This ontology has the following classes and properties.
The Core Ontology of Phenotyping (COP) defines core entities and their relationships that are relevant for modelling phenotypic knowledge and developing phenotyping software.
IRI: https://w3id.org/cop/Algorithm
IRI: https://w3id.org/cop/AttributeSpec
An attribute specification is a specification of an attribute.
IRI: https://w3id.org/gfo-light/Attributive
Qualities (attributes, traits, characteristics, etc.) of concrete individuals, relations (relators) between them and roles that objects can play in different contexts are subsumed under the category Attributive.
Attributives are individuals that depend on other individuals by some kind of dependency relation.
IRI: https://w3id.org/cop/BasicRestrictedPhenotypeClassView
A basic restricted phenotype class view represents a restricted phenotype class that restricts an unrestricted phenotype class represented by a basic view.
Specification of the phenotype class 'Weight over 100 kg'
IRI: https://w3id.org/cop/BasicUnrestrictedPhenotypeClassView
A basic unrestricted phenotype class view represents an unrestricted phenotype class whose instances (phenotypes) have already been determined and can be queried from the data source.
Specification of the phenotype class 'Weight'
IRI: https://w3id.org/cop/BooleanSpec
IRI: https://w3id.org/gfo-light/Category
The notion of category covers all abstract entities that can be instantiated by or are predicated of other entities.
IRI: https://w3id.org/gfo-light/Chronoid
Chronoids are real-valued time intervals with endpoints.
The time (extension) of a football match (from the start point in time to the end point in time)
IRI: https://w3id.org/gfo-light/ConcreteIndividual
Concrete individuals are entities that have an immediate relation to time or to space-time. They exist in time.
IRI: https://w3id.org/gfo-light/Continuant
Social or material (three-dimensional) objects, their groups/aggregates, parts and boundaries (two-, one- and zero-dimensional entities, i.e., surfaces, lines and points) are subsumed under the category Continuant.
Continuants are concrete individuals that persist through time and are wholly present at every point of their existence time (lifetime).
IRI: https://w3id.org/cop/DataTypeSpec
A data type specification is a specification of a data type (e.g., string, decimal, boolean or date-time).
IRI: https://w3id.org/cop/DateTimeSpec
IRI: https://w3id.org/cop/DecimalSpec
IRI: https://w3id.org/cop/DerivationExpression
A derivation expression is an executable formal specification of a combination of different functions/operators and input variables, the execution of which calculates/derives a new value (e.g., of a phenotype) based on the input values.
IRI: https://w3id.org/cop/DerivedRestrictedPhenotypeClassView
A derived restricted phenotype class view represents a restricted phenotype class that restricts an unrestricted phenotype class represented by a derived view.
Specification of the phenotype class 'Overweight (e.g., BMI over 30)'
IRI: https://w3id.org/cop/DerivedUnrestrictedPhenotypeClassView
A derived unrestricted phenotype class view represents an unrestricted phenotype class whose instances (phenotypes) need to be determined (i.e., derived from other phenotypes).
Specification of the phenotype class 'Body Mass Index (BMI)'
IRI: https://w3id.org/cop/Description
A description is a string describing an entity.
IRI: https://w3id.org/cop/DynamicPhenotypeAlgorithm
A dynamic phenotype algorithm is a phenotype algorithm for executing an arbitrary phenotype query.
IRI: https://w3id.org/gfo-light/Entity
Everything that exists is called an entity.
IRI: https://w3id.org/gfo-light/Individual
Individuals are entities which cannot be further instantiated.
IRI: https://w3id.org/gfo-light/InformationObject
Information objects are symbolic entities that denote/designate, describe, specify or represent other entities.
Computer programme
Description
Diagram
Model
Title
IRI: https://w3id.org/gfo-light/Line
Lines are not necessarily straight. They can be, for example, curves or broken lines that pass through various points and form a corner, a triangle or a polygon.
