C880 Alcohol Withdrawal Delirium [Disease/Finding] Alkalosis M0000714 D000471 A pathological condition that removes acid or adds base to the body fluids. Alkalosis N0000000355 1025787 21420006 C0002063 C888 Alkalosis [Disease/Finding] Anuria M0001524 D001002 Absence of urine formation. It is usually associated with complete bilateral ureteral (URETER) obstruction, complete lower urinary tract obstruction, or unilateral ureteral obstruction when a solitary kidney is present. Anuria N0000000431 1023563 2472002 C0003460 C1040 Anuria [Disease/Finding] Aortic Stenosis, Subvalvular M0001552 D001020 A pathological constriction occurring in the region below the AORTIC VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA. Aortic Stenosis, Subvalvular N0000000442 1025918 Aortic Subvalvular Stenosis Subvalvular Aortic Stenosis C0003500 C1062 Aortic Stenosis, Subvalvular [Disease/Finding] Aortic Valve Stenosis M0001557 D001024 A pathological constriction that can occur above (supravalvular stenosis), below (subvalvular stenosis), or at the AORTIC VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA. Aortic Valve Stenosis N0000000445 1021926 60573004 Aortic Stenosis C0003507 C1068 Aortic Valve Stenosis [Disease/Finding] Arrhythmias, Cardiac M0001715 D001145 Any disturbances of the normal rhythmic beating of the heart or MYOCARDIAL CONTRACTION. Cardiac arrhythmias can be classified by the abnormalities in HEART RATE, disorders of electrical impulse generation, or impulse conduction. Arrhythmias, Cardiac N0000000469 1023395 195107004 Arrhythmia Arrythmia Cardiac Arrhythmia Cardiac Arrhythmias Cardiac Dysrhythmia C0003811 C1116 Arrhythmias, Cardiac [Disease/Finding] Ascites M0001791 D001201 Accumulation or retention of free fluid within the peritoneal cavity. Ascites N0000000490 1021930 389026000 C0003962 C1158 Ascites [Disease/Finding] Bacterial Infections and Mycoses M0002125 D001423 Infections caused by bacteria and fungi, general, specified, or unspecified. Bacterial Infections and Mycoses N0000000523 986958 C0004615 C1224 Bacterial Infections and Mycoses [Disease/Finding] Mental Disorders M0002289 D001523 Psychiatric illness or diseases manifested by breakdowns in the adaptational process expressed primarily as abnormalities of thought, feeling, and behavior producing either distress or impairment of function. Mental Disorders N0000000538 1022308 74732009 C0004936 C1254 Mental Disorders [Disease/Finding] Blood Coagulation Disorders M0002683 D001778 Hemorrhagic and thrombotic disorders that occur as a consequence of abnormalities in blood coagulation due to a variety of factors such as COAGULATION PROTEIN DISORDERS; BLOOD PLATELET DISORDERS; BLOOD PROTEIN DISORDERS or nutritional conditions. Blood Coagulation Disorders N0000000575 1022276 362970003 64779008 Coagulation Disorders, Blood Disorders, Blood Coagulation C0005779 C1328 Blood Coagulation Disorders [Disease/Finding] Bone Diseases M0002776 D001847 Diseases of BONES. Bone Diseases N0000000584 1025929 308147009 76069003 C0005940 C1346 Bone Diseases [Disease/Finding] Bone Diseases, Metabolic M0002780 D001851 Bone Diseases, Metabolic N0000000588 1026469 50279003 Metabolic Bone Diseases C0005944 C1354 Bone Diseases, Metabolic [Disease/Finding] Bradycardia M0002863 D001919 Cardiac arrhythmias that are characterized by excessively slow HEART RATE, usually below 50 beats per minute in human adults. They can be classified broadly into SINOATRIAL NODE dysfunction and ATRIOVENTRICULAR BLOCK. Bradycardia N0000000600 1025503 48867003 Bradyarrhythmia Bradyarrhythmias C0428977 C1378 Bradycardia [Disease/Finding] Brain Diseases M0002874 D001927 Pathologic conditions affecting the BRAIN, which is composed of the intracranial components of the CENTRAL NERVOUS SYSTEM. This includes (but is not limited to) the CEREBRAL CORTEX; intracranial white matter; BASAL GANGLIA; THALAMUS; HYPOTHALAMUS; BRAIN STEM; and CEREBELLUM. Brain Diseases N0000000605 986258 81308009 Brain Disorders CNS Disorders, Intracranial Central Nervous System Disorders, Intracranial Central Nervous System Intracranial Disorders Encephalon Diseases Intracranial CNS Disorders Intracranial Central Nervous System Disorders C0006111 C1388 Brain Diseases [Disease/Finding] Calcium Metabolism Disorders M0003174 D002128 Disorders in the processing of calcium in the body: its absorption, transport, storage, and utilization. Calcium Metabolism Disorders N0000000646 1024541 71638002 C0006705 C1470 Calcium Metabolism Disorders [Disease/Finding] Calculi M0003195 D002137 An abnormal concretion occurring mostly in the urinary and biliary tracts, usually composed of mineral salts. Also called stones. Calculi N0000000647 1026851 125243009 56381008 Biliary or Urinary Stones C0006736 C1472 Calculi [Disease/Finding] Candidiasis M0003258 D002177 Infection with a fungus of the genus CANDIDA. It is usually a superficial infection of the moist areas of the body and is generally caused by CANDIDA ALBICANS. (Dorland, 27th ed) Candidiasis N0000000650 1022538 78048006 Moniliasis C0006840 C1478 Candidiasis [Disease/Finding] Candidiasis, Chronic Mucocutaneous M0003259 D002178 A clinical syndrome characterized by development, usually in infancy or childhood, of a chronic, often widespread candidiasis of skin, nails, and mucous membranes. It may be secondary to one of the immunodeficiency syndromes, inherited as an autosomal recessive trait, or associated with defects in cell-mediated immunity, endocrine disorders, dental stomatitis, or malignancy. Candidiasis, Chronic Mucocutaneous N0000000651 1023229 234568006 C0006845 C1480 Candidiasis, Chronic Mucocutaneous [Disease/Finding] Candidiasis, Cutaneous M0003260 D002179 Candidiasis of the skin manifested as eczema-like lesions of the interdigital spaces, perleche, or chronic paronychia. (Dorland, 27th ed) Candidiasis, Cutaneous N0000000652 1025470 49883006 Moniliasis, Cutaneous C0006846 C1482 Candidiasis, Cutaneous [Disease/Finding] Candidiasis, Oral M0003261 D002180 Infection of the mucous membranes of the mouth by a fungus of the genus CANDIDA. (Dorland, 27th ed) Candidiasis, Oral N0000000653 1022622 79740000 Moniliasis, Oral Thrush C0006849 C1484 Candidiasis, Oral [Disease/Finding] Candidiasis, Vulvovaginal M0003262 D002181 Infection of the VULVA and VAGINA with a fungus of the genus CANDIDA. Candidiasis, Vulvovaginal N0000000654 1024776 72605008 Moniliasis, Vulvovaginal C0700345 C1486 Candidiasis, Vulvovaginal [Disease/Finding] Cardiac Output, Low M0003453 D002303 A state of subnormal or depressed cardiac output at rest or during stress. It is a characteristic of CARDIOVASCULAR DISEASES, including congenital, valvular, rheumatic, hypertensive, coronary, and cardiomyopathic. The serious form of low cardiac output is characterized by marked reduction in STROKE VOLUME, and systemic vasoconstriction resulting in cold, pale, and sometimes cyanotic extremities. Cardiac Output, Low N0000000683 1024618 86318000 Low Cardiac Output C0007166 C1544 Cardiac Output, Low [Disease/Finding] Cardiovascular Diseases M0003473 D002318 Pathological conditions involving the CARDIOVASCULAR SYSTEM including the HEART; the BLOOD VESSELS; or the PERICARDIUM. Cardiovascular Diseases N0000000689 1022075 105980002 49601007 C0007222 C1556 Cardiovascular Diseases [Disease/Finding] Central Nervous System Diseases M0003805 D002493 Diseases of any component of the brain (including the cerebral hemispheres, diencephalon, brain stem, and cerebellum) or the spinal cord. Central Nervous System Diseases N0000000709 1023588 23853001 CNS Diseases Central Nervous System Disorders C0007682 C1596 Central Nervous System Diseases [Disease/Finding] Cerebrovascular Disorders M0003914 D002561 A spectrum of pathological conditions of impaired blood flow in the brain. They can involve vessels (ARTERIES; or VEINS) in the CEREBRUM, the CEREBELLUM, and the BRAIN STEM. Major categories include INTRACRANIAL ARTERIOVENOUS MALFORMATIONS; BRAIN ISCHEMIA; CEREBRAL HEMORRHAGE; and others. Cerebrovascular Disorders N0000000730 1022010 62914000 Brain Vascular Disorders Intracranial Vascular Disorders Vascular Diseases, Intracranial C0007820 C1638 Cerebrovascular Disorders [Disease/Finding] Coma M0004841 D003128 A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused. Coma generally occurs when there is dysfunction or injury involving both cerebral hemispheres or the brain stem RETICULAR FORMATION. Coma N0000000819 988251 371632003 Comatose C0009421 C1816 Coma [Disease/Finding] Consciousness Disorders M0005031 D003244 Organic mental disorders in which there is impairment of the ability to maintain awareness of self and environment and to respond to environmental stimuli. Dysfunction of the cerebral hemispheres or brain stem RETICULAR FORMATION may result in this condition. Consciousness Disorders N0000000840 1031236 C0009792 C1858 Consciousness Disorders [Disease/Finding] Corneal Diseases M0005177 D003316 Diseases of the cornea. Corneal Diseases N0000000851 1024256 15250008 C0010034 C1880 Corneal Diseases [Disease/Finding] Crohn Disease M0005335 D003424 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. Crohn Disease N0000000875 1024195 34000006 Crohn's Disease C0010346 C1928 Crohn Disease [Disease/Finding] Cytomegalovirus Infections M0005604 D003586 Infection with CYTOMEGALOVIRUS, characterized by enlarged cells bearing intranuclear inclusions. Infection may be in almost any organ, but the salivary glands are the most common site in children, as are the lungs in adults. Cytomegalovirus Infections N0000000897 1023187 28944009 Cytomegalic Inclusion Disease Inclusion Disease Infections, Cytomegalovirus Salivary Gland Virus Disease C0010823 C1972 Cytomegalovirus Infections [Disease/Finding] Deficiency Diseases M0005753 D003677 A condition produced by dietary or metabolic deficiency. The term includes all diseases caused by an insufficient supply of essential nutrients, i.e., protein (or amino acids), vitamins, and minerals. It also includes an inadequacy of calories. (From Dorland, 27th ed; Stedman, 25th ed) Deficiency Diseases N0000000909 1025258 C0011156 C1996 Deficiency Diseases [Disease/Finding] Dehydration M0005757 D003681 The condition that results from excessive loss of water from a living organism. Dehydration N0000000911 1023412 34095006 C0011175 C2000 Dehydration [Disease/Finding] Dermatitis M0006046 D003872 Any inflammation of the skin. Dermatitis N0000000939 1023378 182782007 C0011603 C2056 Dermatitis [Disease/Finding] Dermatitis, Atopic M0006050 D003876 A chronic inflammatory genetically determined disease of the skin marked by increased ability to form reagin (IgE), with increased susceptibility to allergic rhinitis and asthma, and hereditary disposition to a lowered threshold for pruritus. It is manifested by lichenification, excoriation, and crusting, mainly on the flexural surfaces of the elbow and knee. In infants it is known as infantile eczema. Dermatitis, Atopic N0000000943 1022124 200773006 200775004 24079001 Eczema, Atopic Neurodermatitis, Atopic Neurodermatitis, Disseminated C0011615 C2064 Dermatitis, Atopic [Disease/Finding] Dermatomycoses M0006059 D003881 Superficial infections of the skin or its appendages by any of various fungi. Dermatomycoses N0000000945 1021749 14560005 276206000 Dermatomycosis Fungal Skin Diseases