externally connected to
type: ObjectProperty
type: SymmetricProperty
IAO_0000111: externally_connected_to
sub property of: is related to

is_concretization_of
type: ObjectProperty
sub property of: is related to

is_concretized_as
type: ObjectProperty
inverse of: is_concretization_of
sub property of: is related to

has disposition
type: ObjectProperty
comment: A relation between an entitty and the disposition it realizes
sub property of: is related to

has function
type: ObjectProperty
comment: A relation between an entity and a function
sub property of: is related to

rkb:hasGrain
type: ObjectProperty
IAO_0000111: hasGrain
domain: independent continuant
range: independent continuant
sub property of: is related to

has quality
type: ObjectProperty
comment: A relation between an entity and the quality that inheres in it
sub property of: is related to

has role
type: ObjectProperty
comment: The relation between an entity and a role
sub property of: is related to

rkb:isContainedIn
type: ObjectProperty
IAO_0000111: containedIn
IAO_0000111: isSpecifiedBy
range: continuant
domain: continuant
domain: dependent continuant
range: dependent continuant
sub property of: is related to

is described by
type: ObjectProperty
sub property of: is related to

rkb:isInformationAbout
type: ObjectProperty
IAO_0000111: isInformationAbout
range: independent continuant
domain: information content entity
sub property of: is related to

rkb:isRepresentedAs
type: ObjectProperty
IAO_0000111: is represented as
sub property of: is related to

rkb:isSerializationOf
type: ObjectProperty
IAO_0000111: isSerializationOf
sub property of: is related to

contains
type: ObjectProperty
definition: A spatial relation between two continuants such that one spatially contains the other with no overlap, and one is not a part of the other.
range: continuant
domain: continuant
inverse of: is contained in
sub property of: is spatially related to

denotes
type: ObjectProperty
example: The word 'Boston' denotes the city of Boston by virtue of it being concretized as words on various signs around the city.
definition: g denotes c when a generically dependent continuant g is concretized by a specifically dependent continuant s which inheres in independent continuant c.
domain: generically dependent continuant
range: independent continuant
sub property of: is about

derivative of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
definition: A transitive, symmetric, temporal relation in which one continuant is the derivative of another non-identical continuant.
range: continuant
domain: continuant
sub property of: is temporally related to

derives from
type: ObjectProperty
type: TransitiveProperty
comment: A transitive, temporal relation in which one continuant derives from another non-identical continuant.
example: glucose-6-phosphate derivesFrom glucose in glucose metabolism
range: continuant
domain: continuant
sub property of: derivative of
inverse of: derives into
property chain axiom: immediately derives from

derives into
type: ObjectProperty
type: TransitiveProperty
comment: A transitive, temporal relation in which one continuant derives into another non-identical continuant.
domain: continuant
range: continuant
sub property of: derivative of

has agent
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation between a process and an active continuant.
range: continuant
domain: occurrent
sub property of: has participant

has disposition
type: ObjectProperty
definition: A relation between an entity and the disposition it realizes.
domain: continuant
range: disposition
sub property of: has inherent
inverse of: is disposition of

has function
type: ObjectProperty
definition: A relation between an entity and a function.
example: vase hasFunction containerFunction
domain: continuant
range: function
sub property of: has disposition
inverse of: is function of

has improper part
type: ObjectProperty
definition: A reflexive mereological relational such that the entities are not distinct.
example: cake has improper part slice of cake
range: entity
domain: entity
sub property of: has part
inverse of: is improper part of

has non-tangential proper part
type: ObjectProperty
definition: A proper part relation in which there is no overlap of the edge of spatial regions.
comment: RCC8:non-tangential proper part
range: entity
domain: entity
sub property of: has proper part
inverse of: is non-tangential proper part of

has part
type: ObjectProperty
type: TransitiveProperty
definition: has part is a reflexive (for all p, p has part p), transitive (for all p, p1, p2 if p part_of p1 and p1 part_of p2, then p part_of p2) and anti-symmetric (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical) relation.
comment: Due to nonstructural restrictions in OWL2, no cardinality restriction may be added to this property due to involvement in property chains. One should use hasProperPart to quantify over. hasPart is effectively reflexive due to the reflexivity of hasImproperPart
example: person has part arm, workshop has part coffee break
domain: entity
range: entity
inverse of: part of
sub property of: is related to

has participant
type: ObjectProperty
definition: A relation between a process and its a continuant participant.
comment: 1. no cardinality restriction may be added to this property due to involvement in role chains. One should use hasAgent/realizes to specify knowledge and to quantify over.
range: continuant
domain: occurrent
inverse of: is participant in
sub property of: is related to
property chain axiom: has part

has proper part
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A mereological relation such that when x has proper part y, then x and y are distinct, and the spatial region occupied by y is wholly contained by with that of x.
example: car hasProperPart engine
domain: entity
range: entity
sub property of: has part
inverse of: is proper part of

has quality
type: ObjectProperty
definition: A relation between an entity and the quality that inheres in it.
example: bob hasQuality HappinessQuality
domain: continuant
range: quality
sub property of: has inherent
inverse of: is quality of

has reference
type: ObjectProperty
definition: A relation between an entity and a source of information.
domain: entity
inverse of: is reference for
sub property of: is related to

has role
type: ObjectProperty
definition: The relation between an entity and a role.
example: bob hasRole teacherRole
domain: continuant
range: role
sub property of: has inherent
inverse of: is role of

has tangential proper part
type: ObjectProperty
comment: RCC8:tangential proper part
definition: A proper part relation in which there is overlap on the edge of a spatial region.
domain: entity
range: entity
sub property of: has proper part
inverse of: is tangential proper part of

has unit
type: ObjectProperty
type: FunctionalProperty
definition: A relation between a measurement value and the unit that it was measured with.
sub property of: is related to
inverse of: is unit of

has inherent
type: ObjectProperty
domain: independent continuant
range: specifically dependent continuant
sub property of: bearer of

immediately derives from
type: ObjectProperty
comment: A non-transitive temporal relation in which one continuant immediately derives from a non-identical continuant such that there are no (known) intermediate continuants between them.
example: a molecule of alpha-D-glucose-6-phosphate immediately_derives_from D-glucose in glucose metabolism.
domain: continuant
range: continuant
sub property of: derives from
inverse of: immediately derives into

immediately derives into
type: ObjectProperty
comment: A non-transitive temporal relation in which one continuant immediately derives into a non-identical continuant such that there are no intermediate steps between them.
example: glucose immediatelyDerivesInto glucose-6-phosphate in glucose metabolism
domain: continuant
range: continuant
sub property of: derives into

immediately preceded by
type: ObjectProperty
comment: 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.
range: occurrent
domain: occurrent
inverse of: immediately precedes
sub property of: preceded by

immediately precedes
type: ObjectProperty
comment: A non-transitive temporal relation in which one process is immediately precedes another process, such that there is no interval of time between the two processes.
range: occurrent
domain: occurrent
sub property of: precedes

inheres in
type: ObjectProperty
range: independent continuant
domain: specifically dependent continuant
sub property of: borne by

is about
type: ObjectProperty
definition: i is about c where i is an information content entity or an information carrier and c is an independent continuant.
domain: dependent continuant
range: independent continuant
sub property of: borne by

is adjacent to
type: ObjectProperty
type: SymmetricProperty
definition: Two continuants are adjacent to each other if the edges of their spatial regions are in direct contact.
comment: RCC8:external connection
range: continuant
domain: continuant
sub property of: is connected to

is after
type: ObjectProperty
type: TransitiveProperty
definition: A spatial relation such that when x is after y, then x is positioned numerically greater than y on some spatial coordinate scale.
domain: continuant
range: continuant
inverse of: is before
sub property of: is connected to

is agent in
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation in which a continuant actively participates in the process.
domain: continuant
range: occurrent
inverse of: has agent
sub property of: is participant in

bearer of
type: ObjectProperty
definition: A relation between an independent continuant and dependent continuant.
example: hair bearerOf brown color
domain: continuant
range: dependent continuant
inverse of: borne by
sub property of: is related to
property chain axiom: is participant in