A line is a 1-dimensional object boundary.
Boundary line of the football field
Longitudinal axis of the human skeleton
IRI: https://w3id.org/cop/Model
A model is a representation/specification of an abstraction of an entity.
IRI: https://w3id.org/gfo-light/Object
Objects are social or material entities that can exist independently of each other.
Bone
Chopstick
Computer
Person
IRI: https://w3id.org/gfo-light/ObjectAggregate
Object aggregates are groups of objects that together form a unit.
Research group
Sports team
IRI: https://w3id.org/gfo-light/ObjectBoundary
Object boundaries are 0-, 1-, or 2-dimensional (visible or imaginary) entities (i.e., points, lines and surfaces) that border objects (natural boundaries) or are located inside them (inner boundaries).
IRI: https://w3id.org/gfo-light/ObjectPart
Object parts are material entities that cannot exist independently of the corresponding whole object.
Part of a bone
Part of a chopstick
IRI: https://w3id.org/cop/Organism
An organism is a living object.
IRI: https://w3id.org/cop/Phenotype
A phenotype is a (combination of) bodily feature(s) or observable characteristic(s)/trait(s) of an organism.
Body Mass Index (BMI) of a specific person
Overweight of a specific person
Weight of a specific person
IRI: https://w3id.org/cop/PhenotypeAlgorithm
A phenotype algorithm is an algorithm for executing a phenotype query, i.e., identifying individuals matching the query criteria (i.e., meeting all the inclusion but none of the exclusion criteria) and deriving/outputting further phenotypes (projection entries).
IRI: https://w3id.org/cop/PhenotypeClass
Phenotype classes are categories whose instances are phenotypes.
IRI: https://w3id.org/cop/PhenotypeClassView
A phenotype class view is a formal representation of a phenotype class (its attributes and relationships).
IRI: https://w3id.org/cop/PhenotypeModel
A phenotype model is a formal representation of delimited phenotypic knowledge (i.e., phenotype classes, their attributes, and relationships).
IRI: https://w3id.org/cop/PhenotypeQuery
A phenotype query is a specification of certain phenotype classes as inclusion or exclusion criteria or as projection (output) entries.
IRI: https://w3id.org/cop/Phenotyping
Phenotyping is a process of identifying individuals with certain phenotypes.
IRI: https://w3id.org/cop/PhenotypingSoftware
A run of a phenotyping software (implemented phenotype algorithm) realises a phenotyping process.
Phenotyping software is a software implementing a phenotype algorithm.
IRI: https://w3id.org/gfo-light/Point
A point is a 0-dimensional object boundary.
Gonion
Penalty spot
IRI: https://w3id.org/gfo-light/Process
Processes represent dynamic knowledge.
Processes are concrete individuals that happen in time and have a temporal extension (a chronoid).
A treatment of a patient in a hospital
Football match
The course of an illness
The first half of the match
IRI: https://w3id.org/gfo-light/ProcessAggregate
Process aggregates are sets of processes that are contextually related but not temporally connected.
All football matches in a league season
Series of lectures in a semester
IRI: https://w3id.org/gfo-light/ProcessualEntity
Processual entities include processes and processual aggregates.
IRI: https://w3id.org/gfo-light/Quality
Qualities can possess values.
Qualities are attributives that typically inhere in its bearer.
Observable or measurable characteristics of single objects, e.g., persons, (such as weight and height, laboratory parameters or symptoms)
Qualities of object groups (e.g., goals scored by a football team in a match)
Qualities of processes (e.g., the number of spectators as quality of a football match)
IRI: https://w3id.org/gfo-light/Relator
A relator represents an individual relation instance.
Relators are attributives that connect other entities (role players) by relational roles (played by role players).