Skin Diseases, Fungal C0011630 C2068 Dermatomycoses [Disease/Finding] Digestive System Diseases M0006374 D004066 Diseases in any part of the GASTROINTESTINAL TRACT or the accessory organs (LIVER; BILIARY TRACT; PANCREAS). Digestive System Diseases N0000000973 1023342 53619000 C0012242 C2124 Digestive System Diseases [Disease/Finding] DNA Virus Infections M0006675 D004266 DNA Virus Infections N0000000993 1027612 Infections, DNA Virus C0012922 C2164 DNA Virus Infections [Disease/Finding] Drug Hypersensitivity M0006829 D004342 Immunologically mediated adverse reactions to medicinal substances used legally or illegally. Drug Hypersensitivity N0000000999 1024684 416093006 416098002 Allergy, Drug Drug Allergy Hypersensitivity, Drug C0013182 C2176 Drug Hypersensitivity [Disease/Finding] Drug Toxicity M0006855 D004362 Manifestations of the adverse effects of drugs administered therapeutically or in the course of diagnostic techniques. It does not include accidental or intentional poisoning for which specific headings are available. Drug Toxicity N0000001000 1022029 7895008 Toxicity, Drug C0013221 C2178 Drug Toxicity [Disease/Finding] Edema M0007051 D004487 Abnormal fluid accumulation in TISSUES or body cavities. Most cases of edema are present under the SKIN in SUBCUTANEOUS TISSUE. Edema N0000001057 1022374 20741006 79654002 Dropsy Hydrops C0013604 C2292 Edema [Disease/Finding] Eye Diseases M0008088 D005128 Eye Diseases N0000001181 1023594 194183009 C0015397 C2540 Eye Diseases [Disease/Finding] Female Urogenital Diseases and Pregnancy Complications M0008309 D005261 Pathological processes of the female URINARY TRACT, the reproductive system (GENITALIA, FEMALE), and disorders related to PREGNANCY. Female Urogenital Diseases and Pregnancy Complications N0000001224 985609 C1720765 C2626 Female Urogenital Diseases and Pregnancy Complications [Disease/Finding] Food Hypersensitivity M0008686 D005512 Gastrointestinal disturbances, skin eruptions, or shock due to allergic reactions to allergens in food. Food Hypersensitivity N0000001270 1025015 414285001 Allergy, Food Food Allergy Hypersensitivity, Food C0016470 C2718 Food Hypersensitivity [Disease/Finding] Gastroenteritis M0009018 D005759 INFLAMMATION of any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Causes of gastroenteritis are many including genetic, infection, HYPERSENSITIVITY, drug effects, and CANCER. Gastroenteritis N0000001317 1024672 25374005 C0017160 C2812 Gastroenteritis [Disease/Finding] Gastrointestinal Diseases M0009033 D005767 Diseases in any segment of the GASTROINTESTINAL TRACT from ESOPHAGUS to RECTUM. Gastrointestinal Diseases N0000001320 1022118 119292006 C0017178 C2818 Gastrointestinal Diseases [Disease/Finding] Genital Diseases, Female M0009154 D005831 Pathological processes involving the female reproductive tract (GENITALIA, FEMALE). Genital Diseases, Female N0000001323 1026095 244938009 310789003 Female Genital Diseases Gynecologic Diseases C0017411 C2824 Genital Diseases, Female [Disease/Finding] Genital Diseases, Male M0009155 D005832 Pathological processes involving the male reproductive tract (GENITALIA, MALE). Genital Diseases, Male N0000001324 1021837 64557000 Male Genital Diseases C0017412 C2826 Genital Diseases, Male [Disease/Finding] Graft vs Host Disease M0009578 D006086 The clinical entity characterized by anorexia, diarrhea, loss of hair, leukopenia, thrombocytopenia, growth retardation, and eventual death brought about by the GRAFT VS HOST REACTION. Graft vs Host Disease N0000001384 1024721 234646005 Graft-Versus-Host Disease Graft-vs-Host Disease Homologous Wasting Disease Runt Disease C0018133 C2946 Graft vs Host Disease [Disease/Finding] Heart Arrest M0009938 D006323 Cessation of heart beat or MYOCARDIAL CONTRACTION. If it is treated within a few minutes, heart arrest can be reversed in most cases to normal cardiac rhythm and effective circulation. Heart Arrest N0000001429 1025093 309810002 397829000 410429000 Asystole Cardiac Arrest C0018790 C3036 Heart Arrest [Disease/Finding] Heart Block M0009945 D006327 Impaired conduction of cardiac impulse that can occur anywhere along the conduction pathway, such as between the SINOATRIAL NODE and the right atrium (SA block) or between atria and ventricles (AV block). Heart blocks can be classified by the duration, frequency, or completeness of conduction block. Reversibility depends on the degree of structural or functional defects. Heart Block N0000001430 1023276 233916004 C0018794 C3038 Heart Block [Disease/Finding] Heart Diseases M0009951 D006331 Pathological conditions involving the HEART including its structural and functional abnormalities. Heart Diseases N0000001432 1022072 56265001 Cardiac Diseases C0018799 C3042 Heart Diseases [Disease/Finding] Heart Failure M0009953 D006333 A heterogeneous condition in which the heart is unable to pump out sufficient blood to meet the metabolic need of the body. Heart failure can be caused by structural defects, functional abnormalities (VENTRICULAR DYSFUNCTION), or a sudden overload beyond its capacity. Chronic heart failure is more common than acute heart failure which results from sudden insult to cardiac function, such as MYOCARDIAL INFARCTION. Heart Failure N0000001434 1024953 42343007 Cardiac Failure C0018802 C3046 Heart Failure [Disease/Finding] Heart Valve Diseases M0009972 D006349 Pathological conditions involving any of the various HEART VALVES and the associated structures (PAPILLARY MUSCLES and CHORDAE TENDINEAE). Heart Valve Diseases N0000001443 989613 368009 Valvular Heart Diseases C0018824 C3064 Heart Valve Diseases [Disease/Finding] Hematologic Diseases M0010044 D006402 Disorders of the blood and blood forming tissues. Hematologic Diseases N0000001459 1021953 191402006 267573000 Blood Diseases Hematological Diseases C0018939 C3096 Hematologic Diseases [Disease/Finding] Hemic and Lymphatic Diseases M0010072 D006425 Hematologic diseases and diseases of the lymphatic system collectively. Hemic diseases include disorders involving the formed elements (e.g., ERYTHROCYTE AGGREGATION, INTRAVASCULAR) and chemical components (e.g., BLOOD PROTEIN DISORDERS); lymphatic diseases include disorders relating to lymph, lymph nodes, and lymphocytes. Hemic and Lymphatic Diseases N0000001466 1026878 C0018981 C3110 Hemic and Lymphatic Diseases [Disease/Finding] Hemorrhage M0010152 D006470 Bleeding or escape of blood from a vessel. Hemorrhage N0000001481 1023287 195511004 Bleeding C0019080 C3140 Hemorrhage [Disease/Finding] Hemorrhagic Disorders M0010157 D006474 Spontaneous or near spontaneous bleeding caused by a defect in clotting mechanisms (BLOOD COAGULATION DISORDERS) or another abnormality causing a structural flaw in the blood vessels (HEMOSTATIC DISORDERS). Hemorrhagic Disorders N0000001485 1023732 191331006 Hemorrhagic Diathesis C0019087 C3148 Hemorrhagic Disorders [Disease/Finding] Hepatitis M0010205 D006505 INFLAMMATION of the LIVER. Hepatitis N0000001499 989819 128241005 197351001 C0019158 C3176 Hepatitis [Disease/Finding] Herpes Genitalis M0010276 D006558 Infection of the genitals (GENITALIA) with HERPES SIMPLEX VIRUS in either the males or the females. Herpes Genitalis N0000001527 1025755 271463009 33839006 Genital Herpes Herpes Simplex Virus Genital Infection Herpes Simplex, Genital C0019342 C3232 Herpes Genitalis [Disease/Finding] Herpes Simplex M0010279 D006561 A group of acute infections caused by herpes simplex virus type 1 or type 2 that is characterized by the development of one or more small fluid-filled vesicles with a raised erythematous base on the skin or mucous membrane. It occurs as a primary infection or recurs due to a reactivation of a latent infection. (Dorland, 27th ed.) Herpes Simplex N0000001530 1023866 88594005 C0019348 C3238 Herpes Simplex [Disease/Finding] Herpesviridae Infections M0010285 D006566 Virus diseases caused by the HERPESVIRIDAE. Herpesviridae Infections N0000001533 1024733 23513009 Herpesvirus Infections Infections, Herpesviridae Infections, Herpesvirus C0019372 C3244 Herpesviridae Infections [Disease/Finding] Hypercalcemia M0010814 D006934 Abnormally high level of calcium in the blood. Hypercalcemia N0000001577 1026898 66931009 C0020437 C3332 Hypercalcemia [Disease/Finding] Hyperglycemia M0010824 D006943 Abnormally high BLOOD GLUCOSE level. Hyperglycemia N0000001586 1021913 80394007 C0020456 C3350 Hyperglycemia [Disease/Finding] Hyperkalemia M0010828 D006947 Abnormally high potassium concentration in the blood, most often due to defective renal excretion. It is characterized clinically by electrocardiographic abnormalities (elevated T waves and depressed P waves, and eventually by atrial asystole). In severe cases, weakness and flaccid paralysis may occur. (Dorland, 27th ed) Hyperkalemia N0000001590 1021945 14140009 238142003 Hyperpotassemia C0020461 C3358 Hyperkalemia [Disease/Finding] Hypernatremia M0010837 D006955 Excessive amount of sodium in the blood. (Dorland, 27th ed) Hypernatremia N0000001598 1026718 286926003 39355002 C0020488 C3374 Hypernatremia [Disease/Finding] Hypersensitivity M0010851 D006967 Altered reactivity to an antigen, which can result in pathologic reactions upon subsequent exposure to that particular antigen. Hypersensitivity N0000001610 1022134 106190000 127072000 269284003 Allergy C0020517 C3398 Hypersensitivity [Disease/Finding] Hypersensitivity, Immediate M0010854 D006969 Hypersensitivity reactions which occur within minutes of exposure to challenging antigen due to the release of histamine which follows the antigen-antibody reaction and causes smooth muscle contraction and increased vascular permeability. Hypersensitivity, Immediate N0000001612 1023968 20671006 Atopic Hypersensitivity Hypersensitivity, Atopic Hypersensitivity, Type I IgE-Mediated Hypersensitivity Type I Hypersensitivity C0020523 C3402 Hypersensitivity, Immediate [Disease/Finding] Hypertension M0010859 D006973 Persistently high systemic arterial BLOOD PRESSURE. Based on multiple readings (BLOOD PRESSURE DETERMINATION), hypertension is currently defined as when SYSTOLIC PRESSURE is consistently greater than 140 mm Hg or when DIASTOLIC PRESSURE is consistently 90 mm Hg or more. Hypertension N0000001616 1023354 38341003 Blood Pressure, High C0020538 C3410 Hypertension [Disease/Finding] Hypocalcemia M0010891 D006996 Reduction of the blood calcium below normal. Manifestations include hyperactive deep tendon reflexes, Chvostek's sign, muscle and abdominal cramps, and carpopedal spasm. (Dorland, 27th ed) Hypocalcemia N0000001632 1022560 5291005 C0020598 C3442 Hypocalcemia [Disease/Finding] Hypoglycemia M0010901 D007003 A syndrome of abnormally low BLOOD GLUCOSE level. Clinical hypoglycemia has diverse etiologies. Severe hypoglycemia eventually lead to glucose deprivation of the CENTRAL NERVOUS SYSTEM resulting in HUNGER; SWEATING; PARESTHESIA; impaired mental function; SEIZURES; COMA; and even DEATH. Hypoglycemia N0000001635 1026036 190433001 237630007 271327008 302866003 C0020615 C3448 Hypoglycemia [Disease/Finding] Hyponatremia M0010911 D007010 Deficiency of sodium in the blood; salt depletion. (Dorland, 27th ed) Hyponatremia N0000001640 1022083 238115004 89627008 C0020625 C3458 Hyponatremia [Disease/Finding] Hypoprothrombinemias M0010925 D007020 Absence or reduced levels of prothrombin in the