is before
type: ObjectProperty
type: TransitiveProperty
definition: A spatial relation such that when x is before y, then x is positioned numerically less than y on some spatial coordinate scale.
range: continuant
domain: continuant
sub property of: is connected to

borne by
type: ObjectProperty
definition: A relation between a dependent continuant and an entity.
example: brown colour inheresIn hair
range: continuant
domain: dependent continuant
sub property of: is related to

is concretization of
type: ObjectProperty
example: The ink on the signpost forming the word 'Boston' is a concretization of the word Boston that (generically) denotes the city of Boston.
definition: s is a concretization of g, where s is a specifically dependent continuant and g is a generically dependent continuant.
range: generically dependent continuant
domain: specifically dependent continuant
inverse of: is concretized by
sub property of: is related to

is concretized by
type: ObjectProperty
example: The word 'Boston' is concretized by the specific pattern of ink on the various signs around the city of Boston.
definition: g is concretized by s, where g is a generically dependent continuant and s is a specifically dependent continuant.
domain: generically dependent continuant
range: specifically dependent continuant
sub property of: is related to

is connected to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
definition: Two objects are connected to each other if their spatial regions are indirectly connected via a sequence of direct connections.
domain: continuant
range: continuant
sub property of: is spatially related to

is contained in
type: ObjectProperty
definition: A spatial relation between two continuants such that one is contained in the other, but for which there is no overlap and one is not a part of the other.
domain: continuant
range: continuant
sub property of: is spatially related to

is denoted by
type: ObjectProperty
definition: c is denoted by g when a generically dependent continuant g is concretized by a specifically dependent continuant s which inheres in independent continuant c.
domain: independent continuant
range: information content entity
sub property of: is subject of

is disconnected from
type: ObjectProperty
definition: Two continuants are disconnected when their spatial regions are not adjacent, do not intersect or overlap.
comment: RCC8:disconnection
range: continuant
domain: continuant
sub property of: is spatially related to

is disposition of
type: ObjectProperty
definition: A relation between a disposition and the entity that realizes it.
example: disease isDispositionOf human
range: continuant
domain: disposition
sub property of: inheres in

is function of
type: ObjectProperty
definition: A relation between a function and the entity that realizes it.
example: Catalysis isFunctionOf Enzyme
range: continuant
domain: function
sub property of: is disposition of

is immediately after
type: ObjectProperty
definition: A spatial relation such that when x is immediately after y, then x is positioned adjacent to and numerically greater than y on some spatial coordinate scale.
range: continuant
domain: continuant
sub property of: is adjacent to
sub property of: is after

is immediately before
type: ObjectProperty
definition: A spatial relation such that when x is immediately before y, then x is positioned adjacent to and numerically less than y on some spatial coordinate scale.
range: continuant
domain: continuant
sub property of: is adjacent to
sub property of: is before
inverse of: is immediately after

is improper part of
type: ObjectProperty
definition: A reflexive mereological relation such that the entities are not distinct.
example: slice of cake isImproperPartOf cake
domain: entity
range: entity
sub property of: part of

is located in
type: ObjectProperty
definition: A relation between two entities such that one is located in terms of spatial and/or temporal regions.
example: person isLocatedIn room
range: entity
domain: entity
inverse of: is location of
sub property of: is related to

is location of
type: ObjectProperty
definition: A relation between two entities such that one is the location of another.
domain: entity
range: entity
sub property of: is related to

is non-tangential proper part of
type: ObjectProperty
comment: RCC8:non-tangential proper part of (inv)
sub property of: is proper part of

part of
type: ObjectProperty
type: TransitiveProperty
definition: A transitive relation such that one is a part of itself or another, with disconnected, overlapping or non-overlapping spatial regions.
comment: 1. no cardinality restriction may be added to this property due to involvement in property chains. One should use isProperPartOf to quantify over. 2. isPartOf is effectively reflexive due to the reflexivity of isImproperPartOf
example: arm is part of person; coffee break is part of workshop
range: entity
domain: entity
sub property of: is related to

is participant in
type: ObjectProperty
definition: A relation in which a continuant participates in some way in the process.
comment: 1. no cardinality restriction may be added to this property due to involvement in role chains. One should use isAgentOf/isRealizedIn to specify knowledge and to quantify over.
example: person isParticipantIn his life
domain: continuant
range: occurrent
sub property of: is related to
property chain axiom: part of

is proper part of
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
comment: An irreflexive and anti-symmetric parthood relation such that the entities are distinct.
example: engine isProperPartOf car
range: entity
domain: entity
sub property of: part of

is quality of
type: ObjectProperty
definition: A relation between a quality and some entity.
example: brown colour isQualityOf hair
range: continuant
domain: quality
sub property of: inheres in

is realized in
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation between a realizable entity (role, etc) and a process.
domain: dependent continuant
range: process
sub property of: is participant in

is reference for
type: ObjectProperty
definition: A relation between a source of information and an entity.
range: entity
sub property of: is related to

is related to
type: ObjectProperty
type: SymmetricProperty
definition: is related to is a top level symmetric relation.
range: entity
domain: entity

is represented by
type: ObjectProperty
definition: b is represented by a when a serves as a sign or symbol of b.
range: entity
domain: entity
sub property of: is related to
inverse of: represents

is role of
type: ObjectProperty
definition: A relation between a role and the entity that realizes it.
example: TeacherRole isRoleOf Teacher
range: continuant
domain: role
sub property of: inheres in

is spatial location of
type: ObjectProperty
definition: A relation between a region of space and an oject that occupies that space.
range: continuant
domain: spatial region
sub property of: is location of
inverse of: is spatially located in

is spatially equal to
type: ObjectProperty
comment: RCC8:equality
definition: A spatial relation in which two objects are spatially equivalent when their spatial regions exactly overlap.
domain: continuant
range: continuant
sub property of: is spatially related to

is spatially located in
type: ObjectProperty
definition: A relation between an entity and a spatial region.
example: person isSpatiallyLocatedIn in that three dimensional spatial region
domain: continuant
range: spatial region
sub property of: is located in

is spatially related to
type: ObjectProperty
type: SymmetricProperty
definition: A relation between spatial regions or continuants with respect to the spatial regions they occupy.
range: continuant
domain: continuant
sub property of: is related to

is subject of
type: ObjectProperty
example: carole is the subject of the book "Carole's life"
definition: c is the subject of i where i is an information content entity or an information carrier and c is an independent continuant.
domain: continuant
range: dependent continuant
sub property of: bearer of

is tangential proper part of
type: ObjectProperty
comment: RCC8:tangential proper part of (inv)
sub property of: is proper part of

is temporal location of
type: ObjectProperty
definition: A relation between two temporal entities such that a temporal region is the location of a temporal entity.
range: occurrent
domain: temporal region
sub property of: is location of
inverse of: is temporally located in

is temporally located in
type: ObjectProperty
definition: A relation between an occurant and a temporal region.
example: you are reading this phrase over some time interval
domain: occurrent
range: temporal region
sub property of: is located in

is temporally related to
type: ObjectProperty
definition: A relation between entities at different times.
domain: entity
range: entity
sub property of: is related to

is unit of
type: ObjectProperty
definition: A relation between a unit and the value of a measurement.
sub property of: is related to

partially overlaps with
type: ObjectProperty
definition: A spatial relationship in which two objects partially overlaps when their spatial regions intersect.
comment: RCC8:partial overlap
domain: continuant
range: continuant
sub property of: is spatially related to

preceded by
type: ObjectProperty
type: TransitiveProperty
comment: A transitive, temporal relation in which one process is preceded by (has occured later than) another process.
example: translation preceded_by transcription
range: occurrent
domain: occurrent
sub property of: is temporally related to
inverse of: precedes

precedes
type: ObjectProperty
type: TransitiveProperty
comment: A transitive, temporal relation in which one process precedes (has occured earlier than) another process.
range: occurrent
domain: occurrent
sub property of: is temporally related to
property chain axiom: immediately precedes

realizes
type: ObjectProperty
type: AsymmetricProperty
type: IrreflexiveProperty
definition: A relation between a process and a realizable entity.
range: dependent continuant
domain: occurrent
sub property of: has participant
inverse of: is realized in

represents
type: ObjectProperty
example: The symbol '1994' as it appears on a graph about car sales in the 1990's, represents the year 1994 (an instance of a temporal interval). The 3D geometric mesh generated by a software program represents the surface of a protein.
definition: a represents b when a serves as a sign or symbol of b.
range: entity
domain: entity
sub property of: is related to

has measurement value
type: DatatypeProperty
type: FunctionalProperty
domain: scalar measurement datum
range: float

