Semanticscience Integrated Ontology (SIO)
default language: en
contributor: Contributors are those that engage in discussions in the context of SIO (in alphabetical order): sivaram arabandi christopher baker joachim baran jerven bolleman matthew brush alison callahan leonid chepelev kevin cohen melanie courtot geraint duck laura furlong elisa kendall tatsuya kushida luke mccarthy jim mccusker jose miguel cruz-toledo chris mungall robert hoehndorf simon jupp jin-dong kim dana klassen thomas luetteke james malone chris mungall david osumi-sutherland tazro ohta nuria queralt stephen reed alexandre riazanov matthias samwald robert stevens mark wilkinson karin verspoor natalia villanueva-rosales
creator: Michel Dumontier
creator: http://orcid.org/0000-0003-4727-9435
description: The semanticscience integrated ontology (SIO) provides a simple, integrated ontology (types, relations) for objects, processes and their attributes. This project provides foundational support for the Bio2RDF (http://bio2rdf.org) and SADI (http://sadiframework.org) projects. website: http://semanticscience.org email: sio-ontology@googlegroups.com mailing list: http://groups.google.com/group/sio-ontology
issued: 2010-03-29
license: http://creativecommons.org/licenses/by/4.0/
modified: 2024-03-25
rights: free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/].
cites as authority: http://www.jbiomedsem.com/content/5/1/14
preferred namespace prefix: sio
preferred namespace uri: http://semanticscience.org/resource/
subset: sio-subset-behaviour.owl
subset: sio-subset-camelcase-label.owl
subset: sio-subset-capability.owl
subset: sio-subset-chemical.owl
subset: sio-subset-core.owl
subset: sio-subset-dash-labels.owl
subset: sio-subset-emotion.owl
subset: sio-subset-equivs.owl
subset: sio-subset-geometry.owl
subset: sio-subset-ice.owl
subset: sio-subset-math.owl
subset: sio-subset-nlp.owl
subset: sio-subset-ovopub.owl
subset: sio-subset-process.owl
subset: sio-subset-relations.owl
subset: sio-subset-sadi.owl
comment: general class inclusion axioms: 'is part of' some 'physical entity' subClassOf 'is located in' some 'physical entity' role chains: 'has capability' o 'is realized in' -> 'is participant in'
type: Ontology
version IRI: sio-release.owl
version info: 1.59

entity
description: Every thing is an entity.
subset: core
type: Class

is related to
description: A is related to B iff there is some relation between A and B.
comment: 'is related to' is the top level relation in SIO
subset: core
subset: relations+
type: ObjectProperty
type: SymmetricProperty
domain: entity
range: entity

material entity
description: A material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass.
subset: core
type: Class
subclass of: object
subclass of: Restriction
  on property: has attribute
  some values from: mass
subclass of: Restriction
  all values from: Class
    union of: material entity
    union of: spatial region
  on property: has proper part

quality
description: A quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary.
subset: core
type: Class
subclass of: attribute
subclass of: Restriction
  on property: is quality of
  some values from: entity
disjoint with: realizable entity

process
description: A process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists.
subset: core
subset: process+
type: Class
subclass of: entity
subclass of: Restriction
  all values from: process
  on property: has proper part
subclass of: Restriction
  all values from: time interval
  on property: exists at

has attribute
description: has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.
subset: core
type: ObjectProperty
domain: entity
sub property of: is related to
inverse of: is attribute of

social entity
description: A social entity pertains to the interaction among individuals and groups.
type: Class
subclass of: information content entity

social structure
description: A social structure is a social entity which consists of relationships between two or more entities.
type: Class
subclass of: social entity
subclass of: Restriction
  all values from: object
  on property: has member

is attribute of
description: is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type.
type: ObjectProperty
sub property of: is related to

organization
description: An organization is a collective with a complex articulation of tasks, roles and responsibilities.
type: Class
subclass of: collective

geographic position
description: A geographic position is the coordinate of an entity against some geographic coordinate system.
type: Class
subclass of: position

disposition
description: A disposition is the tendency of a capability to be exhibited under certain conditions or in response to a certain stimulus (trigger).
subset: core
type: Class
subclass of: capability
subclass of: Restriction
  on property: has attribute
  some values from: probability measure
example: solubility (to dissolve when put in fluid); fragility (disposition to break when dropped)

information content entity
description: information content entity is an object that requires some background knowledge or procedure to correctly interpret.
subset: core
subset: ice+
type: Class
subclass of: object
subclass of: Restriction
  all values from: information content entity
  on property: has proper part

role
description: A role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance.
subset: core
type: Class
subclass of: realizable entity

function
description: A function is a capability that satisfies some agentive objective, or (evolutionary) optimization.
subset: core
type: Class
subclass of: capability
disjoint with: dysfunction

site
description: A site is a spatial region bounded (in part or in whole) by material entities and may be occupied by material entities.
type: Class
subclass of: spatial region
example: A nostril; the interior of the heart valve; the interior of a bottle.

denotes
description: denotes is a relation between an entity and what it is a sign or indication of, or what specifically means.
type: ObjectProperty
sub property of: represents
inverse of: is denoted by
example: the symbol '%' denotes a proportion in relation to a whole.

material boundary
description: A material boundary is the boundary of a material entity which exists as a lower dimensional entity at exactly the location where its parts no longer extend into space. Every material entity has a boundary, and a boundary is the boundary of exactly 1 material entity.
type: Class
subclass of: spatial boundary
subclass of: Restriction
  on property: is boundary of
  some values from: material entity
example: the external surface of the window; the surface of the p52 protein

object quality
description: An object quality is quality of an object.
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: object

process quality
description: A process quality is quality that is associated with a process.
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: process

has part
description: has part is a transitive, reflexive and antisymmetric relation between a whole and itself or a whole and its part.
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
sub property of: is location of
inverse of: is part of
example: a collection of cars has as a car as a part;a car has an engine as a part; a car has a piston as a part;

is time boundary of
type: ObjectProperty
domain: time instant
sub property of: is boundary of
inverse of: has time boundary

biopolymer sequence
description: A sequence is a primary structure descriptor in which each of the letters in the string represents a monomeric unit (residue) in which adjacent letters represent the connectivity between the monomeric units.
type: Class
subclass of: primary structure descriptor
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: biopolymer
subclass of: Restriction
  on property: describes
  some values from: biopolymer
subclass of: Restriction
  on property: has value
  some values from: string

start date
description: A start date is a time instant pertaining to the date of the beginning of a process.
type: Class
subclass of: time instant

end date
description: An end date is a time instant pertaining to date of the end of a process.
type: Class
subclass of: time instant

process status
description: process status is a process quality that describes the state of a process.
type: Class
subclass of: process quality
subclass of: Restriction
  on property: is attribute of
  some values from: process

completed
description: completed is that status of a process that successfully unfolds.
type: Class
subclass of: process status

ongoing
description: ongoing is the status of a process that is not yet complete.
type: Class
subclass of: process status

predicted
description: predicted is the quality of an entity that is thought to exist, as evidenced by some rational procedure.
type: Class
subclass of: hypothetical

spatial quantity
alternative: physical dimensional quantity
description: A spatial quantity is a quantity obtained from measuring the spatial extent of an entity
type: Class
subclass of: dimensional quantity
subclass of: Restriction
  on property: is attribute of
  some values from: object
subclass of: Restriction
  on property: has measurement value
  some values from: quantity

1D extent quantity
description: A quantity that extends in single dimension.
type: Class
subclass of: spatial quantity

depth
description: depth is the dimensional extent into a plane of a 3D projection of the object.
type: Class
subclass of: 1D extent quantity

height
description: height is the one dimensional extent along the vertical projection of a 3D object from a base plane of reference.
type: Class
subclass of: 1D extent quantity

length
description: length is the longer dimensional extent along a 2D projection of the object.
type: Class
subclass of: 1D extent quantity

width
description: width is the shorter dimensional extent perpendicular to a 2D projection of the object.
type: Class
subclass of: 1D extent quantity

thickness
description: thickness is the shortest dimensional extent of a 3D projection of an object.
type: Class
subclass of: depth

2D extent quantity
description: A quantity that extends in two dimensions.
type: Class
subclass of: spatial quantity

area
description: area is a quantity that pertains to the extent of a two-dimensional surface or shape, or planar lamina, in the plane.
type: Class
subclass of: 2D extent quantity

length of perimeter
description: A perimeter is a length of the outline that surrounds a two-dimensional shape.
type: Class
subclass of: 2D extent quantity

circumference
description: circumference is the length of the outline of a circle or ellipse. it is defined as c = 2*pi*r, where r is the radius.
type: Class
subclass of: length of perimeter

3D extent quantity
description: A quantity that extends in three dimensions.
type: Class
subclass of: spatial quantity

volume
description: volume is the quantity of three-dimensional space enclosed by some closed boundary.
type: Class
subclass of: 3D extent quantity

compositional quality
description: composition quality is a quality that describes its composition or anatomy.
type: Class
subclass of: object quality

quantity
description: A quantity is an informational entity that gives the magnitude of a property.
type: Class
subclass of: measurement value
subclass of: Restriction
  on property: is attribute of
  some values from: entity
subclass of: Restriction
  on property: is measurement value of
  some values from: entity
equivalent class: Class
  union of: dimensionless quantity
  union of: dimensional quantity

has proper part
description: has proper part is an antisymmetric, irreflexive (normally transitive) relation between a whole and a distinct part.
type: AsymmetricProperty
type: IrreflexiveProperty
type: ObjectProperty
sub property of: has part
inverse of: is proper part of
example: a car has an engine as a proper part; a car has a piston as a proper part;

has boundary
description: has boundary is a mereological relation between a whole and boundary located at its periphery.
type: ObjectProperty
sub property of: has proper part
inverse of: is boundary of
example: the surface of an apple is a 2D boundary of the apple.

shape
description: shape is the quality of a bearer that relates to its spatial extent.
type: Class
subclass of: object quality

position
description: A measurement of a spatial location relative to a frame of reference or other objects.
type: Class
subclass of: measurement value
subclass of: Restriction
  on property: has attribute
  some values from: positional identifier

orientation
description: orientation is an angle between the bearer and an axis, or the angle between the bearer and another object.
type: Class
subclass of: position

has member
description: has member is a mereological relation between a collection and an item.
subset: core
type: IrreflexiveProperty
type: ObjectProperty
domain: collection
sub property of: has attribute
inverse of: is member of
example: a collection of cars has as a car as a member

is denoted by
type: ObjectProperty
sub property of: is represented by

is located in
description: A is located in B iff the spatialtemporial region occupied by A is part of the spatialtemporal region occupied by B. [T][R]
equivalent to: OBO_REL:located_in
subset: core
type: ObjectProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to
inverse of: is location of
example: A parasite in the interior of a person's intestine is located in their intestinal lumen.

is participant in
description: is participant in is a relation that describes the participation of the subject in the (processual) object.
type: ObjectProperty
range: process
sub property of: is spatiotemporally related to
inverse of: has participant
example: a car is a participant in a car race; glucose is a participant in glycolysis

is agent in
description: is agent in is a relation between an entity and a process, where the entity is present throughout the process, no permanent material change occurs, and is a causal participant in the process.
subset: sadi
type: ObjectProperty
sub property of: is participant in
inverse of: has agent
example: hexokinase is an agent in the conversion of glucose to glucose-6-phosphate

is provider of
description: is provider of is a relation between a source and the entity it makes available.
type: ObjectProperty
sub property of: is source of
inverse of: has provider

has provider
description: is provided by is a relation between an entity and the entity that provides it.
equivalent to: dc:source
type: ObjectProperty
sub property of: has source

namespace
description: A namespace is an informational entity that defines a logical container for a set of symbols or identifiers.
type: Class
subclass of: computational entity
subclass of: Restriction
  all values from: identifier
  on property: has member

is part of
description: is part of is a transitive, reflexive and anti-symmetric mereological relation between a whole and itself or a part and its whole.
equivalent to: OBO_REL:part_of
subset: core
type: ObjectProperty
type: ReflexiveProperty
type: TransitiveProperty
sub property of: is located in

data item
description: A data item consists of information that has been collected/generated towards some purpose.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is participant in
  some values from: Class
    intersection of: process
    intersection of: Restriction
      on property: realizes
      some values from: objective

measurement value
description: A measurement value is a quantitative description that reflects the magnitude of some attribute.
type: Class
subclass of: number
subclass of: Class
  union of: Restriction
    on property: has value
    some values from: boolean
  union of: Restriction
    on property: has value
    some values from: dateTime
  union of: Restriction
    on property: has value
    some values from: double
  union of: Restriction
    on property: has value
    some values from: float
  union of: Restriction
    on property: has value
    some values from: integer

coordinate
description: A coordinate is a measurement of position in n-dimensional space.
type: Class
subclass of: position

cartesian coordinate
description: A Cartesian coordinate is the signed distance of a point to some referent line.
type: Class
subclass of: coordinate
subclass of: Restriction
  on property: is proper part of
  some values from: cartesian coordinate system
disjoint with: polar coordinate

polar coordinate
description: A polar coordinate is a position characterized by a distance from a fixed point and an angle from a fixed direction.
type: Class
subclass of: coordinate
subclass of: Restriction
  on property: is proper part of
  some values from: polar coordinate system

unit of measurement
description: A unit of measurement is a definite magnitude of a physical quantity, defined and adopted by convention and/or by law, that is used as a standard for measurement of the same physical quantity.
type: Class
subclass of: quantity

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

plan
description: A plan is a set of intended actions, through which one expects to achieve a goal.
type: Class
subclass of: action specification

generic name
description: A generic name is the preferred name provided by manufacturer.
type: Class
subclass of: name

language entity
description: A language entity implements some language specification for the visual interpretation and is part of some document.
subset: nlp+
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: has value
  some values from: Literal

visual language entity
description: A visual language entity is a language entity that is manifested within the spectrum of light and can be pereceived and processed by a visual system.
type: Class
subclass of: language entity

figure
alternative: diagram
description: A figure is a graphical entity which consists of a visual (n-dimentional) arrangement of information entities.
type: Class
subclass of: media
disjoint with: figure part

image
alternative: depiction
description: An image is an affine projection of a visual entity to a two dimensional surface.
type: Class
subclass of: figure

photograph
alternative: photo
description: A photograph is an image created by light falling on a light-sensitive surface.
type: Class
subclass of: image

statistical graph
alternative: chart
description: A statistical graph is a figure that displays the relationship among numeric data and/or mathematical functions.
type: Class
subclass of: chart

question
description: A question is a linguistic expression used to make a request for information.
type: Class
subclass of: sentence

publication
description: A publication is a document that has been made available by a publisher.
type: Class
subclass of: document

record
description: A record is a document containing a collection of statements about some entity.
type: Class
subclass of: document
subclass of: Restriction
  on property: has unique identifier
  some values from: identifier

dataset
alternative: data set
description: A dataset is a data item that is a collection of data items.
equivalent to: http://www.w3.org/ns/dcat#Dataset
type: Class
subclass of: data item
subclass of: Restriction
  on property: has concretization
  some values from: file
equivalent class: Class
  intersection of: data item
  intersection of: Restriction
    all values from: data item
    on property: has member

specification
description: A specification is a description of the essential technical attributes/requirements for an object or procedure, and may be used to determine that the object / procedure meets its requirements/attributes.
type: Class
subclass of: description
subclass of: Restriction
  on property: specifies
  some values from: entity
subclass of: Restriction
  on property: has component part
  some values from: objective
subclass of: Restriction
  on property: has expression
  some values from: information content entity

action specification
alternative: effective specification
description: An action specification is a specification composed of a sequence of instructions to achieve some objective.
type: Class
subclass of: specification
subclass of: Restriction
  on property: specifies
  some values from: process
subclass of: Restriction
  on property: satisfies
  some values from: objective
subclass of: Restriction
  all values from: process
  on property: is manifested as

biopolymer
description: A biopolymer is an organic polymer that are typically produced by the cells of living organisms.
type: Class
subclass of: organic polymer
subclass of: Restriction
  on property: has direct part
  some values from: Class
    union of: lipid residue
    union of: amino acid residue
    union of: nucleotide residue
    union of: carbohydrate residue
equivalent class: Class
  intersection of: organic polymer
  intersection of: Restriction
    on property: has direct part
    some values from: Class
      union of: lipid residue
      union of: amino acid residue
      union of: nucleotide residue
      union of: carbohydrate residue

is proper part of
description: is proper part of is an asymmetric, irreflexive (normally transitive) relation between a part and its distinct whole.
equivalent to: OBO_REL:proper_part_of
subset: core
type: AsymmetricProperty
type: IrreflexiveProperty
type: ObjectProperty
sub property of: is part of

algorithm
description: An algorithm is an effective method expressed as a finite list of well-defined instructions for calculating a function.
type: Class
subclass of: mathematical entity

is member of
description: is member of is a mereological relation between a item and a collection.
type: ObjectProperty
sub property of: is attribute of

is boundary of
description: is boundary of is a mereological relation between a boundary located at the periphery of a whole.
type: ObjectProperty
sub property of: is proper part of

software entity
description: A software entity is a computational entity that can be interpreted by or directly executed by a processing unit.
type: Class
subclass of: computational entity

software method
description: A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task.
type: Class
subclass of: software entity

software module
description: A software module is software composed of a collection of software methods.
type: Class
subclass of: software entity

software library
description: A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application.
type: Class
subclass of: software entity

software application
description: A software application is software that can be directly executed by some processing unit.
type: Class
subclass of: software entity

software interpreter
description: A software interpreter is a software application that executes some specified input software.
type: Class
subclass of: software application

software script
description: A software script is software whose instructions can be executed using a software interpreter.
type: Class
subclass of: software entity

language
description: Language is a language entity which is the result of encoding and decoding information through systematic creation and usage of systems of symbols, each pairing a specific sign with an intended meaning, established through social conventions
type: Class
subclass of: language entity

symbol
description: A symbol is a proposition about what an entity represents.
type: Class
subclass of: representation
subclass of: Restriction
  on property: represents
  some values from: entity
subclass of: Restriction
  on property: is about
  some values from: entity

book
description: A book is a publication composed of a large number of entries.
type: Class
subclass of: publication

chapter
description: A chapter is a document section of a book or thesis.
type: Class
subclass of: document section

character
description: A character is a language symbol used to construct words.
type: Class
subclass of: language entity

novel
description: A novel is a fictitious prose narrative of book length, typically representing character and action with some degree of realism.
type: Class
subclass of: publication

paragraph
description: A paragraph is a self-contained unit of written discourse consisting of one or more sentences.
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: has direct part
  some values from: sentence

document section
description: A document section is a component of a document.
type: Class
subclass of: document component
subclass of: Restriction
  on property: is proper part of
  some values from: document

capability
description: A capability is a realizable entity whose basis lies in one or more parts or qualities and reflects possibility of an entity to behave in a specified way under certain conditions or in response to a certain stimulus (trigger).
subset: capability+
subset: core
type: Class
subclass of: realizable entity
subclass of: Restriction
  on property: is attribute of
  some values from: Restriction
    on property: is agent in
    some values from: process
subclass of: Restriction
  on property: has basis
  some values from: quality
subclass of: Restriction
  all values from: process
  on property: has trigger

sentence
description: A sentence is a grammatical unit consisting of one or more words that bear minimal syntactic relation to the words that precede or follow it.
type: Class
subclass of: phrase

word
description: A word is the smallest free form (an item that may be expressed in isolation with semantic or pragmatic content) in a language.
type: Class
subclass of: language entity
subclass of: Restriction
  on property: has part
  some values from: morpheme
subclass of: Restriction
  on property: has direct part
  some values from: character

identifier
description: An identifier is a label that specifically refers to (identifies) an entity (instance/type).
type: Class
subclass of: label
subclass of: Restriction
  on property: is identifier for
  some values from: entity

name
description: A name is a label used to identify an entity.
type: Class
subclass of: label
subclass of: Restriction
  on property: has value
  some values from: string

preferred name
description: A preferred name is the name that is generally used by some organization.
type: Class
subclass of: name

common name
description: A common name is a name that is commonly used.
type: Class
subclass of: name

brand name
description: A brand name is a trademarked and marketed name of a product.
type: Class
subclass of: name

scientific name
description: A scientific name is a name given through scientific nomenclature.
type: Class
subclass of: name

magazine
description: A magazine is a periodical that typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports.
equivalent to: http://purl.org/ontology/bibo/Magazine
type: Class
subclass of: periodical

synonym
description: A synonym is a word with the same or very similar meanings.
type: Class
subclass of: term variant
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is similar to
    some values from: term

antonym
description: An antonym is a word with opposite or nearly opposite meaning.
type: Class
subclass of: term variant
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is opposite to
    some values from: term

hypernym
description: A hypernym is a term with a broader meaning.
type: Class
subclass of: term variant
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is broader than
    some values from: term

hyponym
description: A hyponym is a term with a narrower meaning.
type: Class
subclass of: term variant
equivalent class: Class
  intersection of: term variant
  intersection of: Restriction
    on property: is narrower than
    some values from: term

homonym
description: A homonym is a word that sounds the same but has different meaning.
type: Class
subclass of: term variant
subclass of: Restriction
  on property: is dissimilar to
  some values from: term

workflow
description: A workflow is an algorithm that is is a depiction of a sequence of operations to achieve one or more objectives.
type: Class
subclass of: algorithm

is contained in
description: A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. [T]
equivalent to: OBO_REL:contained_in
subset: core
type: ObjectProperty
type: TransitiveProperty
sub property of: is located in
inverse of: contains

ontology document
description: An ontology document is a document that contains an ontology.
type: Class
subclass of: document

pattern
description: A pattern is a generalized representation of some repeatable concrete or informational item.
type: Class
subclass of: mathematical entity

sequence motif
description: A sequence motif is a pattern of nucleotides in a DNA sequence or amino acids in a protein.
type: Class
subclass of: pattern
disjoint with: structural motif

has participant
description: has participant is a relation that describes the participation of the object in the (processual) subject.
equivalent to: OBO_REL:has_participant
subset: core
type: ObjectProperty
domain: process
sub property of: is spatiotemporally related to

descriptor
description: A descriptor (index term, subject term, subject heading) is a term that captures the essence of the topic of a document.
type: Class
subclass of: term

definition
description: A definition is a description that succintly characterizes an entity.
type: Class
subclass of: description

description
description: A description is language entity in which elements of a language (formal or natural) are used to characterize an entity.
type: Class
subclass of: language entity
subclass of: Restriction
  all values from: entity
  on property: describes

category
description: A category is a class of entities having particular shared characteristics.
type: Class
subclass of: concept

class
description: A class is a collection of sets which can be unambiguously defined by a property that all its members share.
type: Class
subclass of: set

has agent
description: has agent is a relation between a process and an entity, where the entity is present throughout the process and is a causal participant in the process.
equivalent to: OBO_REL:has_agent
subset: core
subset: sadi
type: ObjectProperty
sub property of: has participant

web service
description: A web service is a software application that can be accessed over a network, such as the Internet, and executed on a remote system hosting the requested services.
type: Class
subclass of: software application

criterion
description: A criterion is a specification to describe properties used for evaluation.
type: Class
subclass of: design specification

inclusion criterion
description: An inclusion criterion is a criterion that must be present to satisfy some objective.
type: Class
subclass of: criterion
disjoint with: exclusion criterion

exclusion criterion
description: An exclusion criterion is a criterion that must be absent to satistify the objective.
type: Class
subclass of: criterion

parameter
description: A parameter is variable whose value changes the characteristics of a system or a function.
type: Class
subclass of: independent variable

is location of
description: A is location of B iff the spatialtemporal region occupied by A has the spatialtemporal region occupied by B as a part. [T][R]
subset: nlp+
type: ObjectProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to

monomer
description: A monomer is a submolecule that is proper part of some polymer, and is a building block for such polymer.
type: Class
subclass of: submolecule
subclass of: Restriction
  on property: is direct part of
  some values from: biopolymer

keyword
description: A keyword is a descriptor in which the association of the word with the entity facilitates information retrieval.
type: Class
subclass of: descriptor

document
description: A document is a bounded physical or digital representation of a body of information designed with the capacity (and usually intent) to communicate.
type: Class
subclass of: textual entity

list
description: A list is any enumeration of a set of items.
type: Class
subclass of: set
subclass of: Restriction
  on property: has member
  some values from: entity

manuscript
description: A manuscript is a document prior to publication.
type: Class
subclass of: document

note
description: A note is a brief document.
type: Class
subclass of: document

patent
description: A patent is an information entity granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time.
type: Class
subclass of: legal document

article
description: An article is a publication that is stand-alone section of a larger work.
type: Class
subclass of: publication

blog
description: A blog is a publication accessible at some website and is typically about various experiences.
type: Class
subclass of: publication

book volume
description: A book volume is a book that is part of a collection.
type: Class
subclass of: book

conference proceedings
description: A conference proceedings is a book composed of papers presented at a conference.
type: Class
subclass of: book

book series
description: A book series is a collection of books that have been sequentially published.
type: Class
subclass of: collection of documents

edited publication
description: An edited publication is a publication that has been examined and potentially changed by an editor.
type: Class
subclass of: publication

journal
description: A journal is a a peer-reviewed periodical in which scholarship relating to a particular academic discipline is published.
equivalent to: http://purl.org/ontology/bibo/Journal
type: Class
subclass of: periodical

manual
description: A manual is a document that instructs on the usage of a device.
type: Class
subclass of: publication

periodical
description: A periodical is a publication that appears on a regular schedule.
equivalent to: http://purl.org/ontology/bibo/Periodical
type: Class
subclass of: collection of documents

newspaper
description: A newspaper is a periodical publication containing news regarding current events, informative articles, diverse features, editorials, and advertising.
equivalent to: http://purl.org/ontology/bibo/Newspaper
type: Class
subclass of: periodical

technical report
description: A technical report is a publication published by a school or other institution, usually numbered within a series.
type: Class
subclass of: publication

thesis document
description: A thesis document is the written research component of a post-secondary institution that contains a statement supported by arguments.
type: Class
subclass of: publication

honor's thesis
description: An honor's thesis is a thesis prepared as a requirement for an honor's undergraduate degree.
type: Class
subclass of: thesis document

master's thesis
description: A Master's thesis is a thesis prepared as a requirement for a Master's degree.
type: Class
subclass of: thesis document

phd thesis
description: A PhD thesis is a thesis prepared as a requirement for a doctoral degree.
type: Class
subclass of: thesis document

booklet
description: A booklet is a document that lacks a named publisher or sponsoring institution.
type: Class
subclass of: document

diary
description: A diary is a document which describes day-to-day experiences.
type: Class
subclass of: document

document component
description: A bibliographic attribute is an attribute related to publications.
type: Class
subclass of: textual entity

address
description: An address is a position that indicates the physical location of some entity using a social convention.
type: Class
subclass of: positional identifier

affiliation
description: An affiliation is a social relation which indicates the partnership between two or more entities.
type: Class
subclass of: social relation

citation
description: A citation is a textual entity which denotes a source described in the bibliography or reference section of a document.
type: Class
subclass of: document component

document title
description: A document title is a textual entity that summarizes the topic of the document in one sentence.
type: Class
subclass of: title

reference
description: A reference is a textual entity that describes a single source used in the preparation or development of the work.
type: Class
subclass of: document component

page range
description: A page range denotes the start and end page in some document.
type: Class
subclass of: interval

page total
description: A page total is a textual entity that is about the number of pages in some informational entity.
type: Class
subclass of: count

label
description: a label is a term that is associated with some entity
type: Class
subclass of: term

language label
description: A language label is a label that denotes the language of a textual entity.
type: Class
subclass of: label

first name
description: A first name is a name that denotes a specific individual between members of a group of individuals, whose members usually share the same surname.
type: Class
subclass of: name

last name
description: A last name (surname) is a name added to a given name and is part of a personal name and is often the family name.
type: Class
subclass of: name

personal name
alternative: full name
description: A personal name is a name to identify an individual person and usually comprises of a first name and a last name.
type: Class
subclass of: name

legal name
description: A legal name is a name given at birth, or which appears on their birth certificate, marriage certificate, or change of name certificate.
type: Class
subclass of: personal name

title
description: A title is a textual entity that summarily describes some entity.
type: Class
subclass of: label

document version
description: A document version is a version of a work in some sequence of derivative works.
type: Class
subclass of: version label

abstract section
description: An abstract section is a document section that provides brief summary of a document that explains the main argument(s), topic(s) or findings.
type: Class
subclass of: document section

acknowledgements section
description: An acknowledgements section is a document section that identifies individuals, groups or organizations for their support in the development of the work.
type: Class
subclass of: document section

author contribution section
description: An author contribution section is a document section that describes the contribution of the authors.
type: Class
subclass of: document section

author section
description: An author section is a document section that lists the contributing authors.
type: Class
subclass of: document section

bibliography section
description: A bibliography section is a document section that is composed of a list of references used in the development of the work.
type: Class
subclass of: document section

copyright section
description: A copyright section is a document section that contains a notice of copyright.
type: Class
subclass of: document section

correspondence section
description: A correspondence section is a document section that contains the details for contacting the corresponding author.
type: Class
subclass of: document section

discussion section
description: The discussion section is a document section containing a summary of the findings, a reflection on the significance of findings, comparison with related work, among others.
type: Class
subclass of: document section

introduction section
description: An introduction section is a document section that generally provides background, motivation and goals of the work.
type: Class
subclass of: document section

materials and methods section
description: The materials and methods section is a document section containing a description of the materials and methods used in the study.
type: Class
subclass of: document section

materials section
description: The materials section is a document section containing a description of the materials used in the study.
type: Class
subclass of: document section

methods section
description: The methods section is a document section containing a description of the methods used in the study.
type: Class
subclass of: document section

results section
description: The results section is a document section describing the main findings of the study.
type: Class
subclass of: document section

table of contents
description: The table of contents is a document section that lists all sections (and optionally subsections) in a sequential order along with their page number.
type: Class
subclass of: document section

contains
description: A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. [T]
type: ObjectProperty
type: TransitiveProperty
sub property of: is location of

is connected to
alternative: interacts with
description: A is connected to B iff there exists a fiat, material or temporal path between A and B. [S][T]
subset: core
subset: nlp
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to

is adjacent to
description: A is adjacent to B iff there is a small, but non-zero distance between A and B
equivalent to: OBO_REL:adjacent_to
subset: core
subset: nlp
type: ObjectProperty
type: SymmetricProperty
sub property of: is spatiotemporally related to

is represented by
description: is represented by: a relation between an entity and some symbol.
type: ObjectProperty
sub property of: is referred to by
inverse of: represents

is supported by
description: is supported by is a relation between a proposition and something that supports the truth of the assertion.
type: ObjectProperty
sub property of: has evidence
inverse of: is supporting evidence for

is disputed by
description: has disputing evidence is a relation between a proposition and something that disputes (does not directly support) the truth of the assertion.
type: ObjectProperty
sub property of: has evidence
inverse of: is disputing evidence for

is supporting evidence for
type: ObjectProperty
sub property of: is evidence for

is disputing evidence for
type: ObjectProperty
sub property of: is evidence for

represents
description: a represents b when a serves as a sign, symbol or model of b.
subset: core
type: ObjectProperty
sub property of: refers to

is positionally after
description: is positionally after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity.
type: ObjectProperty
type: TransitiveProperty
sub property of: is connected to
inverse of: is positionally before

is referred to by
description: A is referred to by B iff B is an informational entity that makes reference to A.
type: ObjectProperty
sub property of: is related to
inverse of: refers to

has concretization
description: A has concretization B iff A is an informational entity and B is the a quality of some material entity.
type: ObjectProperty
sub property of: is generically related with
inverse of: is concretization of

is concretization of
description: A is concretization of B iff A is a quality of a material entity and B is an informational entity.
type: ObjectProperty
sub property of: is generically related with

is measurement value of
description: is measurement value of is a relation between a value and the entity that it is a measurement of.
type: ObjectProperty
domain: measurement value
sub property of: is attribute of
inverse of: has measurement value

has measurement value
description: has measurement value is a relation between a quality/realizable and a measurement value.
subset: core
type: ObjectProperty
range: measurement value
sub property of: has attribute

has quality
description: has quality is a relation between an entity and the quality that it bears.
type: InverseFunctionalProperty
type: ObjectProperty
range: quality
sub property of: has property
inverse of: is quality of

is quality of
description: is quality of is a relation between a quality and the entity that it is a property of.
type: ObjectProperty
domain: quality
sub property of: is property of

is source of
description: is source of is a relation between a source of information about some entity.
type: ObjectProperty
sub property of: is attribute of
inverse of: has source

implies (->)
description: Implication is a logical operator that holds between a set T of propositions and a proposition B, when every model (or interpretation or valuation) of T is also a model of B.
type: Class
subclass of: logical operator

has unit
description: has unit is a relation between a quantity and the unit it is a multiple of.
subset: core
type: FunctionalProperty
type: ObjectProperty
domain: mathematical entity
range: unit of measurement
sub property of: has attribute
inverse of: is unit of

is unit of
description: is unit of is a relation between a unit and a quantity that it is a multiple of.
type: ObjectProperty
domain: unit of measurement
sub property of: is attribute of

has property
description: has property is a relation between an entity and the quality, capability or role that it and it alone bears.
type: InverseFunctionalProperty
type: ObjectProperty
sub property of: has attribute
inverse of: is property of
example: michel's hair has the quality of being brown in colour.

is property of
description: is property of is a relation betweena quality, capability or role and the entity that it and it alone bears.
type: FunctionalProperty
type: ObjectProperty
sub property of: is attribute of

has function
description: has function is the relation between an entity and a function that is ascribed to it.
type: InverseFunctionalProperty
type: ObjectProperty
range: function
sub property of: has disposition
inverse of: is function of

is function of
description: is function of is a relation between a function and an entity that it is a property of.
type: FunctionalProperty
type: ObjectProperty
domain: function
sub property of: is disposition of

is role of
description: is role of is a relation between a role and the entity that it is a property of.
type: FunctionalProperty
type: ObjectProperty
domain: role
sub property of: is realizable property of
inverse of: has role

has role
description: has role is a relation between an entity and a role that it bears.
type: InverseFunctionalProperty
type: ObjectProperty
range: role
sub property of: has realizable property

has output
description: has output is a relation between an process and an entity, where the entity is present at the end of the process.
subset: core
subset: sadi
type: ObjectProperty
sub property of: has participant
inverse of: is output of

has input
description: has input is a relation between a process and an entity, where the entity is present at the beginning of the process.
subset: core
subset: sadi
type: ObjectProperty
sub property of: has participant
inverse of: is input in

is input in
description: is input in is a relation between an entity and a process, where the entity is present at the beginning of the process.
subset: sadi
type: ObjectProperty
sub property of: is participant in
example: glucose and ATP are inputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.