blood. Hypoprothrombinemias N0000001647 1023756 73975000 Deficiency, Factor II Factor II Deficiency Prothrombin Deficiency C0020640 C3472 Hypoprothrombinemias [Disease/Finding] Immunologic Deficiency Syndromes M0011155 D007153 Syndromes in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral. Immunologic Deficiency Syndromes N0000001667 1022772 191005003 234532001 Deficiency Syndrome, Immunologic Deficiency Syndromes, Immunologic Immunologic Deficiency Syndrome Immunological Deficiency Syndromes C0021051 C3512 Immunologic Deficiency Syndromes [Disease/Finding] Immune System Diseases M0011156 D007154 Disorders caused by abnormal or absent immunologic mechanisms, whether humoral, cell-mediated, or both. Immune System Diseases N0000001668 1022843 41266007 Diseases of Immune System Immune Diseases Immune Disorders Immunologic Diseases Immunological Diseases C0021053 C3514 Immune System Diseases [Disease/Finding] Infant, Newborn, Diseases M0011286 D007232 Diseases of newborn infants present at birth (congenital) or developing within the first month of birth. It does not include hereditary diseases not manifesting at birth or within the first 30 days of life nor does it include inborn errors of metabolism. Both HEREDITARY DISEASES and METABOLISM, INBORN ERRORS are available as general concepts. Infant, Newborn, Diseases N0000001678 1024869 22925008 C0021290 C3534 Infant, Newborn, Diseases [Disease/Finding] Infant, Premature, Diseases M0011290 D007235 Infant, Premature, Diseases N0000001679 990391 C0021295 C3536 Infant, Premature, Diseases [Disease/Finding] Infection M0011294 D007239 Invasion of the host organism by microorganisms that can cause pathological conditions or diseases. Infection N0000001681 1022093 40733004 C0021311 C3540 Infection [Disease/Finding] Intestinal Diseases M0011569 D007410 Pathological processes in any segment of the INTESTINE from DUODENUM to RECTUM. Intestinal Diseases N0000001698 1023320 85919009 C0021831 C3574 Intestinal Diseases [Disease/Finding] Kidney Calculi M0012008 D007669 Stones in the KIDNEY, usually formed in the urine-collecting area of the kidney (KIDNEY PELVIS). Their sizes vary and most contains CALCIUM OXALATE. Kidney Calculi N0000001746 1022167 95570007 Kidney Stones Renal Calculi Renal Calculus C0022650 C3670 Kidney Calculi [Disease/Finding] Kidney Diseases M0012014 D007674 Pathological processes of the KIDNEY or its component tissues. Kidney Diseases N0000001748 1022215 90708001 C0022658 C3674 Kidney Diseases [Disease/Finding] Kidney Failure, Acute M0012015 D058186 Kidney Failure, Acute N0000001749 1022586 14669001 Acute Kidney Failure Acute Renal Failure Renal Failure, Acute C0022660 C3676 Kidney Failure, Acute [Disease/Finding] Kidney Failure, Chronic M0012016 D007676 The end-stage of CHRONIC RENAL INSUFFICIENCY. It is characterized by the severe irreversible kidney damage (as measured by the level of PROTEINURIA) and the reduction in GLOMERULAR FILTRATION RATE to less than 15 ml per min (Kidney Foundation: Kidney Disease Outcome Quality Initiative, 2002). These patients generally require HEMODIALYSIS or KIDNEY TRANSPLANTATION. Kidney Failure, Chronic N0000001750 988914 90688005 Chronic Kidney Failure ESRD End-Stage Kidney Disease End-Stage Renal Disease Renal Disease, End-Stage Renal Failure, Chronic Renal Failure, End-Stage C0022661 C3678 Kidney Failure, Chronic [Disease/Finding] Lacrimal Apparatus Diseases M0012135 D007766 Diseases of the lacrimal apparatus. Lacrimal Apparatus Diseases N0000001774 1025659 31053003 C0022904 C3726 Lacrimal Apparatus Diseases [Disease/Finding] Liver Cirrhosis M0012636 D008103 Liver disease in which the normal microcirculation, the gross vascular anatomy, and the hepatic architecture have been variably destroyed and altered with fibrous septa surrounding regenerated or regenerating parenchymal nodules. Liver Cirrhosis N0000001862 1024193 19943007 Cirrhosis, Liver Hepatic Cirrhosis C0023890 C3902 Liver Cirrhosis [Disease/Finding] Liver Diseases M0012644 D008107 Pathological processes of the LIVER. Liver Diseases N0000001866 1024220 235856003 C0023895 C3910 Liver Diseases [Disease/Finding] Lung Diseases M0012744 D008171 Pathological processes involving any part of the LUNG. Lung Diseases N0000001879 1021971 19829001 Disease, Pulmonary Diseases, Pulmonary Pulmonary Disease Pulmonary Diseases C0024115 C3936 Lung Diseases [Disease/Finding] Lung Neoplasms M0012749 D008175 Tumors or cancer of the LUNG. Lung Neoplasms N0000001883 1023224 126713003 Neoplasms, Lung Neoplasms, Pulmonary Pulmonary Neoplasms C0024121 C3944 Lung Neoplasms [Disease/Finding] Magnesium Deficiency M0012886 D008275 A nutritional condition produced by a deficiency of magnesium in the diet, characterized by anorexia, nausea, vomiting, lethargy, and weakness. Symptoms are paresthesias, muscle cramps, irritability, decreased attention span, and mental confusion, possibly requiring months to appear. Deficiency of body magnesium can exist even when serum values are normal. In addition, magnesium deficiency may be organ-selective, since certain tissues become deficient before others. (Harrison's Principles of Internal Medicine, 12th ed, p1936) Magnesium Deficiency N0000001921 1024574 238118002 Deficiency, Magnesium C0024473 C4020 Magnesium Deficiency [Disease/Finding] Metabolic Diseases M0013493 D008659 Generic term for diseases caused by an abnormal metabolic process. It can be congenital due to inherited enzyme abnormality (METABOLISM, INBORN ERRORS) or acquired due to disease of an endocrine organ or failure of a metabolically important organ such as the liver. (Stedman, 26th ed) Metabolic Diseases N0000002004 1022778 30390004 75934005 Diseases, Metabolic Thesaurismosis C0025517 C4186 Metabolic Diseases [Disease/Finding] Stomatognathic Diseases M0014128 D009057 General or unspecified diseases of the stomatognathic system, comprising the mouth, teeth, jaws, and pharynx. Stomatognathic Diseases N0000002034 1027350 Mouth and Tooth Diseases C0038368 C4246 Stomatognathic Diseases [Disease/Finding] Mouth Diseases M0014130 D009059 Mouth Diseases N0000002036 1027441 118938008 C0026636 C4250 Mouth Diseases [Disease/Finding] Muscle Hypotonia M0014238 D009123 A diminution of the skeletal muscle tone marked by a diminished resistance to passive stretching. Muscle Hypotonia N0000002059 1024653 398151007 398152000 Decreased Muscle Tone Hypomyotonia Hypotonia Hypotony, Muscle Muscle Tone Poor Muscular Hypotonia C0026827 C4296 Muscle Hypotonia [Disease/Finding] Musculoskeletal Diseases M0014259 D009140 Diseases of the muscles and their associated ligaments and other connective tissue and of the bones and cartilage viewed collectively. Musculoskeletal Diseases N0000002067 1022076 928000 C0026857 C4312 Musculoskeletal Diseases [Disease/Finding] Mycoses M0014313 D009181 Mycoses N0000002075 1024676 3218000 Fungus Diseases C0026946 C4328 Mycoses [Disease/Finding] Congenital, Hereditary, and Neonatal Diseases and Abnormalities M0014570 D009358 Diseases existing at birth and often before birth, or that develop during the first month of life (INFANT, NEWBORN, DISEASES), regardless of causation. Of these diseases, those characterized by structural deformities are termed CONGENITAL ABNORMALITIES. Congenital, Hereditary, and Neonatal Diseases and Abnormalities N0000002121 989203 C0027612 C4420 Congenital, Hereditary, and Neonatal Diseases and Abnormalities [Disease/Finding] Neoplasms M0014585 D009369 New abnormal growth of tissue. Malignant neoplasms show a greater degree of anaplasia and have the properties of invasion and metastasis, compared to benign neoplasms. Neoplasms N0000002128 1022284 189525008 189526009 55342001 Tumors C0027651 C4434 Neoplasms [Disease/Finding] Neoplasms by Histologic Type M0014588 D009370 A collective term for the various histological types of NEOPLASMS. It is more likely to be used by searchers than by indexers and catalogers. Neoplasms by Histologic Type N0000002129 986146 Histological Type of Neoplasm Histological Types of Neoplasms Neoplasms by Histological Type C0027652 C4436 Neoplasms by Histologic Type [Disease/Finding] Neoplasms by Site M0014589 D009371 A collective term for precoordinated organ/neoplasm headings locating neoplasms by organ, as BRAIN NEOPLASMS; DUODENAL NEOPLASMS; LIVER NEOPLASMS; etc. Neoplasms by Site N0000002130 1026659 Neoplasms by Sites Site, Neoplasm Sites, Neoplasm C0027653 C4438 Neoplasms by Site [Disease/Finding] Neoplasms, Germ Cell and Embryonal M0014592 D009373 Neoplasms composed of primordial GERM CELLS of embryonic GONADS or of elements of the germ layers of the EMBRYO, MAMMALIAN. The concept does not refer to neoplasms located in the gonads or present in an embryo or FETUS. Neoplasms, Germ Cell and Embryonal N0000002132 1026873 Germ Cell and Embryonal Neoplasms Germ Cell and Embryonic Neoplasms Neoplasms, Germ Cell and Embryonic C0027658 C4442 Neoplasms, Germ Cell and Embryonal [Disease/Finding] Neoplasms, Nerve Tissue M0014605 D009380 Neoplasms composed of nerve tissue. This concept does not refer to neoplasms located in the nervous system or its component nerves. Neoplasms, Nerve Tissue N0000002139 985772 Neoplasms, Nervous Tissue Nerve Tissue Neoplasms Nervous Tissue Neoplasms C0027665 C4456 Neoplasms, Nerve Tissue [Disease/Finding] Nephrosis M0014635 D009401 Pathological processes of the KIDNEY without inflammatory or neoplastic components. Nephrosis may be a primary disorder or secondary complication of other diseases. It is characterized by the NEPHROTIC SYNDROME indicating the presence of PROTEINURIA and HYPOALBUMINEMIA with accompanying EDEMA. Nephrosis N0000002153 1025384 90708001 C0027720 C4484 Nephrosis [Disease/Finding] Nephrotic Syndrome M0014639 D009404 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. Nephrotic Syndrome N0000002155 1026285 52254009 C0027726 C4488 Nephrotic Syndrome [Disease/Finding] Nervous System Diseases M0014667 D009422 Diseases of the central and peripheral nervous system. This includes disorders of the brain, spinal cord, cranial nerves, peripheral nerves, nerve roots, autonomic nervous system, neuromuscular junction, and muscle. Nervous System Diseases N0000002159 1026444 118940003 Nervous System Disorders Neurologic Disorders Neurological Disorders C0027765 C4496 Nervous System Diseases [Disease/Finding] Neurologic Manifestations M0014716 D009461 Clinical signs and symptoms caused by nervous system injury or dysfunction. Neurologic Manifestations N0000002173 1025946 Manifestations, Neurologic Manifestations, Neurological Neurologic Manifestation Neurologic Signs and Symptoms Neurological Manifestations C0027854 C4524 Neurologic Manifestations [Disease/Finding] Nutrition Disorders M0015120 D009748 Disorders caused by nutritional imbalance, either overnutrition or undernutrition. Nutrition Disorders N0000002196 1024039 2492009 Nutritional Disorders C0028709 C4570 Nutrition Disorders [Disease/Finding] Nutritional and Metabolic Diseases M0015124 D009750 A collective term for nutritional disorders resulting from poor absorption or nutritional imbalance, and metabolic disorders resulting from defects in biosynthesis (ANABOLISM) or breakdown (CATABOLISM) of endogenous substances. Nutritional and Metabolic Diseases N0000002197 1026553 C0028715 C4572 Nutritional and Metabolic Diseases [Disease/Finding] Opportunistic Infections M0015350 D009894 An infection caused by an organism which becomes pathogenic under certain conditions, e.g., during immunosuppression. Opportunistic Infections N0000002225 1025670 61274003 C0029118 C4628 Opportunistic Infections [Disease/Finding] Osteoporosis M0015552 D010024 Reduction of bone mass without alteration in the composition of bone, leading to fractures. Primary osteoporosis can be of two major types: postmenopausal osteoporosis (OSTEOPOROSIS, POSTMENOPAUSAL) and age-related or senile osteoporosis. Osteoporosis N0000002260 1022418 203428004 64859006 C0029456 C4698 Osteoporosis [Disease/Finding] Paraganglioma M0015869 D010235 A neural crest tumor usually derived from the chromoreceptor tissue of a paraganglion, such as the carotid body, or medulla of the adrenal gland (usually called a chromaffinoma or pheochromocytoma). It is more common in women than in men. (Stedman, 25th ed; from Segen, Dictionary of Modern Medicine, 1992) Paraganglioma N0000002299 1022619 127027008 253029009 302833002 Paraganglioma, Gangliocytic C0030421 C4776 Paraganglioma [Disease/Finding] Parasitic Diseases M0015919 D010272 Infections or infestations with parasitic organisms. They are often contracted through contact with an intermediate vector, but may occur as the result of direct exposure. Parasitic Diseases N0000002319 987316 17322007 C0030499 C4816 Parasitic Diseases [Disease/Finding] Pathologic Processes M0016012 D010335 The abnormal mechanisms and forms involved in the dysfunctions of tissues and organs. Pathologic Processes N0000002338 1025320 308489006 370135005 Pathological Processes Processes, Pathologic C0030660 C4854 Pathologic Processes [Disease/Finding] Pheochromocytoma M0016586 D010673 A usually benign, well-encapsulated, lobular, vascular tumor of chromaffin tissue of the ADRENAL MEDULLA or sympathetic paraganglia. The cardinal symptom, reflecting the increased secretion of EPINEPHRINE and NOREPINEPHRINE, is HYPERTENSION, which may be persistent or intermittent. During severe attacks, there may be HEADACHE; SWEATING, palpitation, apprehension, TREMOR; PALLOR or FLUSHING of the face, NAUSEA and VOMITING, pain in the CHEST and ABDOMEN, and paresthesias of the extremities. The incidence of malignancy is as low as 5% but the pathologic distinction between benign and malignant pheochromocytomas is not clear. (Dorland, 27th ed; DeVita Jr et al., Cancer: Principles & Practice of Oncology, 3d ed, p1298) Pheochromocytoma N0000002390 1021872 302835009 399343007 C0031511 C4958 Pheochromocytoma [Disease/Finding] Poisoning M0017099 D011041 A condition or physical state produced by the ingestion, injection, inhalation of or exposure to a deleterious agent. Poisoning N0000002447 1026915 75478009 C0032343 C5072 Poisoning [Disease/Finding] Postoperative Complications M0017367 D011183 Pathologic processes that affect patients after a surgical procedure. They may or may not be related to the disease for which the surgery was done, and they may or may not be direct results of the surgery. Postoperative Complications N0000002467 1022600 385486001 Complication, Postoperative C0032787 C5112 Postoperative Complications [Disease/Finding] Psoriasis M0017975 D011565 A common genetically determined, chronic, inflammatory skin disease characterized by rounded erythematous, dry, scaling patches. The lesions have a predilection for nails, scalp, genitalia, extensor surfaces, and the lumbosacral region. Accelerated epidermopoiesis is considered to be the fundamental pathologic feature in psoriasis. Psoriasis N0000002526 1022582 200961000 9014002 C0033860 C5230 Psoriasis [Disease/Finding] Pulmonary Edema M0018125 D011654 Excessive accumulation of extravascular fluid in the lung, an indication of a serious underlying disease or disorder. Pulmonary edema prevents efficient PULMONARY GAS EXCHANGE in the PULMONARY ALVEOLI, and can be life-threatening. Pulmonary Edema N0000002540 1024136 19242006 Edema, Pulmonary Edemas, Pulmonary Pulmonary Edemas Wet Lung C0034063 C5258 Pulmonary Edema [Disease/Finding] Respiratory Tract Diseases M0018918 D012140 Respiratory Tract Diseases N0000002602 1024163 C0035242 C5382 Respiratory Tract Diseases [Disease/Finding] Respiratory Tract Neoplasms M0018921 D012142 Respiratory Tract Neoplasms N0000002604 986366 126667002 C0035244 C5386 Respiratory Tract Neoplasms [Disease/Finding] Retroviridae Infections M0018986 D012192 Virus diseases caused by the RETROVIRIDAE. Retroviridae Infections N0000002623 1025440 105635000 Infections, Retroviridae Infections, Retrovirus Retrovirus Infections C0035369 C5424 Retroviridae Infections [Disease/Finding] RNA Virus Infections M0019160 D012327 RNA Virus Infections N0000002650 1027571 Infections, RNA Virus C0035690 C5478 RNA Virus Infections [Disease/Finding] Sexually Transmitted Diseases M0019758 D012749 Diseases due to or propagated by sexual contact. Sexually Transmitted Diseases N0000002724 1023328 8098009 STDs Venereal Diseases C0036916 C5626 Sexually Transmitted Diseases [Disease/Finding] Shock M0019782 D012769 A pathological condition manifested by failure to perfuse or oxygenate vital organs. Shock N0000002728 1023333 274729009 27942005 Circulatory Collapse Circulatory Failure C0036974 C5634 Shock [Disease/Finding] Shock, Hemorrhagic M0019784 D012771 Acute hemorrhage or excessive fluid loss resulting in HYPOVOLEMIA. Shock, Hemorrhagic N0000002730 1026764 355001 Hemorrhagic Shock C0036982 C5638 Shock, Hemorrhagic [Disease/Finding] Signs and Symptoms M0019845 D012816 Clinical manifestations that can be either objective when observed by a physician, or subjective when perceived by the patient. Signs and Symptoms N0000002748 1024593 C0037088 C5674 Signs and Symptoms [Disease/Finding] Skin Diseases M0019929 D012871 Skin Diseases N0000002761 1022858 95320005 Dermatoses Dermatosis C0037274 C5700 Skin Diseases [Disease/Finding] Skin Diseases, Genetic M0019934 D012873 Diseases of the skin with a genetic component, usually the result of various inborn errors of metabolism. Skin Diseases, Genetic N0000002763 986094 239001006 Genetic Skin Diseases C0037277 C5704 Skin Diseases, Genetic [Disease/Finding] Skin Diseases, Infectious M0019935 D012874 Skin diseases caused by bacteria, fungi, parasites, or viruses. Skin Diseases, Infectious N0000002764 1025346 108365000 Infectious Skin Diseases C0037278 C5706 Skin Diseases, Infectious [Disease/Finding] Skin Neoplasms M0019939 D012878 Tumors or cancer of the SKIN. Skin Neoplasms N0000002768 1025991 126488004 Neoplasms, Skin C0037286 C5714 Skin Neoplasms [Disease/Finding] Substance Withdrawal Syndrome M0020676 D013375 Physiological and psychological symptoms associated with withdrawal from the use of a drug after prolonged administration or habituation. The concept includes withdrawal from smoking or drinking, as well as withdrawal from an administered drug. Substance Withdrawal Syndrome N0000002855 1027256 C0038587 C5888 Substance Withdrawal Syndrome [Disease/Finding] Pathological Conditions, Signs and Symptoms M0020949 D013568 Abnormal anatomical or physiological conditions and objective or subjective manifestations of disease, not classified as disease or syndrome. Pathological Conditions, Signs and Symptoms N0000002872 984268 Symptoms and General Pathology C0039058 C5922 Pathological Conditions, Signs and Symptoms [Disease/Finding] Tetany M0021207 D013746 A disorder characterized by muscle twitches, cramps, and carpopedal spasm, and when severe, laryngospasm and seizures. This condition is associated with unstable depolarization of axonal membranes, primarily in the peripheral nervous system. Tetany usually results from HYPOCALCEMIA or reduced serum levels of MAGNESIUM that may be associated with HYPERVENTILATION; HYPOPARATHYROIDISM; RICKETS; UREMIA; or other conditions. (From Adams et al., Principles of Neurology, 6th ed, p1490) Tetany N0000002916 1024300 10629009 C0039621 C6010 Tetany [Disease/Finding] Thoracic Neoplasms M0021397 D013899 Thoracic Neoplasms N0000002927 1029082 255058005 C0039981 C6032 Thoracic Neoplasms [Disease/Finding] Unconsciousness M0022251 D014474 Loss of the ability to maintain awareness of self and environment combined with markedly reduced responsiveness to environmental stimuli. (From Adams et al., Principles of Neurology, 6th ed, pp344-5) Unconsciousness N0000003064 1026031 418107008 419045004 Consciousness, Loss of Unconscious State C0041657 C6306 Unconsciousness [Disease/Finding] Urinary Calculi M0022362 D014545 Low-density crystals or stones in any part of the URINARY TRACT. Their chemical compositions often include CALCIUM OXALATE, magnesium ammonium phosphate (struvite), CYSTINE, or URIC ACID. Urinary Calculi N0000003077 1023616 197797001 Urinary Stones Urinary Tract Stones C0042018 C6332 Urinary Calculi [Disease/Finding] Urination Disorders M0022377 D014555 Abnormalities in the process of URINE voiding, including bladder control, frequency of URINATION, as well as the volume and composition of URINE. Urination Disorders N0000003082 1025163 C0042035 C6342 Urination Disorders [Disease/Finding] Male Urogenital Diseases M0489510 D052801 Pathological processes of the male URINARY TRACT and the reproductive system (GENITALIA, MALE). Male Urogenital Diseases N0000003085 1027597 Male Genitourinary Diseases C1720894 CMSHM0489510 Male Urogenital Diseases [Disease/Finding] Urologic Diseases M0022400 D014570 Pathological processes of the URINARY TRACT in both males and females. Urologic Diseases N0000003086 1022769 128606002 197951006 41368006 Urinary Tract Diseases Urological Diseases C0042075 C6350 Urologic Diseases [Disease/Finding] Vaginal Diseases M0022482 D014623 Pathological processes of the VAGINA. Vaginal Diseases N0000003104 1026314 25658005 C0042251 C6386 Vaginal Diseases [Disease/Finding] Vaginitis M0022488 D014627 Inflammation of the vagina characterized by pain and a purulent discharge. Vaginitis N0000003107 1021851 198213001 30800001 C0042267 C6392 Vaginitis [Disease/Finding] Vascular Diseases M0022535 D014652 Pathological processes involving any of the BLOOD VESSELS in the cardiac or peripheral circulation. They include diseases of ARTERIES; VEINS; and rest of the vasculature system in the body. Vascular Diseases N0000003111 1024109 27550009 C0042373 C6400 Vascular Diseases [Disease/Finding] Ventricular Fibrillation M0022595 D014693 A potentially lethal cardiac arrhythmia that is characterized by uncoordinated extremely rapid firing of electrical impulses (400-600/min) in HEART VENTRICLES. Such asynchronous ventricular quivering or fibrillation prevents any effective cardiac output and results in unconsciousness (SYNCOPE). It is one of the major electrocardiographic patterns seen with CARDIAC ARREST. Ventricular Fibrillation N0000003118 1024218 71908006 C0042510 C6414 Ventricular Fibrillation [Disease/Finding] Ventricular Outflow Obstruction M0022598 D014694 Occlusion of the outflow tract in either the LEFT VENTRICLE or the RIGHT VENTRICLE of the heart. This may result from CONGENITAL HEART DEFECTS, predisposing heart diseases, complications of surgery, or HEART NEOPLASMS. Ventricular Outflow Obstruction N0000003119 1028258 C0042512 C6416 Ventricular Outflow Obstruction [Disease/Finding] Virus Diseases M0022758 D014777 A general term for diseases produced by