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
domain: cartesian spatial coordinate datum
range: float

begins
type: DatatypeProperty
type: FunctionalProperty
comment: A data property that marks the beginning of a temporal entity.

end
type: DatatypeProperty
type: FunctionalProperty
comment: A data property that marks the end of a temporal entity.

has value
type: DatatypeProperty
type: FunctionalProperty
comment: A data type property to store a value.

has x coordinate value
type: DatatypeProperty
type: FunctionalProperty
definition: A datatype relation between a coordinate and its coordinate value on the x-axis.
sub property of: has value

has y coordinate value
type: DatatypeProperty
type: FunctionalProperty
definition: A datatype relation between a coordinate and its coordinate value on the Y-axis.
sub property of: has value

has z coordinate value
type: DatatypeProperty
type: FunctionalProperty
definition: A datatype relation between a coordinate and its coordinate value on the Z-axis.
sub property of: has value

xanthine [chebi:15318]
type: Class
equivalent class: rkb:RKB 000036
subclass of: purine nucleobases [chebi:26386]

cytosine [chebi:16040]
type: Class
equivalent class: rkb:RKB 000037
subclass of: pyrimidine nucleobases [chebi:26432]

guanine [chebi:16235]
type: Class
equivalent class: rkb:RKB 000035
subclass of: purine nucleobases [chebi:26386]

adenine [chebi:16708]
type: Class
equivalent class: rkb:RKB 000034
subclass of: purine nucleobases [chebi:26386]

deoxyribonucleic acids [chebi:16991]
type: Class
equivalent class: rkb:RKB 000073
subclass of: nucleic acid [chebi:33696]

uracil [chebi:17568]
type: Class
equivalent class: rkb:RKB 000039
subclass of: pyrimidine nucleobases [chebi:26432]

thymine [chebi:17821]
type: Class
equivalent class: rkb:RKB 000038
subclass of: pyrimidine nucleobases [chebi:26432]

nucleobases [chebi:18282]
type: Class
equivalent class: rkb:RKB 000027
subclass of: rkb:RKB 000018

purine nucleobases [chebi:26386]
type: Class
equivalent class: rkb:RKB 000032
subclass of: nucleobases [chebi:18282]

pyrimidine nucleobases [chebi:26432]
type: Class
equivalent class: rkb:RKB 000033
subclass of: nucleobases [chebi:18282]

nucleic acid [chebi:33696]
type: Class
equivalent class: rkb:RKB 000028
subclass of: rkb:RKB 000018

ribonucleic acids [chebi:33697]
type: Class
equivalent class: rkb:RKB 000076
subclass of: nucleic acid [chebi:33696]

UMP residue [chebi:46470]
type: Class
subclass of: canonical ribonucleotide residue [chebi:50299]

canonical nucleotide residue [chebi:50297]
type: Class
subclass of: nucleotide residue [chebi:50319]

canonical deoxyribonucleotide residue [chebi:50298]
type: Class
subclass of: canonical nucleotide residue [chebi:50297]

canonical ribonucleotide residue [chebi:50299]
type: Class
subclass of: canonical nucleotide residue [chebi:50297]

dTMP residue [chebi:50300]
type: Class
subclass of: canonical deoxyribonucleotide residue [chebi:50298]

AMP residue [chebi:50306]
type: Class
subclass of: canonical ribonucleotide residue [chebi:50299]

CMP residue [chebi:50308]
type: Class
subclass of: canonical ribonucleotide residue [chebi:50299]

nucleotide residue [chebi:50319]
type: Class
subclass of: rkb:RKB 000018

dCMP residue [chebi:50321]
type: Class
subclass of: canonical deoxyribonucleotide residue [chebi:50298]

dGMP residue [chebi:50322]
type: Class
subclass of: canonical deoxyribonucleotide residue [chebi:50298]

dAMP residue [chebi:50323]
type: Class
subclass of: canonical deoxyribonucleotide residue [chebi:50298]

GMP residue [chebi:50324]
type: Class
subclass of: canonical ribonucleotide residue [chebi:50299]

RNAO_0000112
type: Class
subclass of: quality
IAO_0000115: The spatial arrangement of the atoms in a molecule or molecular part affording distinction between stereoisomers which can be interconverted by rotations about formally single bonds.
IAO_0000111: conformation
IAO_0000117: http://goldbook.iupac.org/C01258.html

RNAO_0000113
type: Class
subclass of: RNAO_0000112
IAO_0000117: PERSON: Colin Batchelor, based on the Leontis-Westhof classification.
IAO_0000115: A conformation that inheres in an RNA base pair. It may be cis- or trans- depending on the orientations of the ribose rings relative to the edge-edge interaction of the nucleobases.
IAO_0000111: base pair orientation

RNAO_0000114
type: Class
subclass of: RNAO_0000113
subclass of: rkb:RKB 000008
disjoint with: RNAO_0000115
IAO_0000115: A base pair conformation where the ribose rings are on the same side of a plane drawn through the middle of the edge-edge hydrogen bonds.
IAO_0000111: base pair cis-orientation
IAO_0000117: PERSON: Colin Batchelor, based on the Leontis-Westhof classification.

RNAO_0000115
type: Class
subclass of: RNAO_0000113
subclass of: rkb:RKB 000008
IAO_0000115: A base pair conformation where the ribose rings are on opposite sides of a plane drawn through the middle of the edge-edge hydrogen bonds.
IAO_0000117: PERSON: Colin Batchelor, based on the Leontis-Westhof classification.
IAO_0000111: base pair trans-orientation

RNAO_0000121
type: Class
subclass of: RNAO_0000112
IAO_0000111: nucleoside conformation
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: A conformation that inheres in an nucleoside based on the rotation of the nucleobase about the glycosidic torsion angle χ with the furanose.

RNAO_0000122
type: Class
subclass of: RNAO_0000121
disjoint with: RNAO_0000123
IAO_0000115: A syn nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented towards the ribose due to rotation about the glycosidic torsion angle χ. From χ = 0°, where the plane of the base is aligned with the O4’-C1’ bond in a direction towards the O4’ atom, the syn conformation covers the remaining rotations of ±90°: χ = [-90°, 90°].
IAO_0000111: syn nucleoside conformation
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000123
type: Class
subclass of: RNAO_0000121
IAO_0000111: anti nucleoside conformation
IAO_0000115: A anti nucleoside conformation is a nucleoside conformation characterized by the nucleobase being oriented away from the ribose due to rotation about the glycosidic torsion angle χ. From χ = 180°, where the plane of the base is aligned with the O4’-C1’ bond in a direction away from the O4’ atom, the anti conformation covers a rotations of ±90°: χ = [-180°, 90°].
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000124
type: Class
subclass of: RNAO_0000126
disjoint with: RNAO_0000125
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: An envelope conformation is a furan ring conformation in which only one of the five fruan atoms (C1’, C2’, C3’, C4’ or O4’) is out of the plane formed by the four others.
IAO_0000111: envelope conformation

RNAO_0000125
type: Class
subclass of: RNAO_0000126
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: An envelope conformation is a furan ring conformation in which two atoms are in opposite sides of the plane formed by the remaining three.
IAO_0000111: twist conformation

RNAO_0000126
type: Class
subclass of: RNAO_0000112
IAO_0000111: furan ring conformation
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: A furan ring conformation is a conformation that inheres in a furan ring and is characterized by the values of torsion angles: θ0-4.