is output of
description: is output of is a relation between an entity and a process, where the entity is present at the end of the process.
subset: sadi
type: ObjectProperty
sub property of: is participant in
example: glucose-6-phosphate and ADP are outputs in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.

is implementation of
description: is implementation of is a relation between an information entity and a specification that it conforms to.
type: ObjectProperty
sub property of: is attribute of
inverse of: has implementation

has implementation
description: has implementation is a relation between a specification and an implementation that conforms to it.
type: ObjectProperty
sub property of: has attribute

has disposition
description: has disposition is the relation between an entity and a disposition that it bears.
type: InverseFunctionalProperty
type: ObjectProperty
range: disposition
sub property of: has capability
inverse of: is disposition of

is disposition of
description: is disposition of is a relation between a disposition and the entity that it is a property of.
type: FunctionalProperty
type: ObjectProperty
domain: disposition
sub property of: is capability of

namespace label
description: A namespace label is a short name for a namespace.
type: Class
subclass of: label

logical operator
description: A logical operator is a unary or binary relation to construct logical expressions.
type: Class
subclass of: mathematical entity

conjunction (and)
description: AND is a logical operator that has the value true if both of its operands are true, otherwise a value of false.
type: Class
subclass of: logical operator

is positionally before
description: is positionally before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity.
type: ObjectProperty
type: TransitiveProperty
sub property of: is connected to

is directly after
description: is directly after is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically greater than the projection of the position of the second entity, and the entities are adjacent to one another.
type: FunctionalProperty
type: ObjectProperty
sub property of: is positionally after
sub property of: is directly connected to
inverse of: is directly before

is directly before
description: is directly before is a relation between entities placed on a dimensional axis in which the projection of the position of the first entity is numerically less than the projection of the position of the second entity, and the entities are adjacent to one another.
type: FunctionalProperty
type: ObjectProperty
sub property of: is positionally before
sub property of: is directly connected to

is causally related with
description: A transitive, symmetric, temporal relation in which one entity is causally related with another non-identical entity.
subset: core
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is spatiotemporally related to

is derived from
description: A transitive temporal relation in which one entity was materially formed from another non-identical entity.
equivalent to: OBO_REL:derives_from
subset: core
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from
inverse of: derives into

derives into
description: a derives to b if and only if a or some part thereof is consumed in the formation of b.
type: ObjectProperty
type: TransitiveProperty
domain: object
range: object
sub property of: is causally related to

immediately derives into
description: a immediately derives into b if and only if a or some significant part thereof is consumed in the formation of b and there are no identifiable intermediate entities between a and b.
type: ObjectProperty
sub property of: derives into
inverse of: is immediately derived from

is immediately derived from
description: A non-transitive temporal relation in which one entity is immediately derived from a non-identical entity such that there are no intermediate entities between them.
type: ObjectProperty
sub property of: is derived from

precedes
description: A transitive, temporal relation in which one process precedes (has occured earlier than) another process.
subset: core
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from
inverse of: is preceded by

is preceded by
equivalent to: OBO_REL:preceded_by
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related to

immediately precedes
description: 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.
type: ObjectProperty
sub property of: precedes
inverse of: is immediately preceded by

is immediately preceded by
description: A non-transitive temporal relation in which one process is immediately preceded by another process, such that there is no interval of time between the two processes.
type: ObjectProperty
sub property of: is preceded by

is referenced by
description: is reference for is a relation between a document that provides information about an entity.
type: ObjectProperty
sub property of: is referred to by
inverse of: references

has source
description: has source is a relation between an entity and another entity from which it stems from.
type: ObjectProperty
sub property of: has attribute

is annotation of
description: is annotation of is a relation between some textual entity and the entity that it annotates.
type: ObjectProperty
domain: language entity
sub property of: is attribute of
inverse of: has annotation

has annotation
alternative: is annotated with
alternative: was annotated with
description: has annotation is a relation between an entity and some textual anntotation.
type: ObjectProperty
range: language entity
sub property of: has attribute
example: document x is annotated with the keywords 'ontology','semantic web'

proposition
description: A proposition is a sentence expressing something true or false.
type: Class
subclass of: description
subclass of: Restriction
  on property: has quality
  some values from: truth value
subclass of: Restriction
  on property: is about
  some values from: entity

dimensionless quantity
description: A dimensionless quantity is a quantity that has no associated unit.
type: Class
subclass of: quantity
subclass of: Class
  complement of: Restriction
    on property: has unit
    some values from: unit of measurement
disjoint with: dimensional quantity

dimensional quantity
description: A dimensional quantity is a quantity that has an associated unit.
type: Class
subclass of: quantity
subclass of: Restriction
  on property: has unit
  some values from: unit of measurement

argument
description: An argument is a set of one or more declarative sentences (or propositions) known as the premises along with another declarative sentence (or proposition) known as the conclusion.
type: Class
subclass of: proposition
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: premise
  intersection of: Restriction
    on property: has proper part
    some values from: conclusion

premise
description: A premise is a proposition of an argument from which the conclusion is drawn.
type: Class
subclass of: proposition

conclusion
description: A conclusion is a proposition which is reached after considering the evidence, arguments or premises.
type: Class
subclass of: proposition

deductive argument
description: A deductive argument is an argument that asserts that the truth of the conclusion is a logical consequence of the premises.
type: Class
subclass of: argument

inductive argument
description: An inductive argument is an argument that asserts that the truth of the conclusion is supported by the premises.
type: Class
subclass of: argument

sound argument
description: A sound argument is a valid argument with true premises.
type: Class
subclass of: valid argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: premise
    intersection of: Restriction
      on property: has quality
      some values from: true

valid argument
description: A valid argument is an argument where the truth of the conclusion is a logical consequence of the premises and (consequently) its corresponding conditional is a necessary truth.
type: Class
subclass of: argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: conclusion
    intersection of: Restriction
      on property: has quality
      some values from: false

invalid argument
description: An invalid argument is an argument where the truth of the conclusion is false because it is not a logical consequence of the premises.
type: Class
subclass of: argument
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: conclusion
    intersection of: Restriction
      on property: has quality
      some values from: false

truth value
description: truth value is a quality of information that is claimed/verified to be true or false.
type: Class
subclass of: informational quality
equivalent class: Class
  union of: true
  union of: false

true
description: true is a truth value that indicates that it holds under all possible worlds.
type: Class
subclass of: truth value
subclass of: Restriction
  has value: true
  on property: has value
disjoint with: false

false
description: false is a truth value in that indicates that it is not true.
type: Class
subclass of: truth value
subclass of: Restriction
  has value: false
  on property: has value

is variant of
description: is variant of: a relationship indicating that two entities are different (by some measure), but either achieve the same objectives in different ways or are permutations of one another (temporal, logical or otherwise)
subset: core
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is comparable to

has direct part
description: has direct part is a relation to specify a part at a particular level of granularity
type: ObjectProperty
sub property of: has proper part
inverse of: is direct part of
example: a car has an engine as a direct part

is prior version of
description: A is prior version of B iff A is a variant of B and B derives from A.
type: ObjectProperty
sub property of: is derived from
sub property of: is version of
inverse of: is subsequent version of

term
description: A term is a word or phrase used to denote one or more entities.
type: Class
subclass of: language entity
subclass of: Class
  union of: word
  union of: phrase

emotion
description: An emotion is a process (experience) that arises internally or from an involuntary physiological response to a stimulus.
subset: emotion++
type: Class
subclass of: behaviour

cites
description: cites is a relation to refer to by way of example, authority or proof.
type: ObjectProperty
sub property of: references
inverse of: is cited by

is cited by
description: is cited by is a relation from an object that is referred to by way of example, authority or proof.
type: ObjectProperty
sub property of: is referenced by

mass
description: mass is the quality of the amount of substance.
type: Class
subclass of: spatial quantity
subclass of: Restriction
  on property: is attribute of
  some values from: material entity

disjunction (or)
description: OR is a logical operator that results in true whenever one or more of its operands are true.
type: Class
subclass of: logical operator

negation (not)
description: NOT is a logical operator in that has the value true if its operand is false.
type: Class
subclass of: logical operator

exclusive disjunction (xor)
description: XOR, also called exclusive disjunction or (symbolized XOR, EOR, EXOR, or ⊕), is a type of logical disjunction on two operands that results in a value of true if exactly one of the operands has a value of true.
type: Class
subclass of: disjunction (or)

is similar to
description: is similar to is a relation between two entities that share one or more features.
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of

hypothesis
description: A hypothesis is a proposed explanation for a phenomenon.
type: Class
subclass of: proposition

academic organization
description: An academic organization is a lawfully recognized organization that confers diplomas, degrees and other forms of recognition of academic achievement.
type: Class
subclass of: organization

is subsequent version of
description: A is subsequent version of B iff A is a variant of B and A derives from B.
type: ObjectProperty
sub property of: is version of

social relation
description: A social relation is a social entity that describes a relationship between two or more individuals or groups.
type: Class
subclass of: social entity

is covalently connected to (transitive)
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
domain: atom
range: atom
sub property of: is connected to

set
description: A set is a collection of entities, for which there may be zero members.
type: Class
subclass of: mathematical entity
subclass of: Restriction
  all values from: entity
  on property: has member

university
description: A university is an institution of higher education and research which grants academic degrees in a variety of subjects and provides both undergraduate education and postgraduate education.
type: Class
subclass of: academic organization

has target
description: has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.
type: ObjectProperty
sub property of: has input
inverse of: is target in

is target in
description: is target in is a relation between an entity and a process, where the entity is present at the beginning of the process and undergoes a change or transformation in the process.
type: ObjectProperty
sub property of: is input in
example: glucose is a target in the hexokinase-mediated conversion of glucose to glucose-6-phosphate.

is weakly interacting with (transitive)
description: is weakly interacting with is a symmetric relation between two molecular entities (or any part thereof) that are interacting through some weak force (van der waals, hydrogen bonds, electrostatic interactions)
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
domain: Class
  union of: molecule
  union of: Restriction
    on property: is part of
    some values from: molecule
range: Class
  union of: molecule
  union of: Restriction
    on property: is part of
    some values from: molecule
sub property of: is connected to

is causally related to
description: a is causally related to b iff there is a causal chain of events from a to b
type: ObjectProperty
sub property of: is causally related with
inverse of: is causally related from

collection of documents
description: A collection of documents is a non-zero set of documents.
equivalent to: http://purl.org/ontology/bibo/Collection
type: Class
subclass of: collection
subclass of: Restriction
  min qualified cardinality: 2
  on class: document
  on property: has component part

website
description: A website is a collection of documents published on the World Wide Web.
type: Class
subclass of: collection of documents
subclass of: Restriction
  on property: has direct part
  some values from: web page

movie
alternative: film
alternative: moving pictures
description: A movie is a series of images that are displayed in rapid succession to give the impression of movement.
type: Class
subclass of: media

excerpt
description: An excerpt is a contiguous or discontiguous portion of a document.
type: Class
subclass of: textual entity
subclass of: Restriction
  on property: is part of
  some values from: textual entity

quote
description: A quote is a excerpt that is attributed to a particular source.
type: Class
subclass of: excerpt
subclass of: Restriction
  on property: is derived from
  some values from: textual entity

has value
description: A relation between a informational entity and its actual value (numeric, date, text, etc).
subset: core
subset: nlp
subset: relations
subset: sadi
type: DatatypeProperty
type: FunctionalProperty

geographic image
description: A geographic image is a photograph of some geographical area.
type: Class
subclass of: photograph

web page
description: A web page is a document that is published according to World Wide Web standards.
type: Class
subclass of: document

email
description: Email message is a digital document that is composed of a header and a body and is transmitted using the SMTP protocol.
type: Class
subclass of: document

process number
description: process number is a number associated with a process that denotes its ordinal position in a set of processes.
type: Class
subclass of: ordinal position

letter
description: A letter is a document that contains a personal communication from one part to another.
type: Class
subclass of: document

normality
description: normality is the quality in which the value may differ from normal or average
type: Class
subclass of: quality
equivalent class: Class
  union of: normal
  union of: abnormal

edition number
description: An edition number is count of a literary work edited and published, as by a certain editor or in a certain manner including being printed during some interval of time.
type: Class
subclass of: count

volume number
description: volume number is a count of a sequence of periodicals.
type: Class
subclass of: count

is direct part of
description: is direct part of is a relation between a specific part (at some level of granularity) and its whole.
subset: core
type: ObjectProperty
sub property of: is proper part of

is product of
description: is product of is a relation between an entity and a process, where the entity is present at the end of the process as a result of a transformation in the process target.
subset: sadi
type: ObjectProperty
sub property of: is output of
inverse of: has product
example: glucose-6-phosphate is the product of the hexokinase-mediated conversion of glucose to glucose-6-phosphate.

has product
description: has product is a relation between an process and an entity, where a new entity exists at the end of the process.
subset: sadi
type: ObjectProperty
sub property of: has output

is component part of
description: is component part of is a relation between a component and a whole, where the component is instrinsic to the whole, and loss of the part would change the kind that the whole is.
subset: core
type: ObjectProperty
sub property of: is direct part of
inverse of: has component part

polymer
description: A polymer is a molecule composed of a connected set of monomeric residues.
type: Class
subclass of: molecule
subclass of: Restriction
  on property: has direct part
  some values from: monomer
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: has direct part
    some values from: monomer

functional specification
description: A functional specification is a specification that describes the characteristics of an object.
type: Class
subclass of: specification
subclass of: Restriction
  on property: specifies
  some values from: Class
    union of: material entity
    union of: information content entity

design specification
description: A design specification is a specification that provides precise and explicit information about the requirements for a product design.
type: Class
subclass of: functional specification

spatial specification
description: A specification for spatial location is an effective specification towards representation spatial position or spatial data.
type: Class
subclass of: functional specification

longitude
description: Longitude is a geographic position that refers to the angle east or west of a reference meridian between the two geographical poles to another meridian that passes through an arbitrary point.
type: Class
subclass of: geographic position
disjoint with: latitude

latitude
description: Latitude is a geographic coordinate which refers to the angle from a point on the Earth's surface to the equatorial plane
type: Class
subclass of: geographic position

coordinate system
description: A coordinate system is a specification for spatial location that uses a set of numbers, or coordinates, to uniquely determine the position of a point or other geometric element.
type: Class
subclass of: spatial specification

cartesian coordinate system
description: A Cartesian coordinate system specifies each point uniquely in a plane by a pair of numerical coordinates, which are the signed distances from the point to two fixed perpendicular directed lines, measured in the same unit of length.
type: Class
subclass of: coordinate system

is spatiotemporally related to
description: A is spatiotemporally related to B iff A is in the spatial or temporal vicinity of B
subset: core
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to

is surrounded by
description: A 'is surrounded by' B iff the A 'is contained by' B and A 'is adjacent to' B or A 'is directly connected to' B.
type: ObjectProperty
sub property of: is contained in
inverse of: surrounds

surrounds
description: A 'surrounds' B iff the A 'contains' B and A 'is adjacent to' B or A 'is directly connected to' B.
type: ObjectProperty
sub property of: contains

overlaps with
description: A overlaps with B iff there is some C that is part of both A and B. [S][R]
type: ObjectProperty
type: ReflexiveProperty
type: SymmetricProperty
sub property of: is spatiotemporally related to
property chain axiom: overlaps with
property chain axiom: is part of

concept
description: A concept is term that refers to a generalization of a set of attributes or entities.
type: Class
subclass of: term

polar coordinate system
description: A polar coordinate system is a two-dimensional coordinate system in which each point on a plane is determined by a distance from a fixed point and an angle from a fixed direction.
type: Class
subclass of: coordinate system

positional identifier
description: A positional description is a description of location using some system or frame of reference.
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is attribute of
  some values from: position

cylindrical coordinate system
description: A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis, the direction from the axis relative to a chosen reference direction, and the distance from a chosen reference plane perpendicular to the axis.
type: Class
subclass of: coordinate system

spherical coordinate system
description: A spherical coordinate system is a coordinate system for three-dimensional space where the position of a point is specified by three numbers: the radial distance of that point from a fixed origin, its polar angle measured from a fixed zenith direction, and the azimuth angle of its orthogonal projection on a reference plane that passes through the origin and is orthogonal to the zenith, measured from a fixed reference direction on that plane.
type: Class
subclass of: coordinate system

OWL ontology
description: An OWL ontology is an ontology as specified by the W3C OWL specification.
type: Class
subclass of: ontology document

is about
description: is about is a relation between an information content entity and the entity that its primary subject.
type: ObjectProperty
sub property of: describes
inverse of: is subject of

3D cartesian coordinate
description: A 3D cartesian coordinate is a coordinate that is composed of an x, y and z coordinate.
type: Class
subclass of: cartesian coordinate
subclass of: Class
  intersection of: Restriction
    on class: x cartesian coordinate
    on property: has direct part
    qualified cardinality: 1
  intersection of: Restriction
    on class: y cartesian coordinate
    on property: has direct part
    qualified cardinality: 1
  intersection of: Restriction
    on class: z cartesian coordinate
    on property: has direct part
    qualified cardinality: 1

is covalently connected to
description: is covalently connected to is a relation between an atom and another atom.
type: ObjectProperty
type: SymmetricProperty
sub property of: is covalently connected to (transitive)
sub property of: is directly connected to

is weakly interacting with
type: ObjectProperty
type: SymmetricProperty
sub property of: is weakly interacting with (transitive)
sub property of: is directly connected to

objective
description: An objective is a proposition that indicates a planned or anticipated outcome.
type: Class
subclass of: proposition
subclass of: Restriction
  all values from: action specification
  on property: is specified by
subclass of: Restriction
  all values from: process
  on property: is realized in

specifies
description: A relation between an information content entity and a product that it (directly/indirectly) specifies
type: ObjectProperty
sub property of: is causally related with
sub property of: describes
inverse of: is specified by

is specified by
description: a relation between a product and the information content entity that specifies it.
type: ObjectProperty
sub property of: is causally related with
sub property of: is described by

realizable entity
description: A realizable entity is an attribute that is exhibited under some condition and is realized in some process.
subset: core
type: Class
subclass of: attribute
subclass of: Restriction
  on property: is realizable property of
  some values from: entity
subclass of: Restriction
  all values from: entity
  on property: in relation to

is manifested as
description: is manifested as is a relation between an expression and its manifestations.
type: ObjectProperty
sub property of: is generically related with
inverse of: is manifestation of
example: the english language version of 'war of the worlds' is manifested as a collection of english language versions of the book.

term variant
description: A term variant is a term that is a variant of another term.
type: Class
subclass of: term
subclass of: Restriction
  on property: is variant of
  some values from: term
equivalent class: Class
  intersection of: term
  intersection of: Restriction
    on property: is variant of
    some values from: term

to modify
description: to modify is the capability to change some entity.
type: Class
subclass of: to actively interact with

to record
description: to record is the capability to detect and transcribe information in a specified format on some physical medium.
type: Class
subclass of: to actively interact with

to magnify
description: to magnify is the capability to increase the appearance of the size of an object.
type: Class
subclass of: to change appearance

to heat
description: to heat is a capability to increase the internal kinetic energy of a material.
type: Class
subclass of: to supply energy

to cool
description: to cool is the capability to decrease the internal kinetic energy of a material.
type: Class
subclass of: to reduce energy

to freeze
description: to freeze is the capability to decrease the internal kinetic energy of a material such that it changes state from a gas or liquid to a solid.
type: Class
subclass of: to cool

to separate
description: to separate is the capability to i) distinguish some entities based on some attribute(s) and ii) subsequently physically displace them.
type: Class
subclass of: to modify

to ionize
description: to ionize is the capability to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
type: Class
subclass of: to modify electronically

to supply energy
description: to supply energy is the capability to transfer energy from a source to a sink.
type: Class
subclass of: to change energetically

is causally related from
description: a is causally related from b iff there is a causal chain of events from b to a
subset: core
type: ObjectProperty
sub property of: is causally related with

to observe
description: to observe is the capability to watch attentively.
type: Class
subclass of: to passively interact with

dysfunction
description: dysfunction is a capability to act in a manner that is abnormal or opposite to the object's typical function.
type: Class
subclass of: capability

realizes
description: realizes is a relation between a process and a realizable entity (role, function, disposition).
subset: core
type: ObjectProperty
sub property of: has output
inverse of: is realized in

is realized in
type: ObjectProperty
sub property of: is participant in
example: the role of a patient is realized in medical examination

fitness
description: fitness is the quality of an object with respect to some stated functions or evolutionary adaptation.
type: Class
subclass of: object quality

intent
description: intent is a desire to realize a particular outcome.
type: Class
subclass of: desire

purpose
description: purpose is the reason for which something is done or created or for which something exists.
type: Class
subclass of: reason

belief
description: A belief is a proposition that is believed to be true.
type: Class
subclass of: proposition
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: true
    intersection of: Restriction
      on property: is quality of
      some values from: proposition

satisfies
description: satisfies is a relation between an entity and the specification or objective that it conforms to.
type: ObjectProperty
domain: entity
range: description
sub property of: has attribute
inverse of: is satisfied by

is satisfied by
type: ObjectProperty
sub property of: is attribute of

has creator
alternative: is created by
alternative: was created by
description: has creator is a relation between an entity and that which created it.
equivalent to: dc:creator
type: ObjectProperty
domain: entity
range: entity
sub property of: has source
inverse of: is creator of
example: the iPhone was created by Apple Inc

is creator of
alternative: is created by
description: is creator of is a relation between a creator and an entity..
type: ObjectProperty
sub property of: is source of

number
alternative: rank 0 tensor
description: A number is a tensor of rank 0.
type: Class
subclass of: scalar

variable
description: A variable is a value that may change within the scope of a given problem or set of operations.
type: Class
subclass of: mathematical entity

equation
description: An equation is a mathematical statement that asserts the equality of two expressions.
type: Class
subclass of: mathematical entity

has component part
description: has component part is a relation between a whole and a component part where the component is instrinsic to the whole, and loss of the part would change the kind that it is.
type: ObjectProperty
sub property of: has direct part
example: a human has blood as a component part

spatial region
alternative: region
description: A spatial region is an object contained in some region of space.
type: Class
subclass of: object
subclass of: Restriction
  all values from: spatial region
  on property: has part
example: The airspace above Ottawa airport; the band around the northern hemisphere between 50 degrees N and 60 degrees N; the spatial region occupied by a bottle.

to measure
description: to measure is the capability to obtain information about some entity by examining its attributes in relation to some reference metric.
type: Class
subclass of: to investigate

to inject
description: to inject is the capability to administer a substance into some object through its external barrier.
type: Class
subclass of: to modify

to boil
description: to boil is the capability to increase the internal kinetic energy of a material such that it changes state from a solid or liquid to a gas.
type: Class
subclass of: to heat

to reduce energy
description: to reduce energy is the capability to remove energy from a source.
type: Class
subclass of: to change energetically

to supply electricity
description: to supply electricity is the capability to transfer electricity from a source to a sink.
type: Class
subclass of: to supply energy

to change materially
description: to change appearance is the capability to change the material composition of an object.
type: Class
subclass of: to modify

to demagnify
description: to demagnify is the capability to decrease the appearance of the size of an object.
type: Class
subclass of: to change appearance

to change appearance
description: to change appearance is the capability to change the visual attributes of an object.
type: Class
subclass of: to modify

perception
description: perception is the organization, identification, and interpretation of sensory information in order to fabricate a mental representation through the process of transduction, which sensors in the body transform signals from the environment into encoded neural signals.
type: Class
subclass of: observing

to contain
description: to contain is the capability to bound or constrain a physical entity in some site.
type: Class
subclass of: to change spatially

to immobilize
description: to immobilize is the capability to contain an entity in such a way that it may not move in space.
type: Class
subclass of: to contain

to filter
description: to filter is the capability to retain certain entities based on selected attribute(s) while allowing other entities to pass through.
type: Class
subclass of: to separate

to excite
description: to excite is the capability to supply energy to a materila by bombarding it with energetic particles (e.g., photons).
type: Class
subclass of: to supply energy

to emit
description: to emit is the capability to release some physical entity (light, pollution, etc).
type: Class
subclass of: to reduce energy

to change energetically
description: to change energetically is the capability to change the energetic aspects of an object.
type: Class
subclass of: to modify

to positively charge
description: to positively charge is the capability to remove an electron or add a positively charged ion to a chemical entity.
type: Class
subclass of: to ionize

to negatively charge
description: to negatively charge is the capability to add an electron or negatively charged ion to a chemical entity.
type: Class
subclass of: to ionize

to assemble
description: to assemble is the capability to combine entities together into a larger object that persists in time.
type: Class
subclass of: to actively interact with

to extract
description: to extract is the capability to remove certain entities based on selected attribute(s) while allowing other entities to remain.
type: Class
subclass of: to separate

to transport
description: to transport is the capability to displace a material from one location to another.
type: Class
subclass of: to actively interact with

time measurement
description: time measurement is a measurement value of the duration of some interval of time or a particular instant of time (against some frame of reference).
comment: Time intervals are specified as date/datetime ranges.
type: Class
subclass of: dimensional quantity
example: the duration of my life; the duration of a surgical procedure, the moment of death

to change spatially
description: to change spatially is the capability to affect the physical movement of some entity.
type: Class
subclass of: to modify

patient
description: A patient is an individual that is the recepient of medical care.
type: Class
subclass of: person
subclass of: Restriction
  on property: has role
  some values from: patient role

doctor
description: A doctor is an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.
type: Class
subclass of: medical practitioner
subclass of: Restriction
  on property: has role
  some values from: doctor role

to regulate
alternative: to modulate
description: to regulate is to control or maintain the rate or speed of an object or process.
type: Class
subclass of: to modify

file
description: A file is an information-bearing object that contains a physical embodiment of some information using a particular character encoding.
equivalent to: http://www.w3.org/ns/dcat#Distribution
type: Class
subclass of: media

to provide
description: to provide is the capability to make available some object to another that requires it.
type: Class
subclass of: to retrieve

nurse
description: A nurse is an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.
type: Class
subclass of: medical practitioner
subclass of: Restriction
  on property: has role
  some values from: nurse role

study subject
description: A study subject is an individual that is the subject of the study.
type: Class
subclass of: person

x cartesian coordinate
description: An x cartesian coordinate is the coordinate of an object onto the x-axis of a cartesian coordinate system.
type: Class
subclass of: cartesian coordinate

y cartesian coordinate
description: An y cartesian coordinate is the coordinate of an object onto the y-axis of a cartesian coordinate system.
type: Class
subclass of: cartesian coordinate

z cartesian coordinate
description: A z cartesian coordinate is the coordinate of an object onto the z-axis of a cartesian coordinate system.
type: Class
subclass of: cartesian coordinate

study group
description: A study group is a group of individuals that are subjects in an observational or intervention study.
type: Class
subclass of: collective

professor
description: A professor is an individual that is a scholarly teacher.
type: Class
subclass of: academic

student
description: A student is an individual who is attends an educational institution.
type: Class
subclass of: academic

academic
description: An academic is an individual that participates in education and scholarship.
type: Class
subclass of: person

to increase the rate of formation
description: to increase the rate of formation is to regulate the rate of formation in a manner that increases this rate relative to a reference process.
type: Class
subclass of: to regulate the rate of formation

to investigate
description: to investigate is the capability to uncover facts.
type: Class
subclass of: to actively interact with

mutual disposition
description: A mutual disposition is a disposition that simulataneously invokes another disposition when realized.
type: Class
subclass of: disposition

anger
description: anger is disgust directed toward an equal status individual.
type: Class
subclass of: disgust

hate
description: Hate is a deep and emotional extreme dislike, directed against a certain object or class of objects.
type: Class
subclass of: disgust

love
description: love is an emotion of a strong affection and personal attachment.
type: Class
subclass of: positive emotion

geolegal region
description: A geolegal region is a geographic region which has causal powers confered by a legal entity.
type: Class
subclass of: geographic region
example: The 50 kph zones in Ottawa; the geographic region occupied by France.

geographic region
description: A geographic region is a spatial region whose boundaries are typically defined against some material frame of reference (like the earth).
type: Class
subclass of: spatial region
example: The spatial region occupied by the province of ontario; the spatial region occupied by a lake.

geopolitical region
description: a geopolitical region is a geographic region recognized by social or legal convention.
type: Class
subclass of: geolegal region
example: The geographic region bounded by Canada; the spatial region occupied by the US embassy in Ottawa.

time interval
description: A time internval is a contiguous temporal region having some duration.
type: Class
subclass of: time measurement

time instant
description: A time instant is a temporal region which occurs instantaneously, e.g. having no duration.
type: Class
subclass of: time measurement
example: at this moment; the moment at which a finger is detached in an industrial accident; the moment at which a child is born; the moment of death

table
description: A table is a figure that consists of an ordered arrangement of columns and rows.
type: Class
subclass of: figure

has expression
type: ObjectProperty
sub property of: is generically related with
inverse of: is expression of
example: the story 'war of worlds' is expressed as every language edition of the book 'war of the worlds'

is expression of
description: is expression of is a relation between more concrete expression of some conceptualization.
type: ObjectProperty
sub property of: is generically related with
example: every language edition of 'war of the worlds' are expressions of the story of 'war of the worlds'

is broader than (t)
description: A is broader than B (t) iff for A is broader than B.
equivalent to: http://www.w3.org/2004/02/skos/core#narrowerTransitive
type: ObjectProperty
type: TransitiveProperty
domain: term
range: term
sub property of: is similar to
inverse of: is narrower than (t)

scatterplot
alternative: scatter chart
alternative: scatter diagram
alternative: scatter graph
description: A scatterplot is a statistical graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis.
type: Class
subclass of: statistical graph

is narrower than (t)
description: A is narrower than B (t) iff for A is narrower than B.
equivalent to: http://www.w3.org/2004/02/skos/core#broaderTransitive
type: ObjectProperty
type: TransitiveProperty
domain: term
range: term
sub property of: is similar to

is generically related with
description: A is generically related with B iff A is an abstract entity or an information content entity and B is a information content entity or a physical entity, respectively.
type: ObjectProperty
sub property of: is related to

is manifestation of
type: ObjectProperty
sub property of: is generically related with

is narrower than
description: A is narrower than B iff the meaning of term A is narrower in scope than the meaning of term B
equivalent to: http://www.w3.org/2004/02/skos/core#broader
type: ObjectProperty
sub property of: is narrower than (t)
inverse of: is broader than

year
description: A year is a period of time taken by a planet to make one revolution around the sun.
type: Class
subclass of: time interval

month
description: A month is a period of time that divides the year.
type: Class
subclass of: time interval

day
description: A day is a period of 24 hours.
type: Class
subclass of: time interval

century
description: A century is a period of one hundred years.
type: Class
subclass of: time interval

millennium
description: A millenium is a period of 1000 years
type: Class
subclass of: time interval

hour
description: An hour is a period of 60 minutes.
type: Class
subclass of: time interval

minute
description: A minute is a period of 60 seconds.
type: Class
subclass of: time interval

second
description: A second (symbol: s) is the base unit of time in the International System of Units (SI) and is the second division of the hour by sixty, the first division by 60 being the minute.
type: Class
subclass of: time interval

informational quality
description: An informational quality is a quality that pertains to information.
type: Class
subclass of: quality
subclass of: Restriction
  on property: is quality of
  some values from: information content entity

2D cartesian point
description: A 2D cartesian point is a point whose position is specified along two dimensions using Cartesian coordinates.
type: Class
subclass of: point
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    all values from: Class
      union of: x cartesian coordinate
      union of: y cartesian coordinate
    on property: has component part
  intersection of: Restriction
    on class: x cartesian coordinate
    on property: has component part
    qualified cardinality: 1
  intersection of: Restriction
    on class: y cartesian coordinate
    on property: has component part
    qualified cardinality: 1

altitude
description: Altitude is a distance above sea level.
type: Class
subclass of: position

center of mass
description: The center of mass (aka barycenter) is the weighted average location of all the mass in a body or group of bodies.
type: Class
subclass of: position

3D cartesian point
description: A 3D cartesian point is a point whose position is specified along three dimensions using Cartesian coordinates.
type: Class
subclass of: point
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    on class: x cartesian coordinate
    on property: has component part
    qualified cardinality: 1
  intersection of: Restriction
    on class: y cartesian coordinate
    on property: has component part
    qualified cardinality: 1
  intersection of: Restriction
    on class: z cartesian coordinate
    on property: has component part
    qualified cardinality: 1

1D cartesian point
description: A 1D cartesian point is a point whose position is specified along a single dimension using Cartesian coordinates.
type: Class
subclass of: point
equivalent class: Class
  intersection of: point
  intersection of: Restriction
    all values from: z cartesian coordinate
    on property: has component part
  intersection of: Restriction
    on class: z cartesian coordinate
    on property: has component part
    qualified cardinality: 1

line graph
alternative: line chart
description: A line graph is a statistical graph in which lines contains the evaluation of functions or individual points connected by line segments.
type: Class
subclass of: statistical graph
example: Graph 1 in http://tinyurl.com/opwnvm

bar graph
description: A bar graph is a statistical graph with rectangular bars of lengths proportional to that value that they represent.
type: Class
subclass of: statistical graph
example: Graphs 3,4,5 in http://tinyurl.com/opwnvm

horizontal bar graph
description: A horizontal bar graph is a bar graph in which the rectangular bars are horizontally oriented in space.
type: Class
subclass of: bar graph
example: Graph 3 in http://tinyurl.com/opwnvm

vertical bar graph
description: A vertical bar graph is a bar graph in which the rectangular bars are vertically oriented in space.
type: Class
subclass of: bar graph
example: Graph 4,5 in http://tinyurl.com/opwnvm

stacked bar graph
description: A stacked bar graph is a bar graph in which each rectangular bar is partioned by the categorical value of each series of data.
type: Class
subclass of: bar graph
example: Graphs 6,7 in http://tinyurl.com/opwnvm

line-bar graph
description: A line-bar graph statistical graph that contains both lines and bars.
type: Class
subclass of: statistical graph
example: Graph 8 in http://tinyurl.com/opwnvm

figure part
description: A figure part is a part of a figure.
type: Class
subclass of: media
subclass of: Restriction
  on property: is proper part of
  some values from: figure

plot
description: A plot is a part of a figure that corresponds to the spatial region between the set of axes.
type: Class
subclass of: figure part
disjoint with: legend
example: The square portion of the chart bounded by lines that overlap with the two axes in Graph 1 of http://tinyurl.com/opwnvm

axis
description: An axis is a line segment that is part of a statistical graph in which the position along the line corresponds to a numeric or categorical value.
comment: The value of a plotted geometric objects (e.g. point) can be obtained from the perpendicular projection of the position of the object onto the axis. Axis may also be associated with a textual description of what the values on the axis represents.
type: Class
subclass of: directed line segment
subclass of: Restriction
  on property: is component part of
  some values from: statistical graph
example: The left vertical and bottom horizontal lines with tickmarks in Graph 1 http://tinyurl.com/opwnvm

