]> 2011-08-26 imported from part of has part in_neural_circuit_with A relation that holds between two neurons connected directly via a synapse, or indirectly via a series of synaptically connected neurons. David Osumi-Sutherland upstream_in_neural_circuit_with 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. David Osumi-Sutherland downstream_in_neural_circuit_with 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. David Osumi-Sutherland derives from has_soma_location <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) Relation between a neuron and an anatomical structure that its soma is part of. soma part of fasciculates_with 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 fasciculates with 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. axon synapses in <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))) Chris Mungall David Osumi-Sutherland Relation between a neuron and some structure its axon forms (chemical) synapses in. synapsed_by <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?))) Chris Mungall David Osumi-Sutherland Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. has plasma membrane part <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) Chris Mungall Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] PMID:19243617 has_postsynaptic_terminal_in Chris Mungall Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. 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)) David Osumi-Sutherland synapsed in releases neurotransmitter has_presynaptic_terminal_in <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?) Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. synapses in synapsed_to 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)))) Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. <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?))) Chris Mungall David Osumi-Sutherland dendrite synapsed in <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))) Chris Mungall David Osumi-Sutherland Relation between a neuron and some structure (e.g.- a brain region) in which its dendrite receives synaptic input. has_synaptic_terminal_in 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. has synapse in <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?) David Osumi-Sutherland overlaps http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) has_fasciculating_neuron_projection 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 David Osumi-Sutherland The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. has fasciculating component innervates <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?))) David Osumi-Sutherland 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. connected_to David Osumi-Sutherland X connected_to Y if and only if X and Y share a fiat boundary. partially overlaps derived_by_descent_from ancestral_stucture_of 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. evolutionarily_descended_from has_derived_by_descendant shares ancestor with VBO calls this homologous_to 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. only in taxon RO_0002162 only ?Y Chris Mungall PMID:20973947 never in taxon Chris Mungall PMID:20973947 RO_0002162 only not ?Y in taxon Connects a biological entity to its taxon of origin. Chris Mungall PMID:20973947 spatially disjoint from BFO_0000051 exactly 0 (BFO_0000050 some ?Y) Chris Mungall has_component For use in recording has_part with a cardinality constraint. has phenotype Chris Mungall PMID:20971987 Robert Hoehndorf phenotype of Chris Mungall PMID:20971987 Robert Hoehndorf develops from Chris Mungall David Osumi-Sutherland Terry Meehan develops into Chris Mungall David Osumi-Sutherland Terry Meehan entity continuant independent continuant material entity anatomical structure material anatomical entity cell component "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 neuron projection bundle membrane "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 "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 "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 "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 "A prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, http://www.cogsci.princeton.edu/~wn/] neuron projection "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 "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 "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] synapse "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 "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 neuron derived_by_descent_from RO:0002156 ancestral_stucture_of 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. evolutionarily_descended_from