RNAO_0000127
type: Class
subclass of: RNAO_0000124
IAO_0000117: PERSON: Michel Dumontier
IAO_0000111: C2’-endo pucker
IAO_0000115: C2'-endo pucker (2E conformation) is an envelope conformation in which the C2' atom is above the plane formed by the other 4 atoms.

RNAO_0000128
type: Class
subclass of: RNAO_0000124
IAO_0000111: C3’-endo pucker
IAO_0000115: C3'-endo pucker (An 3E conformation) is an envelope conformation in which the C3' atom is above the plane formed by the other 4 atoms.
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000129
type: Class
subclass of: RNAO_0000124
IAO_0000111: C4’-exo pucker
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: C4'-exo pucker (E4 conformation) is an envelope conformation in which the C4' atom is below the plane formed by the other 4 atoms.

RNAO_0000130
type: Class
subclass of: RNAO_0000125
disjoint with: RNAO_0000131
IAO_0000115: C3'-endo - C4' exo pucker (3E4 conformation) is a twist conformation in which the C3' atom is above the plane and the C4' atom is below the plane.
IAO_0000117: PERSON: Michel Dumontier
IAO_0000111: C3'-endo - C4' -exo pucker

RNAO_0000131
type: Class
subclass of: RNAO_0000125
IAO_0000115: C3'-endo - C2' exo pucker (3E2 conformation) is a twist conformation in which the C3' atom is above the plane and the C2' atom is below the plane.
IAO_0000117: PERSON: Michel Dumontier
IAO_0000111: C3'-endo - C2' -exo pucker

RNAO_0000135
type: Class
subclass of: RNAO_0000112
IAO_0000115: A base stack orientation is a conformation that inheres in a base stack by virtue of the orientation of the nucleobases relative to i) the alignment of base normals and ii) their sequence adjacency.
IAO_0000111: base stack orientation
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000138
type: Class
subclass of: RNAO_0000140
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: An base stack straight orientation is a base stack orientation in which the normals of both bases are aligned in the same direction.
IAO_0000111: base stack straight orientation

RNAO_0000139
type: Class
subclass of: RNAO_0000140
IAO_0000115: A base stack reverse orientation is a base stack orientation in which the normals of both bases are aligned in the opposite directions.
IAO_0000111: base stack reverse orientation
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000140
type: Class
subclass of: RNAO_0000135
disjoint with: RNAO_0000144
IAO_0000115: A base stack base-normal orientation is a base stack orientation that depends on the relative orientation of the base normals.
IAO_0000111: base stack base-normal orientation

RNAO_0000142
type: Class
subclass of: RNAO_0000140
IAO_0000115: A base stack above orientation is a base stack orientation in which the second base (B) is in the same direction as the normal to the first base (A).
IAO_0000111: base stack above orientation
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000143
type: Class
subclass of: RNAO_0000140
IAO_0000111: base stack below orientation
IAO_0000115: A base stack below orientation is a base stack orientation in which the normal of the second base (B) is directed towards the first base (A).
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000144
type: Class
subclass of: RNAO_0000135
IAO_0000111: base stack sequence adjacency
IAO_0000115: A base stack sequence adjacency is a base stack orientation that depends on whether the stacked nucleobases are part of nucleotides that are sequence adjacent or not.
IAO_0000117: PERSON: Michel Dumontier

RNAO_0000145
type: Class
subclass of: RNAO_0000144
disjoint with: RNAO_0000146
IAO_0000117: PERSON: Michel Dumontier
IAO_0000115: A base stack adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are sequence adjacent.
IAO_0000111: base stack adjacent base orientation

RNAO_0000146
type: Class
subclass of: RNAO_0000144
IAO_0000115: A base stack non-adjacent orientation is a base stack orientation in which the stacked nucleobases are part of nucleotides that are not sequence adjacent.
IAO_0000117: PERSON: Michel Dumontier
IAO_0000111: base stack non-adjacent base orientation

data item
type: Class
subclass of: information content entity
IAO_0000116: 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum.
IAO_0000116: 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym.
IAO_0000117: PERSON: Alan Ruttenberg
IAO_0000117: PERSON: Chris Stoeckert
IAO_0000117: PERSON: Jonathan Rees
IAO_0000111: data item
IAO_0000116: 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers.
IAO_0000112: Data items include counts of things, analyte concentrations, and statistical summaries.
IAO_0000116: JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief
IAO_0000115: a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements.
IAO_0000118: data

scalar measurement datum
type: Class
subclass of: measurement datum
subclass of: Restriction
  on property: has measurement value
  min cardinality: 1
IAO_0000112: 10 feet. 3 ml.
IAO_0000116: 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form
IAO_0000117: PERSON: Melanie Courtot
IAO_0000116: Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them.
IAO_0000115: a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label.
IAO_0000117: PERSON: Alan Ruttenberg

data set
type: Class
subclass of: data item
IAO_0000119: OBI_0000042
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000124
IAO_0000116: 2/2/2009 Is this what we need. There are also data sets like all measurement taken in a time course experiement on one patient. What is the result of one FACS experiment?
IAO_0000115: A data set is an information content entity that is an aggregate of other data items that have something in common and are considered to form a unit and are packaged together for some purpose, for example depositing into a repository.
IAO_0000111: data set
IAO_0000119: group:OBI
IAO_0000117: person:Allyson
IAO_0000117: person:Chris Stoeckert

measurement datum
type: Class
subclass of: data item
IAO_0000116: 2/2/2009 is_specified_output of some assay?
IAO_0000119: OBI_0000305
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000124
IAO_0000115: A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument.
IAO_0000112: Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
IAO_0000119: group:OBI
IAO_0000111: measurement datum
IAO_0000117: person:Chris Stoeckert

setting datum
type: Class
subclass of: data item
IAO_0000115: A settings datum is a datum that denotes some configuration of an instrument.
IAO_0000116: Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
IAO_0000114: http://purl.obolibrary.org/obo/IAO_0000124
IAO_0000116: 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable.

cartesian spatial coordinate datum
type: Class
subclass of: data item
IAO_0000116: 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617
IAO_0000115: A cartesian spatial coordinate datum is a represenation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude
IAO_0000117: Alan Ruttenberg

one dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region
IAO_0000117: Alan Ruttenberg

two dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region
IAO_0000117: Alan Ruttenberg

three dimensional cartesian spatial coordinate datum
type: Class
subclass of: cartesian spatial coordinate datum
subclass of: Restriction
  on property: has x coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has y coordinate value
  cardinality: 1
subclass of: Restriction
  on property: has z coordinate value
  cardinality: 1
comment: A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region
IAO_0000117: Alan Ruttenberg

length measurement datum
type: Class
subclass of: scalar measurement datum
IAO_0000115: A scalar measurement datum that is the result of measurement of length quality
IAO_0000117: Alan Ruttenberg

rkb:RKB 000000
type: Class
subclass of: information content entity
IAO_0000111: structure model

rkb:RKB 000001
type: Class
subclass of: object
subclass of: Restriction
  on property: has part
  some values from: rkb:RKB 000126
IAO_0000111: nucleotide base pair

rkb:RKB 000002
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: AMP residue [chebi:50306]
      union of: dAMP residue [chebi:50323]
    qualified cardinality: 2
subclass of: rkb:RKB 000001
IAO_0000111: AA base pair

rkb:RKB 000003
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: dTMP residue [chebi:50300]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: AMP residue [chebi:50306]
      union of: dAMP residue [chebi:50323]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: AT base pair

rkb:RKB 000004
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: UMP residue [chebi:46470]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: AMP residue [chebi:50306]
      union of: dAMP residue [chebi:50323]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: AU base pair

rkb:RKB 000005
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: AMP residue [chebi:50306]
      union of: dAMP residue [chebi:50323]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: CMP residue [chebi:50308]
      union of: dCMP residue [chebi:50321]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: CA base pair

rkb:RKB 000006
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: CMP residue [chebi:50308]
      union of: dCMP residue [chebi:50321]
    qualified cardinality: 2
subclass of: rkb:RKB 000001
IAO_0000111: CC base pair

