ro.owl
type: Ontology
imports: ontology-metadata.owl
version info: 2011-08-26

imported from
type: AnnotationProperty

part of
type: ObjectProperty
type: TransitiveProperty
imported from: BFO
inverse of: has part
sub property of: overlaps

has part
type: ObjectProperty
type: TransitiveProperty
imported from: BFO
sub property of: overlaps

in_neural_circuit_with
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons.
IAO_0000117: David Osumi-Sutherland

upstream_in_neural_circuit_with
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
sub property of: in_neural_circuit_with

downstream_in_neural_circuit_with
type: ObjectProperty
type: TransitiveProperty
IAO_0000115: A relation that holds between a neuron that is synapsed_to another neuron or a neuron that is connected indirectly to another by a chain of neurons, each synapsed_to the next.
IAO_0000117: David Osumi-Sutherland
sub property of: in_neural_circuit_with

derives from
type: ObjectProperty
sub property of: topObjectProperty

has_soma_location
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)
IAO_0000115: Relation between a neuron and an anatomical structure that its soma is part of.
IAO_0000111: soma part of
sub property of: overlaps
domain: neuron
property chain axiom: part of

fasciculates_with
type: ObjectProperty
IAO_0000426: x fasciculates_with y iff: ∀'neuron ; CL_0000540’(x), ∃‘neuron projection bundle ; CARO_0001001’(y), ∃‘neuron projection ; GO_0043005(np)’, np part_of x ∧ np overlaps y ∧ np aligned_with y
IAO_0000118: fasciculates with
IAO_0000115: Description: relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.
range: neuron projection bundle
sub property of: overlaps
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

axon synapses in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and some structure its axon forms (chemical) synapses in.
sub property of: has_presynaptic_terminal_in
domain: neuron
property chain axiom: part of

synapsed_by
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it.
sub property of: upstream_in_neural_circuit_with
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

has plasma membrane part
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y)
IAO_0000117: Chris Mungall
IAO_0000112: Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]
IAO_0000119: PMID:19243617
sub property of: has part

has_postsynaptic_terminal_in
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))
IAO_0000117: David Osumi-Sutherland
IAO_0000118: synapsed in
inverse of: axon synapses in
sub property of: has_synaptic_terminal_in
property chain axiom: part of
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

releases neurotransmitter
type: ObjectProperty
sub property of: topObjectProperty

has_presynaptic_terminal_in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input.
IAO_0000118: synapses in
sub property of: has_synaptic_terminal_in
property chain axiom: part of
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

synapsed_to
type: ObjectProperty
comment: N1 synapsed_to some N2 Expands to: N1 SubclassOf ( has_part some ( ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( ‘synapse ; GO:0045202’ that has_part some ( ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))
IAO_0000115: Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
sub property of: downstream_in_neural_circuit_with
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

dendrite synapsed in
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030425> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( http://purl.obolibrary.org/obo/GO_0042734 and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y)))
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input.
sub property of: has_postsynaptic_terminal_in
domain: neuron
property chain axiom: part of

has_synaptic_terminal_in
type: ObjectProperty
IAO_0000115: A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input.
IAO_0000118: has synapse in
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)
IAO_0000117: David Osumi-Sutherland
sub property of: overlaps
domain: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron
property chain axiom: part of

overlaps
type: ObjectProperty
IAO_0000424: http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
sub property of: topObjectProperty
property chain axiom: part of
property chain axiom: has part

has_fasciculating_neuron_projection
type: ObjectProperty
IAO_0000426: T has_fasciculating_neuron_projection np iff: ∀neuron projection bundle ; CARO_0001001’(T), ∃ ‘neuron projection ; GO_0043005’(np), np overlaps T ∧ np aligned_with T
IAO_0000117: David Osumi-Sutherland
IAO_0000115: The relation between a neuron projection bundle and a neuron projection that is fasciculated with it.
IAO_0000118: has fasciculating component
domain: neuron projection bundle
inverse of: fasciculates_with
sub property of: overlaps
range: Class
  union of: neuron
  union of: Restriction
    on property: part of
    some values from: neuron

innervates
type: ObjectProperty
IAO_0000424: <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?)))
IAO_0000117: David Osumi-Sutherland
IAO_0000115: Relation between a ‘neuron projection bundle’ and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.
domain: neuron projection bundle
sub property of: topObjectProperty
property chain axiom: part of

connected_to
type: ObjectProperty
IAO_0000117: David Osumi-Sutherland
IAO_0000115: X connected_to Y if and only if X and Y share a fiat boundary.