A relator describing the relative location of an object (playing the target object role) in relation to another object (playing the reference object role), e.g., the location of a person relative to the city centre or the location of an anatomical structure relative to the longitudinal axis
A winner-loser relator connecting a winner and a loser team by a winner and a loser role
The marriage (relator) of John and Mary (in which Mary plays the wife role and John the husband role)
IRI: https://w3id.org/cop/RestrictedPhenotypeClass
A phenotype class whose extension (the set of instances, i.e., phenotypes) is restricted to a certain value range is called restricted phenotype class.
Overweight (e.g., BMI over 30)
Weight over 100 kg
IRI: https://w3id.org/gfo-light/Role
An object part can play a (e.g., functional) role in the whole object (e.g., the processor is part of the computer and has the task/function/role to process commands). A member (object) of a social group (object aggregate) can play a social role in that group (e.g., John is member of the football team and plays the role of midfielder). Objects can play processual or situational roles in processes (e.g., team A plays the home team role and team B plays the visiting team role in a football match) or situations (e.g., scorer and assistant role in a goal situation or roles played by a doctor and a patient in a risk/adverse situation in hospital) in which they participate. Objects can play relational roles in a relation/relator (e.g., wife role and husband role of the marriage relator).
A role is a relational entity that links a continuant (role player) with some context (object, object aggregate, processual entity, situational entity, relator), in which the continuant plays that role.
John is member of the football team and plays the role of midfielder.
Roles played by a doctor and a patient in a risk/adverse situation in hospital
Target object role and reference object role of a relative location relator (describes the relative location of an object playing the target object role in relation to another object playing the reference object role)
Team A plays the home team role and team B plays the visiting team role in a football match.
The processor is part of the computer and has the task/function/role to process commands.
Wife role and husband role of the marriage relator
Winner team role and loser team role of the winner-loser relator
IRI: https://w3id.org/gfo-light/Situation
A situation can exist at a certain point in time or during a certain period of time and can be part or result of a process or another situation.
Situations are combinations/constellations of attributives that belong together in the context of the use case under consideration.
A risk situation when treating a patient in hospital if his laboratory values (qualities) are in the critical range over a certain period of time
The situation after the wedding of John and Mary (i.e., the situation in which they are married containing the marriage relator with a husband and a wife role)
The situation at the end of a football match containing players' qualities (e.g., number of goals or assists), teams' qualities (e.g., number of goals or ball possession) and a winner-loser relator with one team playing the winner role and the other team playing the loser role
IRI: https://w3id.org/gfo-light/SituationAggregate
Situation aggregates are sets of situations that are contextually related but not temporally connected.
All phases of increased temperature in the course of an illness
IRI: https://w3id.org/gfo-light/SituationalEntity
Situational entities include situations and situational aggregates.
IRI: https://w3id.org/cop/Software
Software refers to executable computer programmes including all their components.
IRI: https://w3id.org/cop/StaticPhenotypeAlgorithm
A static phenotype algorithm is a phenotype algorithm for executing exactly one specific phenotype query.
IRI: https://w3id.org/cop/StringSpec
IRI: https://w3id.org/gfo-light/Surface
A surface is a 2-dimensional object boundary.
Frontal plane of the human skeleton
Surface of the football field
IRI: https://w3id.org/cop/Synonym
A synonym is a string that has a similar meaning to the title.
IRI: https://w3id.org/cop/TerminologyCode
A terminology code is a code of a terminology (code system).
IRI: https://w3id.org/gfo-light/TimeBoundary
Start point in time of a football match
IRI: https://w3id.org/gfo-light/TimeEntity
The time entities defined in GFO-light are points in time (time boundaries) and time intervals/periods (chronoids), which consist of points in time.
IRI: https://w3id.org/cop/Title
A title is a string designating an entity.
IRI: https://w3id.org/cop/UnitOfMeasureSpec
A unit of measure specification is a specification of a unit of measure.
IRI: https://w3id.org/cop/UnrestrictedPhenotypeClass
A phenotype class whose extension (the set of instances, i.e., phenotypes) is not restricted to a certain value range is called unrestricted phenotype class.