Cartesian coordinate axis
description: A Cartesian coordinate axis is an axis whose behavior follows that of a Cartesian coordinate system.
type: Class
subclass of: value axis
subclass of: Restriction
  on property: satisfies
  some values from: cartesian coordinate system

x-axis
alternative: horizontal axis
description: An x-axis is a Cartesian coordinate axis that is aligned with the horizon.
comment: In most figures, this axis represents categories, such as months, market segments, or other non-numeric data.
type: Class
subclass of: Cartesian coordinate axis
disjoint with: y-axis
disjoint with: z-axis
example: The horizontal axis in http://tinyurl.com/opwnvm

y-axis
alternative: vertical axis
description: A y-axis is a Cartesian coordinate axis that is spatially oriented perpendicular to the x-axis.
type: Class
subclass of: Cartesian coordinate axis

z-axis
description: A z-axis is a Cartesian coordinate axis that is spatially oriented normal to the plane formed by the x- and y-axes.
type: Class
subclass of: Cartesian coordinate axis

category axis
description: A category axis is an axis in which the position along the line is partioned into categories.
type: Class
subclass of: axis
disjoint with: value axis
equivalent class: Class
  union of: primary category axis
  union of: secondary category axis
example: The horizontal axis corresponding to months of the year in graph 4 of http://tinyurl.com/opwnvm

primary category axis
description: A primary category axis is a category axis that either defines the sole value range or holds the larger set of categorical values specified by the secondary category axis.
type: Class
subclass of: category axis
disjoint with: secondary category axis
example: The category axis that corresponds to years in Graph 1 of http://tinyurl.com/opwnvm

secondary category axis
description: A secondary category axis is a category axis that defines a finer granular part (or subset) of the value range of the primary category axis.
type: Class
subclass of: category axis
example: The category axis that corresponds to months in Graph 1 of http://tinyurl.com/opwnvm

value axis
description: A value axis is an axis in which the position along the line is partioned into numeric values.
comment: A value axis holds the properties of having a minimum and a maximum value, and is usually associated with tickmarks that indicate intervals along the axis.
type: Class
subclass of: axis
equivalent class: Class
  union of: left value axis
  union of: right value axis
  union of: top value axis
  union of: bottom value axis
example: The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm

left value axis
description: A left value axis is a value axis that is spatially positioned to the left of the plot area.
type: Class
subclass of: value axis
example: The value axis that ranges from 3.0 to 7.4 and corresponds to billions of dollars in Graph 1 of http://tinyurl.com/opwnvm

right value axis
description: A right value axis is a value axis that is spatially positioned to the right of the plot area.
type: Class
subclass of: value axis

scaled value axis
description: A scaled value axis is a value axis in which the value range was subject to a mathematic transformation.
type: Class
subclass of: value axis

linear value axis
description: A linear value axis is a value axis that corresponds to a scaling factor of 1 of the value range.
type: Class
subclass of: scaled value axis
disjoint with: logarithmic value axis

logarithmic value axis
description: A logarithmic value axis is a scaled value axis that corresponds to a scaling factor of the logarithm of the value range.
type: Class
subclass of: scaled value axis

data series
description: A data series is a data set composed of related values displayed in a statistical graph.
type: Class
subclass of: list
example: Example: The two series that correspond to "Seasonally adjusted" and "Trend" are composed of the seasonally adjusted value of permits in each month and values from a trend derived from some mathematical tranformation across those values, respectively, in Graph 1 of http://tinyurl.com/opwnvm

data point
description: A data point is a point that which corresponds to the projection of the values of measurement data against the axes of a statistical graph.
type: Class
subclass of: point
subclass of: Restriction
  on property: denotes
  some values from: entity

global maximal stationary point
description: A global maximum stationary point is a data point that corresponds to a measurement value is larger than that of all other plotted datapoints.
type: Class
subclass of: local maximum stationary point

global minimal stationary point
description: A global minimum data point is a data point that corresponds to a measurement value is smaller than that of all other plotted datapoints.
type: Class
subclass of: local minimum stationary point

legend
description: A legend is a part of a figure that associates textual descriptions with symbols pertaining to plotted entities.
type: Class
subclass of: figure part
example: The colored line segments and the adjacent textual descriptions in Graph 1 of http://tinyurl.com/opwnvm

graph title
description: A graph title is a title that describes a graph.
type: Class
subclass of: title
subclass of: Restriction
  on property: is direct part of
  some values from: statistical graph
equivalent class: Class
  intersection of: title
  intersection of: Restriction
    on property: is direct part of
    some values from: statistical graph
example: Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm

primary title
description: A primary title is a title that should be first used in describing some entity.
type: Class
subclass of: title

secondary title
alternative: subtitle, alternative title
description: A secondary title is a title of lesser importance that should be used after the first title in describing some entity.
type: Class
subclass of: title

scientific data
description: scientific data is data obtained from some scientific procedure.
type: Class
subclass of: data item

primary graph title
description: A primary graph title is a primary title that describes a statistical graph.
type: Class
subclass of: primary title
subclass of: Restriction
  on property: is direct part of
  some values from: statistical graph
example: "Total value of permits increased slightly in December" in Graph 1 of http://tinyurl.com/opwnvm

secondary graph title
description: A secondary graph title is a secondary title that describes a statistical graph.
type: Class
subclass of: primary title
subclass of: Restriction
  on property: is direct part of
  some values from: statistical graph

biological quality
description: A biological quality is a quality held by a biological entity.
type: Class
subclass of: object quality

cellular quality
description: cellular quality is the quality of a cell
type: Class
subclass of: biological quality
subclass of: Restriction
  on property: is quality of
  some values from: cell

is broader than
equivalent to: http://www.w3.org/2004/02/skos/core#narrower
type: ObjectProperty
sub property of: is broader than (t)

sequence variant role
description: A sequence variant role is a comparative role in which the composition of characters in a sequence differs when compared to another entity of similar type.
type: Class
subclass of: variant role

variant role
description: A variant role is a comparative role in which the value of an attribute differs when compared to another entity
type: Class
subclass of: comparative role

insertion variant role
description: An insertion variant role is the role of an sequence that contains a sub-sequence that is considered to be an addition relative to the frame of reference.
type: Class
subclass of: sequence variant role

deletion variant role
description: A deletion variant role is the role of an sequence that lacks a sub-sequence relative to the frame of reference.
type: Class
subclass of: sequence variant role

is match to
description: A is match to B iff A and B are terms with similar (related, broad, close, exact) meanings
equivalent to: http://www.w3.org/2004/02/skos/core#relatedMatch
type: ObjectProperty
type: SymmetricProperty
domain: term
range: term
sub property of: is similar to

phrase
description: A phrase is a group of words functioning as a single unit in the syntax of a sentence.
type: Class
subclass of: language entity
subclass of: Restriction
  min qualified cardinality: 2
  on class: word
  on property: has direct part

is exact match to
equivalent to: http://www.w3.org/2004/02/skos/core#exactMatch
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to

human
description: A human is a primates of the family Hominidae and are characterized by having a large brain relative to body size, with a well developed neocortex, prefrontal cortex and temporal lobes, making them capable of abstract reasoning, language, introspection, problem solving and culture through social learning.
type: Class
subclass of: multicellular organism

mouse
description: A mouse is a small mammal belonging to the order of rodents, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail.
type: Class
subclass of: multicellular organism

rat
description: A rat is a medium-sized, long-tailed rodent of the superfamily Muroidea.
type: Class
subclass of: multicellular organism

worm
description: A worm is a non-arthropod invertebrate animal that typically have a long cylindrical tube-like body and no legs.
type: Class
subclass of: multicellular organism

e.coli
description: Escherichia coli (e coli) is a Gram-negative, rod-shaped bacterium that is commonly found in the lower intestine of warm-blooded organisms.
type: Class
subclass of: unicellular organism

is close match to
equivalent to: http://www.w3.org/2004/02/skos/core#closeMatch
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to

is broad match to
equivalent to: http://www.w3.org/2004/02/skos/core#broadMatch
type: ObjectProperty
type: SymmetricProperty
sub property of: is match to

to consume
description: to consume is the capability to internalize a material entity.
type: Class
subclass of: to actively interact with

clause
description: A clause consists of a subject and a predicate.
type: Class
subclass of: sentence

to actively interact with
description: to actively interact with is the capability to interact with another entity in a way that requires physical contact.
type: Class
subclass of: to interact with

is dissimilar to
description: is dissimilar to is a relation between two entities in which one is considered dissimilar to the other based on some criteria.
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of

is opposite to
description: is opposite to is a relation between two entities in which one is diametrically opposed to the other.
type: ObjectProperty
type: SymmetricProperty
sub property of: is dissimilar to
example: hot is the opposite of cold; left is opposite of right

is version of
description: is version of is a relation that holds between any two versions in which one is a subsequent or alternate version of (through a branch).
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is variant of

person
description: A person is an object that has certain capacities or attributes constituting personhood.
type: Class
subclass of: specialized object

to decrease the rate of formation
description: to decrease the rate of formation is to regulate the rate of formation in a manner that decreases this rate relative to a reference process.
type: Class
subclass of: to regulate the rate of formation

polygon vertex
description: A polygon vertex is a terminal point at which two polygon edges meet and are part of a polygon.
type: Class
subclass of: node
subclass of: Restriction
  min qualified cardinality: 2
  on class: polygon edge
  on property: is component part of
subclass of: Restriction
  on class: vertex normal
  on property: has component part
  qualified cardinality: 1

polygon edge
description: A polygon edge is a line segment joining two polygon vertices.
type: Class
subclass of: line segment
subclass of: Restriction
  on property: is part of
  some values from: polygon
subclass of: Restriction
  on class: polygon vertex
  on property: has component part
  qualified cardinality: 2

polyhedral skeleton
description: A polyhedral skeleton is a collection of polygon edges.
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: has direct part
  some values from: polygon edge

polygonal face
description: A polygonal face is a polygon bounded by a circuit of polygon edges, and includes the flat (plane) region inside the boundary.
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: is part of
  some values from: polygon

polyhedral surface
description: A polyhedral surface is composed of polygonal faces.
type: Class
subclass of: geometric entity
subclass of: Restriction
  on property: has part
  some values from: polygonal face

polygon
description: A polygon is a planar entity that is bounded by a closed path or circuit, composed of a finite connected sequence3 of straight line segments.
type: Class
subclass of: geometric entity

geometric entity
description: A geometric entity is an information content entity that pertains to the structure and topology of a space.
subset: geometry+
type: Class
subclass of: information content entity

point
description: A point is a geometric entity that is located in a zero-dimensional spatial region and whose position is defined by its coordinates in some coordinate system.
type: Class
subclass of: geometric entity

endpoint
description: An endpoint is a terminal point that is the last of an ordered pair of points.
type: Class
subclass of: terminal point

start point
description: A start point is a terminal point which is the first of an ordered pair of points.
type: Class
subclass of: terminal point

model
description: A model is a representation of some thing.
type: Class
subclass of: representation
subclass of: Restriction
  on property: represents
  some values from: entity

line
description: A line is curve that extends in a single dimension (e.g. straight line; exhibits no curvature), and is composed of at least two fully connected points.
type: Class
subclass of: curve
equivalent class: Class
  union of: line segment
  union of: ray
  union of: infinite line

line segment
description: A line segment is a line and a part of a curve that is (inclusively) bounded by two terminal points.
type: Class
subclass of: line
subclass of: Restriction
  on class: terminal point
  on property: has component part
  qualified cardinality: 2

tick mark
description: A tick mark is a line segment that is spatially positioned perpendicular to the axis of a statistical graph and indicates the position of a specific numeric value (which may be indicated by an adjacent value label) on a value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value (which may be indicated by an adjacent category label) on the categorical axis.
type: Class
subclass of: line segment

major tick mark
description: A major tick mark is a tick mark that indicates the position of a specific numeric value and is adjacent to its value label on the value axis, or is one of a pair of tick marks that delineates the boundary of a categorical value indicated by an adjacent category label on the categorical axis.
type: Class
subclass of: tick mark

minor tick mark
description: A minor tick mark is a tick mark that indicates the position of a specific numeric value but has no adjacent value label, or is one of a pair of tick marks that delineates the boundary of a categorical value but has no adjacent category label on the categorical axis.
type: Class
subclass of: tick mark

ray
description: A ray is a line which that is bounded by a startpoint and extends outwards infinitely along one dimension.
type: Class
subclass of: line

quadrilateral
description: A quadrilateral is a polygon with composed of four points and four line segments, in which each point is fully connected to two other points.
type: Class
subclass of: polygon

rectangle
description: A rectangle is a quadrilateral in which one pair of line segments are parallel and the other pair are perpendicular to the first pair.
type: Class
subclass of: quadrilateral

bar
description: A bar is a rectangle that is located in the plot of a statistical graph in which its length is proportional to the values that it represents.
type: Class
subclass of: rectangle

triangle
description: A triangle is a polygon composed of three points and three line segments, in which each point is fully connected to another point along through the line segment.
type: Class
subclass of: polygon

directed line segment
description: A directed line segment is a line segment that is contained by an ordered pair of endpoints (a start point and an endpoint).
type: Class
subclass of: line segment
subclass of: Restriction
  on class: endpoint
  on property: has component part
  qualified cardinality: 1
subclass of: Restriction
  on class: start point
  on property: has component part
  qualified cardinality: 1

arrowed line segment
description: An arrowed line is a directed line segment in which one or both endpoints is tangentially part of a triangle that bisects the line.
type: Class
subclass of: directed line segment
subclass of: Restriction
  on property: has part
  some values from: triangle
subclass of: Restriction
  max qualified cardinality: 2
  on class: triangle
  on property: has component part

single arrowed line segment
description: A single arrowed line is directed line in which the endpoint is tangentially part of a triangle that bisects the line.
type: Class
subclass of: arrowed line segment
subclass of: Restriction
  on class: triangle
  on property: has component part
  qualified cardinality: 1
disjoint with: double arrowed line segment

double arrowed line segment
description: A double arrowed line is an arrowed line in which both terminal points are tangentially part of different triangles that bisect the line.
type: Class
subclass of: arrowed line segment
subclass of: Restriction
  on class: triangle
  on property: has component part
  qualified cardinality: 2

horizontal line
description: A horizontal line is a line that is positionally oriented with the horizon.
type: Class
subclass of: positionally oriented line

vertical line
description: A vertical line is a line that is positionally oriented perpendicular to the horizon.
type: Class
subclass of: positionally oriented line

trend line
description: A trend line is a line, line segment or ray that is part of a statistical graph which indicates a statistical or visual direction across categorical or value data.
type: Class
subclass of: statistical graph line

increasing line
description: An increasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is positive.
type: Class
subclass of: trend line

decreasing line
description: An decreasing line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is negative.
type: Class
subclass of: trend line

plateau line
description: An plateau line is a line segment in which the startpoint and endpoint are ordered along one dimension and the difference of values in a second dimension is zero.
type: Class
subclass of: trend line

drop line
description: A drop line is a statistical graph line that vertically or horizontally connects a data series line with a value axis in a statistical graph.
type: Class
subclass of: statistical graph line

terminal point
description: A terminal point is a point that defines the finite extension of a line.
type: Class
subclass of: point

surface normal
description: A surface normal is a vector that is perpendicular to a flat surface.
type: Class
subclass of: vector line

positionally oriented line
description: A positionally oriented line is a line that is positioned against some axis of reference.
type: Class
subclass of: line

statistical graph line
description: A statistical graph line is a line used in a statistical graph to communicate some trend or feature of the embedded data.
type: Class
subclass of: line

to regulate the rate of formation
description: to regulate the rate of formation is to modify the rate at which an object is formed.
type: Class
subclass of: to regulate

curvature
description: curvature is a quality of a bearer that relates to the presence of curves, bends, or angles.
type: Class
subclass of: shape

straight
description: straight is a quality of a bearer that is free of curves, bends, or angles.
type: Class
see also: PATO:0002180 [for material entities]
subclass of: curvature

infinite line
description: An infinite line is a line that extends outwards in both directions of a single dimensional and is not bounded by terminal points.
type: Class
subclass of: line

vector line
description: A vector line is a line which that is bounded by a startpoint and extends outwards along one dimension.
type: Class
subclass of: ray

vertex normal
description: A vertext normal is the normalized average of the surface normals of the faces that contain that vertex.
type: Class
subclass of: vector line

to serve as
description: to serve as is the capability to act in a manner corresponding to some role.
type: Class
subclass of: to actively interact with

to serve as a host
description: to serve as host is the capability to act in a manner that provides hospitality, serves to harbour an organism in or on itself.
type: Class
subclass of: to serve as
subclass of: Restriction
  on property: is capability of
  some values from: host

to infect
description: to infect is the capability to administer a disease-causing organism into some object.
type: Class
subclass of: to inject

polyline
alternative: polygonal chain, polygonal curve, polygonal path, piecewise linear curve
description: A polyline is a connected sequence of line segments.
type: Class
subclass of: geometric entity
subclass of: Restriction
  min qualified cardinality: 2
  on class: line segment
  on property: has component part

collection of points
description: A collection of points is a geometric entity that contains a non-zero set of geometric points.
type: Class
subclass of: geometric entity
subclass of: collection
subclass of: Restriction
  all values from: point
  on property: has member

to cause disease
description: to cause disease is the capability to materially change a biological object in that it functions abnormally.
type: Class
subclass of: to change materially

to reduce the activation energy
alternative: to activate
description: to reduce the activation energy is to require a smaller amount of energy in order to form or break a chemical bond.
type: Class
subclass of: to change the activation energy
disjoint with: to increase the activation energy

to increase the activation energy
alternative: to inhibit
description: to increase the activation energy is to require a larger amount of energy in order to form or break a chemical bond.
type: Class
subclass of: to change the activation energy

to change the activation energy
description: to change the activation energy is to change the amount of energy required to form or break a chemical bond.
type: Class
subclass of: to change energetically

has parameter
description: has parameter is a relation between a process and an information content entity which modulates the behaviour of some participant.
subset: sadi
type: ObjectProperty
sub property of: has input
inverse of: is parameter in

is parameter in
description: is parameter in is a relation between a data item and some data transformation process.
type: ObjectProperty
sub property of: is input in

normal
description: A quality that has a value that is normal or average.
equivalent to: PATO:0000461
type: Class
subclass of: normality
disjoint with: abnormal

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

lipid residue
description: A lipid residue is a part of an organic molecule that was derived from a lipid molecule.
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: lipid

is described by
description: is described by is a relation between one entity and another entity that provides a description (detailed account) of it.
type: ObjectProperty
sub property of: is referred to by
inverse of: describes

is orthologous to
description: is orthologous to is a relation between two biological entities that share a common ancestor and occur in different species.
type: ObjectProperty
type: SymmetricProperty
sub property of: is homologous to

chemical synthesis
description: chemical synthesis is synthesis of a chemical entity from physical precursors through one or more chemical interactions or reactions.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has agent
  some values from: enzyme
subclass of: Restriction
  on property: has product
  some values from: chemical entity

molecular orbital
description: A molecular orbital (or MO) is a mathematical function describing the wave-like behavior of an electron in a molecule.
type: Class
subclass of: chemical quality

passive transport
description: passive transport is the movement of a substance across a membrane and does not require chemical energy.
type: Class
subclass of: membrane transport
disjoint with: active transport

describes
description: describes is a relation between one entity and another entity that it provides a description (detailed account of).
subset: core
type: ObjectProperty
sub property of: refers to

diffusion
description: diffusion is motion of particles at temperatures above absolute zero.
type: Class
subclass of: passive movement

diffusion equation
description: A diffusion equation describes density fluctuations in a material undergoing diffusion.
type: Class
subclass of: movement equation
subclass of: Restriction
  on property: specifies
  some values from: diffusion

movement equation
description: A movement equation describes the displacement of an object in space over time.
type: Class
subclass of: equation

ordinary differential equation
description: An ordinary differential equation (ODE) is a differential equation in which the unknown function (also known as the dependent variable) is a function of a single independent variable.
type: Class
subclass of: differential equation

partial differential equation
description: A partial differential equation (PDE) is a differential equation in which the unknown function is a function of multiple independent variables and the equation involves its partial derivatives.
type: Class
subclass of: differential equation

differential equation
description: A differential equation is a mathematical equation for an unknown function of one or several variables that relates the values of the function itself and its derivatives of various orders.
type: Class
subclass of: equation

movement
description: movement is the process in which an object is spatially displaced.
subset: core
type: Class
subclass of: process

brownian motion
description: Brownian motion is the seemlingly random movement of particles suspended in a fluid.
type: Class
subclass of: diffusion

osmosis
description: osmosis is the movement of water molecules through a selectively-permeable membrane down a water potential gradient.
type: Class
subclass of: diffusion

passive movement
description: passive movement is the process in which an object is spatially displaced without an expenditure of energy contained in molecular bonds.
type: Class
subclass of: movement

active movement
description: active movement is the process in which an object is spatially displaced using some chemical energy.
type: Class
subclass of: movement

transporting
description: transporting is a process in which one object physically moves another object from one location to another.
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: to transport
  intersection of: Restriction
    on property: realizes
    some values from: to be transported

membrane transport
description: membrane transport is the movement of molecules across a membrane.
type: Class
subclass of: chemical transport

primary active transport
description: primary active transport, also called direct active transport, directly uses energy to transport molecules across a membrane.
type: Class
subclass of: active transport
disjoint with: secondary active transport

secondary active transport
description: secondary active transport or co-transport uses electrochemical potential difference created by pumping ions out of the cell to transport molecules across a membrane.
type: Class
subclass of: active transport

symport enabled secondary active transport
description: symport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in the same direction simultaneously.
type: Class
subclass of: secondary active transport
disjoint with: antiport enabled secondary active transport

antiport enabled secondary active transport
description: antiport enabled secondary active transport is a secondary active transfort in which both ion and molecule are transported in opposite directions simultaneously.
type: Class
subclass of: secondary active transport

locomotion
description: The self-propelled movement of an object.
broader than: GO:0040011
type: Class
subclass of: active movement

birthing
description: birthing is the process by which a biological organism is brought into existence.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: biological entity

dying
description: dying is a process in which a biological entity ceases to exist.
type: Class
subclass of: destroying
subclass of: Restriction
  on property: has substrate
  some values from: biological entity

idea
description: An idea is a proposition about some object of conceptual thought.
type: Class
subclass of: proposition

has capability
description: has capability is a relation between an entity and the capability that it bears.
type: InverseFunctionalProperty
type: ObjectProperty
range: capability
sub property of: has realizable property
inverse of: is capability of
example: SIO has the capability to semantically integrate data.

biological reproduction
description: biological reproduction is the biological process by which one or more biological organisms are produced from their "parents".
type: Class
subclass of: reproducing

creating
alternative: creation
alternative: development
alternative: formulation
alternative: production
alternative: synthesis
description: creating is the process in which an entity comes into existence.
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has product
  some values from: object

regulating
alternative: regulation
description: regulating is a process that modulates the attributes of an object or process.
type: Class
subclass of: interacting
equivalent class: Class
  union of: process maintenance
  union of: process up-regulation
  union of: process down-regulation

biosynthesis
description: biosynthesis is the synthesis of an organic compound in a living organism, usually aided by enzymes.
type: Class
subclass of: chemical synthesis

destroying
alternative: destruction
description: destroying is a process in which something is broken down and/or ceases to exist.
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has substrate
  some values from: object

chemical destruction
description: chemical destruction is destruction of a chemical entity to its chemical constituents through one ormore chemical interactions or reactions.
type: Class
subclass of: destroying
subclass of: Restriction
  on property: has target
  some values from: chemical entity

interacting
description: interacting is a process characterized by the interaction between two or more entities.
subset: core
type: Class
subclass of: process
subclass of: Class
  intersection of: Restriction
    min qualified cardinality: 2
    on class: to interact with
    on property: realizes
  intersection of: Restriction
    min qualified cardinality: 2
    on class: to be interacted with
    on property: realizes
subclass of: Restriction
  on property: has participant
  some values from: object

data transformation
description: data transformation is the process of applying an algorithmic procedure to some input data and producing some output data.
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has output
  some values from: data item
subclass of: Restriction
  on property: has input
  some values from: data item

parameterized data transformation
description: A parameterized data transformation is a data transformation whose behaviour may be modified by one or more parameters.
type: Class
subclass of: data transformation
subclass of: Restriction
  on property: has parameter
  some values from: parameter

data storage device
description: A data storage device is a device that is capable of storing information.
type: Class
subclass of: device

solid state hard drive
description: A solid-state drive (SSD) is a data storage device that uses solid-state memory to store persistent data.
type: Class
subclass of: hard disk drive

hard disk drive
description: A hard disk drive (HDD) is a non-volatile, random access device for digital data. It features rotating rigid platters on a motor-driven spindle within a protective enclosure. Data is magnetically read and written on the platter by read/write heads that float on a film of air above the platters.
type: Class
subclass of: data storage device

structure
description: structure is the specification that refers to the composition and arrangement of parts of an object.
type: Class
subclass of: functional specification

computational entity
description: A computational entity is an information content entity operated on using some computational system.
type: Class
subclass of: information content entity

sound wave
description: A sound wave is a mechanical wave that is an oscillation of pressure transmitted through a solid, liquid, or gas, composed of frequencies within the range of hearing.
type: Class
subclass of: wave

curve
description: A curve is a geometric entity that may be located in n-dimensional spatial region whose extension may be n-dimensional, is composed of at least two fully connected points and does not intersect itself.
type: Class
subclass of: geometric entity

regulation of process
description: regulation of a process is a process that modulates the duration, frequency, spatial extent of a target process.
type: Class
subclass of: regulating
subclass of: Restriction
  on property: regulates
  some values from: process
equivalent class: Class
  union of: regulation of process frequency
  union of: regulation of process duration
  union of: regulation of process spatial extent
  union of: regulation of object quantity

regulation of capability
description: regulation of capability is the regulation of the ability of one party by another.
type: Class
subclass of: regulating
subclass of: Restriction
  on property: affects
  some values from: capability

regulation of catalytic capability
description: the regulation of the enzymatic activity.
type: Class
subclass of: regulation of capability
subclass of: Restriction
  on property: regulates
  some values from: to change materially

representation
description: A representation is a entity that in some way represents another entity (or attribute thereof).
type: Class
subclass of: information content entity
subclass of: Restriction
  on property: is model of
  some values from: entity

ordinal position
alternative: offset
description: A ordinal position is a number that designates the position of an entity from the first entity in an ordered sequence of entities.
type: Class
subclass of: linear position

attribute
description: An attribute is a characteristic of some entity.
subset: core
type: Class
subclass of: entity
subclass of: Restriction
  on property: is attribute of
  some values from: entity

collection
description: A collection is a set for which there exists at least one member, although any member need not to exist at any point in the collection's existence.
type: Class
subclass of: set
subclass of: Restriction
  on property: has member
  some values from: entity

empty set
description: An empty set is a set for which there are exactly 0 members.
type: Class
subclass of: set
subclass of: Restriction
  on class: entity
  on property: has member
  qualified cardinality: 0

standard
description: A standard is a socially-agreed upon specification.
type: Class
subclass of: specification
subclass of: Restriction
  on property: has quality
  some values from: agreement

regulatory authority
description: A regulatory authority is an organization responsible for exercising regulatory or supervisory capacity in some area of human activity.
type: Class
subclass of: organization

collective
alternative: group
description: A collective is a group of entities that share or are motivated by at least one common issue or interest, or work together on a specific project(s) to achieve a common objective.
type: Class
subclass of: social structure

formal specification
description: A formal specification is a mathematical description of software or hardware that may be used to develop an implementation.
type: Class
subclass of: functional specification

RDFS ontology
description: An RDFS ontology is an ontology that conforms to the syntax and semantics of the Resource Description Framework Schema (RDFS).
type: Class
subclass of: ontology document

OBO ontology
description: An OBO ontology is an ontology document as specified by the Open Biological Ontology community.
type: Class
subclass of: ontology document

chemical functional group
alternative: chemical group
description: A chemical functional group is a submolecule that confers specific chemical properties.
type: Class
subclass of: submolecule

chemical structure
description: chemical structure is the structure of a chemical entity in terms of its molecular geometry and electronic structure.
type: Class
subclass of: structure

molecular structure
alternative: molecular geometry
description: molecular structure is the spatial arrangement of atoms in a molecule and the chemical bonds that hold the atoms together.
type: Class
subclass of: chemical structure

refers to
description: refers to is a relation between one entity and the entity that it makes reference to.
subset: core
subset: nlp+
type: ObjectProperty
sub property of: is related to

is subject of
type: ObjectProperty
sub property of: is described by

is paralogous to
description: is paralogous to is a relation between two entities which indicates their common ancestry as a result of a gene duplication.
type: ObjectProperty
type: SymmetricProperty
sub property of: is homologous to

references
alternative: mentions
description: references is a relation between one entity and the entity that it makes reference to by name, but is not described by it.
subset: core
type: ObjectProperty
sub property of: refers to

is model of
description: is model of is a relation between a model (an artifact) and the entity it purports to represent.
type: ObjectProperty
sub property of: represents
inverse of: is modelled by
example: the architect builds a model that represents the building she envisions.

is modelled by
type: ObjectProperty
sub property of: is represented by

is xenologous to
description: a relation between two entities which indicates their common ancestry but due to horizontal gene transfer.
type: ObjectProperty
type: SymmetricProperty
sub property of: is orthologous to

has trigger
description: has trigger is a relation between a realizable and the factor that causes it to be realized.
type: ObjectProperty
sub property of: is causally related to
inverse of: is trigger for

is trigger for
type: ObjectProperty
sub property of: is causally related from

probability measure
description: A probability measure is quantity of how likely it is that some event will occur.
type: Class
subclass of: dimensionless quantity

to passively interact with
description: to passively interact with is the capability to interact with another entity in a way that does not require physical contact.
type: Class
subclass of: to interact with

increased
description: A quality that has a value that is increased compared to normal or average.
equivalent to: PATO:0002300
type: Class
subclass of: abnormal
disjoint with: decreased

has basis
description: has basis is a relation between a realizable entity and the quality that forms the basis for it.
type: ObjectProperty
domain: realizable entity
range: quality
sub property of: has attribute
inverse of: is base for
example: the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization).

is base for
description: is base for is a relation between a quality and the realizable entity that it is the basis for.
type: ObjectProperty
domain: quality
range: realizable entity
sub property of: is attribute of
example: the solubility of salt (the disposition) is based on the molecular structure of NaCl (the quality) that allows the polarized water-molecules (the trigger) to break the ion bonds (the realization).