viruses. Virus Diseases N0000003128 1022696 34014006 Viral Diseases C0042769 C6434 Virus Diseases [Disease/Finding] Vulvar Diseases M0022856 D014845 Pathological processes of the VULVA. Vulvar Diseases N0000003145 1024723 5089007 C0042994 C6468 Vulvar Diseases [Disease/Finding] Vulvitis M0022858 D014847 Inflammation of the VULVA. It is characterized by PRURITUS and painful urination. Vulvitis N0000003147 1023099 266586003 63144007 C0042996 C6472 Vulvitis [Disease/Finding] Vulvovaginitis M0022859 D014848 Inflammation of the VULVA and the VAGINA, characterized by discharge, burning, and PRURITUS. Vulvovaginitis N0000003148 1025805 198215008 53277000 C0042998 C6474 Vulvovaginitis [Disease/Finding] Water-Electrolyte Imbalance M0022901 D014883 Disturbances in the body's WATER-ELECTROLYTE BALANCE. Water-Electrolyte Imbalance N0000003154 1028873 C0043065 C6486 Water-Electrolyte Imbalance [Disease/Finding] Wounds and Injuries M0023019 D014947 Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. Wounds and Injuries N0000003169 1022221 19130008 Injuries and Wounds Injuries, Wounds Trauma Wounds and Injury Wounds, Injury C0043251 C6516 Wounds and Injuries [Disease/Finding] Inflammatory Bowel Diseases M0023374 D015212 Chronic, non-specific inflammation of the GASTROINTESTINAL TRACT. Etiology may be genetic or environmental. This term includes CROHN DISEASE and ULCERATIVE COLITIS. Inflammatory Bowel Diseases N0000003206 1023128 24526004 Bowel Diseases, Inflammatory C0021390 C6590 Inflammatory Bowel Diseases [Disease/Finding] Sexually Transmitted Diseases, Viral M0023402 D015229 Viral diseases which are transmitted or propagated by sexual conduct. Sexually Transmitted Diseases, Viral N0000003211 1027279 Sexually Transmitted Disease, Viral Venereal Diseases, Viral Viral Sexually Transmitted Disease Viral Sexually Transmitted Diseases Viral Venereal Diseases C0036918 C6600 Sexually Transmitted Diseases, Viral [Disease/Finding] Dry Eye Syndromes M0023637 D015352 Corneal and conjunctival dryness due to deficient tear production, predominantly in menopausal and post-menopausal women. Filamentary keratitis or erosion of the conjunctival and corneal epithelium may be caused by these disorders. Sensation of the presence of a foreign body in the eye and burning of the eyes may occur. Dry Eye Syndromes N0000003223 987360 46152009 C0013238 C6624 Dry Eye Syndromes [Disease/Finding] Overdose M0023903 D015537 An accidental or deliberate dose of a medication or street drug that is in excess of what is normally used. Overdose N0000003288 1023841 55680006 C0029944 C6754 Overdose [Disease/Finding] HIV Infections M0023997 D015658 Includes the spectrum of human immunodeficiency virus infections that range from asymptomatic seropositivity, thru AIDS-related complex (ARC), to acquired immunodeficiency syndrome (AIDS). HIV Infections N0000003302 1022756 86406008 HTLV-III Infections HTLV-III-LAV Infections T-Lymphotropic Virus Type III Infections, Human C0019693 C6782 HIV Infections [Disease/Finding] Corneal Edema M0024096 D015715 An excessive amount of fluid in the cornea due to damage of the epithelium or endothelium causing decreased visual acuity. Corneal Edema N0000003307 1024597 193812004 27194006 C0010037 C6792 Corneal Edema [Disease/Finding] Lentivirus Infections M0024697 D016180 Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection. Lentivirus Infections N0000003384 1024090 24907000 Infections, Lentivirus C0079680 C6946 Lentivirus Infections [Disease/Finding] AIDS-Related Opportunistic Infections M0025965 D017088 Opportunistic infections found in patients who test positive for human immunodeficiency virus (HIV). The most common include PNEUMOCYSTIS PNEUMONIA, Kaposi's sarcoma, cryptosporidiosis, herpes simplex, toxoplasmosis, cryptococcosis, and infections with Mycobacterium avium complex, Microsporidium, and Cytomegalovirus. AIDS-Related Opportunistic Infections N0000003524 1025910 HIV-Related Opportunistic Infections Opportunistic Infections, AIDS-Related Opportunistic Infections, HIV-Related C0162526 C7226 AIDS-Related Opportunistic Infections [Disease/Finding] Kidney Failure M0025974 D051437 A severe irreversible decline in the ability of kidneys to remove wastes, concentrate URINE, and maintain ELECTROLYTE BALANCE; BLOOD PRESSURE; and CALCIUM metabolism. Kidney Failure N0000003529 1022860 266553002 42399005 Renal Failure C0035078 C7236 Kidney Failure [Disease/Finding] Skin Diseases, Viral M0026098 D017193 Skin diseases caused by viruses. Skin Diseases, Viral N0000003547 1029386 128937004 Viral Skin Diseases C0162628 C7272 Skin Diseases, Viral [Disease/Finding] Skin and Connective Tissue Diseases M0026454 D017437 A collective term for diseases of the skin and its appendages and of connective tissue. Skin and Connective Tissue Diseases N0000003573 1027511 C0175166 C7324 Skin and Connective Tissue Diseases [Disease/Finding] Skin Diseases, Eczematous M0026466 D017443 Any of a variety of eruptive skin disorders characterized by erythema, oozing, vesiculation, and scaling. Etiology is varied. Skin Diseases, Eczematous N0000003576 1022475 Eczematous Disorders Eczematous Skin Diseases C0162817 C7330 Skin Diseases, Eczematous [Disease/Finding] Skin Diseases, Papulosquamous M0026467 D017444 A group of dermatoses with distinct morphologic features. The primary lesion is most commonly a papule, usually erythematous, with a variable degree of scaling on the surface. Plaques form through the coalescing of primary lesions. Skin Diseases, Papulosquamous N0000003577 1024350 22585003 Papulosquamous Disorders Papulosquamous Skin Diseases C0162818 C7332 Skin Diseases, Papulosquamous [Disease/Finding] Neuroectodermal Tumors M0026668 D017599 Malignant neoplasms arising in the neuroectoderm, the portion of the ectoderm of the early embryo that gives rise to the central and peripheral nervous systems, including some glial cells. Neuroectodermal Tumors N0000003613 1022212 253096008 73676002 C0206093 C7404 Neuroectodermal Tumors [Disease/Finding] Neuroendocrine Tumors M0027590 D018358 Tumors whose cells possess secretory granules and originate from the neuroectoderm, i.e., the cells of the ectoblast or epiblast that program the neuroendocrine system. Common properties across most neuroendocrine tumors include ectopic hormone production (often via APUD CELLS), the presence of tumor-associated antigens, and isozyme composition. Neuroendocrine Tumors N0000003804 1024535 255046005 C0206754 C7786 Neuroendocrine Tumors [Disease/Finding] Neurobehavioral Manifestations M0333801 D019954 Signs and symptoms of higher cortical dysfunction caused by organic conditions. These include certain behavioral alterations and impairments of skills involved in the acquisition, processing, and utilization of knowledge or information. Neurobehavioral Manifestations N0000003967 1025867 Cognitive Manifestations Cognitive Symptoms Neurobehavioral Signs and Symptoms Signs and Symptoms, Neurobehavioral C0525041 C8112 Neurobehavioral Manifestations [Disease/Finding] Delirium, Dementia, Amnestic, Cognitive Disorders M0029645 D019965 Cognitive disorders including delirium, dementia, and other cognitive disorders. These may be the result of substance use, trauma, or other causes. Delirium, Dementia, Amnestic, Cognitive Disorders N0000003976 1022574 106014008 111479008 Mental Disorders, Organic Organic Mental Disorders C0029227 C8130 Delirium, Dementia, Amnestic, Cognitive Disorders [Disease/Finding] Substance-Related Disorders M0029657 D019966 Disorders related to substance abuse, the side effects of a medication, or toxin exposure. Substance-Related Disorders N0000003977 1027904 C0236969 C8132 Substance-Related Disorders [Disease/Finding] Alcohol-Related Disorders M0029672 D019973 Disorders related to or resulting from abuse or mis-use of alcohol. Alcohol-Related Disorders N0000003982 1025655 29212009 C0236664 C8142 Alcohol-Related Disorders [Disease/Finding] Coagulation Protein Disorders M0029880 D020147 Hemorrhagic and thrombotic disorders resulting from abnormalities or deficiencies of coagulation proteins. Coagulation Protein Disorders N0000004004 1024212 Blood Coagulation Factor Deficiencies Coagulation Proteins Disorders C0600503 C8186 Coagulation Protein Disorders [Disease/Finding] Neurotoxicity Syndromes M0328313 D020258 Neurologic disorders caused by exposure to toxic substances through ingestion, injection, cutaneous application, or other method. This includes conditions caused by biologic, chemical, and pharmaceutical agents. Neurotoxicity Syndromes N0000004080 985040 19466003 Nervous System Poisoning Neurotoxic Disorders Neurotoxin Diseases Neurotoxin Disorders Poisoning, Nervous System C0235032 C8338 Neurotoxicity Syndromes [Disease/Finding] Alcohol-Induced Disorders, Nervous System M0328091 D020268 Acute and chronic neurologic disorders associated with the various neurologic effects of ETHANOL. Primary sites of injury include the brain and peripheral nerves. Alcohol-Induced Disorders, Nervous System N0000004088 1023561 Alcohol Abuse, Nervous System Ethanol Induced Nervous System Disorders Ethanol-Induced Disorders, Nervous System Ethanol-Induced Nervous System Disorders Ethyl Alcohol Abuse Neurologic Syndromes Nervous System Disorders, Ethanol-Induced C0751865 C8354 Alcohol-Induced Disorders, Nervous System [Disease/Finding] Intracranial Hemorrhages M0328611 D020300 Bleeding within the SKULL, including hemorrhages in the brain and the three membranes of MENINGES. The escape of blood often leads to the formation of HEMATOMA in the cranial epidural, subdural, and subarachnoid spaces. Intracranial Hemorrhages N0000004102 1026294 1386000 Hemorrhage, Intracranial C0151699 C8382 Intracranial Hemorrhages [Disease/Finding] Alcohol-Induced Disorders M0328025 D020751 Disorders stemming from the misuse and abuse of alcohol. Alcohol-Induced Disorders N0000004170 1025678 C0236970 C8518 Alcohol-Induced Disorders [Disease/Finding] Pathological Conditions, Anatomical M0328642 D020763 An abnormal structural condition of the human body, usually macroscopic, that is common to a variety of different diseases. Pathological Conditions, Anatomical N0000004178 1026773 C0752135 C8534 Pathological Conditions, Anatomical [Disease/Finding] Neuromuscular Manifestations M0328296 D020879 Signs and symptoms associated with diseases of the muscle, neuromuscular junction, or peripheral nerves. Neuromuscular Manifestations N0000004213 1027972 Neuromuscular Signs and Symptoms Signs and Symptoms, Neuromuscular C0752252 C8604 Neuromuscular Manifestations [Disease/Finding] Discrete Subaortic Stenosis M0001558 D021922 A type of constriction that is caused by the presence of a fibrous ring (discrete type) below the AORTIC VALVE, anywhere between the aortic valve and the MITRAL VALVE. It is characterized by restricted outflow from the LEFT VENTRICLE into the AORTA. Discrete Subaortic Stenosis N0000004248 1031927 Subaortic Stenosis, Discrete C0012628 C8674 Discrete Subaortic Stenosis [Disease/Finding] basiliximab M0292349 C113157 basiliximab N0000004374 196102 basiliximab C0676831 C11518 basiliximab [Chemical/Ingredient] Carbohydrates M0003360 D002241 The largest class of organic compounds, including STARCH; GLYCOGEN; CELLULOSE; POLYSACCHARIDES; and simple MONOSACCHARIDES. Carbohydrates are composed of