Body Mass Index (BMI)
Weight
IRI: https://w3id.org/cop/ValueRangeSpec
A value range specification is a specification of the permitted values of an entity (e.g., of a phenotype), either by listing them (e.g., for string values) or by defining the minimum and maximum (e.g., for numerical values).
IRI: https://w3id.org/gfo-light/after
IRI: https://w3id.org/cop/applicableFor
IRI: https://w3id.org/gfo-light/attributiveOf
IRI: https://w3id.org/cop/basedOn
IRI: https://w3id.org/cop/basicRestrictionOf
IRI: https://w3id.org/gfo-light/before
X before Y: Xf < Ys
IRI: https://w3id.org/gfo-light/boundaryOf
IRI: https://w3id.org/gfo-light/causedBy
IRI: https://w3id.org/gfo-light/causes
IRI: https://w3id.org/gfo-light/containsRole
IRI: https://w3id.org/cop/derivedFrom
IRI: https://w3id.org/cop/derivedRestrictionOf
IRI: https://w3id.org/gfo-light/during
X during Y: Xs > Ys and Xf < Yf
IRI: https://w3id.org/gfo-light/hasAttributive
IRI: https://w3id.org/gfo-light/hasBoundary
IRI: https://w3id.org/cop/hasExclusion
IRI: https://w3id.org/cop/hasInclusion
IRI: https://w3id.org/gfo-light/hasInnerBoundary
IRI: https://w3id.org/gfo-light/hasMember
IRI: https://w3id.org/gfo-light/hasNaturalBoundary
IRI: https://w3id.org/gfo-light/hasOwner
IRI: https://w3id.org/gfo-light/hasPart
IRI: https://w3id.org/gfo-light/hasParticipant
IRI: https://w3id.org/gfo-light/hasProcessPart
IRI: https://w3id.org/cop/hasProjection
IRI: https://w3id.org/gfo-light/hasQuality
IRI: https://w3id.org/cop/hasQueryParameter
IRI: https://w3id.org/gfo-light/hasSituationPart
IRI: https://w3id.org/gfo-light/hasTemporalPart
IRI: https://w3id.org/gfo-light/hasTime
IRI: https://w3id.org/cop/hasVariable
IRI: https://w3id.org/cop/identifies
IRI: https://w3id.org/cop/implementedBy
IRI: https://w3id.org/cop/implements
IRI: https://w3id.org/gfo-light/innerBoundaryOf
IRI: https://w3id.org/gfo-light/instanceOf
IRI: https://w3id.org/gfo-light/instantiatedBy
IRI: https://w3id.org/gfo-light/leadsTo
IRI: https://w3id.org/gfo-light/locatedIn
Material objects can be located in other material objects (locatedIn, e.g., the driver is located in the car).