is realizable property of
type: FunctionalProperty
type: ObjectProperty
sub property of: is property of
inverse of: has realizable property

has realizable property
type: InverseFunctionalProperty
type: ObjectProperty
sub property of: has property

is capability of
description: is capability of is a relation between a capability and the entity that bears it.
type: FunctionalProperty
type: ObjectProperty
domain: capability
sub property of: is realizable property of

process model
description: A process model is a representation of some process.
type: Class
subclass of: model
subclass of: Restriction
  on property: is model of
  some values from: process
disjoint with: object model

object model
description: An object model is a representation of an object.
type: Class
subclass of: model

information processing
description: information processing is a process that involves the generation or use of information.
type: Class
subclass of: procedure

wave
description: A wave is a physical entity that travels through space and time, consist of oscillations or vibrations and may be accompanied by the transfer of energy.
type: Class
subclass of: heterogeneous substance

textual entity
description: A textual entity is language entity that is manifested as a sequence of one or more distinct characters.
type: Class
subclass of: language entity

is directly connected to
description: A is directly connected to B iff there exists a path direclty between A and B.
type: ObjectProperty
type: SymmetricProperty
sub property of: is connected to

version label
description: A version label is a label for a particular form or variation of an earlier or original type.
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is identifier for
  some values from: Restriction
    on property: is variant of
    some values from: entity

software version label
description: A software version label is a version label for a piece of software.
type: Class
subclass of: version label
subclass of: Restriction
  on property: is identifier for
  some values from: software entity
example: major.minor[.build[.revision]]

transforms into
description: A transitive temporal relation in which an entity mainstains identity from one state to another.
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related to
inverse of: is transformed from

immediately transforms into
description: A temporal relation in which an entity mainstains identity from one state to another.
type: ObjectProperty
sub property of: transforms into
inverse of: is immediately transformed from

is transformed from
description: A transitive temporal relation in which an entity mainstains identity from one state to another.
type: ObjectProperty
type: TransitiveProperty
sub property of: is causally related from

is immediately transformed from
description: A temporal relation in which an entity mainstains identity from one state to another.
type: ObjectProperty
sub property of: is transformed from

hole
description: A hole is a site that is opening into or through something.
type: Class
subclass of: site

province
description: A province is a territorial unit, almost always an administrative division, within a country or state.
type: Class
subclass of: geopolitical region
subclass of: Restriction
  on property: is proper part of
  some values from: country

state
description: A state is a set of governing and supportive institutions that have sovereignty over a definite territory and population.
type: Class
subclass of: geopolitical region

territory
description: A territory is a non-sovereign geographic region.
type: Class
subclass of: geopolitical region

country
description: A country is a region legally identified as a distinct entity in political geography.
type: Class
subclass of: geopolitical region

city
description: A city is a relatively large and permanent settlement.
type: Class
subclass of: geopolitical region

township
description: A township is a rural or sub-urban settlement.
type: Class
subclass of: geopolitical region

software execution
description: software execution is the process of executing software on a computing device.
type: Class
subclass of: information processing

in relation to
description: in relation to is a comparative relation to indicate that the instance of the class holding the relation exists in relation to another entity.
subset: core
type: ObjectProperty
sub property of: refers to
inverse of: in relation from

start time
description: A start time is a time instant pertaining to the time at which a process begins.
type: Class
subclass of: time instant

end time
description: An end time is a time instant pertaining to the time at which a process ends.
type: Class
subclass of: time instant

has identifier
description: a relation between an entity and an identifier.
type: ObjectProperty
range: identifier
sub property of: has attribute
inverse of: is identifier for

is identifier for
alternative: identifies
description: a relation between an identifier and an entity.
type: ObjectProperty
domain: identifier
sub property of: is attribute of

has unique identifier
description: has unique identifier is an inverse functional relation between an entity and an identifier that uniquely identifies it.
type: InverseFunctionalProperty
type: ObjectProperty
range: unique identifier
sub property of: has identifier
inverse of: is unique identifier for

is unique identifier for
description: is unique identifier for is a relation between an identifier and an entity that it uniquely identifies
type: FunctionalProperty
type: ObjectProperty
domain: unique identifier
sub property of: is identifier for

unique identifier
description: A unique identifier is an identifier that uniquely identifies some thing.
type: Class
subclass of: identifier
subclass of: Restriction
  on property: is unique identifier for
  some values from: entity
equivalent class: Class
  intersection of: identifier
  intersection of: Restriction
    on property: is unique identifier for
    some values from: entity

social role
description: A social role is a role that is ascribed to individuals in a community.
type: Class
subclass of: role

processual role
description: A processual role is a role that can only be realized in a process.
type: Class
subclass of: role

abstract role
description: An abstract role is a role whose basis lies in spatial/temporal or comparative relations.
type: Class
subclass of: role

has time boundary
type: FunctionalProperty
type: ObjectProperty
range: time instant
sub property of: has boundary

has start time
type: FunctionalProperty
type: ObjectProperty
range: time instant
sub property of: has time boundary
inverse of: is start time of

has end time
type: FunctionalProperty
type: ObjectProperty
range: time instant
sub property of: has time boundary
inverse of: is end time of

is start time of
type: ObjectProperty
domain: time instant
sub property of: is time boundary of

justification
description: A justification is a proposition that defends, explains or excuses some argument.
type: Class
subclass of: proposition

is end time of
type: ObjectProperty
domain: time instant
sub property of: is time boundary of

academic department
description: An academic department is a division of a university or school faculty devoted to a particular academic discipline.
type: Class
subclass of: academic organization

exists at
description: exists at is a relation between an entity and a time measurement.
subset: core
type: ObjectProperty
range: time measurement
sub property of: is spatiotemporally related to

institute
description: institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective.
type: Class
subclass of: organization

to be a part of
description: to be a part of is the capability to be assembled into a larger structure that persists in time.
type: Class
subclass of: to be combined

to associate
description: to associate is the capability to physically interact with another object.
type: Class
subclass of: to actively interact with

to be actively interacted with
description: to be actively interacted with is the capability to be manipulated by some device or agent.
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutually related to
  some values from: to actively interact with
disjoint with: to be passively interacted with

corporation
description: A corporation is an organization that is granted a charter recognizing it as a separate legal entity.
type: Class
subclass of: organization

to be passively interacted with
description: to be passively interacted with is the capability of an object to be observed.
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutually related to
  some values from: to passively interact with

to be recorded
description: to be recorded is the capability of an object to be observed in such a way that information about it can be transcribed in a specified format on some physical medium.
type: Class
subclass of: to be observed
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to record

to be observed
description: to be observed is the capability of an object to be perceived.
type: Class
subclass of: to be passively interacted with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to observe

is mutual disposition of
description: a is mutual disposition of b if and only if the realization of the disposition a necessarily causes the realization of the disposition b.
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to

to disassemble
description: to disassemble is to physically separate the parts of an object.
type: Class
subclass of: to change materially

is greater than or equal to
description: is greater than or equal to is a comparison relation between two quantities in which the first has a value larger or equal to the second.
type: ObjectProperty
type: TransitiveProperty
sub property of: is numerically comparable to
inverse of: is lesser than or equal to

to disassociate
description: to disassociate is to cease or break association with some thing.
type: Class
subclass of: to modify

to interact with
description: to interact with is a capabililty that involves another object.
type: Class
subclass of: capability
subclass of: Restriction
  on property: in relation to
  some values from: entity
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to be interacted with

to be interacted with
description: to be interacted with is the capability of an object to be target of a physical interaction.
type: Class
subclass of: capability
subclass of: Restriction
  on property: in relation to
  some values from: entity
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to interact with

evolving
description: evolving is a process that elicits change across successive generations in the inherited characteristics of biological populations.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: entity

positional role
description: A positional role is an abstract role which holds by comparing position to another object of reference.
type: Class
subclass of: abstract role
disjoint with: comparative role

design
description: A specification of an object, manifested by an agent, intended to accomplish goals, in a particular environment, using a set of primitive components, satisfying a set of requirements, subject to constraints.
type: Class
subclass of: functional specification

occupational role
description: An occupational role is a social role that pertains to an organizational structure.
type: Class
subclass of: social role

student role
description: A student role is the role of an individual that is enrolled in courses at an academic institution.
type: Class
subclass of: academic role
subclass of: Restriction
  on property: is role of
  some values from: student
disjoint with: professor role

professor role
description: A professor role is the role of an individual that is involved in teaching of students (undergraduate and/or graduate) at a post-secondary academic institution.
type: Class
subclass of: academic role
subclass of: Restriction
  on property: is role of
  some values from: professor
subclass of: Restriction
  on property: is mutual role of
  some values from: student role

is mutually related to
description: a is mutually related to b if and only if the realization of the relation of a necessarily causes the realization of a relation to b.
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to

is mutual role of
description: a is mutual role of b if and only if the realization of role a necessarily causes the realization of role b.
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to

academic role
description: An academic role is a social role that pertains to the academic institution.
type: Class
subclass of: occupational role

medical role
description: A medical role is the role of an individual that is a participant in the delivery of medical care.
type: Class
subclass of: occupational role

doctor role
alternative: physician
description: A doctor role is the role of an individual who practices medicine, which is concerned with promoting, maintaining or restoring human health through the study, diagnosis, and treatment of disease, injury, and other physical and mental impairments.
type: Class
subclass of: medical role

nurse role
description: A nurse role is the role of an individual that is involved in the protection, promotion, and optimization of health and abilities, prevention of illness and injury, alleviation of suffering through the diagnosis and treatment of human response, and advocacy in the care of individuals, families, communities, and populations.
type: Class
subclass of: medical role

patient role
description: A patient role is the role of an individual that is the recepient of medical care.
type: Class
subclass of: medical role

medical practitioner
description: A medical practioner is an individual that provides medical care.
type: Class
subclass of: person

dentist role
description: A dentist role is the role of an individual that that specializes in the diagnosis, prevention, and treatment of diseases and conditions of the oral cavity.
type: Class
subclass of: medical role

to translocate
alternative: to move
description: to translocate is the capability to displace oneself from one location to another.
type: Class
subclass of: to interact with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to be translocated
disjoint with: to be translocated

to be translocated
alternative: to be moved
description: to be translocated is the capability to be physically displaced from one location to another
type: Class
subclass of: to be interacted with
subclass of: Restriction
  on property: is mutual disposition of
  some values from: to translocate

comparative role
description: A comparative role is an abstract role which holds by comparing some attribute of another object of reference.
type: Class
subclass of: abstract role

to be compared
description: to be compared is the capability of an object to be examined in order to note the similarities or differences among a set of objects.
type: Class
subclass of: to be examined

to compare
description: to compare is the capability to examine in order to note the similarities or differences among a set of objects.
type: Class
subclass of: to examine

to examine
description: to examine is the capability to make detailed observation.
type: Class
subclass of: to observe

to be examined
description: to be examined is the capability of an object to be observed in a detailed manner.
type: Class
subclass of: to be observed

administrative role
description: An administrative role is the role of an individual that performs administrative tasks for some organization.
type: Class
subclass of: occupational role

secretary role
description: A secretary role is the role of an individual that performs administrative tasks to support one or more individuals of the same organization.
type: Class
subclass of: administrative role

chemical identifier
description: A chemical identifier is an identifier for a chemical entity
type: Class
subclass of: physical entity identifier

record identifier
description: A record identifier is an identifier for a database entry.
type: Class
subclass of: informational entity identifier
subclass of: Restriction
  on property: is identifier for
  some values from: database entry

physical entity identifier
description: A physical entity identifier is an identifier for a physical entity.
type: Class
subclass of: identifier

informational entity identifier
description: An informational entity identifier is an identifier for an informational entity.
type: Class
subclass of: identifier

molecular identifier
description: A molecular identifier is an identifier for a molecular entity.
type: Class
subclass of: chemical identifier

is lesser than or equal to
description: is greater than to is a comparison relation between two quantities in which the first has a value smaller or equal to the second.
type: ObjectProperty
type: TransitiveProperty
sub property of: is numerically comparable to

is greater than
description: is greater than to is a comparison relation between two quantities in which the first has a value larger than the second.
type: ObjectProperty
type: TransitiveProperty
sub property of: is greater than or equal to
inverse of: is lesser than

is lesser than
description: is lesser than to is a comparison relation between two quantities in which the first has a value smaller than the second.
type: ObjectProperty
type: TransitiveProperty
sub property of: is lesser than or equal to

is comparable to
description: is comparable to is a relation between two entities that share at least one feature whose value can be compared.
subset: core
type: ObjectProperty
type: SymmetricProperty
sub property of: is related to

is numerically comparable to
description: is numerically comparable to is a comparison relation between two quantities whose datatype value can be compared.
type: ObjectProperty
type: SymmetricProperty
domain: quantity
range: quantity
sub property of: is comparable to

is equal to
description: is equal to is a comparison relation between two quantities whose value are exactly the same.
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is numerically comparable to

planning
description: planning is the agentive process of developing a plan that specifies a set of actions in order to meet a set of goals or objectives.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: Class
    union of: plan
    union of: design

curve segment
description: A curve segment is a part of a curve that consists of at least three points.
type: Class
subclass of: curve

stationary point
description: A stationary point is a point that is part of a curve in which the derivative at that point is zero, and hence its value is at least a local maximum or minimum.
type: Class
subclass of: data point

local maximum stationary point
description: A local maximum stationary point is a point that has a higher value in some axis than adjacent points.
type: Class
subclass of: stationary point

local minimum stationary point
description: A local minimum stationary point is a point that has a lower value in some axis than adjacent points.
type: Class
subclass of: stationary point

learning
description: learning is the agentive process of acquiring knowledge.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: proposition

comparing
alternative: comparison
description: comparing is the process of examining a set of objects and determining their equality or inequality based on one or more features.
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: to be compared
  intersection of: Restriction
    on property: realizes
    some values from: to compare

reasoning
description: reasoning is the agentive process of using knowledge to evaluate the truth value of a proposition.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: Class
    intersection of: truth value
    intersection of: Restriction
      on property: is quality of
      some values from: proposition

investigation
alternative: study
description: investigation is the process of carrying out a plan or procedure so as to discover facts or information about the object of study.
type: Class
subclass of: procedure
subclass of: Restriction
  on property: has product
  some values from: object
subclass of: Restriction
  on property: realizes
  some values from: objective

predicting
description: predicting is the process of formulating a proposition about a state of affairs which might be realized in the future.
type: Class
subclass of: creating
subclass of: Restriction
  on property: has product
  some values from: proposition

is inequal to
description: is inequal to is a comparison relation between two quantities whose value are not the same.
type: ObjectProperty
type: SymmetricProperty
sub property of: is numerically comparable to

database
description: A database is a set of tables.
type: Class
subclass of: computational entity

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

row
description: A row represents a single, implicitly structured data item in a table.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: has proper part
  some values from: cell (informational)
subclass of: Restriction
  on property: has identifier
  some values from: identifier

column
description: A column is a vertical sequence of cells in a cellular automata.
type: Class
subclass of: computational entity
subclass of: Restriction
  all values from: Class
    intersection of: cell (informational)
    intersection of: Restriction
      on property: has value
      some values from: Literal
    intersection of: Restriction
      all values from: Literal
      on property: has value
  on property: specifies
subclass of: Restriction
  min qualified cardinality: 0
  on class: name
  on property: has attribute

database table
description: A database table is a set of named columns with zero or more rows composed of cells that contain column values and is part of a database.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is proper part of
  some values from: database

cell (informational)
description: The minimal unit of a cellular automaton that can change state and has an associated behavior.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: refers to
  some values from: entity

database entry
alternative: database record
description: A database entry is a single, implicitly structured data item in a table.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: is proper part of
  some values from: database

database column
description: A database collumn is a column in a database table.
type: Class
subclass of: column
subclass of: Restriction
  on property: is proper part of
  some values from: database table

disordered
description: disordered is a structural quality in which the parts of an object are non-rigid.
type: Class
subclass of: structural quality
subclass of: Restriction
  on property: is quality of
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has quality
      some values from: abnormal
disjoint with: rigid

unique cell
description: A unique cell is a cell that contains a unique value in the cellular automaton.
type: Class
subclass of: cell (informational)
subclass of: Restriction
  on property: has attribute
  some values from: unique identifier

referencing cell
description: A referenceing cell is a cell of a cellular automata that refers to another cell.
type: Class
subclass of: cell (informational)

referent cell
description: A referent cell is a cell that is the referent of some function or pointer.
type: Class
subclass of: cell (informational)
subclass of: Restriction
  on property: is referred to by
  some values from: cell (informational)

database key
description: A database key is an informational entity whose value is constructed from one or more database columns.
type: Class
subclass of: computational entity
subclass of: Restriction
  on property: has component part
  some values from: column
subclass of: Restriction
  on property: has value
  some values from: Literal

primary database key
description: A primary database key is a database key that identifies every row of a table.
type: Class
subclass of: database key
subclass of: Class
  complement of: Restriction
    has value: null
    on property: has value
subclass of: Restriction
  on property: is unique identifier for
  some values from: row

foreign database key
description: A foreign database key is a database key that refers to a key in some table.
type: Class
subclass of: database key
subclass of: Restriction
  on property: references
  some values from: database key

probability value
alternative: p-value
description: A p-value or probability value is the probability of obtaining a test statistic at least as extreme as the one that was actually observed, assuming that the null hypothesis is true
type: Class
subclass of: probability measure
subclass of: Restriction
  on property: has value
  some values from: Datatype
    on datatype: double
    with restrictions:
      min inclusive: 0.0
    with restrictions:
      max inclusive: 1.0

street name
description: A street name is the token given to identify a particular street.
type: Class
subclass of: positional identifier

postal code
description: A postal code is a geographic coordinate composed of a series of letters and/or digits appended to a postal address for the purpose of sorting mail.
type: Class
subclass of: geographic position

apartment number
description: An apartment number is the number assigned to identify an apartment in a building of apartments.
type: Class
subclass of: positional identifier

uncertainty value
description: The uncertainty value (margin of error) of a measurement is a range of values likely to enclose the true value.
type: Class
subclass of: quantity

standard deviation
description: A standard deviation (represented by the symbol σ) is the quantity of variation from the average (mean, or expected value).
type: Class
subclass of: quantity

versioned record
description: A versioned record is a record for which there exists another variant based that was derived via modification of the facts.
type: Class
subclass of: record

has evidence
description: has evidence is a relation between a proposition and something that demonstrates the truth of the assertion.
type: ObjectProperty
sub property of: references
inverse of: is evidence for

is evidence for
type: ObjectProperty
sub property of: is referenced by

is refuted by
description: has evidence is a relation between a proposition and something that refutes (is incompatible with) the truth of the assertion.
type: ObjectProperty
sub property of: has evidence
inverse of: is refuting evidence for

is refuting evidence for
type: ObjectProperty
sub property of: is evidence for

object
description: An object is an entity that is wholly identifiable at any instant of time during which it exists.
subset: core
type: Class
subclass of: entity
subclass of: Restriction
  all values from: object
  on property: has proper part

to be a member of
description: to be a member of is the capability to be considered a part of a collection.
type: Class
subclass of: to passively interact with

to distort
description: to distort is the capability to change the appearance of an entity by some transformation.
type: Class
subclass of: to change appearance

primer
description: A primer is a nucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.
type: Class
subclass of: Class
  intersection of: nucleic acid
  intersection of: Restriction
    on property: has capability
    some values from: Class
      intersection of: to bind to
      intersection of: Restriction
        on property: has capability
        some values from: to serve as a primer for DNA synthesis
      intersection of: Restriction
        on property: in relation to
        some values from: Class

to bind to
description: to bind to is the capability to physically interact with another object through a set of non-covalent interactions.
type: Class
subclass of: to associate

spatial boundary
description: A spatial boundary is the closure minus the interior of a subset of a topological space.
type: Class
subclass of: spatial region

hermaphrodite
description: hermaphrodite is a biological sex of an individual with both male and female sexual organs.
equivalent to: PATO:0001827
type: Class
subclass of: intersex
disjoint with: male

answer
description: An answer is a reply to a question.
type: Class
subclass of: description

verbal language entity
description: A verbal language entity is a language entity that is manifested through sound.
type: Class
subclass of: language entity

page number
description: A page number is the count of a page in a sequence of pages.
type: Class
subclass of: count

linear position
description: A linear position is the position of some object against a linear positioning system.
type: Class
subclass of: position

sequence element position
description: A sequence element position is the position of an element of a linear sequence.
type: Class
subclass of: linear position

non-protein coding RNA (ncRNA) gene
alternative: ncRNA gene
description: A non-protein coding RNA (ncRNA) gene is a gene that encodes for a RNA transcript that is not further translated into a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001263
type: Class
subclass of: gene

sequence start position
description: A sequence start position is the start position for a sequence of characters.
type: Class
subclass of: sequence element position
subclass of: start position

sequence end position
description: A sequence end position is the position of the last character in a sequence of characters relative to some linear frame of reference.
type: Class
subclass of: sequence element position
subclass of: end position

measured at
description: measured at is a relation between a measurement value and the time measurement.
subset: core
type: ObjectProperty
range: time measurement
sub property of: exists at

count
description: The number of elements of a finite set of objects.
type: Class
subclass of: dimensionless quantity

chemical entity role
description: A chemical role is a processual role held by a chemical entity.
type: Class
subclass of: processual role
subclass of: Restriction
  on property: is role of
  some values from: chemical entity

catalytic role
description: The role of a chemical participant that serves to increase the rate of reaction by lowering the activiation energy.
type: Class
subclass of: regulator role

substrate role
description: The role of a chemical entity that is modified in a chemical reaction.
type: Class
subclass of: reactant role

product role
description: The role of a chemical entity present at the end of a chemical reaction.
type: Class
subclass of: molecular entity role
subclass of: Restriction
  on property: is role of
  some values from: product

cofactor role
description: The role of a chemical entity involved in the mechanism for enzyme-mediated catalysis.
type: Class
subclass of: molecular entity role

co-enzyme role
description: A co-factor role in which the chemical entity is modified during catalysis and must be regenerated.
type: Class
subclass of: substrate role
subclass of: cofactor role

prosthetic group role
description: A coenzyme role of a chemical entity that is covalently bonded to the enzyme.
type: Class
subclass of: co-enzyme role

co-substrate role
description: A co-enzyme role of a chemical entity that is transiently associated, and is regenerated in a separate reaction.
type: Class
subclass of: co-enzyme role

inhibitor role
description: The role of a chemical entity that reduces the rate of reaction.
type: Class
subclass of: regulator role

activator role
description: The role of a chemical entity that increases the rate of reaction.
type: Class
subclass of: regulator role

charged
description: The quality of having a charge.
type: Class
subclass of: charge quality
disjoint with: uncharged

uncharged
description: The quality of not having a charge.
type: Class
subclass of: charge quality

partial positive charge
description: A partial negative charge is a negative charge where the value of the charge is negative.
type: Class
subclass of: partial charge
disjoint with: partial negative charge

partial negative charge
description: A partial positive charge is a partial charge where the value of the charge is positive.
type: Class
subclass of: partial charge

partial charge
description: The quality of having a charge that is not a full multiple of 1 unit charge.
type: Class
subclass of: charged
equivalent class: Class
  union of: partial positive charge
  union of: partial negative charge

complete charge
description: A complete charge is a charge where the value of the charge is a multiple of 1.
type: Class
subclass of: charged
equivalent class: Class
  union of: positive charge
  union of: negative charge

URL
alternative: Uniform Resource Locator
description: A Uniform Resource Locator or Universal Resource Locator (URL) is a specific character string that constitutes a reference to an Internet resource.
type: Class
subclass of: informational entity identifier
subclass of: Restriction
  on property: has value
  some values from: anyURI

affection
description: affection is an emotion characterized with a feeling or type of love for another living thing.
type: Class
subclass of: positive emotion

angst
description: angst is the intense feeling of apprehension, anxiety or inner turmoil.
type: Class
subclass of: anxiety

annoyance
description: Annoyance is an unpleasant emtion that is characterized by a abnormal or excessive sensitivity to some external stimulus.
type: Class
subclass of: negative emotion

anxiety
description: anxiety is an emotion charactersized by intense feeling of fear and concern coupled with a physical response.
type: Class
subclass of: apprehension

apathy
description: apathy is an emotion characterized by lack of interest, enthusiasm, or concern.
type: Class
subclass of: indifference

arousal
description: arousal is an emotion characterized by state of reactive to stimuli. It involves the activation of the reticular activating system in the brain stem, the autonomic nervous system and the endocrine system, leading to increased heart rate and blood pressure and a condition of sensory alertness, mobility and readiness to respond.
type: Class
subclass of: positive emotion

awe
description: awe is an emotion produced by that which is grand, sublime or powerful and is characterized by a combination of joy, fear and admiration/reverence/respect.
type: Class
subclass of: positive emotion

boldness
description: boldness is the trait of being willing to undertake things that involve risk or danger.
type: Class
subclass of: positive emotion

boredom
description: boredom is the emotion experience by those not interested in their surroundings or available activities.
type: Class
subclass of: negative emotion

contempt
description: contempt is disgust towards a lower status individual.
type: Class
subclass of: disgust

contentment
description: contentment is an emotion characterized by acknowledgement and satisfaction of the current state of affairs.
type: Class
subclass of: happiness

curiosity
description: curiosity is the strong desire to know or learn something.
type: Class
subclass of: desire

depression
alternative: depressed
description: depression is an unpleasant emotion linked to aversion to activity that can affect a person's thoughts, behavior, feelings and physical well-being. Depressed individuals may feel sad, anxious, empty, hopeless, worried, helpless, worthless, guilty, irritable, or restless.
type: Class
subclass of: sadness

desire
description: desire is a strong emotion of wanting to have something or wishing for something to happen.
type: Class
subclass of: interest

despair
description: despair is depression, hopelessness or lack of hope.
type: Class
subclass of: sadness

disappointment
alternative: disappointed
alternative: disappointing
description: disappointment is the feeling of dissatisfaction that follows the failure of expectations or hopes to manifest.
type: Class
subclass of: negative emotion

disgust
description: Disgust is a feeling of revulsion or profound disapproval aroused by something unpleasant or offensive.
type: Class
subclass of: hostility

dread
description: dread is the instense negative emotion that induces fear and apprehension.
type: Class
subclass of: fear

ecstasy
description: ecstacy is an emotion characterized by a heightened state of consciousness with total involvement of a subject.
type: Class
subclass of: positive emotion

positive emotion
description: A positive emotion is an emotion that feels good.
type: Class
subclass of: emotion
subclass of: Restriction
  on property: has quality
  some values from: positive

negative emotion
description: negative emotion is an emotion that does not feel good.
type: Class
subclass of: emotion
subclass of: Restriction
  on property: has quality
  some values from: negative

embarassment
description: Embarrassment is the emotion of intense discomfort with oneself, experienced upon having a socially unacceptable act or condition witnessed by or revealed to other.
type: Class
subclass of: negative emotion

envy
description: envy is an emotion that occurs when a person lacks another's (perceived) superior quality, achievement or possession and wishes that the other lacked it.
type: Class
subclass of: negative emotion

euphoria
description: euphoria is an emotion characterized by intense feelings of well-being, elation, happiness, ecstasy, excitement, and joy.
type: Class
subclass of: happiness

excitement
description: excitement is a positive emotion of feeling great enthusiasm and eagerness.
type: Class
subclass of: positive emotion

fear
description: Fear is a negative emotion induced by a perceived threat that induces one to hide or move quickly away from the location of the perceived threat.
type: Class
subclass of: apprehension

frustration
description: Frustration is an emotion that arises from the perceived resistance to the fulfillment of individual will.
type: Class
subclass of: annoyance

gratitude
alternative: appreciation
alternative: gratefulness
alternative: gratification
alternative: thankfullness
description: Gratitude, thankfulness, gratefulness, or appreciation is a feeling, emotion or attitude in acknowledgment of a benefit that one has received or will receive.
type: Class
subclass of: positive emotion

happiness
description: happiness is an emotion characterized by positive or pleasant emotions ranging from contentment to intense joy.
type: Class
subclass of: positive emotion

guilt
alternative: guilty
description: Guilt is the emotion borne from feeling responsible for the commission of an offense and arises out of public humiliation.
type: Class
subclass of: negative emotion

grief
description: grief is an emotion in response to loss, whether physical or abstract including death, unemployment, ill health or the end of a relationship.
type: Class
subclass of: sadness

hope
description: hope is an emotion of belief in a positive outcome related to events and circumstances in one's life.
type: Class
subclass of: positive emotion

hostility
description: Hostility is the intense negative emotion of being in conflict or opposition to someone or something.
type: Class
subclass of: negative emotion

hurt
description: hurt is an unpleasant feeling, emotion or sensation.
type: Class
subclass of: negative emotion

hysteria
description: Hysteria is an unmanageable emotion.
type: Class
subclass of: negative emotion

indifference
description: indifference is an emotion characterized by lack of interest, concern, or sympathy.
type: Class
subclass of: emotion
subclass of: Class
  intersection of: Class
    complement of: Restriction
      on property: has quality
      some values from: positive
  intersection of: Class
    complement of: Restriction
      on property: has quality
      some values from: negative

interest
description: interest is the emotion of wanting to know or learn about something or someone.
type: Class
subclass of: positive emotion

jealousy
description: jealousy is an emotion and typically refers to the negative thoughts and feelings of insecurity, fear, and anxiety over an anticipated loss of something that the person values, particularly in reference to a human connection.
type: Class
subclass of: envy

joy
description: joy is an emotion of intense happiness.
type: Class
subclass of: happiness

loathing
description: loathing is an intense dislike or disgust.
type: Class
subclass of: disgust

loneliness
description: Loneliness is an unpleasant emotion in which a person feels a strong sense of emptiness, yearning distress and solitude resulting from inadequate quantity or quality of social relationships.
type: Class
subclass of: negative emotion

lust
description: lust is the strong desire for sex.
type: Class
subclass of: desire

misery
description: misery is a feeling of great unhappiness, suffering and/or pain.
type: Class
subclass of: sadness

panic
description: Panic is a sudden emotion of fear which is so strong as to dominate or prevent reason and logical thinking, replacing it with overwhelming feelings of anxiety and frantic agitation consistent with an animalistic fight-or-flight reaction.
type: Class
subclass of: fear

passion
description: passion is the intense desire for something.
type: Class
subclass of: desire

pity
description: Pity is the emotion of sadness or sorrow for another.
type: Class
subclass of: negative emotion

pleasure
description: pleasure is an emotion of happy satisfaction and enjoyment.
type: Class
subclass of: happiness

pride
description: pride is an emotion of satisfaction of attachment toward one's own or another's choices and actions, or toward a whole group of people, and is a product of praise, independent self-reflection, or a fulfilled feeling of belonging.
type: Class
subclass of: satisfaction

rage
description: Rage is a feeling of intense anger that is associated with the Fight-or-flight response.
type: Class
subclass of: anger

regret
description: regret is a feeling of sadness, repentance, or disappointment over something that has happened or been done.
type: Class
subclass of: worry

remorse
description: remorse is an emotion of personal regret felt by a person after he or she has committed an act which they deem to be shameful, hurtful, or violent.
type: Class
subclass of: regret

sadness
alternative: sad
alternative: unhappiness
alternative: unhappy
description: sadness is emotional pain associated with, or characterized by feelings of disadvantage, loss, despair, helplessness, sorrow, and rage.
type: Class
subclass of: negative emotion

satisfaction
description: satisfaction is an emotion of fulfillment of one's wishes, expectations, or needs, or the pleasure derived from this.
type: Class
subclass of: contentment

shame
description: shame is the emotion borne from feeling responsible for the commission of an offense.
type: Class
subclass of: negative emotion

shock
description: shock is an emotion of sudden upset or surprise.
type: Class
subclass of: negative emotion

shyness
description: shyness is an emotion of apprehension, lack of comfort, or awkwardness experienced when in proximity to, approaching, or being approached by other individuals, especially in new situations or with unfamiliar individuals.
type: Class
subclass of: negative emotion

sorrow
description: sorrow is the emotion that is characterized by a long term state of intense sadness, distress and a degree of resignation (not accepting).
type: Class
subclass of: sadness

suffering
description: Suffering is the unpleasant emotion and aversion associated with the perception of harm or threat of harm in an individual.
type: Class
subclass of: hurt

surprise
description: surprise is a brief emotion experienced as the result of an unexpected event.
type: Class
subclass of: positive emotion

terror
description: terror is the extreme feeling of fear.
type: Class
subclass of: dread

wonder
description: wonder is an emotion of perceiving something very rare or unexpected, but not threatening.
type: Class
subclass of: surprise

worry
description: worry is the emotion characterized by concer over a real or imaginary issue.
type: Class
subclass of: apprehension

department chair role
description: A department chain role is the role of an individual that heads a department at a academic organization.
type: Class
subclass of: academic role

student advisor role
description: A student advisor role is the role of an individual employed at an academic organization that is involved in advising students.
type: Class
subclass of: academic role

undergraduate student advisor role
description: An undergraduate student advisor role is the role of an individual employed at an academic organization that is involved in advising undergraduate students.
type: Class
subclass of: student advisor role

graduate student advisor role
description: A graduate student advisor role is the role of an individual employed at an academic organization that is involved in advising graduate students.
type: Class
subclass of: student advisor role

reactant role
description: The role of a chemical entity present at the beginning of a chemical reaction.
type: Class
subclass of: molecular entity role

regulator role
description: The role of a chemical entity that modifies the rate of reaction.
type: Class
subclass of: molecular entity role

investigational role
description: An investigational role is a role held by participants involved in an investigation.
type: Class
subclass of: processual role

host role
description: The role of an organism in providing resources to maintain the survival and/or reproduction of another organism.
type: Class
subclass of: chemical substance role

subject role
description: A subject role is the role of an individual that is the target of the study.
type: Class
subclass of: investigational role

publishing role
description: A publishing role is the role of an individual that is involved in the preparation and issue of creative works for consumption by a wider audience.
type: Class
subclass of: occupational role

publisher role
description: A publisher role is the role of an individual that prepares and issues creative works.
type: Class
subclass of: publishing role

author role
description: An author role is the role of an individual that creates a creative, written work.
type: Class
subclass of: publishing role

buffer role
description: A buffer role is the role of a chemical substance which maintains a pH at a near constant value.
type: Class
subclass of: chemical substance role
subclass of: Restriction
  on property: is role of
  some values from: buffer

chemical substance role
description: A chemical substance role is a chemical entity role held by a chemical substance.
type: Class
subclass of: chemical entity role
subclass of: Restriction
  on property: is role of
  some values from: chemical substance

molecular entity role
description: A molecular entity role is a chemical entity role held by a molecule.
type: Class
subclass of: chemical entity role
subclass of: Restriction
  on property: is role of
  some values from: molecule

toxin role
description: A toxin role is a toxic role of a chemical substance that is poisonous and is produced by an organism.
type: Class
subclass of: poison role

toxic role
description: A toxic role is the role of a chemical substance that is poisonous.
type: Class
subclass of: chemical substance role

in relation from
description: a in relation from b is a comparative relation in a is the object of reference in a relation with b.
type: ObjectProperty
sub property of: is referred to by

reagent role
description: A role of a chemical substance that participates in a chemical reaction as part of some scientific investigation.
type: Class
subclass of: chemical substance role
subclass of: Restriction
  on property: is role of
  some values from: reagent

to luminesce
description: to luminesce is to emit light through cold body radiation
type: Class
subclass of: to be actively interacted with

to fluoresce
description: to fluoresce is to emit light as a result of absorbing light or other electromagnetic radiation.
type: Class
subclass of: to luminesce

molecular tracer role
description: A molecular tracer role is a reactant role of a molecular entity that serves as a marker for the presence, abundance, or location of a molecular target that it associates with.
type: Class
subclass of: reactant role

association
description: An association is a relationship between two or more entities derived by some informational analysis.
type: Class
subclass of: mathematical entity
subclass of: Restriction
  min qualified cardinality: 2
  on class: entity
  on property: refers to

statistical association
description: A statistical association is any relationship between two measured quantities that renders them statistically dependent.
type: Class
subclass of: association

chromosome
description: A chromosome is a molecular complex of circular or linear DNA and bound proteins.
type: Class
subclass of: molecular complex
subclass of: Restriction
  on property: has direct part
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has direct part
  some values from: protein

has frequency
description: has frequency is a relation that specifies the occurence of an object or event
type: ObjectProperty
sub property of: has measurement value
inverse of: is frequency of

is frequency of
description: is frequency of is a relation between a temporal unit and an object or event
type: ObjectProperty
sub property of: is measurement value of

top value axis
description: A top value axis is a value axis that is spatially positioned to the top of the plot area.
type: Class
subclass of: value axis

bottom value axis
description: A bottom value axis is a value axis that is spatially positioned to the bottom of the plot area.
type: Class
subclass of: value axis

chart
description: A chart is a figure that displays the relationship among tabular numeric data, functions or some kinds of qualitative structures.
type: Class
subclass of: figure

has substrate
description: has substrate is a relation between a process and an object where the object is destroyed by its participation in the process.
type: ObjectProperty
sub property of: has target

map
description: A map is a a visual representation of an area that depicts the relationship between elements of that space.
type: Class
subclass of: chart

heatmap
description: A heatmap is a graphical representation of data where the individual values contained in a matrix are represented as colors.
type: Class
subclass of: chart

streamgraph
description: A streamgraph is a multi-line stacked graph that yields the appearance of continuous y-values across the x-axis.
type: Class
subclass of: stack graph

boxplot
description: A boxplot (box-and-whisker diagram) is a convenient way of graphically depicting groups of numerical data through their five-number summaries: the smallest observation (sample minimum), lower quartile (Q1), median (Q2), upper quartile (Q3), and largest observation (sample maximum).
type: Class
subclass of: line-bar graph

geographic heatmap
description: A geographic heatmap is a graphical representation of data over a geographic region where individual values are represented as colors.
type: Class
subclass of: heatmap

histogram
description: A histogram is a graphical representation of data which consists of tabular frequencies, shown as adjacent rectangles, over discrete intervals (bins) , with an area equal to the frequency of the observations in the interval.
type: Class
subclass of: chart

measurement scale
description: A measurement scale is a functional specification that specifies an allowed range of categories or values.
type: Class
subclass of: functional specification

nomimal scale
description: A nominal scale of measurement only specifies a limited set of categories.
type: Class
subclass of: measurement scale

binary scale
description: A binary scale is a measurement scale that specifies a choice between two values.
type: Class
subclass of: measurement scale

numeric scale
description: A numeric scale of measurement is one that only specifies numeric values.
type: Class
subclass of: measurement scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: Literal

decimal scale
description: A decimal scale of measurement is one that only specifies decimal values.
type: Class
subclass of: numeric scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: decimal

integer scale
description: An integer scale of measurement is one that only specifies integer values.
type: Class
subclass of: numeric scale
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has value
      some values from: integer

modifying
alternative: modification
description: modifying is the process by which an entity gains or loses parts, qualities, roles, dispositions, functions, etc, but maintains their identity through these changes.
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: object
subclass of: Restriction
  on property: has target
  some values from: object

reproducing
description: reproducing is a process characterized by creation of an entity that is similar or exactly the same as the template from which it is derived.
type: Class
subclass of: creating
subclass of: Class
  intersection of: Restriction
    on property: has input
    some values from: object
  intersection of: Restriction
    on property: has product
    some values from: object

independent variable
description: An independent variable is a variable that may take on different values independent of other elements in a system.
type: Class
subclass of: variable

dependent variable
description: A dependent variable is one whose value changes as a consequence of changes in other values in the system.
type: Class
subclass of: variable