rkb:RKB 000007
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: UMP residue [chebi:46470]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: CMP residue [chebi:50308]
      union of: dCMP residue [chebi:50321]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: CU base pair

rkb:RKB 000008
type: Class
subclass of: RNAO_0000113
IAO_0000111: glycosyl bond base pair orientation

rkb:RKB 000009
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: AMP residue [chebi:50306]
      union of: dAMP residue [chebi:50323]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: dGMP residue [chebi:50322]
      union of: GMP residue [chebi:50324]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: GA base pair

rkb:RKB 000010
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: CMP residue [chebi:50308]
      union of: dCMP residue [chebi:50321]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: dGMP residue [chebi:50322]
      union of: GMP residue [chebi:50324]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: GC base pair

rkb:RKB 000011
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: dGMP residue [chebi:50322]
      union of: GMP residue [chebi:50324]
    qualified cardinality: 2
subclass of: rkb:RKB 000001
IAO_0000111: GG base pair

rkb:RKB 000012
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: UMP residue [chebi:46470]
    qualified cardinality: 1
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: Class
      union of: dGMP residue [chebi:50322]
      union of: GMP residue [chebi:50324]
    qualified cardinality: 1
subclass of: rkb:RKB 000001
IAO_0000111: GU base pair

rkb:RKB 000013
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: dTMP residue [chebi:50300]
    qualified cardinality: 2
subclass of: rkb:RKB 000001
IAO_0000111: TT base pair

rkb:RKB 000014
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000001
  intersection of: Restriction
    on property: rkb:hasProperPart
    on class: UMP residue [chebi:46470]
    qualified cardinality: 2
subclass of: rkb:RKB 000001
IAO_0000111: UU base pair

rkb:RKB 000015
type: Class
subclass of: object
IAO_0000111: chemical

rkb:RKB 000016
type: Class
subclass of: rkb:RKB 000015
IAO_0000111: molecule

rkb:RKB 000017
type: Class
subclass of: rkb:RKB 000016
comment: A molecule whose formula can be reduced into (CH20)n, for n >= 3
IAO_0000111: carbohydrate

rkb:RKB 000018
type: Class
subclass of: rkb:RKB 000016
comment: Components that comprise Nucleic Acids
IAO_0000111: nucleic acid or component

rkb:RKB 000019
type: Class
subclass of: rkb:RKB 000016
comment: Components that comprise Phosphates
IAO_0000111: phosphate component

rkb:RKB 000020
type: Class
subclass of: rkb:RKB 000017
comment: Basic carbohydrate unit
IAO_0000111: monosaccharide

rkb:RKB 000021
type: Class
subclass of: rkb:RKB 000020
comment: A five-carbon carbohydrate
IAO_0000111: pentose

rkb:RKB 000022
type: Class
subclass of: rkb:RKB 000021
comment: A pentose with an aldehyde functional group in position 1.
IAO_0000111: aldopentose

rkb:RKB 000023
type: Class
subclass of: rkb:RKB 000021
comment: A pentose with an ketone functional group in position 2.
IAO_0000111: ketopentose

rkb:RKB 000024
type: Class
subclass of: rkb:RKB 000022
comment: A five-membered-cyclic carbohydrate
IAO_0000111: furanose

rkb:RKB 000025
type: Class
subclass of: rkb:RKB 000024
disjoint with: rkb:RKB 000026
comment: pubchem:439576
IAO_0000111: deoxyribose

rkb:RKB 000026
type: Class
subclass of: rkb:RKB 000024
comment: chebi:45506
IAO_0000111: ribose

rkb:RKB 000027
type: Class
subclass of: rkb:RKB 000018
comment: Structural parts of nucleotides, generally attached to the 1' carbon of the cognate ribose
IAO_0000111: nucleobase

rkb:RKB 000028
type: Class
subclass of: rkb:RKB 000018
subclass of: Class
  union of: rkb:RKB 000078
  union of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000078
IAO_0000111: nucleic acid

rkb:RKB 000029
type: Class
subclass of: rkb:RKB 000018
subclass of: Class
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000024
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000027
IAO_0000111: nucleoside residue

rkb:RKB 000030
type: Class
subclass of: rkb:RKB 000018
subclass of: Class
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000019
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000029
comment: Purine or pyrimidine base that is attached to a ribose or deoxyribose, (Nucleoside) and is also attached to at least one phosphate group
IAO_0000111: nucleotide

rkb:RKB 000031
type: Class
subclass of: rkb:RKB 000019
IAO_0000111: phosphate
comment: pubchem:1061

rkb:RKB 000032
type: Class
subclass of: rkb:RKB 000027
comment: pubchem:1044 chebi:26389
comment: heterocyclic aromatic compound consisting of a pyrimidine ring fused to an imidazole ring
IAO_0000111: purine nucleobase

rkb:RKB 000033
type: Class
subclass of: rkb:RKB 000027
comment: Six member heterocyclic aromatic compound containing two nitrogen atoms at positions 1 and 3
comment: pubchem:9260 chebi:26432
IAO_0000111: pyrimidine nucleobase

rkb:RKB 000034
type: Class
subclass of: rkb:RKB 000032
comment: pubchem:190 chebi:16708
IAO_0000111: adenine

rkb:RKB 000035
type: Class
subclass of: rkb:RKB 000032
comment: pubchem:764 chebi:16235
IAO_0000111: guanine

rkb:RKB 000036
type: Class
subclass of: rkb:RKB 000032
comment: pubchem:6021 chebi:17368
IAO_0000111: xanthine

rkb:RKB 000037
type: Class
subclass of: rkb:RKB 000033
comment: pubchem:597 chebi:16040
IAO_0000111: cytosine

rkb:RKB 000038
type: Class
subclass of: rkb:RKB 000033
comment: pubchem:1135 chebi:17821
IAO_0000111: thymine

rkb:RKB 000039
type: Class
subclass of: rkb:RKB 000033
comment: pubchem:1174 chebi:17568
IAO_0000111: uracil

rkb:RKB 000040
type: Class
subclass of: RNAO_0000113
comment: A spatial interaction between nucleotides that depends on the direction of their normals.
IAO_0000111: normal vector base pair orientation

rkb:RKB 000041
type: Class
subclass of: rkb:RKB 000030
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000025
disjoint with: rkb:RKB 000042
comment: A nucleotide that has a deoxyribose as its sugar
IAO_0000111: deoxyribonucleotide

rkb:RKB 000042
type: Class
subclass of: rkb:RKB 000030
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000026
comment: A nucleotide that has a ribose as its sugar
IAO_0000111: ribonucleotide

rkb:RKB 000043
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: adenosine monophosphate

rkb:RKB 000044
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: adenosine triphosphate

rkb:RKB 000045
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: cytidine monophosphate

rkb:RKB 000046
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: cytidine triphosphate

rkb:RKB 000047
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: guanosine monophosphate

rkb:RKB 000048
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: guanosine triphosphate

rkb:RKB 000049
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: uridine monophosphate

rkb:RKB 000050
type: Class
subclass of: rkb:RKB 000042
IAO_0000111: uridine triphosphate

rkb:RKB 000051
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: thymidine monophosphate

rkb:RKB 000052
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxyadenosine monophosphate

rkb:RKB 000053
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxycytosine monophosphate

rkb:RKB 000054
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxyguanosine monophosphate

rkb:RKB 000055
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: thymidine triphosphate

rkb:RKB 000056
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxyguanosine triphosphate

rkb:RKB 000057
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxycytosine triphosphate

rkb:RKB 000058
type: Class
subclass of: rkb:RKB 000041
IAO_0000111: deoxyadenosine triphosphate

rkb:RKB 000059
type: Class
subclass of: rkb:RKB 000030
IAO_0000111: nucleotide monophosphate

rkb:RKB 000060
type: Class
subclass of: rkb:RKB 000030
IAO_0000111: nucleotide diphosphate

rkb:RKB 000061
type: Class
subclass of: rkb:RKB 000030
IAO_0000111: nucleotide triphosphate