carbon, hydrogen, and oxygen in a ratio of Cn(H2O)n. Carbohydrates N0000005723 2028 C0007004 C21790 Carbohydrates [Chemical/Ingredient] Metolazone M0013684 D008788 A quinazoline-sulfonamide that is considered a thiazide-like diuretic which is long-acting so useful in chronic RENAL FAILURE. It also tends to lower BLOOD PRESSURE and increase POTASSIUM loss. Metolazone N0000005746 6916 Metolazone 6-Quinazolinesulfonamide, 7-chloro-1,2,3,4-tetrahydro-2-methyl-3-(2-methylphenyl)-4-oxo- C0025854 C21836 Metolazone [Chemical/Ingredient] Proteins M0017890 D011506 Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Proteins N0000005817 8859 Proteins C0033684 C21978 Proteins [Chemical/Ingredient] torsemide M0086132 C026116 torsemide N0000006018 38413 torsemide 1-isopropyl-3-((4-(3-methylphenylamino)pyridine)-3-sulfonyl)urea 1-isopropyl-3-((4-m-toluidino-3-pyridyl)sulfonyl)urea torasemide C0076840 C22380 torsemide [Chemical/Ingredient] Dobutamine M0006696 D004280 A catecholamine derivative with specificity for BETA-1 ADRENERGIC RECEPTORS. It is commonly used as a cardiotonic agent after CARDIAC SURGERY and during DOBUTAMINE STRESS ECHOCARDIOGRAPHY. Dobutamine N0000006055 3616 Dobutamine 1,2-Benzenediol, 4-(2-((3-(4-hydroxyphenyl)-1-methylpropyl)amino)ethyl)-, (+-)- C0012963 C22454 Dobutamine [Chemical/Ingredient] Dopamine M0006756 D004298 One of the catecholamine NEUROTRANSMITTERS in the brain. It is derived from TYROSINE and is the precursor to NOREPINEPHRINE and EPINEPHRINE. Dopamine is a major transmitter in the extrapyramidal system of the brain, and important in regulating movement. A family of receptors (RECEPTORS, DOPAMINE) mediate its action. Dopamine N0000006091 3628 Dopamine 1,2-Benzenediol, 4-(2-aminoethyl)- 3,4-Dihydroxyphenethylamine 4-(2-Aminoethyl)-1,2-benzenediol Hydroxytyramine C0013030 C22526 Dopamine [Chemical/Ingredient] Lipids M0012553 D008055 A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed) Lipids N0000006185 6411 C0023779 C22714 Lipids [Chemical/Ingredient] Vitamin D M0022797 D014807 A vitamin that includes both CHOLECALCIFEROLS and ERGOCALCIFEROLS, which have the common effect of preventing or curing RICKETS in animals. It can also be viewed as a hormone since it can be formed in SKIN by action of ULTRAVIOLET RAYS upon the precursors, 7-dehydrocholesterol and ERGOSTEROL, and acts on VITAMIN D RECEPTORS to regulate CALCIUM in opposition to PARATHYROID HORMONE. Vitamin D N0000006277 11253 Vitamin D C0042866 C22900 Vitamin D [Chemical/Ingredient] Vitamin K M0022806 D014812 A lipid cofactor that is required for normal blood clotting. Several forms of vitamin K have been identified: VITAMIN K 1 (phytomenadione) derived from plants, VITAMIN K 2 (menaquinone) from bacteria, and synthetic naphthoquinone provitamins, VITAMIN K 3 (menadione). Vitamin K 3 provitamins, after being alkylated in vivo, exhibit the antifibrinolytic activity of vitamin K. Green leafy vegetables, liver, cheese, butter, and egg yolk are good sources of vitamin K. Vitamin K N0000006290 11258 Vitamin K C0042878 C22926 Vitamin K [Chemical/Ingredient] Magnesium M0012884 D008274 A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION. Magnesium N0000006335 6574 Magnesium C0024467 C23018 Magnesium [Chemical/Ingredient] Glucose M0009339 D005947 A primary source of energy for living organisms. It is naturally occurring and is found in fruits and other parts of plants in its free state. It is used therapeutically in fluid and nutrient replacement. Glucose N0000006402 4850 Glucose D-Glucose Dextrose C0017725 C23152 Glucose [Chemical/Ingredient] Hydrochloric Acid M0010701 D006851 A strong corrosive acid that is commonly used as a laboratory reagent. It is formed by dissolving hydrogen chloride in water. GASTRIC ACID is the hydrochloric acid component of GASTRIC JUICE. Hydrochloric Acid N0000006448 5486 Hydrochloric Acid Hydrochloric acid Muriatic Acid C0020259 C23244 Hydrochloric Acid [Chemical/Ingredient] Calcifediol M0003141 D002112 The major circulating metabolite of VITAMIN D3. It is produced in the LIVER and is the best indicator of the body's vitamin D stores. It is effective in the treatment of RICKETS and OSTEOMALACIA, both in azotemic and non-azotemic patients. Calcifediol also has mineralizing properties. Calcifediol N0000006507 1889 Calcifediol 25-Hydroxycholecalciferol 25-Hydroxyvitamin D 3 25-Hydroxyvitamin D3 9,10-Secocholesta-5,7,10(19)-triene-3,25-diol, (3beta,5Z,7E)- Calcidiol C0006657 C23362 Calcifediol [Chemical/Ingredient] Calcium M0003153 D002118 A basic element found in nearly all organized tissues. It is a member of the alkaline earth family of metals with the atomic symbol Ca, atomic number 20, and atomic weight 40. Calcium is the most abundant mineral in the body and combines with phosphorus to form calcium phosphate in the bones and teeth. It is essential for the normal functioning of nerves and muscles and plays a role in blood coagulation (as factor IV) and in many enzymatic processes. Calcium N0000006512 1895 Calcium Blood Coagulation Factor IV Coagulation Factor IV Factor IV C0006675 C23372 Calcium [Chemical/Ingredient] Calcium Chloride M0003166 D002122 A salt used to replenish calcium levels, as an acid-producing diuretic, and as an antidote for magnesium poisoning. Calcium Chloride N0000006545 1901 Calcium Chloride Calcium Chloride, Anhydrous Calcium chloride C0006686 C23438 Calcium Chloride [Chemical/Ingredient] Sodium Lactate M0028809 D019354 The sodium salt of racemic or inactive lactic acid. It is a hygroscopic agent used intravenously as a systemic and urinary alkalizer. Sodium Lactate N0000006559 56489 Sodium Lactate C0142874 C23466 Sodium Lactate [Chemical/Ingredient] Lactates M0012155 D007773 Salts or esters of LACTIC ACID containing the general formula CH3CHOHCOOR. Lactates N0000006568 6201 C0022924 C23484 Lactates [Chemical/Ingredient] Atracurium M0001922 D001279 A non-depolarizing neuromuscular blocking agent with short duration of action. Its lack of significant cardiovascular effects and its lack of dependence on good kidney function for elimination provide clinical advantage over alternate non-depolarizing neuromuscular blocking agents. Atracurium N0000006674 1218 Atracurium Isoquinolinium, 2,2'-(1,5-pentanediylbis(oxy(3-oxo-3,1-propanediyl)))bis(1-((3,4-dimethoxyphenyl)methyl))-1,2,3,4-tetrahydro-6,7-dimethoxy-2-methyl- C0004234 C23696 Atracurium [Chemical/Ingredient] Nystatin M0015146 D009761 Macrolide antifungal antibiotic complex produced by Streptomyces noursei, S. aureus, and other Streptomyces species. The biologically active components of the complex are nystatin A1, A2, and A3. Nystatin N0000006699 7597 Nystatin C0028741 C23746 Nystatin [Chemical/Ingredient] Sulbactam M0020733 D013407 A beta-lactamase inhibitor with very weak antibacterial action. The compound prevents antibiotic destruction of beta-lactam antibiotics by inhibiting beta-lactamases, thus extending their spectrum activity. Combinations of sulbactam with beta-lactam antibiotics have been used successfully for the therapy of infections caused by organisms resistant to the antibiotic alone. Sulbactam N0000006841 10167 Sulbactam 4-Thia-1-azabicyclo(3.2.0)heptane-2-carboxylic acid, 3,3-dimethyl-7-oxo-, 4,4-dioxide, (2S-cis)- Penicillanic Acid Sulfone C0038665 C24032 Sulbactam [Chemical/Ingredient] Fatty Acids M0008265 D005227 Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed) Fatty Acids N0000006847 4297 C0015684 C24044 Fatty Acids [Chemical/Ingredient] Chlorothiazide M0004186 D002740 A thiazide diuretic with actions and uses similar to those of HYDROCHLOROTHIAZIDE. (From Martindale, The Extra Pharmacopoeia, 30th ed, p812) Chlorothiazide N0000006932 2396 Chlorothiazide 2H-1,2,4-Benzothiadiazine-7-sulfonamide, 6-chloro-, 1,1-dioxide C0008273 C24214 Chlorothiazide [Chemical/Ingredient] Cholecalciferol M0004229 D002762 Derivative of 7-dehydroxycholesterol formed by ULTRAVIOLET RAYS breaking of the C9-C10 bond. It differs from ERGOCALCIFEROL in having a single bond between C22 and C23 and lacking a methyl group at C24. Cholecalciferol N0000006996 2418 Cholecalciferol (3 beta,5Z,7E)-9,10-Secocholesta-5,7,10(19)-trien-3-ol 9,10-Secocholesta-5,7,10(19)-trien-3-ol, (3beta,5Z,7E)- Calciol Vitamin D 3 Vitamin D3 C0008318 C24342 Cholecalciferol [Chemical/Ingredient] Foscarnet M0026166 D017245 An antiviral agent used in the treatment of cytomegalovirus retinitis. Foscarnet also shows activity against human herpesviruses and HIV. Foscarnet N0000007166 33562 Foscarnet Phosphinecarboxylic acid, dihydroxy-, oxide Phosphonoformic Acid C0070895 C24684 Foscarnet [Chemical/Ingredient] Magnesium Chloride M0023974 D015636 Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys. Magnesium Chloride N0000007198 6579 Magnesium Chloride Magnesium chloride (MgCl2) MgCl2 C0024472 C24748 Magnesium Chloride [Chemical/Ingredient] Sodium Chloride M0020094 D012965 A ubiquitous sodium salt that is commonly used to season food. It plays an important biological role in maintaining the osmotic tension of blood and tissues. The OSMOLAR CONCENTRATION this and other SALTS accounts for SALINITY which influences the types of organisms that live in an ENVIRONMENT. Sodium Chloride N0000007207 9863 Sodium Chloride Sodium chloride (NaCl) C0037494 C24766 Sodium Chloride [Chemical/Ingredient] Tacrolimus M0025261 D016559 A macrolide isolated from the culture broth of a strain of Streptomyces tsukubaensis that has strong immunosuppressive activity in vivo and prevents the activation of T-lymphocytes in response to antigenic or mitogenic stimulation in vitro. Tacrolimus N0000007302 42316 Tacrolimus 15,19-Epoxy-3H-pyrido(2,1-c)(1,4)oxaazacyclotricosine-1,7,20,21(4H,23H)-tetrone, 5,6,8,11,12,13,14,15,16,17,18,19,24,25,26,26a-hexadecahydro-5,19-dihydroxy-3-(2-(4-hydroxy-3-methoxycyclohexyl)-1-methylethenyl)-14,16-dimethoxy-4,10,12,18-tetramethyl-8-(2-p C0085149 C24956 Tacrolimus [Chemical/Ingredient] Alkaloids M0000713 D000470 Organic nitrogenous bases. Many alkaloids of medical importance occur in the animal and vegetable kingdoms, and some have been synthesized. (Grant & Hackh's Chemical Dictionary, 5th ed) Alkaloids N0000007503 496 C0002062 C25362 Alkaloids [Chemical/Ingredient] Phenethylamines M0016506 D010627 A group of compounds that are derivatives of beta- aminoethylbenzene which is structurally and pharmacologically related to amphetamine. (From Merck Index, 11th ed) Phenethylamines N0000007526 8127 Phenylethylamines C0031399 C25408 Phenethylamines [Chemical/Ingredient] Macrolides M0028311 D018942 A group of macrocyclic compounds formed by chain extension of multiple PROPIONATES and cyclized into a large (typically 12, 14, 16) membered lactone. They are often glycosylated. Many of them are ANTIBIOTICS. Macrolides N0000007529 586370 C0282563 C25414 Macrolides [Chemical/Ingredient] Anions M0001248 D000838 Negatively charged atoms, radicals or groups of atoms which travel to the anode or positive pole during electrolysis. Anions N0000007541 853 C0003075 C25438 Anions [Chemical/Ingredient] Benzothiadiazines M0002371 D001581 Heterocyclic compounds of a ring with SULFUR and two NITROGEN atoms fused to a BENZENE ring. Members inhibit SODIUM-POTASSIUM-CHLORIDE SYMPORTERS and are used as DIURETICS. Benzothiadiazines N0000007554 1414 C0005084 C25464 Benzothiadiazines [Chemical/Ingredient] Biogenic Monoamines M0023566 D015306 Biogenic amines having only one amine moiety. Included in this group are all natural monoamines formed by the enzymatic decarboxylation of natural amino acids. Biogenic Monoamines N0000007586 1565 Monoamines, Biogenic C0005497 C25528 Biogenic Monoamines [Chemical/Ingredient] Hexoses M0010338 D006601 Hexoses N0000007604 5318 C0019494 C25568 Hexoses [Chemical/Ingredient] Quinazolines M0018336 D011799 Quinazolines N0000007605 9064 C0034407 C25570 Quinazolines [Chemical/Ingredient] Globulins M0009293 D005916 Globulins N0000007615 4825 C0017649 C25590 Globulins [Chemical/Ingredient] Acids M0000220 D000143 Chemical compounds which yield hydrogen ions or protons when dissolved in water, whose hydrogen can be replaced by metals or basic radicals, or which react with bases to form salts and water (neutralization). An extension of the term includes substances dissolved in media other than water. (Grant & Hackh's Chemical Dictionary, 5th ed) Acids N0000007626 230 C0001128 C25612 Acids [Chemical/Ingredient] Acids, Acyclic M0000221 D000144 Carboxylic acids that have open-chain molecular structures as opposed to ring-shaped structures. Acids, Acyclic N0000007627 231 Acyclic Acids C0001129 C25614 Acids, Acyclic [Chemical/Ingredient] Acids, Noncarboxylic M0000225 D000148 Inorganic acids with a non metal, other than carbon, attached to hydrogen, or an acid radical containing no carbon. Acids, Noncarboxylic N0000007630 235 Noncarboxylic Acids C0001133 C25620 Acids, Noncarboxylic [Chemical/Ingredient] Lactams M0012143 D007769 Cyclic AMIDES formed from aminocarboxylic acids by the elimination of water. Lactims are the enol forms of lactams. Lactams N0000007642 6195 C0022914 C25644 Lactams [Chemical/Ingredient] Lactones M0012175 D007783 Cyclic esters of hydroxy carboxylic acids, containing a 1-oxacycloalkan-2-one structure. Large cyclic lactones of over a dozen atoms are MACROLIDES. Lactones N0000007646 6209 C0022947 C25652 Lactones [Chemical/Ingredient] Organic Chemicals M0015401 D009930 A broad class of substances containing carbon and its derivatives. Many of these chemicals will frequently contain hydrogen with or without oxygen, nitrogen, sulfur, phosphorus, and other elements. They exist in either carbon chain or carbon ring form. Organic Chemicals N0000007676 7692 C0029224 C25712 Organic Chemicals [Chemical/Ingredient] Amides M0000897 D000577 Organic compounds containing the -CO-NH2 radical. Amides are derived from acids by replacement of -OH by -NH2 or from ammonia by the replacement of H by an acyl group. (From Grant & Hackh's Chemical Dictionary, 5th ed) Amides N0000007681 633 C0002482 C25722 Amides [Chemical/Ingredient] Organophosphorus Compounds M0015421 D009943 Organic compounds that contain phosphorus as an integral part of the molecule. Included under this heading is broad array of synthetic compounds that are used as PESTICIDES and DRUGS. Organophosphorus Compounds N0000007684 7696 C0029254 C25728 Organophosphorus Compounds [Chemical/Ingredient] Phosphorus Acids M0027146 D017976 Inorganic acids that contain phosphorus as an integral part of the molecule. Phosphorus Acids N0000007696 67101 C0206451 C25752 Phosphorus Acids [Chemical/Ingredient] Chlorides M0004143 D002712 Inorganic compounds derived from hydrochloric acid that contain the Cl- ion. Chlorides N0000007711 2364 C0008203 C25782 Chlorides [Chemical/Ingredient] Catecholamines M0003647 D002395 A general class of ortho-dihydroxyphenylalkylamines derived from tyrosine. Catecholamines N0000007715 2146 Sympathins C0007412 C25790 Catecholamines [Chemical/Ingredient] Steroids M0020527 D013256 A group of polycyclic compounds closely related biochemically to TERPENES. They include cholesterol, numerous hormones, precursors of certain vitamins, bile acids, alcohols (STEROLS), and certain natural drugs and poisons. Steroids have a common nucleus, a fused, reduced 17-carbon atom ring system, cyclopentanoperhydrophenanthrene. Most steroids also have two methyl groups and an aliphatic side-chain attached to the nucleus. (From Hawley's Condensed Chemical Dictionary, 11th ed) Steroids N0000007720 10072 C0038317 C25800 Steroids [Chemical/Ingredient] Phosphonoacetic Acid M0016688 D010746 A simple organophosphorus compound that inhibits DNA polymerase, especially in viruses and is used as an antiviral agent. Phosphonoacetic Acid N0000007721 8250 Acetic acid, phosphono- Phosphonacetic Acid C0031681 C25802 Phosphonoacetic Acid [Chemical/Ingredient] Biogenic Amines M0002518 D001679 A group of naturally occurring amines derived by enzymatic decarboxylation of the natural amino acids. Many have powerful physiological effects (e.g., histamine, serotonin, epinephrine, tyramine). Those derived from aromatic amino acids, and also their synthetic analogs (e.g., amphetamine), are of use in pharmacology. Biogenic Amines N0000007726 1564 Amines, Biogenic Biogenic Amine C0005496 C25812 Biogenic Amines [Chemical/Ingredient] Sterols M0020532 D013261 Steroids with a hydroxyl group at C-3 and most of the skeleton of cholestane. Additional carbon atoms may be present in the side chain. (IUPAC Steroid Nomenclature, 1987) Sterols N0000007730 10077 C0038323 C25820 Sterols [Chemical/Ingredient] Cholestenes M0004266 D002782 Steroids with methyl groups at C-10 and C-13 and a branched 8-carbon chain at C-17. Members include compounds with any degree of unsaturation; however, CHOLESTADIENES is available for derivatives containing two double bonds. Cholestenes N0000007759 2436 C0008375 C25878 Cholestenes [Chemical/Ingredient] Chlorine Compounds M0026679 D017606 Inorganic compounds that contain chlorine as an integral part of the molecule. Chlorine Compounds N0000007794 67167 Chlorine Compounds, Inorganic C0206759 C25948 Chlorine Compounds [Chemical/Ingredient] Calcium Compounds M0026683 D017610 Inorganic compounds that contain calcium as an integral part of the molecule. Calcium Compounds N0000007800 66999 C0206106 C25960 Calcium Compounds [Chemical/Ingredient] Magnesium Compounds M0026689 D017616 Inorganic compounds that contain magnesium as an integral part of the molecule. Magnesium Compounds N0000007803 67004 C0206112 C25966 Magnesium Compounds [Chemical/Ingredient] Naphthalenes M0014459 D009281 Two-ring crystalline hydrocarbons isolated from coal tar. They are used as intermediates in chemical synthesis, as insect repellents, fungicides, lubricants, preservatives, and, formerly, as topical antiseptics. Naphthalenes N0000007809 7251 C0027378 C25978 Naphthalenes [Chemical/Ingredient] Bicyclo Compounds, Heterocyclic M0028488 D019086 A class of saturated compounds consisting of two rings only, having two or more atoms in common, containing at least one hetero atom, and that take the name of an open chain hydrocarbon containing the same total number of atoms. (From Riguady et al., Nomenclature of Organic Chemistry, 1979, p31) Bicyclo Compounds, Heterocyclic N0000007813 82186 Bicyclic Heterocyclic Compounds Heterocyclic Bicyclo Compounds Heterocyclic Cpds, Bicyclic C0282650 C25986 Bicyclo Compounds, Heterocyclic [Chemical/Ingredient] Naphthoquinones M0014463 D009285 Naphthalene rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups. Naphthoquinones N0000007814 7255 Naphthalenediones C0027388 C25988 Naphthoquinones [Chemical/Ingredient] Membrane Lipids M0013338 D008563 Lipids, predominantly phospholipids, cholesterol and small amounts of glycolipids found in membranes including cellular and intracellular membranes. These lipids may be arranged in bilayers in the membranes with integral proteins between the layers and peripheral proteins attached to the outside. Membrane lipids are required for active transport, several enzymatic activities and membrane formation. Membrane Lipids N0000007818 6723 Cell Membrane Lipids C0025249 C25996 Membrane Lipids [Chemical/Ingredient] Amino Acids, Peptides, and Proteins M0000928 D000602 Amino acids and chains of amino acids connected by peptide linkages. Amino Acids, Peptides, and Proteins N0000007833 664 C0002526 C26026 Amino Acids, Peptides, and Proteins [Chemical/Ingredient] Sodium Compounds M0026726 D017670 Inorganic compounds that contain sodium as an integral part of the molecule. Sodium Compounds N0000007844 67017 C0206134 C26048 Sodium Compounds [Chemical/Ingredient] Peptides M0016238 D010455 Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES. Peptides N0000007874 8036 C0030956 C26108 Peptides [Chemical/Ingredient] Glycosides M0009500 D006027 Any compound that contains a constituent sugar, in which the hydroxyl group attached to the first carbon is substituted by an alcoholic, phenolic, or other group. They are named specifically for the sugar contained, such as glucoside (glucose), pentoside (pentose), fructoside (fructose), etc. Upon hydrolysis, a sugar and nonsugar component (aglycone) are formed. (From Dorland, 28th ed; From Miall's Dictionary of Chemistry, 5th ed) Glycosides N0000007897 4958 C0017977 C26154 Glycosides [Chemical/Ingredient] Elements M0007227 D004602 Substances that comprise all matter. Each element is made up of atoms that are identical in number of electrons and protons and in nuclear charge, but may differ in mass or number of neutrons. Elements N0000007912 3802 C0013879 C26186 Elements [Chemical/Ingredient] Blood Coagulation Factors M0002684 D001779 Endogenous substances, usually proteins, that are involved in the blood coagulation process. Blood Coagulation Factors N0000007914 1637 Blood Coagulation Factor Coagulation Factor Coagulation Factor, Blood Coagulation Factors Coagulation Factors, Blood Factor, Coagulation Factors, Coagulation C0005789 C26190 Blood Coagulation Factors [Chemical/Ingredient] Secosteroids M0019588 D012632 Steroids in which fission of one or more ring structures and concomitant addition of a hydrogen atom at each terminal group has occurred. Secosteroids N0000007915 9626 C0036532 C26192 Secosteroids [Chemical/Ingredient] Immunoglobulins M0011122 D007136 Multi-subunit proteins which function in IMMUNITY. They are produced by B LYMPHOCYTES from the IMMUNOGLOBULIN GENES. They are comprised of two heavy (IMMUNOGLOBULIN HEAVY CHAINS) and two light chains (IMMUNOGLOBULIN LIGHT CHAINS) with additional ancillary polypeptide chains depending on their isoforms. The variety of isoforms include monomeric or polymeric forms, and transmembrane forms (B-CELL ANTIGEN RECEPTORS) or secreted forms (ANTIBODIES). They are divided by the amino acid sequence of their heavy chains into five classes (IMMUNOGLOBULIN A; IMMUNOGLOBULIN D; IMMUNOGLOBULIN E; IMMUNOGLOBULIN G; IMMUNOGLOBULIN M) and various subclasses. Immunoglobulins N0000007920 5720 Immunoglobulins Globulins, Immune Immune Globulins Immunoglobulin C0021027 C26202 Immunoglobulins [Chemical/Ingredient] Blood Proteins M0002710 D001798 Proteins that are present in blood serum, including SERUM ALBUMIN; BLOOD COAGULATION FACTORS; and many other types of proteins. Blood Proteins N0000007921 1653 C0005832 C26204 Blood Proteins [Chemical/Ingredient] Terpenes M0021183 D013729 A class of compounds composed of repeating 5-carbon units of HEMITERPENES. Terpenes N0000007940 10372 Terpenoids C0039561 C26242 Terpenes [Chemical/Ingredient] Recombinant Proteins M0018641 D011994 Proteins prepared by recombinant DNA