Gantt chart
description: A Gantt chart is a bar chart that illustrates a project schedule.
type: Class
subclass of: chart

correlation
description: A correlation is a statistical relationship involving dependence between two random variables or datasets.
type: Class
subclass of: statistical association

television program
description: A television program is a audiovisual media that is produced and broadcast using a television.
type: Class
subclass of: media

radio receiver
description: A radio receiver is a communication device that receives its input from an antenna, uses electronic filters to separate a wanted radio signal from all other signals picked up by this antenna, amplifies it to a level suitable for further processing, and finally converts through demodulation and decoding the signal into a form usable for the consumer, such as sound, pictures, digital data, measurement values, navigational positions.
type: Class
subclass of: communication device

telephone
description: The telephone is a communications device that transmits and receives sounds, and are minimally composed of a microphone to speak into, a speaker'which reproduces the voice of the other person and a ringer which makes a sound to alert the owner when a call is coming in.
type: Class
subclass of: communication device

radar
description: A radar is an object-detection system which uses radio waves to determine the range, altitude, direction, or speed of objects.
type: Class
subclass of: device

pie chart
description: A pie chart is a circular chart divided into sectors each of whose length is proportional to the quantity it represents.
type: Class
subclass of: mereological chart

matrix chart
description: A matrix chart summarizes a multidimensional data set in a grid.
type: Class
subclass of: chart

network diagram
description: A network diagram consists of a set of vertices connected by edges.
type: Class
subclass of: chart

block histogram
description: A block histogram contains an x-axis that is divided into bins which correspond to value ranges. Each item in the data set is drawn as a rectangular block, and the blocks are piled into the bins to show how many values in each range.
type: Class
subclass of: histogram

bubble chart
description: A bubble chart contains circles whose area corresponds to a value.
type: Class
subclass of: chart

stack graph
description: A stack graph is a statistical graph which presents multiple series in which the distance between one series and another indicates the relative contribution to the total for any x-value.
type: Class
subclass of: statistical graph

treemap
description: A treemap is a chart that fully partitions the area into a set of rectangles whose area represents its relative value.
type: Class
subclass of: mereological chart

word tree
description: A word tree is a chart that links phrases with contexts through a tree-like branching structure.
type: Class
subclass of: textual chart

textual chart
description: A textual chart is a chart containing text.
type: Class
subclass of: chart
subclass of: Restriction
  on property: has direct part
  some values from: textual entity

tag cloud
alternative: word cloud
description: A tag cloud is a visualization of word frequencies.
type: Class
subclass of: textual chart

phrase net diagram
description: A phrase net diagram illustrates the relationship between different words used in a text.
type: Class
subclass of: textual chart

mereological chart
description: A mereological chart is a chart that illustrates the parts in the context of the whole.
type: Class
subclass of: chart

conversing
description: conversing a form of interactive, spontaneous communication between two or more agents who are following rules of etiquette.
type: Class
subclass of: communicating

numeric label
description: A numeric label is a number used as a label.
type: Class
subclass of: label

start position
description: A start position is the proximal position of an object relative to an origin in a linear system.
type: Class
subclass of: linear position

interval
description: An interval is a set of real numbers that includes all numbers between any two numbers in the set.
type: Class
subclass of: mathematical entity

tree diagram
description: A tree diagram is a hierarchical network diagram in which a root vertex is connected to one or more other vertices through a directed edge, which in turn may be connected to other vertices.
type: Class
subclass of: directed acyclic graph

flowchart
description: A flowchart is a diagram that represents an algorithm or process, showing the steps as boxes of various kinds, and their order by connecting these with arrows.
type: Class
subclass of: chart

venn diagram
description: A Venn diagram is a chart that illustrates all possible logical relations between a finite collection of sets as overlapping circles.
type: Class
subclass of: chart

dendrogram
description: A dendrogram is a tree diagram used to illustrate the arrangement of the clusters produced by hierarchical clustering.
type: Class
subclass of: tree diagram

apprehension
description: apprehension is the negative emotion that something unpleasant will occur.
type: Class
subclass of: negative emotion

resentment
description: resentment is disgust directed toward a higher status individual.
type: Class
subclass of: disgust

pain
description: Pain is an unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage.
type: Class
subclass of: hurt

default parameter
description: A default parameter is a parameter which has a default value.
type: Class
subclass of: parameter

end position
alternative: stop position
description: An end position is the distal position of an object relative to an origin in a linear system.
type: Class
subclass of: linear position

sick
description: sick is the status of a living organism that is behaving at a sub-optimal level.
type: Class
subclass of: alive

environment
description: An environment is a geographic region that hosts certain processes or objects.
type: Class
subclass of: geographic region

device
description: A device is usually a constructed tool.
type: Class
subclass of: heterogeneous substance

communication device
description: A communication device is a device that facilitates the transmission of information through encoded in an audio or digital signal between a sender and a receiver.
type: Class
subclass of: device

existence quality
description: existence quality is the quality of an entity that describe in what environment it is known to exist.
type: Class
subclass of: quality

real
description: real is the quality of an entity that exists in real space and time.
type: Class
subclass of: existence quality
disjoint with: fictional
disjoint with: virtual

fictional
description: fictional is the quality of an entity that exists only in a creative work of fiction.
type: Class
subclass of: hypothetical

virtual
description: virtual is the quality of an entity that exists only in a virtual setting such as a simulation or game environment.
type: Class
subclass of: existence quality

not started
description: not started is the status of a process that is predicted to exist but has not yet begun.
type: Class
subclass of: process status

standard operating procedure
description: A standard operating procedure is a specification approved for use in specific environments.
type: Class
subclass of: experimental protocol

agreement quality
description: agreement quality is a quality that exhibits the degree of consensus for some set of assertions.
type: Class
subclass of: informational quality
equivalent class: Class
  union of: agreement
  union of: disagreement

agreement
description: agreement is the result of consensus decision making when members of the group agree.
type: Class
subclass of: agreement quality
disjoint with: disagreement

disagreement
description: agreement is the result of consensus decision making when members of the group do not all agree.
type: Class
subclass of: agreement quality

poison role
description: A poison role is the role of a substance that causes some negative disturbance in an organism.
type: Class
subclass of: toxic role
subclass of: Restriction
  on property: is role of
  some values from: poison

communicating
alternative: communication
description: communicating is the process of conveying information through the exchange of thoughts, messages, or information, as by speech, visuals, signals, writing, or behaviour.
type: Class
subclass of: interacting

is first part of
description: is first part of is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: is ordered part of
inverse of: has first part

has first part
description: has first part is a proper part relation in which the part is the first of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: has ordered part

has last part
description: has last part is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: has ordered part
inverse of: is last part of

is last part of
description: is last part of is a proper part relation in which the part is the last of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: is ordered part of

has ordered part
description: has ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: has proper part

is ordered part of
description: is ordered part of is a proper part relation in which the part is one of a set of linearly ordered parts resulting from the projection of the whole on a linear coordinate system.
type: ObjectProperty
sub property of: is proper part of

observational study
description: observational study draws inferences about the possible effect of a treatment on subjects, where the assignment of subjects into a treated group versus a control group is outside the control of the investigator
type: Class
subclass of: experiment
subclass of: Restriction
  on property: has participant
  some values from: hypothesis
subclass of: Restriction
  on property: specifies
  some values from: Class
    intersection of: truth value
    intersection of: Restriction
      on property: is quality of
      some values from: hypothesis

syllable
description: A syllable is a verbal entity of language having one vowel sound, with or without surrounding consonants, forming the whole or a part of a word.
type: Class
subclass of: verbal language entity

consonant
description: A consonant is a verbal entity of language that is articulated with complete or partial closure of the vocal tract.
type: Class
subclass of: verbal language entity

vowel
description: A vowel is a verbal entity of language that is pronounced with an open vocal tract so that there is no build-up of air pressure at any point above the glottis.
type: Class
subclass of: verbal language entity

sign language
description: A sign language (also signed language) is a language that involves manual communication and body language to convey meaning. This can involve simultaneously combining hand shapes, orientation and movement of the hands, arms or body, and facial expressions to fluidly express a speaker's thoughts.
type: Class
subclass of: language

verbal language
description: A verbal language is a language that uses sounds to communicate.
type: Class
subclass of: language

written language
description: written language is a language that is communicated through a writing system.
type: Class
subclass of: language

gene-disease association
description: A gene-disease association is an association between a gene and a disease.
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: gene
subclass of: Restriction
  on property: refers to
  some values from: disease

genome
description: A genome is a collection of nucleic acids.
type: Class
subclass of: biological entity

protein coding gene
description: A gene that contains an open reading frame which codes for a protein.
equivalent to: http://purl.obolibrary.org/obo/SO_0001217
type: Class
subclass of: gene

functional rna coding gene
description: A gene that codes for a functional RNA molecule.
type: Class
subclass of: rna gene

predicted gene
description: A predicted gene is a gene that was identified through computational method but has not been experimentally validated.
type: Class
subclass of: gene
subclass of: Restriction
  on property: has attribute
  some values from: predicted

pseudogene
description: A pseudo gene is a region of a nucleic acid that either cannot be transcribed, or its RNA transcript cannot be translated.
equivalent to: http://purl.obolibrary.org/obo/SO_0000336
type: Class
subclass of: nucleic acid part

sequence assembly
description: A sequence assembly is a sequence that is produced as by the alignment of two or more sequences.
type: Class
subclass of: biopolymer sequence

validated gene
description: An experimentally validated gene is a gene whose existence has been demonstrated through experimental methods.
type: Class
subclass of: gene
subclass of: Restriction
  on property: has attribute
  some values from: real

unsupported
description: unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical)
type: Class
subclass of: existence quality

chemical-disease association
description: A chemical-disease association is an association between a chemical and a disease.
type: Class
subclass of: association
subclass of: Class
  intersection of: Restriction
    on property: refers to
    some values from: chemical entity
  intersection of: Restriction
    on property: refers to
    some values from: disease

experiment
alternative: study
description: An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
type: Class
subclass of: investigation

suspended
description: suspended is the status of a process that is no longer progressing towards completion.
type: Class
subclass of: process status

cancelled
description: cancelled is a process status in which the process, while planned to occur, will not occur.
type: Class
subclass of: not started

aborted
description: aborted is a process status in which a started process will not complete as intended.
type: Class
subclass of: process status

literature curation
description: literature curation is the process of an agent selecting and extracting terms and phrases from a document.
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has output
  some values from: phrase
subclass of: Restriction
  on property: has input
  some values from: document

procedure
description: A procedure is a process that attempts to achieve one or more objectives by following an established set of actions.
type: Class
subclass of: process
subclass of: Restriction
  on property: is manifestation of
  some values from: action specification
subclass of: Restriction
  all values from: Class
    union of: capability
    union of: objective
  on property: realizes

clinical trial
description: A clinical trial is an intervention trial to determine the safety and efficacy of medical interventions (e.g., drugs, diagnostics, devices, therapy protocols).
type: Class
subclass of: intervention study
subclass of: Restriction
  on property: is specified by
  some values from: experimental protocol

medical diagnosis
description: A medical diagnosis (often simply termed diagnosis) refers to the process of attempting to determine or identify a possible disease or disorder.
type: Class
subclass of: medical procedure
subclass of: Restriction
  on property: has output
  some values from: diagnostic opinion
subclass of: Restriction
  on property: has input
  some values from: Class
    intersection of: biological entity
    intersection of: Restriction
      on property: has quality
      some values from: disordered

differential diagnosis
description: A differential diagnosis (sometimes abbreviated DDx, ddx, DD, D/Dx, or ΔΔ) is a systematic diagnostic method used to identify the presence of an entity where multiple alternatives are possible (and the process may be termed differential diagnostic procedure), and may also refer to any of the included candidate alternatives (which may also be termed candidate condition).
type: Class
subclass of: medical procedure

diagnostic opinion
description: A diagnostic opinion is an opinion resulting from a medical diagnostic procedure.
type: Class
subclass of: opinion

opinion
description: An opinion is a belief that is the result of emotion or interpretation of facts.
type: Class
subclass of: belief
subclass of: Restriction
  on property: is product of
  some values from: medical diagnosis

chemical effect
description: A chemical effect is a chemical interaction in which a chemical elicits a marked characteristic of a biological system.
type: Class
subclass of: chemical interaction
subclass of: Restriction
  on property: has agent
  some values from: drug

drug drug interaction
description: A drug-drug interaction is an interaction in which two drugs interact in such a way to produce a non-additive biological response.
type: Class
subclass of: chemical effect
subclass of: Restriction
  min qualified cardinality: 2
  on class: drug
  on property: has participant

assay
alternative: bioassay
description: An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
type: Class
subclass of: procedure
subclass of: Restriction
  on property: has output
  some values from: Class
    intersection of: Class
      union of: measurement value
      union of: existence quality
    intersection of: Restriction
      on property: is attribute of
      some values from: entity
subclass of: Restriction
  on property: has input
  some values from: object

toxicity
description: toxicity is the quality of a chemical substance to cause injury to an organism in a dose dependent manner.
type: Class
subclass of: chemical quality
equivalent class: Class
  union of: toxic
  union of: non toxic

toxic
description: toxic is the quality of a substance imparing the normal functioning of a system.
type: Class
subclass of: toxicity
disjoint with: non toxic

non toxic
description: non toxic is the quality of a substance having no damaging effect to a system.
type: Class
subclass of: toxicity

chemical quality
description: chemical quality is the quality of a chemical entity.
type: Class
subclass of: object quality

healthy
description: healthy is an organismal state of complete physical, mental and social well-being.
type: Class
subclass of: alive

age
description: age is the length of time that a person has lived or a thing has existed.
type: Class
subclass of: dimensional quantity

ethnicity
description: ethnicity is the biological quality of membership in a social group based on a common heritage.
type: Class
subclass of: biological quality

race
description: race is a characteristic of an individual by heritable phenotypic characteristics, geographic ancestry, physical appearance, ethnicity, and social status.
type: Class
subclass of: biological quality

ethnic group
description: An ethnic group is a group of people whose members identify with each other through a common heritage, consisting of a common culture, including a shared language or dialect.
type: Class
subclass of: human population

syndrome
description: A syndrome is composed of a set of several clinically recognizable features, signs (observed by someone other than the patient), symptoms (reported by the patient), phenomena or characteristics that often occur together.
type: Class
subclass of: description

ratio
description: A ratio is a relationship between two numbers of the same kind expressed arithmetically as a dimensionless quotient of the two which explicitly indicates how many times the first number contains the second.
type: Class
subclass of: dimensionless quantity

dose
description: A dose is the quantity of a chemical substance administered to a biological system.
type: Class
subclass of: dimensional quantity

effective dose
description: effective dose is the amount of a substance required to produce an effect on a predefined percentage of a population.
type: Class
subclass of: dose

expected value
description: An expected value (or e-value) is the weighted average of all possible values that a random variable can take on.
type: Class
subclass of: probability measure

diagnostic test
alternative: clinical laboratory test
description: A diagnostic test is a procedure performed to confirm, or determine the presence of disease in an individual suspected of having the disease, usually following the report of symptoms, or based on the results of other medical tests.
type: Class
subclass of: medical procedure

medical screening
description: A medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce
type: Class
subclass of: medical procedure

medical procedure
description: A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder.
type: Class
subclass of: procedure

prognosis
description: A prognosis is a proposition about the likely course of a disease, the chance of recovery or recurrence.
type: Class
subclass of: proposition

report
description: A report is a textual document made that present focused, salient content to a specific audience.
type: Class
subclass of: document

medical health record
description: A medical health record is a record of a single patient's medical history.
type: Class
subclass of: record

medical report
description: A medical report is a report prepared by a health care practioner about test outcomes or health status of an individual.
type: Class
subclass of: report

peer reviewed article
description: A peer reviewed article is an article that has undergone peer-review and deemed acceptable for publication.
type: Class
subclass of: article
subclass of: Restriction
  on property: has quality
  some values from: peer-reviewed

major version number
description: A major version number is a version of a software that exhibits a significant change in functionalilty from a prior version.
type: Class
subclass of: software version label

minor version number
description: A minor version number is a version of a software that exhibits minor features or significant fix from a prior version.
type: Class
subclass of: software version label

revision number
description: A revision number is a version of a software in which bugs have been fixed from a prior version.
type: Class
subclass of: software version label

text quality
description: text quality is the quality of a textual entity.
type: Class
subclass of: object quality
subclass of: Restriction
  on property: is quality of
  some values from: textual entity

reviewed
description: reviewed is the quality of a textual entity that has been examined and commented on by another party.
type: Class
subclass of: written

peer-reviewed
description: peer-reviewed is the quality of a textual entity that has been examined and commented by a peer expert reviewer.
type: Class
subclass of: reviewed
disjoint with: editor reviewed

draft
alternative: drafted
description: draft is the quality of text that has not yet complete.
type: Class
subclass of: written

finalized
description: finalized is the quality of a textual entity that is in its final form.
type: Class
subclass of: written

editor reviewed
description: editor reviewed is the quality of a textual entity that has been examined and commented on by an editor.
type: Class
subclass of: reviewed

written
description: written is the quality of information that is embodied as visual glyphs in some material form.
type: Class
subclass of: text quality

morpheme
description: A morpheme is the smallest semantically meaningful unit in a language.
type: Class
subclass of: language entity

study design
alternative: study protocol
description: A study design is a protocol for the proper execution of a study which normally requires a carefullly crafted research question or hypothesis and at least one variable under observation and observed values for that variable.
type: Class
subclass of: experimental protocol
subclass of: Restriction
  all values from: Restriction
    on property: is part of
    some values from: investigation
  on property: is manifested as

recipe
description: A recipe is a set of instructions that describe how to prepare or make something.
type: Class
subclass of: action specification

experimental protocol
description: An experimental protocol is an action specification with respect to the design and implementation of experiments. In addition to providing a detailed set of procedures and lists of required equipment and instruments, experimental protocols often include information on safety precautions, the calculation of results and reporting standards, including statistical analysis and rules for predefining and documenting excluded data to avoid bias.
type: Class
subclass of: action specification

viroid
description: A viroid is a molecule of RNA that does not code for and is not protected by a protein coat.
type: Class
subclass of: non-cellular organism

polar quality
description: The quality of being polar or not polar.
type: Class
subclass of: chemical quality
equivalent class: Class
  union of: polar
  union of: non-polar

polar
description: polar is the quality of having a dipole.
type: Class
subclass of: polar quality
disjoint with: non-polar

non-polar
description: non-polar is the quality of not having a dipole.
type: Class
subclass of: polar quality

intervention study
description: An intervention study has the objective of improving the condition of an individual or a group of individuals, and demonstrates the magnitude of that capability by comparing it to a control group.
type: Class
subclass of: experiment

sampling
description: sampling is the act of obtaining a sample, whether through selection, collection or preparation.
type: Class
subclass of: interacting
subclass of: Class
  intersection of: Restriction
    on property: has output
    some values from: sample
  intersection of: Restriction
    on property: has input
    some values from: object

sample
description: A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
type: Class
subclass of: heterogeneous substance
subclass of: Class
  union of: Restriction
    on property: is member of
    some values from: collection
  union of: Restriction
    on property: is derived from
    some values from: object

data analysis
description: data analysis is a process of inspecting, cleaning, transforming, and modeling data with the goal of highlighting useful information, suggesting conclusions, and supporting decision making.
type: Class
subclass of: information processing
subclass of: Class
  intersection of: Restriction
    on property: has output
    some values from: proposition
  intersection of: Restriction
    on property: has input
    some values from: data item

data collection
description: data collection is the process of acquiring information.
type: Class
subclass of: information processing
subclass of: Restriction
  on property: has product
  some values from: data item

reason
description: A reason is a justification that specifies the motive for an action or a determination.
type: Class
subclass of: justification

measuring
alternative: measurement
description: measuring is the process of determining the size, amount, or degree of (something) by using an instrument or device marked in standard units
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: measurement value
subclass of: Restriction
  on property: has input
  some values from: Class
    union of: quality
    union of: process
    union of: object

observing
alternative: observation
description: observing is a process of passive interaction in which one entity makes note of attributes of one or more entities.
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has output
  some values from: entity
subclass of: Restriction
  on property: has input
  some values from: entity

character position
alternative: character offset
description: The ordinal position of a character in a sequence of characters.
type: Class
subclass of: ordinal position
subclass of: Restriction
  all values from: integer
  on property: has value

word start position
description: The position of the first character in a word as an offset from the first character of the text in which it is found.
type: Class
subclass of: text span start position
subclass of: Restriction
  on property: is part of
  some values from: textual entity

word end position
description: word end position is the position of the last character in a word as an offset from the first character of the text in which it is found.
type: Class
subclass of: text span end position

gesturing
description: gesturing is a form of non-verbal communication in which visible bodily actions communicate particular messages, either in place of speech or together and in parallel with spoken words. Gestures include movement of the hands, face, or other parts of the body.
type: Class
subclass of: communicating

planned
description: planned is a process status for a process that has not yet started, but is referred to in a plan.
type: Class
subclass of: not started

population
description: A population is all the organisms that both belong to the same group or species and live in the same geographical area.
type: Class
subclass of: collective

human population
description: A human population refers to a collection of human beings.
type: Class
subclass of: population

family
description: A group of people affiliated by consanguinity, affinity, or co-residence.
type: Class
subclass of: collective

community
description: A community is a sizeable social unit that shares common values.
type: Class
subclass of: collective

speculation
description: speculation is an opinion based on incomplete evidence.
type: Class
subclass of: opinion

study
description: A study is a process that realizes the steps of a study design.
type: Class
subclass of: investigation
subclass of: Restriction
  on property: realizes
  some values from: objective
subclass of: Restriction
  on property: is manifestation of
  some values from: study design

controlled observational cohort study
description: In a controlled observational cohort study, two groups of subjects are selected from two populations that are thought to differ in only one characteristic. The groups of subjects are studied for a specific period and contrasted at the end of the study period.
type: Class
subclass of: observational study

control group
description: A control group is a group of individuals that are not subject to an intervention of interest, but rather serve as a baseline to compare the outcomes in the intervention group.
type: Class
subclass of: study group

intervention group
description: An intervention group is a group of individuals that are subject to an intervention.
type: Class
subclass of: study group

control variable
alternative: controlled variable
alternative: extraneous variable
description: A control variable that is believed to alter the dependent or independent variables, but may not actually be the focus of the experiment. So that variable will be kept constant or monitored to try to minimise its effect on the experiment.
type: Class
subclass of: variable

text span start position
description: text span start position is the position (offset) of the first character of a text span in relation the text it is from.
type: Class
subclass of: start position

text span end position
description: text span end position is the position (offset) of the last character of a text span in relation the text it is from.
type: Class
subclass of: end position

text span
alternative: selector
description: A text span is a subset of contiguous sequence of characters of a textual entity.
type: Class
subclass of: textual entity
subclass of: Class
  intersection of: Restriction
    on property: has attribute
    some values from: text span start position
  intersection of: Restriction
    on property: has attribute
    some values from: text span end position

t-statistic
description: A t-statistic is a ratio of the departure of an estimated parameter from its notional value and its standard error.
type: Class
subclass of: ratio

microarray probe set identifier
description: A microarray probe set identifier is an identifier for a set of probe pairs selected to represent expressed sequences on an array.
type: Class
subclass of: molecular identifier

microarray experiment
description: A microarray experiment is an experiment that involves a microarray device to measure the expression of one or more genes.
type: Class
subclass of: experiment

gene expression value
description: A gene expression value is a measured value obtained from a gene expression experiment.
type: Class
subclass of: dimensional quantity

differential gene expression ratio
description: A differential gene expression ratio is the ratio of gene expression values from a test sample compared to a control sample.
type: Class
subclass of: ratio

genotype
description: A genotype is a functional specification of a biological entity in terms of its genetic composition (or lack thereof).
type: Class
subclass of: functional specification

vocabulary
description: A vocabulary is a collection of terms.
type: Class
subclass of: functional specification
subclass of: formal specification

t-statistic based increased differential gene expression
description: A t-statistic based increased differential gene expression is a differential gene expression ratio in which the t-statistic is greater than zero.
type: Class
subclass of: differential gene expression ratio
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: t-statistic
    intersection of: Restriction
      on property: has value
      some values from: Datatype
        on datatype: double

t-statistic based decreased differential gene expression
description: A t-statistic based decreased differential gene expression is a differential gene expression ratio in which the t-statistic is less than zero.
type: Class
subclass of: differential gene expression ratio
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: t-statistic
    intersection of: Restriction
      on property: has value
      some values from: Datatype
        on datatype: double

date of database submission
description: A date of database submission refers to the moment in time in which some information was submitted/received to a database system.
type: Class
subclass of: time instant

liquid solution
description: A liquid solution is a heterogeneous substance in a liquid state.
type: Class
subclass of: heterogeneous substance

to remove a covalent bond
description: to remove a covalent bond is the capability to covalently modify a chemical entity by removing a covalent bond.
type: Class
subclass of: to covalently modify

to add a covalent bond
description: to add a covalent bond is the capability to covalently modify a chemical entity by adding a covalent bond.
type: Class
subclass of: to covalently modify

to modify electronically
description: to modify electronically is the capability to change the electronic properties of an object.
type: Class
subclass of: to change energetically

concentration
description: concentration is the amount of substance per unit volume of a solution
type: Class
subclass of: 3D extent quantity
subclass of: Restriction
  on property: is attribute of
  some values from: Class
    intersection of: chemical substance
    intersection of: Restriction
      on property: is proper part of
      some values from: heterogeneous substance
    intersection of: Restriction
      on property: in relation to
      some values from: chemical substance

pH
description: pH is a measure of the activity of the (solvated) hydrogen ion.
comment: pH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution.
type: Class
subclass of: dimensionless quantity

homogeneous
description: homogeneous is a quality that describes the uniform composition of an object.
type: Class
subclass of: compositional quality
disjoint with: heterogeneous

heterogeneous
description: homogeneous is a quality that describes the varied composition of an object.
type: Class
subclass of: compositional quality

structural quality
description: A structural quality is a quality of an object that describes its structure.
type: Class
subclass of: object quality

rigid
description: rigid is the quality of maintaining structural integrity (and not bending) under pressure.
type: Class
subclass of: structural quality

bent
description: bent is the quality of a line being sharply curved or having an angle.
type: Class
subclass of: curvature

curved
description: curved is the quality of a line that deviates from straightness in a smooth, continuous fashion.
type: Class
subclass of: curvature

is specialization of
description: is specialization of is a relation between a more specific instance (in terms of spatial/temporal localization & other attributres) than the other.
equivalent to: http://www.w3.org/ns/prov#specializationOf
type: ObjectProperty
sub property of: is variant of
inverse of: is generalization of
example: a weather forecast for the city of London produced at a specific time is a specialization of a weather forecast for the city of London.

is generalization of
description: is generalization of is a relation between a more general instance (in terms of spatial/temporal localization & other attributres) than the other.
type: ObjectProperty
sub property of: is variant of

is alternate of
description: is alternate of relates two specialized instances.
equivalent to: http://www.w3.org/ns/prov#alternateOf
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of
example: two weather forecasts for the city of London produced at different times or by different organizations (etc) are alternates of each other, and instances of / specializations of forecasts for the city of London.

electronic structure
alternative: electronic configuration
description: electronic structure is the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals.
type: Class
subclass of: chemical structure
example: the electron configuration of the neon atom is 1s2 2s2 2p6.

crystal structure
description: A crystal structure is the arrangement of atoms or molecules in a crystalline liquid or solid.
type: Class
subclass of: molecular structure

is mutual capability of
description: a is mutual capability of b if and only if the realization of capability a necessarily causes the realization of capability b.
type: ObjectProperty
type: SymmetricProperty
sub property of: is mutually related to

to interact and to be interacted with
description: to interact and to be interacted with is a mutual disposition of interacting objects.
type: Class
subclass of: mutual disposition
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: to interact with
  intersection of: Restriction
    on property: has proper part
    some values from: to be interacted with

to gain a covalent bond
description: to gain a covalent bond is the capability of a chemical entity to have bonds added.
type: Class
subclass of: to be covalently modified

to lose a covalent bond
description: to lose a covalent bond is the capability of a chemical entity to have bonds removed.
type: Class
subclass of: to be covalently modified

to ingest
description: to ingest is the capability to take into the body by the mouth for digestion or absorption.
type: Class
subclass of: to consume

to produce
description: to produce is the capability to create new objects
type: Class
subclass of: to actively interact with

pathway
alternative: biological pathway
description: A pathway is an effective specification that outlines a set of actions that forms a way to achieve an objective.
type: Class
subclass of: action specification

centrality measure
description: A central tendency measure is a central value or a typical value for a probability distribution.
type: Class
subclass of: quantity

mean
alternative: arithmeritic mean
alternative: average
description: A mean is the central tendency of a collection of numbers taken as the sum of the numbers divided by the size of the collection.
type: Class
subclass of: centrality measure

median
description: A median is the numerical value separating the higher half of a sample, a population, or a probability distribution, from the lower half.
type: Class
subclass of: centrality measure

mode
description: A mode is the value that appears most often in a set of data.
type: Class
subclass of: centrality measure

sum
description: A sum is the result of adding a set of values together.
type: Class
subclass of: quantity

minimal value
alternative: min
description: A minimal value is smallest value of an attribute for the entities in the defined set.
type: Class
subclass of: quantity
subclass of: Restriction
  on property: is attribute of
  some values from: collection

maximal value
alternative: max
description: A maximal value is largest value of an attribute for the entities in the defined set.
type: Class
subclass of: quantity
subclass of: Restriction
  on property: is attribute of
  some values from: collection

member count
description: A count of the instances of a class or members in a collection.
type: Class
subclass of: count

union
description: A union is a list of all of the values of an attribute for the entities in the defined set.
type: Class
subclass of: list
disjoint with: intersection

intersection
description: An intersection is a list of only the values of an attribute for the entities in the defined set where all entities have that value.
type: Class
subclass of: list

sequence
alternative: ordered list
description: A sequence is an ordered list of entities. Like a set, it contains members (also called elements, or terms).
type: Class
subclass of: list
subclass of: Restriction
  on property: has member
  some values from: Class
    intersection of: entity
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
    intersection of: Restriction
      on property: refers to
      some values from: entity
example: For example, (M, A, R, Y) is a sequence of letters that differs from (A, R, M, Y), as the ordering matters, and (1, 1, 2, 3, 5, 8), which contains the number 1 at two different positions, is a valid sequence.

gene-disease association linked with causal mutation
description: A gene-variant disease association in which a mutation in the gene/protein results in the development or maintenance of the disease.
type: Class
subclass of: gene-disease association linked with genetic variation

therapeutic gene-disease association
alternative: gene-disease association arising from a therapeutic role of the gene/protein
description: A gene disease association in which the gene is a therapeutic marker for the disease.
type: Class
subclass of: gene-disease association

gene-disease biomarker association
description: A gene-disease association in which the gene/protein is involved in the etiology or maintenance of the disease.
type: Class
subclass of: gene-disease association

gene-disease association linked with genetic variation
alternative: gene variant-disease association
description: A gene-disease association in which a sequence variation (a mutation, a SNP) is associated with the disease.
type: Class
subclass of: gene-disease association linked with genomic alterations

gene-disease association linked with altered gene expression
description: A gene-disease association in which the disease phenotype is associated with an altered expression of the gene.
type: Class
subclass of: gene-disease biomarker association

gene-disease association linked with post-translational modification
description: A gene-disease association in which the disease phenotype is associated with post-translational modifications in the protein product.
type: Class
subclass of: gene-disease biomarker association
example: methylation or phosphorylation of protein product

regulation of transcription
description: A process that modulates the frequency, rate or extent of transcription.
type: Class
subclass of: regulation of biochemical process

regulation of translation
description: A process that modulates the frequency, rate or extent of translation.
type: Class
subclass of: regulation of biochemical process

regulation of molecular quantity
description: A process that modulates the frequency, rate or extent of process involved in the creation or destruction of a molecule.
type: Class
subclass of: regulation of object quantity

regulation of molecular production
description: A process that modulates the frequency, rate or extent of process involved in the production of a molecule.
type: Class
subclass of: regulation of molecular quantity

regulation of molecular degradation
description: A process that modulates the frequency, rate or extent of process involved in the destruction of a molecule.
type: Class
subclass of: regulation of molecular quantity
subclass of: Restriction
  on property: regulates
  some values from: chemical destruction

protein mediated regulation of translation
description: A process mediated by a protein that modulates the frequency, rate or extent of translation.
type: Class
subclass of: regulation of translation
subclass of: Restriction
  on property: has agent
  some values from: protein

rna mediated regulation of translation
description: A process mediated by rna that modulates the frequency, rate or extent of translation.
type: Class
subclass of: regulation of translation
subclass of: Restriction
  on property: has agent
  some values from: RNA transcript

process maintenance
description: The process of maintaining some the frequency, rate or extent of another process.
type: Class
subclass of: regulation of process

increased frequency of process from increased regulation
description: The increase of regulation leads to a increased occurence of processes of the target type.
type: Class
subclass of: regulation of process frequency

decreased frequency of process from increased regulation
description: The increase of regulation leads to a decreased occurence of processes of the target process type.
type: Class
subclass of: regulation of process frequency

regulation of process frequency
description: regulation of a process duration is a process that modulates the frequency of another process relative to some reference process.
type: Class
subclass of: regulation of process

regulation of process duration
description: regulation of a process duration is a process that modulates the duration of another process relative to some reference process.
type: Class
subclass of: regulation of process

increased duration of process from increased regulation
description: increased duration of process from increased regulation is a process in which the duration of the target process is increased as a result of increased regulation.
type: Class
subclass of: regulation of process duration

decreased duration of process from increased regulation
description: decreased duration of process from increased regulation is a process in which the duration of the target process is decreased as a result of increased regulation.
type: Class
subclass of: regulation of process duration

regulation of process spatial extent
description: regulation of a process spatial extent is a process that modulates the spatial extent of another process relative to some reference process.
type: Class
subclass of: regulation of process
example: heating the solution causes greater diffusion of a chemical.