rkb:RKB 000062
type: Class
subclass of: rkb:RKB 000029
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000025
comment: A nucleoside that has a deoxyribose as its sugar
IAO_0000111: deoxyribonucleoside residue

rkb:RKB 000063
type: Class
subclass of: rkb:RKB 000029
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000026
comment: A nucleoside that has a ribose as its sugar
IAO_0000111: ribonucleoside residue

rkb:RKB 000064
type: Class
subclass of: rkb:RKB 000029
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000032
IAO_0000111: purine nucleoside residue

rkb:RKB 000065
type: Class
subclass of: rkb:RKB 000029
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000033
IAO_0000111: pyrimidine nucleoside residue

rkb:RKB 000066
type: Class
subclass of: rkb:RKB 000064
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000036
IAO_0000111: inosine residue

rkb:RKB 000067
type: Class
subclass of: rkb:RKB 000064
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000034
IAO_0000111: adenosine residue

rkb:RKB 000068
type: Class
subclass of: rkb:RKB 000064
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000035
IAO_0000111: guanosine residue

rkb:RKB 000069
type: Class
subclass of: rkb:RKB 000065
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000037
IAO_0000111: cytidine residue

rkb:RKB 000070
type: Class
subclass of: rkb:RKB 000065
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000038
IAO_0000111: deoxythymidine residue

RKB_000071
type: Class
label: atom orientation in plane role
subclass of: role

rkb:RKB 000072
type: Class
subclass of: rkb:RKB 000065
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000039
IAO_0000111: uridine residue

rkb:RKB 000073
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000028
  intersection of: Class
    union of: rkb:RKB 000081
    union of: rkb:RKB 000084
subclass of: rkb:RKB 000028
IAO_0000111: deoxyribonucleic acid

rkb:RKB 000074
type: Class
subclass of: rkb:RKB 000028
subclass of: Restriction
  on property: rkb:hasProperPart
  on class: rkb:RKB 000078
  qualified cardinality: 2
IAO_0000111: double stranded nucleic acid

RKB_000075
type: Class
label: nucleotide interaction role
subclass of: role

rkb:RKB 000076
type: Class
equivalent class: Class
  intersection of: rkb:RKB 000028
  intersection of: Class
    union of: rkb:RKB 000082
    union of: rkb:RKB 000083
subclass of: rkb:RKB 000028
IAO_0000111: ribonucleic acid

rkb:RKB 000077
type: Class
subclass of: rkb:RKB 000028
subclass of: Class
  union of: rkb:RKB 000078
  union of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000078
IAO_0000111: single stranded nucleic acid

rkb:RKB 000078
type: Class
subclass of: rkb:RKB 000028
subclass of: Class
  complement of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000078
subclass of: Restriction
  on property: rkb:hasProperPart
  on class: rkb:RKB 000030
  min qualified cardinality: 2
IAO_0000111: polynucleotide

rkb:RKB 000079
type: Class
subclass of: information content entity
IAO_0000111: molecular structure specification

rkb:RKB 000080
type: Class
subclass of: quality
IAO_0000111: atom orientation in plane

rkb:RKB 000081
type: Class
subclass of: rkb:RKB 000074
IAO_0000111: double stranded DNA

rkb:RKB 000082
type: Class
subclass of: rkb:RKB 000074
IAO_0000111: double stranded RNA

rkb:RKB 000083
type: Class
subclass of: rkb:RKB 000077
subclass of: Class
  intersection of: rkb:RKB 000078
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000026
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: Class
      union of: rkb:RKB 000043
      union of: rkb:RKB 000045
      union of: rkb:RKB 000047
      union of: rkb:RKB 000049
IAO_0000111: single stranded RNA

rkb:RKB 000084
type: Class
subclass of: rkb:RKB 000077
subclass of: Class
  intersection of: rkb:RKB 000078
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000025
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: Class
      union of: rkb:RKB 000051
      union of: rkb:RKB 000052
      union of: rkb:RKB 000053
      union of: rkb:RKB 000054
IAO_0000111: single stranded DNA

rkb:RKB 000085
type: Class
equivalent class: Class
  union of: rkb:RKB 000086
  union of: rkb:RKB 000087
  union of: rkb:RKB 000088
subclass of: fiat object part
subclass of: Restriction
  on property: part of
  some values from: nucleotide residue [chebi:50319]
IAO_0000111: nucleotide edge

rkb:RKB 000086
type: Class
subclass of: rkb:RKB 000085
subclass of: Restriction
  on property: has proper part
  some values from: rkb:RKB 000092
comment: Edge composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 7), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Carbon 5), R (Carbon 8) Where R = Purines and Y = Pyrimidines
IAO_0000111: hoogsteen edge

rkb:RKB 000087
type: Class
subclass of: rkb:RKB 000085
subclass of: Restriction
  on property: has proper part
  some values from: rkb:RKB 000104
comment: Edge composed by the following atoms: Adenine (Carbon 2) or Guanine (Nitrogen 2), R (Nitrogen 3), Y (Oxygen 2), Furanose (Oxygen 2) Where R = Purines and Y = Pyrimidines
IAO_0000111: sugar edge

rkb:RKB 000088
type: Class
subclass of: rkb:RKB 000085
subclass of: Restriction
  on property: has proper part
  some values from: rkb:RKB 000103
comment: Edge composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), R (Nitrogen 1), Adenine (Carbon 2) or Guanine (Nitrogen 2), Uracil (Oxygen 4) or Cytosine (Nitrogen 4), Y (Nitrogen 3), Y (Oxygen 2) Where R = Purines and Y = Pyrimidines
IAO_0000111: watson edge

rkb:RKB 000089
type: Class
subclass of: fiat object part
subclass of: Restriction
  on property: part of
  some values from: rkb:RKB 000085
comment: Equivalent to Major-Lemiux faces
comment: A part of the nucleotide ribose or base, capable of forming hydrogen bonds.
IAO_0000111: nucleotide sub edge

rkb:RKB 000090
type: Class
subclass of: rkb:RKB 000089
IAO_0000111: bifurcated sub edge

rkb:RKB 000091
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000086
comment: Face composed by the following atom: R (Carbon 8) Where R = Purines
comment: c8 face
IAO_0000111: c8 sub edge

rkb:RKB 000092
type: Class
equivalent class: Class
  union of: rkb:RKB 000091
  union of: rkb:RKB 000093
  union of: rkb:RKB 000094
  union of: rkb:RKB 000101
subclass of: rkb:RKB 000089
IAO_0000111: hoogsteen sub edge

rkb:RKB 000093
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000086
comment: Face composed by the following atoms: R(Nitrogen 7) , Y (Carbon 5) Where Y = Pyrimidines and R = Purines
comment: hoogsteen hoogsteen face
IAO_0000111: hoogsteen hoogsteen sub edge

rkb:RKB 000094
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000086
comment: Face composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4)
comment: hoogsteen watson face
IAO_0000111: hoogsteen watson sub edge

rkb:RKB 000095
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000087
comment: Face composed by the following atom: Furanose O2'
comment: O2prime face
IAO_0000111: o2 prime sub edge

rkb:RKB 000096
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000087
comment: sugar sugar face
comment: Face composed by the following atoms: R (Nitrogen 3) Where R = Purines
IAO_0000111: sugar sugar sub edge

rkb:RKB 000097
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000087
comment: Face composed by the following atoms: Guanine (Nitrogen 2), Y (Oxygen 2) Where Y = Pyrimidines
comment: sugar watson face
IAO_0000111: sugar watson sub edge

rkb:RKB 000098
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000088
comment: watson hoogsteen face
comment: Face composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4)
IAO_0000111: watson hoogsteen sub edge

rkb:RKB 000099
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000088
comment: Face composed by the following atoms: Guanine (Nitrogen 2), Y (Oxygen 2) Where Y = Pyrimidines
comment: watson sugar face
IAO_0000111: watson sugar sub edge