partially overlaps
type: ObjectProperty
sub property of: overlaps

derived_by_descent_from
type: ObjectProperty
type: TransitiveProperty
IAO_0000118: ancestral_stucture_of
IAO_0000115: d derived_by_descent_from a if d is specified by some genetic program that is sequence-inherited-from a genetic program that specifies a.
IAO_0000118: evolutionarily_descended_from
sub property of: connected_to
inverse of: has_derived_by_descendant
IAO id: RO:0002156

has_derived_by_descendant
type: ObjectProperty
type: TransitiveProperty

shares ancestor with
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
comment: VBO calls this homologous_to
IAO_0000115: two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a.
property chain axiom: derived_by_descent_from
property chain axiom: has_derived_by_descendant

only in taxon
type: ObjectProperty
IAO_0000424: RO_0002162 only ?Y
IAO_0000117: Chris Mungall
IAO_0000119: PMID:20973947

never in taxon
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000119: PMID:20973947
IAO_0000424: RO_0002162 only not ?Y

in taxon
type: ObjectProperty
comment: Connects a biological entity to its taxon of origin.
IAO_0000117: Chris Mungall
IAO_0000119: PMID:20973947

spatially disjoint from
type: ObjectProperty
IAO_0000424: BFO_0000051 exactly 0 (BFO_0000050 some ?Y)
IAO_0000117: Chris Mungall

has_component
type: ObjectProperty
comment: For use in recording has_part with a cardinality constraint.
sub property of: has part

has phenotype
type: ObjectProperty
IAO_0000117: Chris Mungall
IAO_0000119: PMID:20971987
IAO_0000117: Robert Hoehndorf
sub property of: topObjectProperty

phenotype of
type: ObjectProperty
type: FunctionalProperty
IAO_0000117: Chris Mungall
IAO_0000119: PMID:20971987
IAO_0000117: Robert Hoehndorf
inverse of: has phenotype
sub property of: topObjectProperty

develops from
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
sub property of: topObjectProperty

develops into
type: ObjectProperty
type: TransitiveProperty
IAO_0000117: Chris Mungall
IAO_0000117: David Osumi-Sutherland
IAO_0000117: Terry Meehan
inverse of: develops from
sub property of: topObjectProperty

entity
type: Class
imported from: BFO

continuant
type: Class
subclass of: entity
imported from: BFO

independent continuant
type: Class
subclass of: continuant
imported from: BFO

material entity
type: Class
subclass of: independent continuant
imported from: BFO

anatomical structure
type: Class
subclass of: material anatomical entity

material anatomical entity
type: Class
subclass of: material entity

cell component
type: Class
subclass of: anatomical structure
IAO_0000115: "The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators]

multi-cell-component structure
type: Class
subclass of: anatomical structure

neuron projection bundle
type: Class
subclass of: multi-cell-component structure

membrane
type: Class
subclass of: cell part
IAO_0000115: "Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." [GOC:mah, ISBN:0815316194]

axon
type: Class
subclass of: neuron projection
IAO_0000115: "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." [GOC:nln, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

dendrite
type: Class
subclass of: neuron projection
IAO_0000115: "A branching protoplasmic process of a neuron that receives and integrate signals coming from axons of other neurons, and conveys the resulting signal to the body of the cell." [GOC:nln, ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

presynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
IAO_0000115: "A specialized area of membrane of the axon terminal that faces the plasma membrane of the neuron or muscle fiber with which the axon terminal establishes a synaptic junction; many synaptic junctions exhibit structural presynaptic characteristics, such as conical, electron-dense internal protrusions, that distinguish it from the remainder of the axon plasma membrane." [GOC:jl, http://cancerweb.ncl.ac.uk/]

cell projection
type: Class
subclass of: cell part
IAO_0000115: "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]

neuron projection
type: Class
subclass of: cell projection
IAO_0000115: "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." [GOC:jl, http://www.cogsci.princeton.edu/~wn/]

synapse part
type: Class
subclass of: cell component
IAO_0000115: "Any constituent part of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." [GOC:jl]

cell part
type: Class
subclass of: cell component
IAO_0000115: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl]

synapse
type: Class
subclass of: cell component
IAO_0000115: "The junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell; the site of interneuronal communication. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

postsynaptic membrane
type: Class
subclass of: membrane
subclass of: synapse part
IAO_0000115: "A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters across the synaptic cleft and transmit the signal to the postsynaptic membrane." [ISBN:0198506732 "Oxford Dictionary of Biochemistry and Molecular Biology"]

cell
type: Class
subclass of: anatomical structure
imported from: CL

neuron
type: Class
subclass of: cell
imported from: CL