increased spatial extent of process from increased regulation
description: The increase of regulation leads to a increased spatial extent of the target process.
type: Class
subclass of: regulation of process spatial extent

decreased spatial extent of process from decreased regulation
description: The increase of regulation leads to a decreased spatial extent of the target process.
type: Class
subclass of: regulation of process spatial extent

maintenance of spatial extent of process
description: maintenance of spatial extent of process is a regulation of a process' spatial extent within some specified parameter.
type: Class
subclass of: regulation of process spatial extent

maintenance of duration of process
description: maintenance of duration of process is a process that regulates a target process to maintain its duration within an expected interval.
type: Class
subclass of: regulation of process duration

maintenance of frequency of process
description: maintenance of frequency of process is a process that regulates the number of occurences of a target process type to a specified number or interval.
type: Class
subclass of: regulation of process frequency

regulation of object quantity
description: regulation of a participant quantity is the regulation of a process in which the quantity of its partcipants is changed.
type: Class
subclass of: regulation of process
subclass of: Restriction
  on property: regulates
  some values from: quantity

increased object production from increased regulation
description: increased regulation leads to an increase in the number of target objects of a specified type.
type: Class
subclass of: regulation of object production

decreased object production from increased regulation
description: increased regulation leads to a decrease in the number of target objects of a specified type.
type: Class
subclass of: regulation of object production

increased object consumption from increased regulation
description: increased regulation leads to an increase in the consumption of an object of specified type.
type: Class
subclass of: regulation of object consumption

decreased object consumption from increased regulation
description: increased regulation leads to an decrease in the consumption of an object of specified type.
type: Class
subclass of: regulation of object consumption

regulation of object consumption
description: A process that modulates the frequency, rate or extent of process involved in the consumption of an object.
type: Class
subclass of: regulation of object quantity

regulation of object production
description: regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is increased.
type: Class
subclass of: regulation of object quantity

maintenance of quantity of object production
description: maintenance of quantity of object production is a regulation of object production in which the number of objects produced is held more or less constant.
type: Class
subclass of: regulation of object production

maintenance of level of object consumption
description: regulation of a participant quantity is the regulation of a process in which the quantity of a selected participant is maintained at a steady level.
type: Class
subclass of: regulation of object consumption

regulates
description: x regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect on the frequency, rate or extent of y
type: ObjectProperty
sub property of: is causally related to
inverse of: is regulated by

is regulated by
type: ObjectProperty
sub property of: is causally related from

results in
type: ObjectProperty
sub property of: is causally related to
inverse of: is result of

is result of
type: ObjectProperty
sub property of: is causally related from

affects
type: ObjectProperty
sub property of: has output
inverse of: is affected by

is affected by
type: ObjectProperty
sub property of: is participant in

number of objects produced
description: number of objects produced is a count of objects that were produced in some process.
type: Class
subclass of: count

number of objects consumed
description: number of objects consumed is a count of objects that were consumed in some process.
type: Class
subclass of: count

difference in number of objects produced
description: A difference in number of objects produced is a count of the number of objects produced with respect to a second variable (space, time, etc)
type: Class
subclass of: count

increase in number of objects produced
description: An increase in the number of objects produced is the positive value of a difference in number of objects produced.
type: Class
subclass of: difference in number of objects produced

decrease in number of objects produced
description: An decrease in the number of objects produced is the negative value of a difference in number of objects produced.
type: Class
subclass of: difference in number of objects produced

user account
description: user account allows a user to authenticate to system services and be granted authorization to access them.
type: Class
subclass of: computational entity

annotation
description: An annotation is a written explanatory or critical description, or other in-context information (e.g., pattern, motif, link), that has been associated with data or other types of information.
type: Class
subclass of: description
subclass of: Restriction
  on property: in relation to
  some values from: entity

comment
description: A comment is a verbal or written remark often related to an added piece of information, or an observation or statement.
type: Class
subclass of: proposition

audio recording
description: An audio recording is an electrical or mechanical inscription and re-creation of sound waves, such as spoken voice, singing, instrumental music, or sound effects.
type: Class
subclass of: media

issue
description: An issue is a single instance of a periodically published journal, magazine, or newspaper.
type: Class
subclass of: edited publication
subclass of: Restriction
  on property: is proper part of
  some values from: periodical

slideshow
description: A slideshow is a visual presentation of information contained within a collection of slides.
type: Class
subclass of: media
subclass of: Restriction
  on property: has proper part
  some values from: slide

database cross-reference
alternative: dbxref
description: A database cross-reference is an association between one data item and another.
type: Class
subclass of: association

exact cross-reference
description: An exact cross-reference is a database cross-reference in which one entity is equivalent to the other based on all the entitie's attributes (minus the source).
type: Class
subclass of: database cross-reference

double stranded DNA
description: double stranded nucleic acid is a molecular complex composed of two weakly connected deoxyribonucleic acids.
type: Class
subclass of: double stranded nucleic acid
subclass of: Restriction
  on class: deoxyribonucleic acid
  on property: has proper part
  qualified cardinality: 2
disjoint with: double stranded RNA

nucleic acid strand
description: A nucleic acid strand is a single-stranded nucleic acid that is part of a double stranded nucleic acid complex.
type: Class
subclass of: nucleic acid
subclass of: Restriction
  on property: is proper part of
  some values from: double stranded nucleic acid
equivalent class: Class
  union of: positive nucleic acid strand
  union of: negative nucleic acid strand

positive nucleic acid strand
alternative: forward strand
description: The positive nucleic acid strand refers to the strand that is to be read 5' to 3'.
type: Class
subclass of: nucleic acid strand

negative nucleic acid strand
alternative: reverse strand
description: The negative nucleic acid strand is the strand that is that is complimentary to the forward strand and appears from 3' to 5'.
type: Class
subclass of: nucleic acid strand

double stranded nucleic acid
description: double stranded nucleic acid is a molecular complex composed of two weakly connected nucleic acids.
type: Class
subclass of: molecular complex
subclass of: Restriction
  on class: nucleic acid
  on property: has proper part
  qualified cardinality: 2

double stranded RNA
description: double stranded nucleic acid is a molecular complex composed of two weakly connected ribonucleic acids.
type: Class
subclass of: double stranded nucleic acid
subclass of: Restriction
  on class: ribonucleic acid
  on property: has proper part
  qualified cardinality: 2

full agreement
description: full agreement is the result of consensus decision making when members of the group unanimously agree.
type: Class
subclass of: agreement

mass spectrometry experiment
description: A mass spectrometry experiment is an experiment that involves the use of a mass spectrometer.
type: Class
subclass of: experiment

full disagreement
description: full agreement is the result of consensus decision making when members of the group unanimously disagree.
type: Class
subclass of: disagreement

ribosomal RNA gene
alternative: rRNA gene
description: A ribosomal RNA gene is a gene that codes for a ribosomal RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001637
type: Class
subclass of: non-protein coding RNA (ncRNA) gene

statement
description: A statement is a proposition that is either (a) a meaningful declarative sentence that is either true or false, or (b) that which a true or false declarative sentence asserts.
type: Class
subclass of: proposition

slope
description: A slope or gradient of a line describes its steepness, incline, or grade. A higher slope value indicates a steeper incline. Slope is normally described by the ratio of the "rise" divided by the "run" between two points on a line.
type: Class
subclass of: ratio

software process identifier
description: A software process identifier is an identifier for a software process in some operating system.
type: Class
subclass of: informational entity identifier

hypothetical
description: hypothetical is the quality of an entity that is conjectured to exist.
type: Class
subclass of: existence quality

database row
description: A database row is a row that is part of a database table.
type: Class
subclass of: row
subclass of: Restriction
  on property: is proper part of
  some values from: database table

SADI semantic web service
description: a SADI semantic web service is a semantic web service that follows the SADI specification
subset: sadi
type: Class
subclass of: semantic web service

semantic web service
description: a semantic web service is a web service that provides a formal, machine understanble description of its functionality.
type: Class
subclass of: web service

REST web service
description: a REST web service is a web service that provides functionality according to the Representational State Transfer (REST) specification.
type: Class
subclass of: web service

SOAP web service
description: a SOAP web service is a web service that implements Simple Object Access Protocol (SOAP).
type: Class
subclass of: web service

web service invocation
description: A web service invocation involves the execution of a web service.
type: Class
subclass of: software execution

SADI web service invocation
description: A SADI web service invocation is the excution of a SADI web service.
subset: sadi
type: Class
subclass of: web service invocation
subclass of: Restriction
  on property: has agent
  some values from: SADI semantic web service

media
description: media are audo/visual/audiovisual modes of communicating information for mass consumption.
type: Class
subclass of: information content entity

behaviour
description: Behaviour is the set of actions and mannerisms made by systems (biological or otherwise) in response to stimuli or inputs, whether internal or external, conscious or subconscious, overt or covert, and voluntary or involuntary.
subset: behaviour+
subset: core
type: Class
subclass of: process

history
description: history is a sequence of past events.
type: Class
subclass of: description

structural motif
description: A structural motif is a pattern in a structure formed by a spatial arrangement of objects (e.g. atoms).
type: Class
subclass of: pattern

consensus
description: consensus is an acceptable resolution, one that can be supported, even if not the preferred outcome for each individual.
type: Class
subclass of: agreement

increased molecular degradation from increased regulation
description: A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.
type: Class
subclass of: regulation of molecular degradation

decreased molecular degradation from decreased regulation
description: A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.
type: Class
subclass of: regulation of molecular degradation

increased molecular degradation from decreased regulation
description: A process that increases the frequency, rate or extent of process involved in the destruction of a molecule as a result of decreased regulation.
type: Class
subclass of: regulation of molecular degradation

decreased molecular degradation from increased regulation
description: A process that decreases the frequency, rate or extent of process involved in the destruction of a molecule as a result of increased regulation.
type: Class
subclass of: regulation of molecular degradation
subclass of: Restriction
  on property: has quality
  some values from: increased
subclass of: Restriction
  on property: results in
  some values from: Class
    intersection of: chemical destruction
    intersection of: Restriction
      on property: has quality
      some values from: decreased

increased molecular production from increased regulation
description: A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.
type: Class
subclass of: regulation of molecular production

decreased molecular production from increased regulation
description: A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of increased regulation.
type: Class
subclass of: regulation of molecular production

increased molecular production from decreased regulation
description: A process that increases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.
type: Class
subclass of: regulation of molecular production

decreased molecular production from decreased regulation
description: A process that decreases the frequency, rate or extent of process involved in the production of a molecule as a result of decreased regulation.
type: Class
subclass of: regulation of molecular production

increased chemical destruction
description: increased chemical destruction is a process in which there is an increase in the amount of chemical destroyed relative to some reference process
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is greater than
      some values from: Class
        intersection of: count
        intersection of: Restriction
subclass of: Restriction
  on property: has quality
  some values from: increased

decreased chemical destruction
description: decreased chemical destruction is a process in which there is a decrease in the amount of chemical destroyed relative to some reference process
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has attribute
  some values from: Class
    intersection of: count
    intersection of: Restriction
      on property: is greater than
      some values from: Class
        intersection of: count
        intersection of: Restriction
subclass of: Restriction
  on property: has quality
  some values from: increased
subclass of: Restriction
  on property: in relation to
  some values from: chemical destruction

assertional qualifier
description: An assertional qualifier is the quality of affirmation, either being positive or negative.
type: Class
subclass of: quality
equivalent class: Class
  union of: positive
  union of: negative

positive
description: positive is an assertional qualifier that expresses the validity or truth of a basic assertion.
type: Class
subclass of: assertional qualifier
disjoint with: negative

negative
description: negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion.
type: Class
subclass of: assertional qualifier

intensity
description: intensity is a quality that represents the strength or degree of something.
type: Class
subclass of: quality

mild
description: mild is a qualitative intensity value that is more intense than weak, but less intense than moderate.
type: Class
subclass of: intensity

moderate
description: moderate is a qualitative intensity value that is more intense than mild, but less intense than strong.
type: Class
subclass of: intensity

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

fatal
description: fatal is a qualitative intensity value that is more intense than severe, leading to the death/non-functioning of a system.
type: Class
subclass of: intensity

strong
description: strong is a qualitative intensity value that is more intense than moderate, but less intense than severe.
type: Class
subclass of: intensity

weak
description: weak is a qualitative intensity value that is more intense than none, but less intense than mild.
type: Class
subclass of: intensity

to test a hypothesis
description: to test a hypothesis is the capability to evaluate the truth value of a proposition based on gathered evidence.
type: Class
subclass of: to examine

to characterize
description: to characterize is the capability to classify the attributes or features of an entity against a reference classification.
type: Class
subclass of: to describe

to describe
description: to describe is the capabilty to communicate facts about an entity.
type: Class
subclass of: to passively interact with

5' splice site
description: The 5' splice site is the terminal region of an exon that is 5' to the intron that is to be excised.
type: Class
subclass of: splice site

3' splice site
description: The 3' splice site is the terminal region of an exon that is 3' to the intron that is to be excised.
type: Class
subclass of: splice site

amino acid
description: An amino acid is an organic molecule composed of a carbon bonded to four different groups: a carboxyl group, an amino group, an R group, and a hydrogen atom. In the case of glycine, the R group is another hydrogen atom.
type: Class
subclass of: organic molecule

cis regulatory element
description: A cisregulatory element is a DNA sequence located on the same DNA strand or chromosome as the gene whose expression it affects.
type: Class
subclass of: nucleic acid part

trans-regulatory element
description: A trans-regulatory element is a DNA sequence associated with the regulation of a gene located outside the genomic region supporting the corresponding structural DNA region of the trans-regulatory element (i.e., a different DNA strand or different chromosome).
type: Class
subclass of: nucleic acid part

small cytoplasmic RNA (scRNA) gene
description: A small cytoplasmic RNA (scRNA) gene is a gene that encodes a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001266
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small cytoplasmic RNA (scRNA)

small nuclear RNA (snRNA) gene
description: A small nuclear RNA (snRNA) gene is a gene that encodes a small niuclear RNA molecule.
equivalent to: http://purl.obolibrary.org/obo/SO_0001268
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small nuclear RNA (snRNA)

small nucleolar RNA (snoRNA) gene
description: A small nucleolar RNA (snoRNA) gene is a gene that encodes a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
equivalent to: http://purl.obolibrary.org/obo/SO_0001267
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: small nucleolar RNA (snoRNA)

transfer RNA (tRNA) gene
alternative: solube RNA (sRNA) gene
alternative: tRNA gene
description: A transfer RNA (tRNA) gene is a gene that codes for a tRNA used in the translation of a messenger RNA (mRNA) to produce a protein product.
equivalent to: http://purl.obolibrary.org/obo/SO_0001272
type: Class
subclass of: non-protein coding RNA (ncRNA) gene
subclass of: Restriction
  on property: encodes
  some values from: transfer RNA (tRNA)

small cytoplasmic RNA (scRNA)
alternative: scRNA
description: A small cytoplasmic RNA (scRNA) molecule is a small (7S; 129 nucleotides) RNA molecule found in the cytosol and rough endoplasmic reticulum that are normally associated with proteins that are involved in specific selection and transport of other proteins.
type: Class
subclass of: non-protein coding RNA (ncRNA)
subclass of: Restriction
  on property: is encoded by
  some values from: small cytoplasmic RNA (scRNA) gene

transfer RNA (tRNA)
alternative: tRNA
description: A transfer RNA (tRNA) is an RNA molecule that aids in the translation of a messenger RNA (mRNA) to produce a protein product.
type: Class
subclass of: non-protein coding RNA (ncRNA)

small nuclear RNA (snRNA)
alternative: snRNA
description: A small nuclear RNA (snRNA) is a small RNA molecule that is located in the nucleus of a cell.
type: Class
subclass of: non-protein coding RNA (ncRNA)

small nucleolar RNA (snoRNA)
alternative: snoRNA
description: A small nucleolar RNA (snoRNA) is a small RNA that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins.
type: Class
subclass of: non-protein coding RNA (ncRNA)

non-protein coding RNA (ncRNA)
description: A non-protein coding RNA (ncRNA) is a RNA molecular that cannot be used as a template for generating a protein product.
type: Class
subclass of: RNA transcript

data collection device
description: A data collection device is a device that collects information about one or more objects.
type: Class
subclass of: device

mass spectrometer
description: A mass spectrometer is a device that identifies ions based on their mass to charge ratio using an electromagnetic field.
similar to: http://purl.obolibrary.org/obo/OBI_0000049
type: Class
subclass of: data collection device

microarray device
alternative: microarray platform
description: A microarray device is a device that identifies the binding of a target substance to a physically immobile substrate placed in an array or lattice.
similar to: http://purl.obolibrary.org/obo/OBI_0000052
type: Class
subclass of: data collection device

to identify
description: to identify is the capability to determine the identity of something.
type: Class
subclass of: to investigate

nmr device
alternative: nuclear magnetic resonance device
description: A nuclear magnetic resonance (NMR) device is a device that applies a magnetic field to perturb nuclei with an odd number of protons and/or of neutrons in order to hav them absort and re-emit electromagnetic radiation.
equivalent to: http://purl.obolibrary.org/obo/OBI_0000566
type: Class
subclass of: data collection device

catalog
alternative: registry
description: A catalog is a systemic collection of items of the same type.
type: Class
subclass of: collection

is identical to
description: is identical to is a relation between two objects that are conceptually the same notwithstanding provenance or other non-intrinsic attributes.
type: ObjectProperty
type: SymmetricProperty
sub property of: is comparable to

likelihood
description: Likelihood is the hypothetical probability that an event that has already occurred would yield a specific outcome.
type: Class
subclass of: quantity

log likelihood
description: Log likelihood is the natural logarithm of the likelihood function
type: Class
subclass of: likelihood

standard score
alternative: z-value, z-score, normal score, standardadized variable.
description: A standard score is the (signed) number of standard deviations an observation or datum is above the mean.
type: Class
subclass of: probability measure

interval
description: an interval is a set of real numbers with the property that any number that lies between two numbers in the set is also included in the set.
type: Class
subclass of: set
example: The set of all numbers x satisfying 0<=x<=1 is an interval which contains 0 and 1, as well as numbers between them.

is transitively related to
comment: not implemented in standard distribution
subset: ovopub
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty

open interval
description: an open interval is an interval that does not include its endpoints.
type: Class
subclass of: left open interval
subclass of: right open interval
example: (0,1) is an open interval that is greater than 0 and less than 1.

closed interval
description: A closed interval is an interval that includes its endpoints, and is denoted with square brackets.
type: Class
subclass of: right closed interval
subclass of: left closed interval
example: [0,1] is a closed interval that is greater than or equal to 0 and less than or equal to 1.

chemical-pathway association
alternative: drug-pathway association
description: a chemical-pathway association is an association between a chemical and a pathway.
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: pathway
subclass of: Restriction
  on property: refers to
  some values from: chemical entity

left open interval
description: a left open interval is an interval in which there is no element that is smaller than all other elements.
type: Class
subclass of: interval

right open interval
description: a right open interval is an interval in which there is no element that is greater than all other elements.
type: Class
subclass of: interval

right closed interval
description: a right closed interval is an interval in which there is a real number that is larger than all of its elements.
type: Class
subclass of: interval

left closed interval
description: a left closed interval is an interval in which there is a real number that is smaller than all its elements.
type: Class
subclass of: interval

pharmacokinetic pathway
description: a pharmacokinetic pathway is a metabolic pathway which describes the metabolism of a drug molecule.
type: Class
subclass of: metabolic pathway

pharmacodynamic pathway
description: a pharmacodynamic pathay is a regulatory pathway in which a drug molecule regulates the activity of one or more components organized in a pathway.
type: Class
subclass of: regulatory pathway

chemical-gene association
description: a chemical-gene association is an association between a chemical and a gene.
type: Class
subclass of: association
subclass of: Restriction
  on property: refers to
  some values from: chemical entity
subclass of: Restriction
  on property: refers to
  some values from: gene

set item
description: set item is an item in a set.
type: Class
subclass of: mathematical entity
subclass of: Restriction
  on property: is member of
  some values from: set

collection item
description: a collection item is an item in a collection.
type: Class
subclass of: set item
subclass of: Restriction
  on property: is member of
  some values from: collection

list item
description: a list item is an item in a list.
type: Class
subclass of: set item
subclass of: Restriction
  on property: refers to
  some values from: entity
subclass of: Restriction
  on property: is ordered part of
  some values from: list

ordered list item
description: an ordered list item is an item in an ordered list.
type: Class
subclass of: list item
subclass of: Class
  intersection of: list item
  intersection of: Restriction
    on property: has attribute
    some values from: ordinal position
  intersection of: Restriction
    on property: is part of
    some values from: list

anatomical entity
description: an anatomical entity is an object that is a structural part (material or immaterial) of a biological entity.
type: Class
subclass of: specialized object
equivalent class: Class
  intersection of: Class
    union of: material entity
    union of: spatial region
  intersection of: Restriction
    on property: is direct part of
    some values from: biological entity

zygosity
description: zygosity is the quality pertaining to the allelic complement of a biological system at a single locus on the DNA.
type: Class
subclass of: biological quality

homozygous
description: homozygous is the quality of a biological organism in which there are two identical alleles at a given locus.
type: Class
subclass of: zygosity

heterozygous
description: homozygous is the quality of a biological organism in which there are two different alleles at a given locus.
type: Class
subclass of: zygosity

hemizygous
description: hemizygous is the quality of a biological organism in which, based on the ploidy of the organism, there is half the number of alleles than normal at a given locus.
type: Class
subclass of: zygosity

nullizygous
description: nullizygous is the quality of a biological organism in which there are no allelles at a given locus.
type: Class
subclass of: zygosity

parental transmission
description: parental transmition is the quality of a biological organism in which the (genetic) material is transmitted from a parental unit.
type: Class
subclass of: biological quality

maternally transmitted
description: maternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the maternal line.
type: Class
subclass of: parental transmission
disjoint with: paternally transmitted

paternally transmitted
description: paternally transmitted is the quality of a biological organism in which the (genetic) material is transmitted from the paternal line.
type: Class
subclass of: parental transmission

helicity
description: helicity is the quality of being helical
type: Class
subclass of: structural quality

circularly helical
description: a circularly helical quality is the quality of a helix that is connected in a circle or loop.
type: Class
subclass of: helicity

left-handed helical
description: left-handed helical quality is the quality in which a clockwise screwing motion moves the helix towards the observed along the line of sight along the helix's axis.
type: Class
subclass of: helicity
disjoint with: right-handed helical

right-handed helical
description: right-handed helical quality is the quality in which a clockwise screwing motion moves the helix away from the observed along the line of sight along the helix's axis.
type: Class
subclass of: helicity

coding frame offset
description: a coding frame offset is a numeric value that indicates the number of bases from a reference start codon position.
type: Class
subclass of: chemical quality

coding sequence
description: a coding sequence is a sequence of nucleotides which encode a RNA or protein product..
type: Class
subclass of: nucleic acid sequence

has data item
description: has data item is a relation between a dataset and any described / referrenced entity.
subset: core
type: ObjectProperty
domain: dataset
sub property of: refers to
inverse of: is data item in

is data item in
description: 'is data item in' is a relation between an entity that is described or referenced in a dataset.
subset: core
type: ObjectProperty
range: dataset
sub property of: refers to

has phenotype
description: has phenotype is a relation between an object and an observable/measurable characteristic.
type: ObjectProperty
sub property of: has attribute
inverse of: is phenotype of

is phenotype of
description: is phenotype of is a relation between an observable/measurable characteristic and an object.
type: ObjectProperty
sub property of: is attribute of

humiliation
description: Humiliation is the abasement of pride, which creates mortification or leads to a state of being humbled or reduced to lowliness or submission.
type: Class
subclass of: hurt

hunger
description: hunger is the craving for food.
type: Class
subclass of: negative emotion

discouragement
alternative: discouraged
description: Discouragement is the emtion of having lost confidence or enthusiasm.
type: Class
subclass of: negative emotion

satisfaction
alternative: contentment
alternative: pleasure
description: satisfaction is the emotion of fulfillling one's wishes, expectations, or needs.
type: Class
subclass of: positive emotion

suicidal
description: suicidal is the emotion of being deeply unhappy or depressed with thoughts of killing one's self.
type: Class
subclass of: negative emotion

irritability
alternative: irritable
description: irritability is the negative emotion of quick excitability to annoyance, impatience, or anger.
type: Class
subclass of: negative emotion

indecision
alternative: indecisiveness
description: indecision is the emotion of being unable to choose between two or more possible courses of action.
type: Class
subclass of: negative emotion

temporal qualifier
description: a temporal qualifier is pertains to the frequency of the event of interest.
type: Class
subclass of: informational quality

never
alternative: none of the time
description: never refers to in none of the occasions.
type: Class
subclass of: temporal qualifier

some of the time
alternative: some of the time
description: some refers to in the minority of occasions
type: Class
subclass of: temporal qualifier

most of the time
alternative: most of the time
description: most refers to in the majority of occasions
type: Class
subclass of: temporal qualifier

always
alternative: all of the time
description: always indicates that the event occurs at all times.
type: Class
subclass of: temporal qualifier

quality descriptor
type: Class
subclass of: informational quality

very poor quality
type: Class
subclass of: quality descriptor

poor quality
type: Class
subclass of: quality descriptor

neither good nor poor quality
type: Class
subclass of: quality descriptor

good quality
type: Class
subclass of: quality descriptor

very good quality
type: Class
subclass of: quality descriptor

quantity modifier
type: Class
subclass of: informational quality

ovopub
description: An ovopub is an information content entity that contains and links to one or more resources and/or statements, including those describing its provenance, and is itself a dereferenceable resource.
subset: ovopub+
type: Class
subclass of: computational entity

collection ovopub
description: A collection ovopub is an ovopub that contains and links to one or more assertion subgraphs and/or ovopubs, as well as statements describing its provenance. It is used to share a specific set of items or restrict a search to the resources contained therein.
type: Class
subclass of: ovopub
disjoint with: assertion ovopub

assertion ovopub
description: An assertion ovopub is an ovopub that contains and links to an assertion subgraph with one or more statements that may be true or false, as well as statements describing its provenance.
type: Class
subclass of: ovopub

none quantifier
type: Class
subclass of: quantity modifier

a little quantifier
type: Class
subclass of: quantity modifier

moderately quantifier
type: Class
subclass of: quantity modifier

mostly quantifier
type: Class
subclass of: quantity modifier

completely quantifier
type: Class
subclass of: quantity modifier

satisfaction qualifier
type: Class
subclass of: informational quality

very dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

neither satisfied or dissatisfied qualifier
type: Class
subclass of: satisfaction qualifier

satisfied qualifier
type: Class
subclass of: satisfaction qualifier

excellent quality
type: Class
subclass of: quality descriptor

date of issue
description: the date at which an information content entity was made public.
type: Class
subclass of: time instant

author list
description: an ordered list of authors.
type: Class
subclass of: ordered list
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: list item
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
    intersection of: Restriction
      on property: refers to
      some values from: Class
        union of: organization
        union of: person

ordered list
description: an ordered list is a list in which items are sequentially ordered.
type: Class
subclass of: list
subclass of: Restriction
  on property: has proper part
  some values from: Class
    intersection of: list item
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position

middle name
description: a middle name is a name assigned to an individual that is not the first or last name.
type: Class
subclass of: name

middle initial
description: a middle initial is an abbreviated middle name.
type: Class
subclass of: middle name

telephone number
description: a telephone number is an identifier used to connect to a physical device capable of transfering voice or data over a network.
type: Class
subclass of: informational entity identifier

cellular phone number
description: a cellular phone number is a number to connect to a mobile device
type: Class
subclass of: telephone number

fax number
description: a fax number is a number to connect to fax device
type: Class
subclass of: telephone number

IP number
alternative: IP address
description: an IP number is an number to connect to a device on the internet.
type: Class
subclass of: informational entity identifier

email address
description: an email address is an identifier to send mail to particular electronic mailbox.
type: Class
subclass of: informational entity identifier

work phone number
description: a work phone number is the number to connect to an phone at a place of work.
type: Class
subclass of: telephone number

home phone number
description: a home phone number is the number to connect to an phone at a place of residence.
type: Class
subclass of: telephone number

status descriptor
description: status descriptor is a descriptor for the state of a process or object.
type: Class
subclass of: informational quality

protein expression value
description: A protein expression value is a quantity obtained from a protein expression experiment.
type: Class
subclass of: dimensional quantity

copy number variation
alternative: CNV
description: copy number variation refers to the number of deletions/duplications of a DNA region as compared to some reference state.
type: Class
subclass of: count

single nucleotide polymorphism
alternative: SNP
alternative: SNV
alternative: single nucleotide variation
description: a single nucleotide variation (SNV) is a nucleotide residue that is a variant compared to some reference nucleic acid sequence.
type: Class
subclass of: nucleotide residue

metadata
description: metadata is data that provides information about data.
type: Class
subclass of: data item

diagnosis
description: A diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms.
type: Class
subclass of: conclusion

directed acyclic graph
alternative: dag
description: a directed acyclic graph or DAG is a network digram that contains directed edges in which nodes may have multiple parents, but there are no cycles.
type: Class
subclass of: network diagram

arc
description: an arc is a closed segment of a differentiable curve.
type: Class
subclass of: curve

edge
description: an edge is a line connecting two graph vertices.
type: Class
subclass of: line

node
alternative: vertex
description: a node or vertex is a point in a graph.
type: Class
subclass of: point

epimer
description: An epimer is a stereoisomer that differs in configuration at only one stereogenic center.
type: Class
subclass of: stereoisomer

epimer association
type: Class
subclass of: association
subclass of: Restriction
  on class: epimer
  on property: refers to
  qualified cardinality: 2

mereological quality
description: a mereological quality is a quality of an entity vis-a-vis containment or parthood
type: Class
subclass of: object quality

empty
description: empty is the quality of not containing some thing
type: Class
subclass of: containment quality

full
description: full is the quality of contain an entity such that there is no more space for any additional entity.
type: Class
subclass of: containment quality

containment quality
description: a containment quality is a quality of being able to contain another entity.
type: Class
subclass of: mereological quality

gene-disease association linked with modifying mutation
description: A gene-disease association in which a gene mutation is known to modify the clinical presentation of the disease.
type: Class
subclass of: gene-disease association linked with genetic variation

gene-disease association linked with susceptibility mutation
description: A gene-disease association in which a germline mutation in the gene predisposes to the development of the disease, and it is necessary but not sufficient for the manifestation of the disease.
type: Class
subclass of: gene-disease association linked with genetic variation

gene-disease association linked with germline causal mutation
description: A gene-variant disease association in which a germline mutation in the gene/protein results in the development or maintenance of the disease, and it may be passed on to offspring.
type: Class
subclass of: gene-disease association linked with causal mutation

gene-disease association linked with somatic causal mutation
description: A gene-variant disease association in which a somatic mutation in the gene/protein results in the development or maintenance of the disease, and it may not be passed on to offspring.
type: Class
subclass of: gene-disease association linked with causal mutation

gene-disease association linked with somatic modifying mutation
description: A gene-variant disease association in which a somatic mutation in the gene modifies the clinical presentation of the disease, and it may not be passed on to offspring.
type: Class
subclass of: gene-disease association linked with modifying mutation

gene-disease association linked with germline modifying mutation
description: A gene-variant disease association in which a germline mutation in the gene modifies the clinical presentation of the disease, and it may be passed on to offspring.
type: Class
subclass of: gene-disease association linked with modifying mutation

fusion gene-disease association
description: A gene-disease association in which the fusion between two different genes (promotor and/or other coding DNA regions) is associated with the disease.
type: Class
subclass of: gene-disease association linked with genomic alterations

gene-disease association linked with chromosomal rearrangement
description: A gene-disease association in which the gene is included in a chromosomal rearrangement associated with a particular manifestation of the disease.
type: Class
subclass of: gene-disease association linked with genomic alterations

gene-disease association linked with genomic alterations
description: a gene-disease association that is linked with some genomic alteration
type: Class
subclass of: gene-disease biomarker association

DisGeNET disease specificity
description: DisGeNET Disease specificity is a measure of disease coverage. It is calculated from the negative base 2 log of the ratio of number of diseases associated to the total number of diseases. The measure is described here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#specificity
type: Class
subclass of: ratio

DisGeNET Pleiotropy Index
description: The DisGeNET pleiotropy index is a measure of specificity as it pertains to classes of disease. The disease pleotropy index is computed from the ratio of the number of disease classes associated with an entity over the total number of disease classes multplied by 100. The measure is defined here: http://www.disgenet.org/web/DisGeNET/menu/dbinfo#pleiotropy
type: Class
subclass of: ratio

specialized object
type: Class
subclass of: object
equivalent class: Class
  intersection of: object
  intersection of: Restriction
    on property: has realizable property
    some values from: realizable entity

week
description: A week is a period of 7 consecutive days.
type: Class
subclass of: time interval

specific gravity
description: Specific gravity is the ratio of the density of a substance to the density of a reference substance; equivalently, it is the ratio of the mass of a substance to the mass of a reference substance for the same given volume.
type: Class
subclass of: ratio

information encoding
type: Class
subclass of: information translation

speech
description: speech is the expression of thoughts and feelings by sound.
type: Class
subclass of: communicating

to retrieve
description: the capability to retrieve a (digitial/physical/mental) object from a location.
type: Class
subclass of: to actively interact with

information translation
type: Class
subclass of: information processing

information decoding
type: Class
subclass of: information translation

to store
description: to store is the capability to place an object into a medium in which it can be retrieved in the future.
type: Class
subclass of: to actively interact with

to encode information
description: the capability to encode information in a different representation
type: Class
subclass of: to actively interact with

to maintain information
description: the capability to maintain information such that it can be retrieved in the future.
type: Class
subclass of: to actively interact with

to decode information
description: the ability to reverse an encoding operation
type: Class
subclass of: to actively interact with

rate of change
description: The amount of change accumulated per unit time.
type: Class
subclass of: dimensional quantity

information maintenance
alternative: regulation of information
description: the regulation or maintenance of information
type: Class
subclass of: process maintenance

frequency
description: Frequency is the number of occurrences of a repeating event per unit time
type: Class
subclass of: rate of change

speed
description: Speed is the rate of change of an object's position.
type: Class
subclass of: rate of change

velocity
description: The rate of change of an object's position and the direction of that change
type: Class
subclass of: speed

slide
description: A slide is an visual representation meant to communicate some information.
type: Class
subclass of: media

statute
description: A statute is a formal written enactment of a legislative authority that governs a state, city or country.
type: Class
subclass of: legal document

legislation
description: A legal document proposing or enacting a law or a group of laws.
type: Class
subclass of: legal document

legal document
description: A legal document is a formally executed written document that can be formally attributed to its author, records and formally expresses a legally enforceable act, process, or contractual duty, obligation, or right, and therefore evidences that act, process, or agreement.
type: Class
subclass of: document

brief
description: A brief is a written legal document used in various legal adversarial systems that is presented to a court arguing why one party to a particular case should prevail.
type: Class
subclass of: legal document

book section
type: Class
subclass of: document section
subclass of: Restriction
  on property: is proper part of
  some values from: book
equivalent class: Class
  intersection of: document section
  intersection of: Restriction
    on property: is proper part of
    some values from: book

bill
description: A bill is proposed legislation under consideration by a legislature.
type: Class
subclass of: legal document

versioned dataset
description: a versioned dataset is a dataset with a particular release date or release number.
type: Class
subclass of: dataset
subclass of: Restriction
  on property: has attribute
  some values from: version label

analyte
description: an analyte is a substance or chemical constituent of interest in an analytical procedure.
type: Class
subclass of: chemical substance

protein domain
description: A protein domain is a part of a protein that maintains its structure and function independently of the rest of the protein.
type: Class
subclass of: amino acid polymer submolecule

protein family
description: a protein family is a collection of proteins that share a common evolutionary origin, reflected by their related function and similarity in composition or structure.
type: Class
subclass of: collection

genomic sequence variant
description: a genomic sequence variant is part of a nucleic acid which is compositionally different than another reference genomic part.
alternative: variant
type: Class
subclass of: nucleic acid part

unigene cluster
description: a unigene cluster is a collection of transcripts (ESTs and mRNAs) that map to a particular genomic region.
alternative: cluster of transcripts
type: Class
subclass of: collection

gene symbol
description: a gene symbol is a short name assigned to a gene.
type: Class
subclass of: scientific name

statement of consequence
description: a statement of consequence is a statement concerning the result or effect of an action or condition.
type: Class
subclass of: statement

notation
description: a notation is a series or system of written symbols used to represent numbers, amounts, or elements.
type: Class
subclass of: specification

chemical notation
description: a notation to describe a chemical entity
type: Class
subclass of: notation