technology. Recombinant Proteins N0000007956 9218 Biosynthetic Proteins Proteins, Biosynthetic C0034861 C26276 Recombinant Proteins [Chemical/Ingredient] Isoquinolines M0011785 D007546 A group of compounds with the heterocyclic ring structure of benzo(c)pyridine. The ring structure is characteristic of the group of opium alkaloids such as papaverine. (From Stedman, 25th ed) Isoquinolines N0000007960 6056 C0022248 C26284 Isoquinolines [Chemical/Ingredient] Hydrocarbons M0010687 D006838 Hydrocarbons N0000007973 5476 C0020242 C26310 Hydrocarbons [Chemical/Ingredient] Hydroxy Acids M0010745 D006880 Organic compounds containing both the hydroxyl and carboxyl radicals. Hydroxy Acids N0000007983 5515 C0020317 C26330 Hydroxy Acids [Chemical/Ingredient] Hydroxycholecalciferols M0010754 D006887 Hydroxy analogs of vitamin D 3; (CHOLECALCIFEROL); including CALCIFEDIOL; CALCITRIOL; and 24,25-DIHYDROXYVITAMIN D 3. Hydroxycholecalciferols N0000007988 5522 Hydroxycholecalciferol Hydroxyvitamins D C0020337 C26340 Hydroxycholecalciferols [Chemical/Ingredient] Metals, Alkaline Earth M0013518 D008673 Metals that constitute the group 2 (formerly group IIa) of the periodic table. Metals, Alkaline Earth N0000007992 6800 Alkaline Earth Metals Group 2 Elements C0025555 C26348 Metals, Alkaline Earth [Chemical/Ingredient] Metals, Light M0029055 D019565 Metals with low specific gravity, typically smaller than 5, characterized by a single valence (1, 2, or 3), a simple spectrum, strong electromotive force (positive), and colorless compounds. (From Grant & Hackh's Chemical Dictionary, 5th ed) Metals, Light N0000008004 114297 Light Metals C0376709 C26372 Metals, Light [Chemical/Ingredient] Ethylamines M0007897 D005021 Ethylamines N0000008011 4146 C0015069 C26386 Ethylamines [Chemical/Ingredient] Sulfites M0020784 D013447 Inorganic salts of sulfurous acid. Sulfites N0000008046 10211 Inorganic Sulfites Sulfites, Inorganic C0038750 C26456 Sulfites [Chemical/Ingredient] Sulfonamides M0020790 D013449 A group of compounds that contain the structure SO2NH2. Members of this group, also known as sulfa drugs, are derivatives of sulfanilamide, which competitively inhibit folic acid synthesis in microorganisms, and are bacteriostatic. They have been largely supplanted by more effective and less toxic antibiotics. (From Dorland, 28th ed) Sulfonamides N0000008048 10215 C0038760 C26460 Sulfonamides [Chemical/Ingredient] Sulfones M0020791 D013450 Sulfones N0000008053 10216 C0038761 C26470 Sulfones [Chemical/Ingredient] Heterocyclic Compounds M0010290 D006571 Ring compounds having atoms other than carbon in their nuclei. (Grant & Hackh's Chemical Dictionary, 5th ed) Heterocyclic Compounds N0000008095 5283 C0019398 C26554 Heterocyclic Compounds [Chemical/Ingredient] Acetic Acids M0000132 D000088 Acetic acid and its derivatives which may be formed by substitution reactions. Mono- and di-substituted, as well as halogenated compounds have been synthesized. Acetic Acids N0000008114 169 C0000985 C26592 Acetic Acids [Chemical/Ingredient] Carboxylic Acids M0003405 D002264 Organic compounds containing the carboxy group (-COOH). This group of compounds includes amino acids and fatty acids. Carboxylic acids can be saturated, unsaturated, or aromatic. Carboxylic Acids N0000008137 2060 C0007066 C26638 Carboxylic Acids [Chemical/Ingredient] Bridged Compounds M0002922 D001952 Cyclic hydrocarbons that contain multiple rings and share one or more atoms. Bridged Compounds N0000008149 1740 C0006174 C26662 Bridged Compounds [Chemical/Ingredient] Phosphorus Compounds M0026614 D017553 Inorganic compounds that contain phosphorus as an integral part of the molecule. Phosphorus Compounds N0000008156 67164 C0206756 C26676 Phosphorus Compounds [Chemical/Ingredient] Polycyclic Hydrocarbons, Aromatic M0017164 D011084 A major group of unsaturated cyclic hydrocarbons containing two or more rings. The vast number of compounds of this important group, derived chiefly from petroleum and coal tar, are rather highly reactive and chemically versatile. The name is due to the strong and not unpleasant odor characteristic of most substances of this nature. (From Hawley's Condensed Chemical Dictionary, 12th ed, p96) Polycyclic Hydrocarbons, Aromatic N0000008164 8504 Polycyclic Aromatic Hydrocarbons Polynuclear Aromatic Hydrocarbons C0032458 C26692 Polycyclic Hydrocarbons, Aromatic [Chemical/Ingredient] Amines M0000913 D000588 A group of compounds derived from ammonia by substituting organic radicals for the hydrogens. (From Grant & Hackh's Chemical Dictionary, 5th ed) Amines N0000008168 823705 C0002508 C26700 Amines [Chemical/Ingredient] Bicyclo Compounds M0002469 D001643 Bicyclo Compounds N0000008171 1530 C0005378 C26706 Bicyclo Compounds [Chemical/Ingredient] Fatty Acids, Volatile M0008273 D005232 Short-chain fatty acids of up to six carbon atoms in length. They are the major end products of microbial fermentation in the ruminant digestive tract and have also been implicated in the causation of neurological diseases in humans. Fatty Acids, Volatile N0000008176 4303 Fatty Acids, Short-Chain C0015691 C26716 Fatty Acids, Volatile [Chemical/Ingredient] Phosphonic Acids M0016684 D010745 Inorganic or organic derivatives of phosphonic acid with the general formula ROP(OH)2 or RP(=O)(OH)2. The tautomeric form of this compound (P(OH)3) is PHOSPHOROUS ACIDS. Nucleoside phosphonates have a phosphate-carbon bond that is more resistant to enzymatic cleavage than the normal phosphate-oxygen bond. Phosphonic Acids N0000008178 8248 C0031679 C26720 Phosphonic Acids [Chemical/Ingredient] Quinones M0018356 D011809 Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups. Quinones N0000008181 9083 C0034435 C26726 Quinones [Chemical/Ingredient] Cholestanes M0004254 D002776 Derivatives of the saturated steroid cholestane with methyl groups at C-18 and C-19 and an iso-octyl side chain at C-17. Cholestanes N0000008187 2432 C0008366 C26738 Cholestanes [Chemical/Ingredient] Ions M0011678 D007477 An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS. Ions N0000008197 5964 C0022023 C26758 Ions [Chemical/Ingredient] Diterpenes M0006609 D004224 Twenty-carbon compounds derived from MEVALONIC ACID or deoxyxylulose phosphate. Diterpenes N0000008216 3557 Diterpenoids C0012780 C26796 Diterpenes [Chemical/Ingredient] Immunoglobulin Fragments M0011106 D007128 Partial immunoglobulin molecules resulting from selective cleavage by proteolytic enzymes or generated through PROTEIN ENGINEERING techniques. Immunoglobulin Fragments N0000008221 5710 C0021009 C26806 Immunoglobulin Fragments [Chemical/Ingredient] Immunoproteins M0011167 D007162 Blood proteins whose activities affect or play a role in the functioning of the immune system. Immunoproteins N0000008223 5744 C0021072 C26810 Immunoproteins [Chemical/Ingredient] Hydrocarbons, Aromatic M0010690 D006841 Organic compounds containing carbon and hydrogen in the form of an unsaturated, usually hexagonal ring structure. The compounds can be single ring, or double, triple, or multiple fused rings. Hydrocarbons, Aromatic N0000008229 5479 Aromatic Hydrocarbons C0020245 C26822 Hydrocarbons, Aromatic [Chemical/Ingredient] Metals M0013515 D008670 Electropositive chemical elements characterized by ductility, malleability, luster, and conductance of heat and electricity. They can replace the hydrogen of an acid and form bases with hydroxyl radicals. (Grant & Hackh's Chemical Dictionary, 5th ed) Metals N0000008237 6797 C0025552 C26838 Metals [Chemical/Ingredient] Serum Globulins M0019698 D012712 All blood proteins except albumin ( = SERUM ALBUMIN, which is not a globulin) and FIBRINOGEN (which is not in the serum). The serum globulins are subdivided into ALPHA-GLOBULINS; BETA-GLOBULINS; and GAMMA-GLOBULINS on the basis of their electrophoretic mobilities. (From Dorland, 28th ed) Serum Globulins N0000008244 9701 C0036800 C26852 Serum Globulins [Chemical/Ingredient] Sulfur Compounds M0020800 D013457 Inorganic or organic compounds that contain sulfur as an integral part of the molecule. Sulfur Compounds N0000008249 10225 C0038776 C26862 Sulfur Compounds [Chemical/Ingredient] Monosaccharides M0014043 D009005 Simple sugars, carbohydrates which cannot be decomposed by hydrolysis. They are colorless crystalline substances with a sweet taste and have the same general formula CnH2nOn. (From Dorland, 28th ed) Monosaccharides N0000008250 7044 C0026492 C26864 Monosaccharides [Chemical/Ingredient] Inorganic Chemicals M0011365 D007287 A broad class of substances encompassing all those that do not include carbon and its derivatives as their principal elements. However, carbides, carbonates, cyanides, cyanates, and carbon disulfide are included in this class. Inorganic Chemicals N0000008257 5824 C0021521 C26878 Inorganic Chemicals [Chemical/Ingredient] Heterocyclic Compounds, Bridged-Ring M0010291 D006572 A class of organic compounds which contain two rings that share a pair of bridgehead carbon atoms. Heterocyclic Compounds, Bridged-Ring N0000008258 5288 Bridged-Ring Heterocyclic Compounds C0019403 C26880 Heterocyclic Compounds, Bridged-Ring [Chemical/Ingredient] Heterocyclic Compounds, 1-Ring M0010292 D006573 A class of organic compounds containing a ring structure made up of more than one kind of atom, usually carbon plus another atom. The ring structure can be aromatic or nonaromatic. Heterocyclic Compounds, 1-Ring N0000008259 5284 Heterocyclic Cpds, 1-Ring C0019399 C26882 Heterocyclic Compounds, 1-Ring [Chemical/Ingredient] Heterocyclic Compounds, 2-Ring M0010293 D006574 A class of organic compounds containing two ring structures, one of which is made up of more than one kind of atom, usually carbon plus another atom. The heterocycle may be either aromatic or nonaromatic. Heterocyclic Compounds, 2-Ring N0000008260 5285 C0019400 C26884 Heterocyclic Compounds, 2-Ring [Chemical/Ingredient] Electrolytes M0007189 D004573 Substances that dissociate into two or more ions, to some extent, in water. Solutions of electrolytes thus conduct an electric current and can be decomposed by it (ELECTROLYSIS). (Grant & Hackh's Chemical Dictionary, 5th ed) Electrolytes N0000008272 3793 C0013832 C26910 Electrolytes [Chemical/Ingredient] Hydrocarbons, Cyclic M0010694 D006844 Organic compounds composed exclusively of carbon and hydrogen forming a closed ring that may be either alicyclic or aromatic. Hydrocarbons, Cyclic N0000008280 5482 Cyclic Hydrocarbons C0020248 C26926 Hydrocarbons, Cyclic [Chemical/Ingredient] Alveolar Surface Tension Alteration N0000008293 989276 C1371276 C26952 Alveolar Surface Tension Alteration [PE] Alveolar Surface Tension Reduction N0000008294 988631 C1371492 C26954 Alveolar Surface Tension Reduction [PE] Arterial Vasoconstriction N0000008298 986283 C1371490 C26962 Arterial Vasoconstriction [PE] Arterial Vasodilation N0000008299 984618 C1371278 C26964 Arterial Vasodilation [PE] Blood & Lymphatic Fluid Function Alteration N0000008307 988284 C1371289 C26980 Blood & Lymphatic Fluid Function Alteration [PE] Carbohydrate Metabolism Alteration N0000008327 1033881 C1371294 C27020 Carbohydrate Metabolism Alteration [PE] Cardiac Contractility Alteration N0000008328 986415 C1371293 C27022 Cardiac Contractility Alteration [PE] Cardiac Rate Alteration N0000008329 985479 C2825066 C27024 Cardiac Rate Alteration [PE]