rkb:RKB 000100
type: Class
subclass of: rkb:RKB 000089
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000088
comment: watson watson face
comment: Face composed by the following atoms: R (Nitrogen 1), Y (Nitrogen 3) Where Y = Pyrimidines and R = Purines
IAO_0000111: watson watson sub edge

rkb:RKB 000101
type: Class
subclass of: rkb:RKB 000090
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000086
comment: Face composed by the following atoms: Adenine (Nitrogen 6) or Guanine (Oxygen 6), Uracil (Oxygen 4) or Cytosine (Nitrogen 4)
comment: bifurcated hoogsteen face
IAO_0000111: bifurcated hoogsteen sub edge

rkb:RKB 000102
type: Class
subclass of: rkb:RKB 000090
subclass of: Restriction
  on property: is proper part of
  some values from: rkb:RKB 000087
comment: bifurcated sugar face
comment: Face composed by the following atoms: Adenine (Carbon 2) or Guanine (Nitrogen 2), Y (Oxygen 2) Where Y = Pyrimidines
IAO_0000111: bifurcated sugar sub edge

rkb:RKB 000103
type: Class
equivalent class: Class
  union of: rkb:RKB 000098
  union of: rkb:RKB 000099
  union of: rkb:RKB 000100
subclass of: rkb:RKB 000089
IAO_0000111: watson sub edge

rkb:RKB 000104
type: Class
equivalent class: Class
  union of: rkb:RKB 000095
  union of: rkb:RKB 000096
  union of: rkb:RKB 000097
  union of: rkb:RKB 000102
subclass of: rkb:RKB 000089
IAO_0000111: sugar sub edge

rkb:RKB 000105
type: Class
subclass of: rkb:RKB 000080
comment: When considering a horizontal plane on the furanose, and the C5' atom is on the left side, the atoms located over the plane are said to be endo to the C5'
IAO_0000111: endo

rkb:RKB 000106
type: Class
subclass of: rkb:RKB 000080
comment: When considering a horizontal plane on the furanose, and teh C5' atom is on the left side, the atoms located under the plane are said to be exo to the C5'
IAO_0000111: exo

rkb:RKB 000107
type: Class
subclass of: rkb:RKB 000105
IAO_0000111: c1 prime endo

rkb:RKB 000108
type: Class
subclass of: rkb:RKB 000105
IAO_0000111: c2 prime endo

rkb:RKB 000109
type: Class
subclass of: rkb:RKB 000105
IAO_0000111: c3 prime endo

rkb:RKB 000110
type: Class
subclass of: rkb:RKB 000105
IAO_0000111: c4 prime endo

rkb:RKB 000111
type: Class
subclass of: information content entity
IAO_0000111: molecular structure file

rkb:RKB 000112
type: Class
subclass of: object
IAO_0000111: collection of molecules

rkb:RKB 000113
type: Class
subclass of: rkb:RKB 000015
IAO_0000111: atom

rkb:RKB 000115
type: Class
subclass of: RNAO_0000140
comment: Downward stacking occurs between bases A and B when the normal of B faces the underside of A, whose normal faces away from B.
IAO_0000111: downward stacking

rkb:RKB 000116
type: Class
subclass of: RNAO_0000140
comment: Inward stacking occurs between bases A and B when their normals face each other.
IAO_0000111: inward stacking

rkb:RKB 000117
type: Class
subclass of: RNAO_0000140
comment: Outward stacking occurs between bases A and B when their normals face away from each other.
IAO_0000111: outward stacking

rkb:RKB 000118
type: Class
subclass of: RNAO_0000140
comment: Upward stacking occurs between bases A and B when the normal of base A faces the underside of base B, whose normal faces away from A.
IAO_0000111: upward stacking

rkb:RKB 000119
type: Class
subclass of: rkb:RKB 000001
subclass of: Restriction
  on property: rkb:hasProperPart
  on class: rkb:RKB 000085
  qualified cardinality: 2
IAO_0000111: edge base pair

rkb:RKB 000120
type: Class
subclass of: rkb:RKB 000119
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000086
IAO_0000111: hoogsteen-hoogsteen base pair

rkb:RKB 000121
type: Class
subclass of: rkb:RKB 000119
subclass of: Class
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000086
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000087
IAO_0000111: hoogsteen-sugar base pair

rkb:RKB 000122
type: Class
subclass of: rkb:RKB 000119
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000087
IAO_0000111: sugar-sugar base pair

rkb:RKB 000123
type: Class
subclass of: rkb:RKB 000119
subclass of: Class
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000086
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000088
IAO_0000111: watson-hoogsteen base pair

rkb:RKB 000124
type: Class
subclass of: rkb:RKB 000119
subclass of: Class
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000087
  intersection of: Restriction
    on property: rkb:hasProperPart
    some values from: rkb:RKB 000088
IAO_0000111: watson-sugar base pair

rkb:RKB 000125
type: Class
subclass of: rkb:RKB 000119
subclass of: Restriction
  on property: rkb:hasProperPart
  some values from: rkb:RKB 000088
IAO_0000111: watson-watson base pair

rkb:RKB 000126
type: Class
subclass of: object
subclass of: Restriction
  on property: rkb:hasProperPart
  on class: rkb:RKB 000089
  min qualified cardinality: 2
IAO_0000111: sub-edge interaction

rkb:RKB 000129
type: Class
subclass of: rkb:RKB 000040
comment: A base pair where the normals are antiparallel.
IAO_0000111: antiparallel base pair

rkb:RKB 000130
type: Class
subclass of: rkb:RKB 000040
comment: A base pair where the normals are parallel.
IAO_0000111: parallel base pair

rkb:RKB 000134
type: Class
subclass of: rkb:RKB 000105
IAO_0000111: o4 prime endo

rkb:RKB 000135
type: Class
subclass of: rkb:RKB 000106
IAO_0000111: c1 prime exo

rkb:RKB 000136
type: Class
subclass of: rkb:RKB 000106
IAO_0000111: c2 prime exo

rkb:RKB 000137
type: Class
subclass of: rkb:RKB 000106
IAO_0000111: c3 prime exo

rkb:RKB 000138
type: Class
subclass of: rkb:RKB 000106
IAO_0000111: c4 prime exo

rkb:RKB 000139
type: Class
subclass of: rkb:RKB 000106
IAO_0000111: o4 prime exo

rkb:RKB 000142
type: Class
subclass of: RKB_000071
IAO_0000111: endo role

rkb:RKB 000143
type: Class
subclass of: RKB_000071
IAO_0000111: exo role

rkb:RKB 000144
type: Class
subclass of: rkb:RKB 000142
IAO_0000111: c1 prime endo role

rkb:RKB 000145
type: Class
subclass of: rkb:RKB 000142
IAO_0000111: c2 prime endo role

rkb:RKB 000146
type: Class
subclass of: rkb:RKB 000142
IAO_0000111: c3 prime endo role

rkb:RKB 000147
type: Class
subclass of: rkb:RKB 000142
IAO_0000111: c4 prime endo role

rkb:RKB 000148
type: Class
subclass of: rkb:RKB 000142
IAO_0000111: o4 prime endo role

rkb:RKB 000149
type: Class
subclass of: rkb:RKB 000143
IAO_0000111: c1 prime exo role

rkb:RKB 000150
type: Class
subclass of: rkb:RKB 000143
IAO_0000111: c2 prime exo role

rkb:RKB 000151
type: Class
subclass of: rkb:RKB 000143
IAO_0000111: c3 prime exo role

rkb:RKB 000152
type: Class
subclass of: rkb:RKB 000143
IAO_0000111: c4 prime exo role

rkb:RKB 000153
type: Class
subclass of: rkb:RKB 000143
IAO_0000111: o4 prime endo role

rkb:RKB 000154
type: Class
subclass of: RKB_000075
IAO_0000111: nucleotide stacking role

rkb:RKB 000155
type: Class
subclass of: rkb:RKB 000154
IAO_0000111: face away role

rkb:RKB 000156
type: Class
subclass of: rkb:RKB 000154
IAO_0000111: facing towards role

conceptual entity
type: Class
subclass of: generically dependent continuant
disjoint with: information content entity
example: An idea; A unicorn; E=MC^2;
definition: A conceptual entity is a generically dependent continuant that is abstract, conceptual or mathematical.