InCHI notation
type: Class
subclass of: chemical notation

sequence variation notation
type: Class
subclass of: notation

hgvs notation
description: The HGVS (human genome variation society) notation is a notation to specify a sequence variation in dna, rna, proteins, and other biomolecules.
type: Class
subclass of: sequence variation notation

protein coding sequence
description: A protein coding sequence (CDS) is the region of DNA that is translated to form proteins. The CDS refers to those nucleotides (concatenated exons) that can be divided into codons which are actually translated into amino acids by the ribosomal translation machinery.
alternative: CDS
alternative: coding sequence
type: Class
subclass of: gene component

ontology
description: an ontology is a formal specification of entities, their attributes and relationships.
type: Class
subclass of: formal specification

biologic
description: A biologic, also known as a biologic medical product, biological, or biopharmaceutical, is any pharmaceutical drug product manufactured in, extracted from, or semisynthesized from biological sources.
type: Class
subclass of: pharmaceutical drug

post-translational modification
description: a post-translational modification is a part of a protein that was added, removed, or modified as a result of a chemical reaction after synthesis.
type: Class
subclass of: amino acid polymer submolecule

evidence
description: evidence is the body of facts or information indicating whether a belief or proposition is true or valid.
type: Class
subclass of: proposition

carbohydrate
alternative: oligosaccharide
alternative: saccharide
description: a carbohydrate is an organic molecule composed of two or more monosaccharides.
type: Class
subclass of: organic polymer
subclass of: Restriction
  min qualified cardinality: 2
  on class: carbohydrate residue
  on property: has direct part

terminology
description: A terminology is a set of terms used for a specified application.
type: Class
subclass of: vocabulary

microRNA (miRNA)
description: A microRNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals and some viruses, that functions in RNA silencing and post-transcriptional regulation of gene expression.
alternative: miRNA
type: Class
subclass of: non-protein coding RNA (ncRNA)

medical intervention
description: a medical intervention is a medical procedure to treat (to cure or alleviate) a health condition.
type: Class
subclass of: medical procedure

chemical exposure
description: chemical exposure is a process to expose one or more individuals to a chemical substance.
type: Class
subclass of: chemical interaction

subcellular entity
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: is part of
  some values from: cell

positively regulates
description: x positively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an effect that increases the frequency, rate or extent of y
type: ObjectProperty
sub property of: regulates

negatively regulates
description: x negatively regulates y if and only if x is a process and y is either a process or a quality, and the progression of x exerts an reduced effect on the frequency, rate or extent of y
type: ObjectProperty
sub property of: regulates

is associated with
description: x is associated with y when x and y are logically or statistically related to one another.
type: ObjectProperty
sub property of: is related to

is correlated with
description: x is correlated with y when x holds a statistical relationship with y
type: ObjectProperty
sub property of: is associated with

intersex
description: intersex is a biological sex characterised by birth with genitalia and/or secondary sexual characteristics of indeterminate sex, or which combine features of both sexes.
type: Class
subclass of: biological sex
disjoint with: female

density
description: Density (volumetric mass density) is the quantity of mass per unit volume of a substance.
type: Class
subclass of: 3D extent quantity

surface area
description: The surface area of a is a measure of the total area that the surface of the object occupies.
type: Class
subclass of: area

aspect ratio
description: The aspect ratio of a geometric shape is the ratio of its sizes in different dimensions.
type: Class
subclass of: ratio

object relational quality
description: object relational quality refers to a quality in relation to one or more objects
type: Class
subclass of: object quality

synthetic quality
description: synthetic quality is the quality of a manufactured object that has similar properties as naturally occuring objects.
type: Class
subclass of: object relational quality

sample quality
description: sample quality is the quality of an object that is drawn from a larger population.
type: Class
subclass of: object relational quality

replica quality
description: replica quality is the quality of an object that is an exact copy of another object.
type: Class
subclass of: object relational quality

percentage
description: A percentage is a number that is a ratio expressed as a fraction of 100. It is denoted using the percent sign "%".
type: Class
subclass of: ratio

quantile
description: A quantile is a quantity that divides the range of a probability distribution into continuous intervals with equal probabilities, or dividing the observations in a sample in the same way.
type: Class
subclass of: dimensionless quantity

percentile
description: A percentile (or a centile) is a quantile that divides the given probability distribution, or sample, into 100 equal-sized intervals.
type: Class
subclass of: quantile

duplicate role
description: a duplicate role is a comparative role that holds when one item is an exact copy of another in a specific set.
type: Class
subclass of: comparative role

replicate role
description: a replicate role is a comparative role that holds when one item is a reproduction, facsimile, or a copy of another.
type: Class
subclass of: comparative role

replicate
description: a replicate is an object that is a facsimile, reproduction, or copy of another item.
type: Class
subclass of: collection item
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: replicate role
    intersection of: Restriction
      on property: in relation to
      some values from: object

a collection of replicates
alternative: replicates
description: a collection of replicates is a collection composed of items that are a facsimile, reproduction, or copy of other items in the collection.
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: replicate

duplicate
description: a duplicate is an object that is an exact copy of another item
type: Class
subclass of: collection item
subclass of: Restriction
  on property: has role
  some values from: Class
    intersection of: duplicate role
    intersection of: Restriction
      on property: in relation to
      some values from: object

a collection of duplicates
alternative: duplicates
description: a collection of duplicates is a collection composed of items that are an exact copy of other items in the collection.
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: duplicate

chemical salt
alternative: salt
description: a chemical salt is a molecular complex composed of an ionic assembly of cations and anions.
type: Class
subclass of: molecular complex

strong chemical salt
description: a strong chemical salt is a chemical salt that is composed of strong electrolytes. Strong chemical salts contain Na,K,NH4 or NO3, CIO4, CH3COO.
type: Class
subclass of: chemical salt

weak chemical salt
description: a weak chemical salt is a chemical salt composed of weak eletrolytes.
type: Class
subclass of: chemical salt

peptide
description: a peptide is an organic polymer composed of between two and fifty amino acids.
type: Class
subclass of: amino acid polymer

oligopeptide
description: an oligopeptide is an organic polymer composed of fewer than 10 or 15 amino acids.
type: Class
subclass of: amino acid polymer

amino acid polymer
description: an amino acid polymer is an organic polymer composed of two or more amino acid residues.
type: Class
subclass of: organic polymer
subclass of: Restriction
  min qualified cardinality: 2
  on class: amino acid residue
  on property: has direct part

ingredient
description: an ingredient is a chemical substance that forms part of a mixture.
type: Class
subclass of: chemical substance
equivalent class: Class
  intersection of: chemical substance
  intersection of: Restriction
    on property: derives into
    some values from: chemical substance

tensor
description: a tensor is a n-dimensional array.
type: Class
subclass of: mathematical entity

vector
alternative: rank 1 tensor
description: a vector is a rank 1 tensor that is described by n-dimension of scalars.
type: Class
subclass of: rank nonzero tensor
subclass of: Restriction
  on property: is part of
  some values from: vector space
subclass of: Restriction
  all values from: scalar
  on property: has proper part

scalar
alternative: rank 0 tensor
description: a scalar is a rank 0 tensor and is an element of a field that is used to define a vector space.
type: Class
subclass of: tensor

vector space
description: a vector space is a set of vectors.
type: Class
subclass of: mathematical entity
subclass of: Restriction
  min qualified cardinality: 0
  on class: vector
  on property: has member

matrix
alternative: rank 2 tensor
description: a matrix is a rank 2 tensor. It is represented as a rectangular array or table of numbers, symbols, or expressions arranged in rows and columns.
type: Class
subclass of: rank nonzero tensor
subclass of: Restriction
  all values from: vector
  on property: has proper part

rank nonzero tensor
description: a rank nonzero tensor is a tensor with a rank greater than zero.
type: Class
subclass of: tensor
subclass of: Restriction
  all values from: Class
    intersection of: tensor
    intersection of: Restriction
      on property: has attribute
      some values from: ordinal position
  on property: has proper part

chemical-chemical association
description: A chemical-chemical association is an association between two chemical entities.
type: Class
subclass of: association
subclass of: Restriction
  on class: chemical entity
  on property: refers to
  qualified cardinality: 2

disease-disease association
type: Class
comment: A disease-disease association is an association between two diseases.
subclass of: association
subclass of: Restriction
  on class: disease
  on property: refers to
  qualified cardinality: 2

gene-gene association
type: Class
comment: A gene-gene association is an association between two genes.
subclass of: association
subclass of: Restriction
  on class: gene
  on property: refers to
  qualified cardinality: 2

protein-protein association
type: Class
comment: A protein-protein association is an association between two proteins.
subclass of: association
subclass of: Restriction
  on class: protein
  on property: refers to
  qualified cardinality: 2

protein-disease association
type: Class
comment: A protein-disease association is an association between a protein and a disease.
subclass of: association

chemical-protein association
type: Class
comment: A chemical-protein association is an association between a chemical and a protein.
subclass of: association

imaginary number
description: An imaginary number is a complex number whose real part is zero e.g. 0 + bi, and is expressed as a multiple of the square root of -1.
example: 5i is an imaginary number, and its square is -25.
type: Class
subclass of: complex number
disjoint with: real number

real number
description: a real number is a complex number whose imaginary part is zero, e.g. a + 0i.
type: Class
subclass of: complex number

complex number
description: a complex number is an element of a number system that extends the real numbers with an imaginary unit i. Every complex number can be expressed in the form a + bi, where a and b are real numbers.
type: Class
subclass of: number
subclass of: Class
  intersection of: Restriction
    on class: imaginary number
    on property: has component part
    qualified cardinality: 1
  intersection of: Restriction
    on class: real number
    on property: has component part
    qualified cardinality: 1

imaginary
description: the quality of existing only in the imagination. it can be used to describe concepts, ideas, or things that are the product of a cognitive process.
type: Class
subclass of: hypothetical

protein isoform
description: a protein isoform is a protein that is a structural variant (different sequence of amino acids and/or post-translational modifications) of another protein, but encoded by the same gene.
type: Class
subclass of: protein
subclass of: isomer
subclass of: Restriction
  on property: is encoded by
  some values from: protein coding gene

salt
description: a salt is a heterogeneous substance that is coposed of positively charged ions (cations) and negatively charged ions (anions) held together by electrostatic forces.
type: Class
subclass of: heterogeneous substance

organism
description: A biological organisn is a biological entity that consists of one or more cells and is capable of genomic replication (independently or not).
type: Class
subclass of: biological entity
equivalent class: Class
  union of: cellular organism
  union of: non-cellular organism

cell
description: A cell is a biological entity that is contained by a plasma membrane.
type: Class
subclass of: biological entity

tissue
description: A tissue is a mereologically maximal collection of cells that together perform some function.
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: has direct part
  some values from: cell

organ
description: An organ is a collection of tissues joined in structural unit to serve a common function.
type: Class
subclass of: biological entity

chemical entity
description: A chemical entity is a material entity that pertains to chemistry.
equivalent to: CHEBI:23367
subset: chemical+
type: Class
subclass of: material entity
example: atom, ion, molecule, chemical substance,

weak submolecular component
description: A weak submolecular component is a submolecular component that weakly connects submolecular components.
type: Class
subclass of: submolecular entity
disjoint with: strong submolecular component

polypeptide
description: A polypeptide is an organic polymer composed of amino acid residues, typically of less than 50 amino acids in length.
type: Class
subclass of: amino acid polymer
subclass of: Restriction
  min qualified cardinality: 2
  on class: amino acid residue
  on property: has component part
disjoint with: nucleic acid

nucleic acid
description: A nucleic acid is an organic polymer composed of a sequence of nucleotide residues.
type: Class
subclass of: organic polymer
subclass of: Restriction
  min qualified cardinality: 2
  on class: nucleotide residue
  on property: has component part

ribonucleic acid
description: A ribonucleic acid is an organic polymer composed of a sequence of ribonucleotide residues.
type: Class
subclass of: nucleic acid
subclass of: Restriction
  min qualified cardinality: 2
  on class: ribonucleotide residue
  on property: has component part
disjoint with: deoxyribonucleic acid

deoxyribonucleic acid
description: A deoxyribonucleic acid is an organic polymer composed of a sequence of deoxyribonucleotide residues.
type: Class
subclass of: nucleic acid
subclass of: Restriction
  min qualified cardinality: 2
  on class: deoxyribonucleotide residue
  on property: has component part

lipid
description: A lipid is a water-insoluable organic molecule.
type: Class
subclass of: organic molecule

chemical interaction
description: A chemical interaction is a biochemical process in which chemical entities interact through some set of attractive forces.
equivalent to: biopax:Interaction
type: Class
subclass of: interacting
subclass of: Restriction
  on property: has participant
  some values from: chemical entity

primary structure descriptor
description: A primary structure descriptor describes a biomolecular object in terms of a 1D or 2D topology.
type: Class
subclass of: biomolecular structure descriptor

protein sequence
alternative: amino acid sequence
alternative: polypeptide sequence
description: A protein acid sequence is the character representation of the molecular structure of a protein.
type: Class
subclass of: biopolymer sequence
subclass of: Restriction
  on property: is attribute of
  some values from: polypeptide
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: polypeptide

nucleic acid sequence
description: A nucleic acid sequence is a symbolic representation of the sequence of nucleic acid residues in a nucleic acid.
type: Class
subclass of: biopolymer sequence
subclass of: Restriction
  on property: is attribute of
  some values from: nucleic acid
subclass of: Restriction
  on property: represents
  some values from: Class
    intersection of: molecular structure
    intersection of: Restriction
      on property: is attribute of
      some values from: nucleic acid

ribonucleic acid sequence
alternative: RNA sequence
description: A ribonucleic acid sequence is a symbolic representation of the sequence of ribonucleic acid residues in a ribonucleic acid.
type: Class
subclass of: nucleic acid sequence
subclass of: Restriction
  on property: is about
  some values from: ribonucleic acid

deoxyribonucleic acid sequence
alternative: DNA sequence
description: A deoxyribonucleic acid sequence is a symbolic representation of the sequence of deoxyribonucleic acid residues in a deoxyribonucleic acid.
type: Class
subclass of: nucleic acid sequence
subclass of: Restriction
  on property: is about
  some values from: deoxyribonucleic acid

biological data
description: biological data is scientific data relevant to biology.
type: Class
subclass of: scientific data

submolecular entity
description: A submolecular entity is a chemical entity that is a part of a molecule.
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: is part of
  some values from: chemical entity

secondary structure descriptor
description: A secondary structure descriptor describes local topological patterns in a biopolymer.
type: Class
subclass of: biomolecular structure descriptor

tertiary structure descriptor
description: A tertiary structure descriptor describes 3D topological patterns in a biopolymer.
type: Class
subclass of: biomolecular structure descriptor

quaternary structure
description: A quaternary structure descriptor describes topological patterns in a multi-unit biopolymer complex.
type: Class
subclass of: biomolecular structure descriptor

genetic polymorphism
description: genetic polymorphism is the description of a difference in genetic composition at some location.
type: Class
subclass of: nucleic acid part

genetic data
description: genetic data is data pertaining to genetics.
type: Class
subclass of: biological data

biological sex
description: biological sex is the quality of a biological organism based on reproductive function or organs.
type: Class
subclass of: biological quality

monosaccharide
description: A monosaccharide is an organic molecule that consists of a single polyhydroxy aldehyde or ketone group.
type: Class
subclass of: organic molecule

PDB chain identifier
description: A PDB chain identifier is a alphabetical label to identify a molecule in a structure provided by the Protein DataBank .
type: Class
subclass of: molecular identifier

PDB record identifier
description: A PDB record identifier is an identifier for a PDB generated record.
type: Class
subclass of: record identifier

hydrogen bond
description: A hydrogen bond is a weak submolecular interaction formed between a hydrogen atom and a electronegative atom.
type: Class
subclass of: weak submolecular component

cation pi interaction
description: A cation pi interaction is an ionic interaction between the localized negative charge of π orbital electrons, located above and below the plane of an aromatic ring, and a positive charge.
type: Class
subclass of: ionic interaction

gene
description: A gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript.
equivalent to: biopax:Gene
equivalent to: http://purl.obolibrary.org/obo/SO_0000704
type: Class
subclass of: nucleic acid part

biochemical reaction
description: A biochemical reaction is a biochemical process that involves the conversion of at least one chemical participant (target) into another (product) by an enzyme (agent).
equivalent to: biopax:BiochemicalReaction
equivalent to: biopax:Conversion
type: Class
subclass of: catalyzed reaction
subclass of: Class
  intersection of: catalyzed reaction
  intersection of: Restriction
    on property: has agent
    some values from: enzyme
  intersection of: Restriction
    on property: has target
    some values from: substrate
  intersection of: Restriction
    on property: has product
    some values from: product

chemical element
description: A chemical element is a (effectively) homogeneous substance composed of one type of atom.
type: Class
subclass of: homogeneous substance
subclass of: Restriction
  all values from: atom
  on property: has direct part

drug
description: A drug is a chemical substance that contains one or more active ingredients that regulate one or more biological processes.
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has capability
  some values from: Class
    intersection of: to regulate
    intersection of: Restriction
      on property: in relation to
      some values from: biological entity

pharmaceutical drug
alternative: medicine
description: A pharmaceutical preparation is a chemical substance that is approved for use in the medical diagnosis, cure, treatment, or prevention of disease.
type: Class
subclass of: drug
subclass of: Restriction
  on property: has direct part
  some values from: active ingredient

binding site
description: A binding site is a molecular site which when occupied with particular ligands leads to structural transformations that initiatiate new moelcular processes.
type: Class
subclass of: molecular site

active site
description: An active site is a molecular site in which a chemical event occurs (structural transformation or conformational change).
type: Class
subclass of: molecular site

haplotype
description: A haplotype is one of a set of genomic sequence variants.
type: Class
subclass of: genomic sequence variant

protein
description: A protein is an organic polymer that is composed of one or more linear polymers of amino acids.
equivalent to: CHEBI:36080
type: Class
subclass of: amino acid polymer
subclass of: Restriction
  on property: has direct part
  some values from: amino acid residue
subclass of: Restriction
  on property: has component part
  some values from: polypeptide

atom
description: An atom is composed of a core of protons and/or neutrons which may be surrounded by a cloud of electrons.
type: Class
subclass of: chemical entity

base pair
description: A base pair is a weak molecular interaction composed of hydrogen bonds between nucleobases.
type: Class
subclass of: weak submolecular component

biological entity
description: A biological entity is a heterogeneous substance that contains genomic material or is the product of a biological process.
subset: chemical-
type: Class
subclass of: heterogeneous substance
subclass of: Restriction
  on property: is part of
  some values from: organism

strong submolecular component
description: A strong submolecular component is a submolecular component that strongly connects submolecular components.
type: Class
subclass of: submolecular entity

male
description: male is a biological sex of an individual with male sexual organs.
equivalent to: PATO:0000384
type: Class
subclass of: biological sex
disjoint with: female

molecular site
description: A moleclar site is a spatial region bounded (in part or in whole) by a molecule and may be occupied by other material entities (e.g. drugs).
type: Class
subclass of: site

allosteric site
description: An allosteric site is a binding site that when bound to particular ligand changes the conformational state and affects its functionality.
type: Class
subclass of: binding site

biological fluid
description: A biological fluid is a fluid of biological origin.
type: Class
subclass of: biological entity
subclass of: Restriction
  on property: is derived from
  some values from: biological entity

female
description: female is a biological sex of an individual with female sexual organs.
type: Class
subclass of: biological sex

evolutionary lineage
description: evolutionary lineage is a sequence of species, that form a line of descent, each new species the direct result of speciation from an immediate ancestral species.
type: Class
subclass of: history

cell line
description: A cell line is a collection of genetically identifical cells.
type: Class
subclass of: biological entity

strain
description: A strain is a genetic variant or kind of microorganism.
type: Class
subclass of: organism
subclass of: Restriction
  on property: is variant of
  some values from: organism

phenotype
description: A phenotype is an observable characteristic of an individual.
type: Class
subclass of: biological quality

life status
description: life status is the quality of whether something is alive or dead.
type: Class
subclass of: biological quality
equivalent class: Class
  union of: alive
  union of: dead

alive
description: alive is the state of a biological organism that exhibits biological functions.
type: Class
subclass of: life status
disjoint with: dead

dead
description: dead is the quality of an object in which there is a cessation of all biological functions.
type: Class
subclass of: life status

family history
description: family history is the systematic narrative and research of past events relating to a specific family, or specific families.
type: Class
subclass of: history

generation number
description: generation number is a count of the number of biological reproduction events elapsed from some starting reference point.
type: Class
subclass of: count

5' untranslated region
description: The five prime untranslated region (5' UTR) is a section of messenger RNA (mRNA) and the DNA that codes for it that starts at the +1 position (where transcription begins) and ends one nucleotide before the start codon (usually AUG) of the coding region.
type: Class
subclass of: gene component

bioinformatic data
description: bioinformatic data is data genereated or used for computer-based investigations of biological phenomena.
type: Class
subclass of: biological data

sequence alignment
description: A sequence alignment is the character-based alignment of sequences using some method.
type: Class
subclass of: collection

multiple sequence alignment
description: A multiple sequence alignment is a sequence alignment involving more than two sequences.
type: Class
subclass of: sequence alignment

pairwise sequence alignment
description: A pairwise sequence alignment is the alignment of exactly 2 sequences.
type: Class
subclass of: sequence alignment

3' untranslated region
description: A three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon.
type: Class
subclass of: gene component

organic submolecule
description: An organic submolecule is connected region of a molecule.
type: Class
subclass of: submolecule
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: carbon atom
  intersection of: Restriction
    on property: has part
    some values from: oxygen atom
subclass of: Restriction
  on property: is part of
  some values from: organic molecule

organic molecule
description: An organic molecule is a molecule composed of organic atoms (at least carbon, hydrogen, and optionally oxygen, phosphorus, nitrogen, sulfur)
type: Class
subclass of: molecule
subclass of: Class
  intersection of: Restriction
    on property: has part
    some values from: carbon atom
  intersection of: Restriction
    on property: has part
    some values from: hydrogen atom

open reading frame
description: An open reading frame (ORF) is a part of a gene that encodes a protein but does not contain a stop codon.
type: Class
subclass of: gene component
subclass of: Class
  intersection of: Restriction
    on class: start codon
    on property: has component part
    qualified cardinality: 1
  intersection of: Restriction
    on class: stop codon
    on property: has component part
    qualified cardinality: 1
subclass of: Restriction
  on property: is transcribed into
  some values from: Class
    intersection of: RNA transcript
    intersection of: Restriction
      on property: is translated into
      some values from: polypeptide

amino acid residue
description: An amino acid residue is a submolecule of an amino acid that is part of a larger molecule.
type: Class
subclass of: amino acid polymer submolecule
subclass of: Restriction
  on property: is derived from
  some values from: amino acid

nucleotide residue
description: A nucleotide residue is a part of a molecule that derives from a nucleotide.
type: Class
subclass of: nucleic acid part

poison
description: A poison is a drug that is harzardous or toxic to an organism when ingested at a certain quantity.
type: Class
subclass of: drug

active ingredient
description: An active ingredient is a molecular entity that exhibits biological activity.
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.

encodes
description: A relation between two objects, in which the first object contains information that is used to produce the second object.
type: ObjectProperty
sub property of: specifies
inverse of: is encoded by
example: an open reading frame encodes a protein (it contains information that specifies the amino acid composition and topology)

is encoded by
description: A relation between two objects, in which the first object is produced from the information contained in the second object.
type: ObjectProperty
sub property of: is specified by

is transcribed into
description: a relation between two information content entities in which one is transcribed into (an exact or similar kind) another through some process.
type: ObjectProperty
sub property of: encodes
inverse of: is transcribed from
example: DNA is transcribed into RNA

is transcribed from
type: ObjectProperty
sub property of: is encoded by

is translated into
type: ObjectProperty
sub property of: encodes
inverse of: is translated from
example: RNA is translated into Protein
example: a relation between two information content entities in which one is translated into (a completely different kind of entity) another through some process.

is translated from
type: ObjectProperty
sub property of: is encoded by

operon
description: An operon is a collection of contiguous genes transcribed as a single (polycistronic) mRNA.
similar to: SO:0000178
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is proper part of
  some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has component part
  some values from: gene
subclass of: Restriction
  on property: is transcribed into
  some values from: RNA transcript

gene regulatory component
description: A gene regulatory component is a gene component that exerts a regulatory function.
type: Class
subclass of: gene component
subclass of: Restriction
  on property: has function
  some values from: to regulate

gene enhancer
description: A gene enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster.
type: Class
subclass of: gene regulatory component

inactive ingredient
description: Aninactive ingredient is a molecular entity that does not exhibit biological activity.
type: Class
subclass of: A pharmaceutical ingredient is a part of a pharmaceutical preparation.

to serve as a template for molecular synthesis
description: to serve as a template for molecular synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which another molecule may be produced.
type: Class
subclass of: to serve as

to serve as a template for protein synthesis
description: to serve as a template for protein synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a protein may be produced.
type: Class
subclass of: to serve as a template for molecular synthesis

to serve as a template for RNA synthesis
description: to serve as a template for RNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which an RNA molecule may be produced.
type: Class
subclass of: to serve as a template for molecular synthesis

to serve as a template for DNA synthesis
description: to serve as a template for DNA synthesis is the capability of a chemical entity to provide the necessary information or scaffold by which a DNA molecule may be produced.
type: Class
subclass of: to serve as a template for molecular synthesis

deoxyribonucleic acid template
description: A deoxyribonucleic acid template is a deoxyribonucleic acid that provides the template to synthesize a complementary strand of DNA through transcription.
type: Class
subclass of: deoxyribonucleic acid
subclass of: Restriction
  on property: has function
  some values from: Class
    union of: to serve as a template for RNA synthesis
    union of: to serve as a template for DNA synthesis

deoxyribonucleic acid primer
description: A deoxyribonucleic acid primer is a deoxyribonucleic acid that enables the synthesis of a complement strand of DNA by binding to it and acting as a point of transcription initiation.
type: Class
subclass of: primer
subclass of: deoxyribonucleic acid
subclass of: Restriction
  on property: has function
  some values from: to serve as a template for DNA synthesis

to serve as a primer for DNA synthesis
description: to serve as a primer for DNA synthesis is the capability of a short nucleic acid to bind to the 5' end of single strand of DNA template and help initiate DNA replication.
type: Class
subclass of: to serve as

RNA transcript component
description: An RNA transcript component is a region of an RNA transcript.
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is part of
  some values from: messenger RNA
subclass of: Restriction
  on property: is proper part of
  some values from: RNA transcript

mature mRNA
description: A mature RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.
type: Class
subclass of: messenger RNA
subclass of: Class
  complement of: Restriction
    on property: has proper part
    some values from: intron
subclass of: Class
  complement of: Restriction
    on property: derives into
    some values from: RNA transcript
subclass of: Restriction
  on property: is derived from
  some values from: RNA transcript
subclass of: Restriction
  on property: is translated into
  some values from: protein

pre-mRNA
description: Precursor mRNA (pre-mRNA) is a single strand of messenger ribonucleic acid (mRNA) that is synthesized from a DNA template throught transcription.
type: Class
subclass of: messenger RNA
subclass of: Restriction
  on property: derives into
  some values from: mature mRNA

mRNA splice variant
description: An mRNA splice variant is an mRNA molecule that varies from another mRNA molecule of the same gene origin but having a different final sequence due to differences in its assembly from splice sites.
type: Class
subclass of: messenger RNA
subclass of: Restriction
  on property: is derived from
  some values from: Class
    intersection of: messenger RNA
    intersection of: Restriction
      on property: has direct part
      some values from: splice site

messenger RNA
description: A messenger RNA is a ribonucleic acid that contains an untranslated region (UTR) and protein coding sequence and lacks introns.
type: Class
subclass of: RNA transcript
subclass of: Restriction
  on property: encodes
  some values from: protein

dna gene
description: A gene that is located on DNA.
type: Class
subclass of: gene
subclass of: Restriction
  on property: is proper part of
  some values from: deoxyribonucleic acid
disjoint with: rna gene

rna gene
description: A gene that is located on RNA.
type: Class
subclass of: gene
subclass of: Restriction
  on property: is proper part of
  some values from: ribonucleic acid

allele
description: An allele is one of a set of sequence variants of a gene.
type: Class
subclass of: gene
subclass of: Restriction
  on property: is variant of
  some values from: gene

ploidy
description: ploidy is the cellular quality relating to the amount of DNA contained in a cell.
type: Class
subclass of: cellular quality

chemical transport
description: chemical transport is the directed movement of a chemical entity by some agent (e.g. transporter).
equivalent to: biopax:Transport
type: Class
subclass of: transporting
subclass of: Restriction
  on property: has participant
  some values from: chemical entity

active transport
description: active transport is the movement of a substance across a membrane against its concentration gradient (from low to high concentration) and requires chemical energy.
equivalent to: biopax:TransportWithBiochemicalReaction
type: Class
subclass of: membrane transport

molecular complex formation
description: molecular complex formation is the process of forming a molecular complex from its constituent parts.
type: Class
subclass of: chemical synthesis
subclass of: Restriction
  on property: has product
  some values from: molecular complex

molecular complex dissociation
description: molecular complex disassociation is the process of dissambly of a molecular complex into its constitutent parts.
type: Class
subclass of: chemical destruction
subclass of: Restriction
  on property: has target
  some values from: molecular complex

regulation of biochemical process
description: regulation of biochemical process is a process that changes the frequency, rate or extent of a target biochemical process.
type: Class
subclass of: regulation of process

biochemical activation
description: biochemical activation is a molecular interaction that increases the catalytic rate of the target enzyme.
type: Class
subclass of: regulation of catalytic capability
subclass of: Restriction
  on property: realizes
  some values from: to decrease the rate of formation
disjoint with: biochemical inhibition

biochemical inhibition
description: biochemical inhibition is a molecular interaction that decreases the catalytic rate of the target enzyme.
type: Class
subclass of: regulation of catalytic capability
subclass of: Restriction
  on property: realizes
  some values from: to increase the activation energy

process up-regulation
alternative: positive regulation
description: process up-regulation is a process that increases the frequency, rate or extent of one or more processes in relation to a reference state.
type: Class
subclass of: regulation of process
disjoint with: process down-regulation

process down-regulation
alternative: negative regulation
description: process down-regulation is a process that decreases the frequency, rate or extent of one or more processes in relation to a reference state.
type: Class
subclass of: regulation of process

medical data
description: medical data is data of interest to medicine.
type: Class
subclass of: biological data

disease
description: disease is the outward manifestation of one or more disorders.
type: Class
subclass of: biological quality
subclass of: Restriction
  on property: is quality of
  some values from: Class
    intersection of: material entity
    intersection of: Restriction
      on property: has quality
      some values from: abnormal

transcription
description: transcription is the process of creating a complementary RNA copy of a sequence of DNA.
type: Class
subclass of: biosynthesis
subclass of: Restriction
  on property: has output
  some values from: Class
    intersection of: ribonucleic acid
    intersection of: Restriction
      on property: is transcribed from
      some values from: deoxyribonucleic acid
subclass of: Restriction
  on property: has input
  some values from: deoxyribonucleic acid

translation
description: translation is the process of producing a polypeptide from a ribonucleic acid by a ribosome.
type: Class
subclass of: biosynthesis
subclass of: Restriction
  on property: has input
  some values from: ribonucleic acid
subclass of: Restriction
  on property: has product
  some values from: polypeptide

is homologous to
description: a relation between two entities which indicates their common ancestry.
type: ObjectProperty
type: SymmetricProperty
sub property of: is variant of

molecular modification
description: Molecular modification is chemical alteration of a known and previously characterized lead compound for the purpose of enhancing its usefulness as a drug. This could mean enhancing its specificity for a particular body target site, increasing its potency, improving its rate and extent of absorption, modifying to advantage its time course in the body, reducing its toxicity, changing its physical or chemical properties (like solubility) to provide desired features.
type: Class
subclass of: chemical reaction

metabolism
description: Metabolism is the set of chemical processes that occur within a living organism in order to maintain life.
type: Class
subclass of: chemical interaction

catabolism
description: Anabolism is the set of metabolic processes that take apart larger chemical entities units into smaller chemical entities.
type: Class
subclass of: metabolism
disjoint with: anabolism

anabolism
description: Anabolism is the set of metabolic processes that construct larger chemical entities units from smaller chemical entities.
type: Class
subclass of: metabolism

carbohydrate residue
description: A carbohydrate residue is a part of a molecule that was derived from a monosaccharide molecule.
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: carbohydrate
subclass of: Restriction
  on property: is derived from
  some values from: monosaccharide

nucleic acid part
description: A nucleic acid part is a component of a nucleic acid.
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: nucleic acid
subclass of: Restriction
  on property: has direct part
  some values from: nucleotide residue

deoxyribonucleotide residue
description: A deoxyribonucleotide residue is a part of a molecule that derives from a deoxyribonucleotide.
type: Class
subclass of: nucleotide residue
disjoint with: ribonucleotide residue

ribonucleotide residue
description: A ribonucleotide residue is a part of a molecule that derives from a ribonucleotide.
type: Class
subclass of: nucleotide residue