IRI: https://w3id.org/gfo-light/locationOf
IRI: https://w3id.org/gfo-light/memberOf
IRI: https://w3id.org/gfo-light/naturalBoundaryOf
IRI: https://w3id.org/gfo-light/ownerOf
IRI: https://w3id.org/gfo-light/partOf
IRI: https://w3id.org/gfo-light/participatesIn
IRI: https://w3id.org/gfo-light/playedBy
IRI: https://w3id.org/gfo-light/plays
IRI: https://w3id.org/gfo-light/processPartOf
IRI: https://w3id.org/gfo-light/qualityOf
IRI: https://w3id.org/cop/realises
IRI: https://w3id.org/gfo-light/relates
IRI: https://w3id.org/gfo-light/representedBy
IRI: https://w3id.org/gfo-light/represents
IRI: https://w3id.org/cop/restrictionOf
IRI: https://w3id.org/gfo-light/resultsFrom
IRI: https://w3id.org/gfo-light/roleIn
IRI: https://w3id.org/gfo-light/situationPartOf
IRI: https://w3id.org/gfo-light/spatiallyEndsOn
IRI: https://w3id.org/gfo-light/spatiallyPassesThrough
IRI: https://w3id.org/gfo-light/spatiallyStartsOn
IRI: https://w3id.org/gfo-light/temporalPartOf
X temporal part of Y: X starts Y or X finishes Y or X during Y
IRI: https://w3id.org/gfo-light/temporallyContains
IRI: https://w3id.org/gfo-light/temporallyEqual
X equal Y: Xs = Ys and Xf = Yf
IRI: https://w3id.org/gfo-light/temporallyFinishedBy
IRI: https://w3id.org/gfo-light/temporallyFinishes
X finishes Y: Xs > Ys and Xf = Yf
IRI: https://w3id.org/gfo-light/temporallyMeets
X meets Y: Xf = Ys
IRI: https://w3id.org/gfo-light/temporallyMetBy
IRI: https://w3id.org/gfo-light/temporallyOverlappedBy
IRI: https://w3id.org/gfo-light/temporallyOverlaps
X overlaps Y: Xs < Ys and Xf > Ys and Xf < Yf
IRI: https://w3id.org/gfo-light/temporallyRelatedWith
If a temporal relation is applied to other concrete individuals as time intervals (attributive, continuant, process, situation), it is propagated to their existence times (hasTime).
Temporal relations between time intervals based on Allen, J. F. (1983). Maintaining knowledge about temporal intervals. Communications of the ACM, 26(11), 832-843.
IRI: https://w3id.org/gfo-light/temporallyStartedBy
IRI: https://w3id.org/gfo-light/temporallyStarts
X starts Y: Xs = Ys and Xf < Yf
IRI: https://w3id.org/gfo-light/timeOf
IRI: https://w3id.org/gfo-light/afterDateTimeValue
Shortcut for 'after'
IRI: https://w3id.org/gfo-light/beforeDateTimeValue
Shortcut for 'before'
IRI: https://w3id.org/gfo-light/booleanValue
IRI: https://w3id.org/gfo-light/containsDateTimeValue
Shortcut for 'temporallyContains'
IRI: https://w3id.org/gfo-light/dateTimeValue
IRI: https://w3id.org/gfo-light/decimalValue
IRI: https://w3id.org/gfo-light/finishedByDateTimeValue
Shortcut for 'temporallyFinishedBy'
IRI: https://w3id.org/gfo-light/hasTemporalPartDateTimeValue
Shortcut for 'hasTemporalPart'
IRI: https://w3id.org/gfo-light/startedByDateTimeValue
Shortcut for 'temporallyStartedBy'
IRI: https://w3id.org/gfo-light/stringValue
IRI: https://w3id.org/gfo-light/unit
IRI: http://www.w3.org/2004/02/skos/core#altLabel
IRI: http://www.w3.org/2000/01/rdf-schema#comment
IRI: http://purl.org/dc/elements/1.1/contributor
IRI: http://purl.org/dc/elements/1.1/created
IRI: http://purl.org/dc/elements/1.1/creator
IRI: http://www.w3.org/2004/02/skos/core#definition
IRI: http://purl.org/dc/elements/1.1/description
IRI: http://purl.org/ontology/bibo/doi
IRI: http://www.w3.org/2004/02/skos/core#example
IRI: http://xmlns.com/foaf/0.1/homepage
IRI: http://purl.org/dc/terms/license
IRI: http://purl.org/dc/elements/1.1/modified
IRI: http://purl.org/vocab/vann/preferredNamespacePrefix
IRI: http://purl.org/vocab/vann/preferredNamespaceURI
IRI: http://purl.org/dc/terms/references
IRI: http://usefulinc.com/ns/doap#repository
IRI: http://purl.org/dc/elements/1.1/title
IRI: http://www.w3.org/2002/07/owl#versionInfo
The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.
An algorithm is a specification of instructions to solve a problem or a class of problems.