connected spatial temporal region
type: Class
subclass of: spatial temporal region
disjoint with: scattered spatial temporal region
definition: A connected spatial temporal region is a spatial temporal region that is maximally connected in both space and in time.

continuant
type: Class
equivalent class: Class
  union of: dependent continuant
  union of: independent continuant
subclass of: entity
disjoint with: occurrent
example: a molecule, the mass of a molecule, the role of a transcription factor, a transcription factor, a collection of molecules in the cell, a binding site, a region of a cell.
definition: A continuant is an entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and whose parts are only continuants.

dependent continuant
type: Class
equivalent class: Class
  union of: generically dependent continuant
  union of: specifically dependent continuant
subclass of: continuant
disjoint with: independent continuant
example: the mass of a molecule, the role of a transcription factor
definition: A dependent continuant is a continuant which is borne by an independent continuant.

entity
type: Class
equivalent class: Class
  union of: continuant
  union of: occurrent
  union of: spatial temporal region
subclass of: Thing
definition: Everything is an entity.

fiat object part
type: Class
subclass of: material entity
example: the part of the cell that is involved in cell adhesion
definition: A fiat object part is a material entity that is part of an object but is not *wholly* demarcated by any physical discontinuities.

function
type: Class
subclass of: disposition
definition: A function is realizable entity in which the capacity to execute some end directed activity under a specific circumstance is intrinsic to its composition.

generically dependent continuant
type: Class
subclass of: dependent continuant
disjoint with: specifically dependent continuant
example: The PDF file being displayed on my screen which is also is stored in memory or in the hard drive. The triangle formed by the peaks of those three mountains.
definition: A generically dependent continuant is a dependent continuant that is borne by one or more independent continuants.

independent continuant
type: Class
equivalent class: Class
  union of: material entity
  union of: site
subclass of: continuant
definition: An independent continuant is a continuant that is the bearer of qualities and realizable entities.
example: a molecule, a transcription factor, a collection of molecules in the cell, a binding site, a region of a cell.

information content entity
type: Class
subclass of: generically dependent continuant
example: The introduction of a scientific article; a sequence that is the concretization of the quality of primary structure; a geometric mesh that represents a molecular surface; the angle from the sun during the the bee waggle dance gives information about the direction to housing or sustenance.
definition: An information content entity is a generically dependent continuant that is an abstraction of, a representation for, or information about some entity.

instantaneous process
type: Class
subclass of: process
definition: An instantaneous process is a process that occurs as a boundary to other processes, and whose beggining and end are exactly the same.
example: cell death

material entity
type: Class
equivalent class: Class
  union of: fiat object part
  union of: object
  union of: object aggregate
subclass of: independent continuant
disjoint with: site
definition: A material entity is an independent continuant that is spatially extended and whose identity is independent of that of other entities and can be maintained through time.

object
type: Class
subclass of: material entity
example: a molecule, a cell, a protein complex
definition: An object is a material entity that is spatially extended, maximally self-connected and self-contained.

object aggregate
type: Class
subclass of: material entity
definition: An object aggregate is a material entity that is the mereological sum of separate objects and may possess non-connected boundaries.
example: a collection of molecules, a collection of rocks

object boundary
type: Class
subclass of: fiat object part
example: the surface of the earth, the surface of a molecule
definition: An object boundary (aka surface) is a fiat object part that exists exactly at the point where the object is separated from other entities.

occurrent
type: Class
equivalent class: Class
  union of: process
  union of: process aggregate
subclass of: entity
definition: An occurrent is an entity happens, unfolds or develops through time and whose parts are also occurrents.
example: cell division, cell death, a set of asynchronous cell divisions.

one dimensional region
type: Class
subclass of: spatial region by dimension
comment: A spatial region with one dimension.
example: an edge of a cube-shaped part of space

process
type: Class
subclass of: occurrent
disjoint with: process aggregate
example: molecular interaction, cell division, cell death
definition: A process is an occurrent that is a maximally connected in spacetime and has bona fide beginnings and endings corresponding to real discontinuities in time.

process aggregate
type: Class
subclass of: occurrent
definition: A process aggregate is an occurent that is a meriological sum of processes and possesses non-connected temporal boundaries.
example: a set of asynchronous cell divisions.

quality
type: Class
subclass of: specifically dependent continuant
disjoint with: realizable entity
example: the mass of a molecule, the color of a fluorophore
definition: A quality is an specifically dependent continuant that is intrinsically associated with an independent continuant, but whose observed/measured value may change with time.

realizable entity
type: Class
subclass of: specifically dependent continuant
example: the disposition to be clumsy, the function of email to deliver messages, the role of a catalyst to increase the rate of reaction.
definition: A realizable entity is a specifically dependent continuant that is solely realized during a process. Realizable entities include dispositions, functions and roles.

disposition
type: Class
subclass of: realizable entity
definition: A disposition is a realizable entity that reflects a tendency under certain circumstances to cause a specific process or transformation in the object in which it inheres.

role
type: Class
subclass of: realizable entity
definition: A role is a realizable entity that reflects the behavior of an independent continuant in a specific circumstance involving two or more independent continuants.

scattered spatial temporal region
type: Class
subclass of: spatial temporal region
definition: A scattered spatial temporal region is a spatial temporal region that is not contiguous in either space or time.
example: The space occupied by the individual substrate molecules in a test tube during several experiments.

site
type: Class
subclass of: independent continuant
definition: A site is an independent continuant defined by a characteristic spatial shape in relation to some arrangement of other continuants and a medium in which it is enclosed in whole or in part. Sites are entities that can be occupied by other continuants.
example: a binding site, the mitochondrial matrix

spatial boundary
type: Class
subclass of: spatial region
example: a point is the boundary of a 1D object, a line is the boundary of a 2D object, a surface is the boundary of a 3D object.
definition: A spatial boundary is a spatial region that is tangential proper part of a larger spatial region.

spatial region
type: Class
subclass of: spatial temporal region
disjoint with: temporal region
definition: A spatial region is a spatial temporal region that is restricted to space.
example: The spatial location occupied by a cell.

spatial region by dimension
type: Class
subclass of: spatial region
definition: A region of space characterized by its spatial dimension.

spatial temporal region
type: Class
equivalent class: Class
  union of: connected spatial temporal region
  union of: scattered spatial temporal region
equivalent class: Class
  union of: spatial region
  union of: temporal region
subclass of: entity
example: cell division occurred in the laboratory over a period of 48 hours.
definition: A spatial temporal region is an entity composed of spatial regions that are parts of space and temporal regions that are parts of time and is the spatial location of continuants and is the temporal location of occurrents.

specifically dependent continuant
type: Class
equivalent class: Class
  union of: quality
  union of: realizable entity
subclass of: dependent continuant
example: the mass of a molecule, the color of a fluorophore, the disposition to be clumsy, the function of email to deliver messages, the role of a catalyst to increase the rate of reaction.
definition: A specifically dependent continuant is a continuant that inheres in a specific and unchanging independent continuant.

temporal boundary
type: Class
subclass of: temporal interval
comment: A temporal boundary is a temporal region that forms at the instantaneous edge of a point in time.
example: the time between cell life and death.

temporal interval
type: Class
subclass of: temporal region
definition: A temporal interval is a a temporal region that is finitely delimited by having a start and end time.
example: the time it takes for a cell to replicate.

temporal region
type: Class
subclass of: spatial temporal region
definition: A temporal region is a spatial temporal region that is restricted to time.
example: The temporal region occupied by cell division.

three dimensional region
type: Class
subclass of: spatial region by dimension
example: a cube-shaped part of space.
comment: A spatial region with three dimensions.

two dimensional region
type: Class
subclass of: spatial region by dimension
comment: A spatial region with two dimensions.
example: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space.

zero dimensional region
type: Class
subclass of: spatial region by dimension
comment: A spatial region with zero dimensions.
example: a point