A pharmaceutical ingredient is a part of a pharmaceutical preparation.
type: Class
label: pharmaceutical ingredient
subclass of: ingredient
subclass of: Restriction
  on property: is proper part of
  some values from: pharmaceutical drug
equivalent class: Class
  intersection of: ingredient
  intersection of: Restriction
    on property: is part of
    some values from: pharmaceutical drug

to covalently modify
description: to covalently modify is to materially change a molecule by adding or removing covalent bonds between atoms.
type: Class
subclass of: to change materially

chemical complex
description: A chemical complex is a chemical substance composed of weakly connected molecules and ions in a known stoichiometry.
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has part
  some values from: Restriction
    on property: is weakly interacting with
    some values from: material entity

enzyme
description: An enzyme is a protein or protein complex that realizes its disposition to covalently modify some molecule during a chemical reaction.
type: Class
subclass of: protein
subclass of: Class
  union of: protein
  union of: protein complex
equivalent class: Class
  intersection of: Class
    union of: protein
    union of: protein complex
  intersection of: Restriction
    on property: has function
    some values from: Class
      intersection of: to covalently modify
      intersection of: Restriction
        on property: is realized in
        some values from: chemical reaction
      intersection of: Restriction
        on property: in relation to
        some values from: chemical entity

catalyst
description: A catalyst is a molecule that has the capability to reduce the activation energy of a reaction and hence increase the overall rate of reaction.
type: Class
subclass of: chemical substance
subclass of: Restriction
  on property: has capability
  some values from: to regulate the rate of formation
subclass of: Restriction
  on property: has capability
  some values from: to reduce the activation energy

chemical reaction
description: A chemical reaction is a process that leads to the transformation of one set of chemical substances to another.
type: Class
subclass of: chemical interaction
subclass of: Class
  intersection of: Restriction
    on property: has proper part
    some values from: chemical synthesis
  intersection of: Restriction
    on property: has proper part
    some values from: chemical destruction

organic polymer
description: An organic polymer is an organic molecule composed of connected set of monomeric units.
type: Class
subclass of: organic molecule
subclass of: Restriction
  on property: has direct part
  some values from: organic submolecule
equivalent class: Class
  intersection of: organic molecule
  intersection of: Restriction
    on property: has direct part
    some values from: monomer
  intersection of: Restriction
    on property: has direct part
    some values from: organic submolecule

to modify conformation of
description: to modify conformation of is to affect the spatial arrangement of an entity.
type: Class
subclass of: to modify

to cleave
description: to cleave is to split or sever an object along a natural line or grain.
type: Class
subclass of: to disassemble

to combine
description: to combine is the capability to modify a set of objects in a way that the object is merged with another object to form a new object or substance.
type: Class
subclass of: to change materially

to breathe
description: to breathe is the capability to inhale and exhale air into the body during respiration.
type: Class
subclass of: capability

to conformationally activate
description: to conformationally activate is to modify the conformation of an entity in such a way that it becomes activated or functional.
type: Class
subclass of: to modify conformation of

to conformationally inhibit
description: to conformationally inhibit is to modify the conformation of an entity in such a way that it functionally is reduced or inhibited.
type: Class
subclass of: to modify conformation of

to oxidize
description: to oxidize is the capability to remove an electron or an increase in oxidation state of a chemical entity.
type: Class
subclass of: to modify oxidation state of

to reduce
description: to reduce is the capability to add an electron or an decrease in oxidation state of a chemical entity.
type: Class
subclass of: to modify oxidation state of

to modify oxidation state of
description: to modify the oxidation state of is to change the number of electrons of a molecule, atom or ion.
type: Class
subclass of: to modify electronically

substrate
description: A substrate is a molecule that is consumed in the course of a biochemical reaction.
type: Class
subclass of: target
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: derives into
    some values from: product
  intersection of: Restriction
    on property: is target in
    some values from: chemical reaction

product
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is output of
  some values from: chemical reaction
subclass of: Restriction
  on property: is derived from
  some values from: substrate
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is output of
    some values from: chemical reaction
  intersection of: Restriction
    on property: is derived from
    some values from: substrate

to be modified
description: to be modified is the capability to be actively interacted with in such a way that it leads to a physical reconfiguration.
type: Class
subclass of: to be actively interacted with

to be cleaved
description: to be cleaved is the capability to be modified in a way that splits one part of the object from the other.
type: Class
subclass of: to be modified

to be covalently modified
description: to be covalently modified is the capability of a chemical entity to have bonds added or removed
type: Class
subclass of: to be modified

to be combined
description: to be combined is the capability to be modified in a way that the object is merged with another object to form a new object or substance.
type: Class
subclass of: to be modified

to be transported
description: to be transported is the disposition to undergo motion.
type: Class
subclass of: to be actively interacted with

to be electronically modified
description: to be electronically modified is the capability of a chemical entity to have electrons added or removed.
type: Class
subclass of: to be modified

to gain an electron
description: to gain an electron is the capability of a chemical entity to receive an electron.
type: Class
subclass of: to be electronically modified

to lose an electron
description: to lose an electron is the capability of a chemical entity to lose an electron.
type: Class
subclass of: to be electronically modified

to be activated
description: to be activated is the capability to be modified in such a way that the conformational change leads to an increase in another capability.
type: Class
subclass of: to be conformationally changed

to be inhibited
description: to be inhibited is the capability to be modified in such a way that the conformational change leads to an decrease in another capability.
type: Class
subclass of: to be conformationally changed

to be conformationally changed
description: to be conformationally changed is the capability to be modified in such a way that the object's conformation is changed.
type: Class
subclass of: to be modified

multicellular organism
description: A multi-cellular organism is an organism that consists of more than one cell.
type: Class
subclass of: cellular organism
subclass of: Restriction
  min qualified cardinality: 2
  on class: cell
  on property: has proper part
disjoint with: unicellular organism

unicellular organism
description: A unicellular organism is a organism that is composed of a single cell.
type: Class
subclass of: cell
subclass of: cellular organism
subclass of: Class
  complement of: Restriction
    on property: is proper part of
    some values from: biological entity

cellular organism
description: A cellular organism is an organism that contains one or more cells.
type: Class
subclass of: organism
disjoint with: non-cellular organism
equivalent class: Class
  union of: multicellular organism
  union of: unicellular organism

non-cellular organism
description: A non-cellular organism is an organism that does not contain a cell.
type: Class
subclass of: organism

virus
description: A virus is a non-cellular organism that can replicate only inside the living cells of an organism.
type: Class
subclass of: non-cellular organism

drug regulatory authority
description: A drug regulatory authority is a regulatory authority which acts to control what substances may be used to treat individuals.
type: Class
subclass of: regulatory authority

specialized material entity
description: A specialized material entity is a material entity that is defined by having some quality, role or capability.
type: Class
subclass of: specialized object
equivalent class: Class
  intersection of: material entity
  intersection of: Restriction
    on property: has realizable property
    some values from: realizable entity

reagent
description: A reagent is a substance that is added to a system in order to bring about a chemical reaction, or added to see if a reaction occurs.
type: Class
subclass of: heterogeneous substance

specimen
description: A specimen is a portion of material for use in testing, examination, or study.
type: Class
subclass of: sample

pathogen
description: A pathogen or infectious agent is a microorganism that causes disease in its host.
type: Class
subclass of: organism

host
description: A host is an organism that harbors a parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter.
type: Class
subclass of: organism

buffer
description: A buffer is a dissolved chemical substance that resists change in pH upon addition of small amounts of acid or base.
type: Class
subclass of: liquid solution component

solvent
description: A solvent is a substance that can dissolve other substances (solutes).
type: Class
subclass of: liquid solution component

solute
description: A solute is a substance that becomes dissolved in a solvent.
type: Class
subclass of: liquid solution component

antigen
description: An antigen is a molecule that can be bound by a major histocompatibility complex (MHC) and presented to a T-cell receptor.
type: Class
subclass of: molecule

receptor
description: A receptor molecule is a molecule that has the capability to bind to a signal and propogate a response to that signal.
type: Class
subclass of: signal transducer

target
type: Class
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is target in
    some values from: process

centrifugation pellet
description: A centrifugation pellet is a solid substance that forms as a result of compaction by a centrifuge.
type: Class
subclass of: centrifugation substance
disjoint with: supernatant

supernatant
description: A supernatent is a liquid substance that remains after centrifugation.
type: Class
subclass of: centrifugation substance

centrifugation substance
description: A centrifugation substance is a substance that is the target or product of centrifugation.
type: Class
subclass of: chemical substance

liquid solution component
description: A liquid solution component is a part of a liquid solution.
type: Class
subclass of: heterogeneous substance

evaluation role
description: An evaluation role is a processual role held by an entity during some evaluation.
type: Class
subclass of: investigational role

placebo
description: A placebo is a medically ineffectual treatment for a medical condition intended to deceive the recipient.
type: Class
subclass of: heterogeneous substance

test role
description: A test role is the role of an individual that is a participant in the study and is the target of the intervention.
type: Class
subclass of: evaluation role

control role
description: A control role is the role of an individual that is part of a study, but is not subject to the intervention that is to be tested.
type: Class
subclass of: evaluation role

ligand
description: A ligand is a molecule that is part of a complex by weakly interacting with another molecule.
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is direct part of
  some values from: molecular complex
subclass of: Restriction
  on property: is weakly interacting with
  some values from: molecule
equivalent class: Class
  intersection of: molecule
  intersection of: Class
    intersection of: Restriction
      on property: is direct part of
      some values from: molecular complex
    intersection of: Restriction
      on property: is weakly interacting with
      some values from: molecule

low barrier hydrogen bond
description: A low barrier hydrogen bond is a shorter, stronger hydrogen bond that is formed between both heteroatoms.
type: Class
subclass of: hydrogen bond

activator
description: A molecular activator is a molecular regulator that realizes its disposition to conformationally change a target molecule and increase its functionality.
type: Class
subclass of: molecular regulator

inhibitor
description: A molecular inhibitor is a molecular regulator that realizes its disposition to conformationally change a target molecule and decrease its functionality.
type: Class
subclass of: molecular regulator

molecular regulator
description: A molecular regulator is a molecule that regulates the function of another chemical entity.
type: Class
subclass of: molecule
subclass of: Restriction
  on property: has capability
  some values from: Class
    intersection of: to regulate
    intersection of: Restriction
      on property: in relation to
      some values from: chemical entity

signal transducer
description: A signal transducer is a molecule that responds to and amplifies a signal in a signalling system.
type: Class
subclass of: molecule

signal
description: A signal is an object that initiates a sequence of events.
type: Class
subclass of: molecule

messenger
description: A mesenger is a molecule involved in either signal detection or signal propagation from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.
type: Class
subclass of: signal transducer

second messenger
description: A second messenger is a molecule that relay signals from receptors on the cell surface to target molecules inside the cell, in the cytoplasm or nucleus.
type: Class
subclass of: messenger

submolecule
description: A submolecule is any part of a molecule.
type: Class
subclass of: submolecular entity
subclass of: Restriction
  on property: is component part of
  some values from: molecule
subclass of: Restriction
  on property: has component part
  some values from: atom

charge quality
description: charge quality is the quality pertaining to electric charge.
type: Class
subclass of: chemical quality
equivalent class: Class
  union of: charged
  union of: uncharged

intron
description: An intron is a region of a gene that is removed from the final protein open reading frame.
type: Class
subclass of: gene component
subclass of: Restriction
  on property: is proper part of
  some values from: gene

gene component
description: A gene component is a component of a gene.
type: Class
subclass of: nucleic acid part
subclass of: Restriction
  on property: is proper part of
  some values from: gene

exon
description: An exon is a nucleotide sequence encoded by a gene that remains present within the final mature RNA product of that gene after introns have been removed by RNA splicing.
type: Class
subclass of: gene component

gene promoter
description: A gene promoter is a region of DNA that initiates transcription of a particular gene.
type: Class
subclass of: gene regulatory component

start codon
description: A start codon is the first codon of a messenger RNA (mRNA) transcript translated by a ribosome. The start codon is almost always preceded by an untranslated region 5' UTR.
type: Class
subclass of: RNA transcript component
disjoint with: stop codon

stop codon
description: A stop codon (or termination codon) is a nucleotide triplet within messenger RNA that signals a termination of translation.
type: Class
subclass of: RNA transcript component
subclass of: Restriction
  on property: is part of
  some values from: messenger RNA

RNA transcript
description: An RNA transcript is an RNA molecule that is produced from transcription of a nucleic acid template.
type: Class
subclass of: ribonucleic acid
subclass of: Restriction
  on property: is transcribed from
  some values from: Class
    union of: deoxyribonucleic acid
    union of: Restriction
      on property: is part of
      some values from: deoxyribonucleic acid

splice site
description: A splice site is a region required for the excision of an intron and connection to another exon.
type: Class
subclass of: RNA transcript component

molecular pocket
description: A molecular pocket is a site on a molecule that appears as a depression into the structure.
type: Class
subclass of: molecular site

acid
description: An acid is a molecular entity in solution capable of donating a hydron (Bronsted acid) or capable of forming a covalent bond with an electron pair (Lewis acid).
type: Class
subclass of: liquid solution component

base
description: A base is a molecular entity dissolved in a solvent that is capable of accepting a proton (Bronsted base) or forming a covalent bond with a hydron (Lewis base) .
type: Class
subclass of: liquid solution component

isomer
description: An isomer is a molecule that is compositionally identical to another molecule as a result of a different atomic connectivity.
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is variant of
  some values from: molecule
equivalent class: Class
  intersection of: molecule
  intersection of: Restriction
    on property: is variant of
    some values from: molecule

ion
description: An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge.
type: Class
subclass of: chemical entity
equivalent class: Class
  intersection of: Class
    union of: atom
    union of: molecule
  intersection of: Restriction
    on property: has quality
    some values from: charge quality

cation
description: An anion is an atom or molecule with a net positive electrical charge.
type: Class
subclass of: ion
subclass of: Restriction
  on property: has quality
  some values from: positive charge
equivalent class: Class
  intersection of: ion
  intersection of: Restriction
    on property: has quality
    some values from: positive charge

anion
description: An anion is an atom or molecule with a net negative electrical charge.
type: Class
subclass of: ion
subclass of: Restriction
  on property: has quality
  some values from: negative charge
equivalent class: Class
  intersection of: ion
  intersection of: Restriction
    on property: has quality
    some values from: negative charge

polar solvent
description: A polar solvent is a solvent that exhibits a polar quality.
type: Class
subclass of: solvent
subclass of: Restriction
  on property: has quality
  some values from: polar
disjoint with: nonpolar solvent

nonpolar solvent
description: A non-polar solvent is a solvent that exhibits a non-polar quality.
type: Class
subclass of: solvent
subclass of: Restriction
  on property: has quality
  some values from: non-polar

positive charge
description: A positive charge is a charge where the value is positive.
type: Class
subclass of: complete charge
disjoint with: negative charge

heterogeneous substance
description: A heterogeneous substance is a chemical substance that is composed of more than one different kind of component.
type: Class
subclass of: chemical substance
disjoint with: homogeneous substance

homogeneous substance
description: A homogeneous substance is a substance that is composed of a uniform type of entity.
type: Class
subclass of: chemical substance

negative charge
description: A negative charge is a charge where the value is negative.
type: Class
subclass of: complete charge

antibody
description: An antibody (also known as immunoglobulins, abbreviated Ig) are gamma globulin proteins that are used by the immune system to identify and neutralize foreign objects. They are typically made of two large heavy chains and two small light chains.
type: Class
subclass of: protein complex

alpha helix
description: An alpha helix is structural region of a protein that is characterized by 3.6 residues per turn, a translation of 1.5 angstroms along the helical axis in which backbone N-H groups form a hydrogen bond to the backbone carboxyl group of the amino acid four residues prior.
type: Class
subclass of: amino acid polymer submolecule

beta strand
description: A beta strand is structural region of a protein that is characterized by a roughly planar sequence of amino acid residues forming hydrogen bonds between the N-O and the C=O of another part of the peptide and having their side chains perpendicular to the planar axis.
type: Class
subclass of: amino acid polymer submolecule

amino acid polymer submolecule
description: An amino acid polymer submolecule is a submolecule of an amino acid polymer.
type: Class
subclass of: organic submolecule
subclass of: Restriction
  on property: is part of
  some values from: amino acid polymer

ionic interaction
description: An ionic interaction is a weak submolecular interaction between a charged submolecules.
type: Class
subclass of: weak submolecular component

protein complex
description: A protein complex is a molecular complex composed of at least two polypeptide chains.
type: Class
subclass of: molecular complex
subclass of: Restriction
  min qualified cardinality: 2
  on class: polypeptide
  on property: has component part

single bond
description: A single bond is a covalent bond between a pair of atoms in which one pair of electrons are shared.
type: Class
subclass of: covalent bond

double bond
description: A double bond is a covalent bond between a pair of atoms in which two pairs of electrons are shared.
type: Class
subclass of: covalent bond

triple bond
description: A triple bond is a covalent bond between a pair of atoms in which three pairs of electrons are shared.
type: Class
subclass of: covalent bond

aromatic bond
description: An aromatic bond is an interaction between a set of atoms across which pairs of electrons are shared.
type: Class
subclass of: covalent bond

disulfide bond
description: A disulfide bond is a bond between two sulfur atoms.
type: Class
subclass of: single bond

dipole-dipole interaction
description: A dipole-dipole interaction is a weak submolecular interaction between strongly electronegative atoms.
type: Class
subclass of: weak submolecular component

van der Waals interaction
description: van der Waals' interaction is an a weak submolecular interaction between an instantaneous dipole and induced dipole.
type: Class
subclass of: weak submolecular component

base stack
description: A base stack is a stabilizing interaction of DNA and RNA between spatially adjacent nucleotides and possibly involving London dispersion, hydrophobic and electrostatic forces.
type: Class
subclass of: weak submolecular component

molecular complex
description: A molecular complex is a chemical complex composed of at least one weakly interacting molecule.
type: Class
subclass of: chemical complex
subclass of: Restriction
  on property: has direct part
  some values from: molecule

acid-base reaction
description: An acid-base reaction is a chemical reaction between an acid and a base.
type: Class
subclass of: chemical reaction

catalyzed reaction
description: A catalyzed reaction is a chemical reaction that is facilitated by a catalyst.
type: Class
subclass of: chemical reaction
subclass of: Restriction
  on property: has agent
  some values from: catalyst

redox reaction
description: A redox reaction is a chemical reaction in which there is a net movement of electrons from one reactant to another.
type: Class
subclass of: chemical reaction
subclass of: Class
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: to oxidize
      intersection of: Restriction
        on property: is disposition of
        some values from: molecule
  intersection of: Restriction
    on property: realizes
    some values from: Class
      intersection of: to reduce
      intersection of: Restriction
        on property: is disposition of
        some values from: molecule

inorganic reaction
description: An inorganic reaction is a chemical reaction that involves the transformation of inorganic molecules.
type: Class
subclass of: chemical reaction

decomposition reaction
description: A decomposition reaction is an inorganic reaction in which molecule is fragmented into submolecules or atoms.
type: Class
subclass of: inorganic reaction

displacement reaction
description: A displacement reaction is an inorganic reaction in which a elementary substance displaces and sets free a constituent atom from a molecule.
type: Class
subclass of: inorganic reaction

double displacement reaction
description: A double displacement reaction is a displacement reaction in which two molecules swap ions, effectively displacing each other to form two new molecules.
type: Class
subclass of: displacement reaction

single displacement reaction
description: A single displacement reaction where one atom is transferred out of one molecule and into another.
type: Class
subclass of: displacement reaction

synthesis reaction
description: A synthesis reaction is an inorganic reaction in which two or more molecules are chemically bonded together to produce a single product.
type: Class
subclass of: inorganic reaction

organic reaction
description: An organic reaction is a chemical reaction involving at least one organic molecule.
type: Class
subclass of: chemical reaction

isomerization reaction
description: An isomerization reaction is a chemical reaction in which a molecule is converted into its isomer.
type: Class
subclass of: chemical reaction

addition reaction
description: An addition reaction is an organic reaction where two or more molecules combine to form a larger one. Addition reactions are limited to chemical compounds that have multiply-bonded atoms: * Molecules with carbon-carbon double bonds or triple bonds * Molecules with carbon - hetero double bonds like C=O or C=N
type: Class
subclass of: organic reaction

polar addition reaction
description: A polar addition reaction is an addition reaction involving polar residues.
type: Class
subclass of: addition reaction

non-polar addition reaction
description: A non-polar addition reaction is an addition reaction involving non-polar residues.
type: Class
subclass of: addition reaction

free radical addition
description: A free radical addition is a non-polar addition reaction involving free radicals.
type: Class
subclass of: non-polar addition reaction

nucleophilic addition reaction
description: A nucleophilic addition reaction is an addition reaction where a pi bond is removed by the creation of two new covalent bonds by the addition from a nucleophile.
type: Class
subclass of: polar addition reaction

electrophilic addition reaction
description: An electrophilic addition reaction is a polar addition reaction where a pi bond is removed by the creation of two new covalent bonds.
type: Class
subclass of: polar addition reaction

biochemical pathway
description: A biochemical pathway specifies a series of biochemical modifications and transformations towards achieving some biological outcome.
type: Class
subclass of: chemical reaction pathway

chemical reaction pathway
description: A chemical reaction pathway specifies a series of chemical reactions towards producing some chemical product.
type: Class
subclass of: pathway
subclass of: Restriction
  on property: specifies
  some values from: Restriction
    on property: has proper part
    some values from: chemical reaction
subclass of: Restriction
  on property: is model of
  some values from: process
subclass of: Restriction
  all values from: chemical reaction
  on property: has member

chemical synthesis pathway
description: A chemical synthesis pathway is a pathway involved in the assembly of a chemical.
type: Class
subclass of: chemical reaction pathway

chemical degradation pathway
description: A chemical degradation pathway is a pathway involved in the disassembly of a chemical.
type: Class
subclass of: chemical reaction pathway

3d structure model
description: A 3D structure model is a representation of the spatial arrangement of one or more chemical entities.
type: Class
subclass of: tertiary structure descriptor

sequence profile
description: A sequence profile is provides the preference for a character at each position of an abstracted sequence.
type: Class
subclass of: pattern

metabolic pathway
description: A metabolic pathway is a series of biochemical reactions that begins with one or more substrates and ends with one or more products.
type: Class
subclass of: biochemical pathway
disjoint with: regulatory pathway

regulatory pathway
description: A regulatory pathway is a series of biochemical reactions that lead to the increase or decrease of activity of participating molecular components.
type: Class
subclass of: biochemical pathway

medical history
description: A medical history is a record of the events of a recipient of medical care.
type: Class
subclass of: history

binary compound
description: A binary compound is a mereological maximum sum of two kinds of weakly connected entities.
type: Class
subclass of: chemical substance
subclass of: Restriction
  on class: molecule
  on property: has direct part
  qualified cardinality: 2

stereoisomer
description: A stereoisomer is an isomer in which the atomic connectivity is the same, but differs in its spatial arrangement of atoms.
type: Class
subclass of: isomer

diastereomer
description: A diastereomer is a stereoisomer that is not a mirror image of its isomer.
type: Class
subclass of: stereoisomer

enantiomer
description: An enantiomer is a stereoisomer that is a mirror image of its isomer.
type: Class
subclass of: stereoisomer

optical isomer
description: An optical isomer is a stereoisomer that rotates the plane of polarization of a beam of plane polarized light.
type: Class
subclass of: stereoisomer

structural isomer
description: A structural isomer is an isomer in which the atoms are joined together in different ways.
type: Class
subclass of: isomer

ring
description: A ring is a submolecule with a circular topology.
type: Class
subclass of: chemical functional group
subclass of: Restriction
  min qualified cardinality: 3
  on class: atom
  on property: has component part
equivalent class: Class
  union of: heterocyclic ring
  union of: homocyclic ring

aromatic ring
description: An aromatic ring is a ring in which the electrons are delocalized across all atoms in the ring.
type: Class
subclass of: ring

heterocyclic ring
description: A heterocyclic ring is a ring containing a hetero atom.
type: Class
subclass of: ring
disjoint with: homocyclic ring

homocyclic ring
description: A homocyclic ring is a ring where the atoms are of a single type.
type: Class
subclass of: ring

ionic compound
description: An ionic compound is a mereological maximal sum of weakly connected paired positive and negative ions.
type: Class
subclass of: binary compound
subclass of: Restriction
  on class: cation
  on property: has direct part
  qualified cardinality: 1
subclass of: Restriction
  on class: anion
  on property: has direct part
  qualified cardinality: 1

allotrope
description: An allotrope is a structural variant of a chemical element.
type: Class
subclass of: chemical element

carbon allotrope
description: A carbon allotrope is a chemical substance composed of carbon.
type: Class
subclass of: allotrope
subclass of: Restriction
  all values from: carbon atom
  on property: has direct part

diamond
description: diamond is a carbon allotrope in which each carbon atom in diamond is covalently bonded to four other carbons in a tetrahedron. These tetrahedrons together form a 3-dimensional network of puckered six-membered rings of atoms.
type: Class
subclass of: carbon allotrope

graphite
description: graphite is an allotrope of carbon which is a conductor, and is the most stable form of solid carbon.
type: Class
subclass of: carbon allotrope

fullerene
description: fullerene is a carbon allotrope which take the form of a hollow sphere, ellipsoid, or tube.
type: Class
subclass of: carbon allotrope

aggregated carbon nanorods
description: aggregate of carbon nanorods is an allotrope of carbon considered to be the least compressible material known, as measured by its isothermal bulk modulus; aggregated diamond nanorods have a modulus of 491 gigapascals (GPa), while a conventional diamond has a modulus of 442 GPa. ADNRs are also 0.3% denser than regular diamond.
type: Class
subclass of: carbon allotrope

amorphous carbon
description: amorphous carbon is an allotrope of carbon that does not have any crystalline structure. As with all glassy materials, some short-range order can be observed, but there is no long-range pattern of atomic positions.
type: Class
subclass of: carbon allotrope

carbon nanofoam
description: carbon nanofoam is an allotrope of carbon that consists of a low-density cluster-assembly of carbon atoms strung together in a loose three-dimensional web. Each cluster is about 6 nanometers wide and consists of about 4000 carbon atoms linked in graphite-like sheets that are given negative curvature by the inclusion of heptagons among the regular hexagonal pattern.
type: Class
subclass of: carbon allotrope

chaoite
description: chaoite is an allotrope of carbon that is slightly harder than graphite with a reflection colour of grey to white.
type: Class
subclass of: carbon allotrope

glassy carbon
description: glassy carbon is an allotrope of carbon which is widely used as an electrode material in electrochemistry, as well as for high temperature crucibles and as a component of some prosthetic devices.
type: Class
subclass of: carbon allotrope

ionsdaleite
description: ionsdaleite is a hexagonal allotrope of the carbon allotrope diamond.
type: Class
subclass of: carbon allotrope

boron atom
type: Class
subclass of: atom

carbon atom
type: Class
subclass of: atom

hydrogen atom
type: Class
subclass of: atom

helium atom
type: Class
subclass of: atom

lithium atom
type: Class
subclass of: atom

beryllium atom
type: Class
subclass of: atom

nitrogen atom
type: Class
subclass of: atom

oxygen atom
type: Class
subclass of: atom

fluorine atom
type: Class
subclass of: atom

neon atom
type: Class
subclass of: atom

sodium atom
type: Class
subclass of: atom

magnesium atom
type: Class
subclass of: atom

aluminium atom
type: Class
subclass of: atom

silicon atom
type: Class
subclass of: atom

phosphorus atom
type: Class
subclass of: atom

sulfur atom
type: Class
subclass of: atom

chlorine atom
type: Class
subclass of: atom

argon atom
type: Class
subclass of: atom

potassium atom
type: Class
subclass of: atom

calcium atom
type: Class
subclass of: atom

scandium atom
type: Class
subclass of: atom

titanium atom
type: Class
subclass of: atom

vanadium atom
type: Class
subclass of: atom

chromium atom
type: Class
subclass of: atom

manganese atom
type: Class
subclass of: atom

iron atom
type: Class
subclass of: atom

cobalt atom
type: Class
subclass of: atom

nickel atom
type: Class
subclass of: atom

copper atom
type: Class
subclass of: atom

zinc atom
type: Class
subclass of: atom

gallium atom
type: Class
subclass of: atom

germanium atom
type: Class
subclass of: atom

arsenic atom
type: Class
subclass of: atom

selenium atom
type: Class
subclass of: atom

bromine atom
type: Class
subclass of: atom

krypton atom
type: Class
subclass of: atom

rubidium atom
type: Class
subclass of: atom

strontium atom
type: Class
subclass of: atom

yttrium atom
type: Class
subclass of: atom

zirconium atom
type: Class
subclass of: atom

niobium atom
type: Class
subclass of: atom

molybdemum atom
type: Class
subclass of: atom

technetium atom
type: Class
subclass of: atom

ruthenium atom
type: Class
subclass of: atom

rhodium atom
type: Class
subclass of: atom

palladium atom
type: Class
subclass of: atom

silver atom
type: Class
subclass of: atom

cadmium atom
type: Class
subclass of: atom

indium atom
type: Class
subclass of: atom

tin atom
type: Class
subclass of: atom

antimony atom
type: Class
subclass of: atom

tellurium atom
type: Class
subclass of: atom

iodine atom
type: Class
subclass of: atom

xenon atom
type: Class
subclass of: atom

caesium atom
type: Class
subclass of: atom

barium atom
type: Class
subclass of: atom

lanthanum atom
type: Class
subclass of: atom

hafnium atom
type: Class
subclass of: atom

tantalum atom
type: Class
subclass of: atom

tungsten atom
type: Class
subclass of: atom

rhenium atom
type: Class
subclass of: atom

osmium atom
type: Class
subclass of: atom

iridium atom
type: Class
subclass of: atom

platinum atom
type: Class
subclass of: atom

gold atom
type: Class
subclass of: atom

mercury atom
type: Class
subclass of: atom

thallium atom
type: Class
subclass of: atom

lead atom
type: Class
subclass of: atom

bismuth atom
type: Class
subclass of: atom

polonium atom
type: Class
subclass of: atom

astatine atom
type: Class
subclass of: atom

radon atom
type: Class
subclass of: atom

francium atom
type: Class
subclass of: atom

radium atom
type: Class
subclass of: atom

actinium atom
type: Class
subclass of: atom

rutherfordium atom
type: Class
subclass of: atom

dubnium atom
type: Class
subclass of: atom

seaborgium atom
type: Class
subclass of: atom

bohrium atom
type: Class
subclass of: atom

hassium atom
type: Class
subclass of: atom

meitnerium atom
type: Class
subclass of: atom

darmstadtium atom
type: Class
subclass of: atom

roentgenium atom
type: Class
subclass of: atom

copernicium atom
type: Class
subclass of: atom

unutrium atom
type: Class
subclass of: atom

ununquadium atom
type: Class
subclass of: atom

ununpentium atom
type: Class
subclass of: atom

ununhexium atom
type: Class
subclass of: atom

ununseptium atom
type: Class
subclass of: atom

ununoctium atom
type: Class
subclass of: atom

cerium atom
type: Class
subclass of: atom

praseodymium atom
type: Class
subclass of: atom

neodymium atom
type: Class
subclass of: atom

promethium atom
type: Class
subclass of: atom

samarium atom
type: Class
subclass of: atom

europium atom
type: Class
subclass of: atom

gadolinium atom
type: Class
subclass of: atom

terbium atom
type: Class
subclass of: atom

dysprosium atom
type: Class
subclass of: atom

holmium atom
type: Class
subclass of: atom

erbium atom
type: Class
subclass of: atom

thulium atom
type: Class
subclass of: atom

ytterbium atom
type: Class
subclass of: atom

lutetium atom
type: Class
subclass of: atom

thorium atom
type: Class
subclass of: atom

protactinium atom
type: Class
subclass of: atom

uranium atom
type: Class
subclass of: atom

neptunium atom
type: Class
subclass of: atom

plutonium atom
type: Class
subclass of: atom

americium atom
type: Class
subclass of: atom

curium atom
type: Class
subclass of: atom

berkelium atom
type: Class
subclass of: atom

californium atom
type: Class
subclass of: atom

einsteinium atom
type: Class
subclass of: atom

fermium atom
type: Class
subclass of: atom

mendelevium atom
type: Class
subclass of: atom

nobelium atom
type: Class
subclass of: atom

lawrencium atom
type: Class
subclass of: atom

covalent bond
description: A covalent bond is a strong submolecular interaction between atoms.
type: Class
subclass of: strong submolecular component
subclass of: Restriction
  on class: atom
  on property: has component part
  qualified cardinality: 2

biomolecular structure descriptor
description: A biomolecular structure descriptor is structure description for organic compounds.
type: Class
subclass of: molecular structure descriptor
subclass of: Restriction
  on property: is about
  some values from: organic molecule

molecular structure file
description: A molecular structure file is a file that contains a description of molecular structure.
type: Class
subclass of: file
subclass of: Restriction
  on property: has part
  some values from: cartesian coordinate
subclass of: Restriction
  on property: has part
  some values from: molecular structure descriptor
subclass of: Restriction
  on property: is concretization of
  some values from: biomolecular structure descriptor

molecular structure descriptor
description: molecular structure descriptor is data that describes some aspect of the molecular structure (composition) and is about some chemical entity.
type: Class
subclass of: chemical quality
subclass of: Restriction
  on property: represents
  some values from: molecular structure
subclass of: Restriction
  on property: is about
  some values from: molecule

chemical data
description: A chemical datum is a scientific data item which conforms to some specification, either for how it is calculated or for how it is measured, and is commonly used in the domain of chemistry to name and differentiate different numeric properties (both calculated and measured) which are about chemical entities.
type: Class
subclass of: scientific data

molecule
description: A molecule is a single chemical entity composed of fully covalently bonded atoms.
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: has part
  some values from: atom

chemical substance
alternative: mixture
description: A chemical substance is a chemical entity composed of two or more weakly (non-covalently) interacting chemical entities.
type: Class
subclass of: chemical entity
equivalent class: Class
  union of: heterogeneous substance
  union of: homogeneous substance

PDB file
description: A PDB file is a molecular structure file specified by the Protein DataBank (PDB).
type: Class
subclass of: molecular structure file

collection of 3d molecular structure models
description: A collection of 3D molecular structure models is just that.
type: Class
subclass of: collection
subclass of: Restriction
  on property: has member
  some values from: 3d structure model

min exclusive: 0.0

max exclusive: 0.0